Epidemiologic Analyses of 

Virulent Newcastle Disease in 

Poultry in California

March 2021
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

ii USDA APHIS VS

Suggested bibliographic citation for this report: 

USDA-APHIS (2021). “Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California, 

March 2021.” USDA:APHIS:VS:Center for Epidemiology and Animal Health. Fort Collins, CO. 

March 2021. 101 pgs.

For more information, contact: 

Amy Delgado, DVM PhD

Director, Monitoring and Modeling

Center for Epidemiology and Animal Health

USDA:APHIS:Veterinary Services

2150 Centre Avenue, Bldg. B-2E7, Fort Collins, CO, 80526-8117

Phone (970) 494-7302 | Mobile (970) 420-2567 | Fax (970) 494-7228

Email: Amy.H.Delgado@usda.gov

The U.S. Department of Agriculture (USDA) prohibits 

discrimination in all its programs and activities on the basis of 

race, color, national origin, age, disability, and where applicable, 

sex, marital status, familial status, parental status, religion, sexual 

orientation, genetic information, political beliefs, reprisal, or 

because all or part of an individual's income is derived from any 

public assistance program. (Not all prohibited bases apply to all 

programs.) Persons with disabilities who require alternative 

means for communication of program information (Braille, large 

print, audiotape, etc.) should contact USDA's TARGET Center at 

(202) 720-2600 (voice and TDD). 

To file a complaint of discrimination, write USDA, Director, Office 

of Civil Rights, 1400 Independence Avenue, SW, Washington, DC 

20250-9410 or call (800) 795-3272 or (202) 720-6382 (TDD). USDA 

is an equal opportunity provider and employer.

Mention of companies or commercial products does not imply 

recommendation or endorsement by the U.S. Department of 

Agriculture over others not mentioned. USDA neither guarantees 

nor warrants the standard of any product mentioned. Product 

names are mentioned solely to report factually on available data 

and to provide specific information.

USDA–APHIS–VS–S&P–CEAH

NRRC Building B, M.S. 2W4

2150 Centre Avenue

Fort Collins, CO 80526-8117

(970) 494–7000

Email: vs.ceah@usda.gov

https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/SAEpidemiology-AnimalHealth-CEAH
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS i

Contents

Executive Summary ..................................................................................................................................2

Introduction .............................................................................................................................................5

A. Disease Overview...........................................................................................................................................5

B. Description of Outbreak................................................................................................................................6

C. Surveillance Overview .................................................................................................................................11

D. References....................................................................................................................................................13

II. Phylogenetic Analysis and Diagnostics...........................................................................................14

A. Virulent Newcastle Disease Virus...............................................................................................................14

Methods....................................................................................................................................................14

Results.......................................................................................................................................................14

B. Comparison to Other Viruses/Lineages .....................................................................................................19

C. Diagnostics...................................................................................................................................................20

D. References....................................................................................................................................................20

III. Population at Risk...........................................................................................................................21

A. Predicting Areas of Backyard Bird Ownership ...........................................................................................21

Methods....................................................................................................................................................21

Results.......................................................................................................................................................21

Summary....................................................................................................................................................24

IV. Epidemiologic Risk..........................................................................................................................25

A. Case Control Study ......................................................................................................................................25

Methods....................................................................................................................................................25

Results.......................................................................................................................................................25

Summary....................................................................................................................................................27

Summary of Historical Epidemiologic Risk Factors....................................................................................27

B. Epidemiologic Investigation of vNDv-Infected Commercial and Backyard Non-Commercial Laying 

Chicken Premises.........................................................................................................................................29

Methods....................................................................................................................................................29

Results.......................................................................................................................................................30

C. References....................................................................................................................................................36

V. Estimating Disease Spread..............................................................................................................37

A. Flock Disease Spread Model–Early Outbreak............................................................................................37

Methods....................................................................................................................................................37

Results.......................................................................................................................................................37

B. Comparing Alternative Control Strategies–Mid-Outbreak.......................................................................39

Methods....................................................................................................................................................39

Results.......................................................................................................................................................40

C. Estimating Within-Flock Transmission Parameters and Predicting the Time to Detect vND in 

Unvaccinated Flocks....................................................................................................................................41

Methods....................................................................................................................................................41

Results.......................................................................................................................................................42

D. Predicted Disease Mortality and Infection Prevalence in vNDV Infected Flocks Using a Disease 

Transmission Simulation Model .................................................................................................................42

Methods....................................................................................................................................................43

Results.......................................................................................................................................................43
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

ii USDA APHIS VS

Conclusions................................................................................................................................................48

E. Estimating the Time of Disease Introduction in vNDv Infected Commercial Layer Barns Using Egg 

Production and Mortality Data...................................................................................................................49

Summary....................................................................................................................................................49

Methods....................................................................................................................................................49

Results.......................................................................................................................................................50

Discussion..................................................................................................................................................53

F. Spatial and Spatiotemporal Patterns of the Outbreak .............................................................................55

Methods....................................................................................................................................................55

Results.......................................................................................................................................................55

Conclusions................................................................................................................................................60

G. Measuring the Spatial Dependence of Virulent Newcastle Disease Transmission Risk .........................60

Methods....................................................................................................................................................61

Results.......................................................................................................................................................62

Conclusions................................................................................................................................................66

Implementation During Outbreak .............................................................................................................66

H. References....................................................................................................................................................67

VI. Acknowledgements........................................................................................................................69

Appendix A: Questionnaire ....................................................................................................................70

Appendix B: Modeling Scenario Design..................................................................................................75

Appendix C. Predicted Disease Mortality and Infection Prevalence Under Additional Flock Size And 

Vaccination Scenarios.....................................................................................................................77

Predicted mortality and disease prevalence in a 50-bird unvaccinated backyard flock ...........................79

Predicted mortality and disease prevalence in a 50-bird vaccinated backyard flock................................81

Predicted mortality and disease prevalence in a 5000-bird unvaccinated commercial flock ...................82

Predicted mortality and disease prevalence in a 20,000-bird unvaccinated commercial flock ................84

Predicted mortality and disease prevalence in a 5000-bird vaccinated commercial flock .......................86

Appendix D. Technical Details for estimating the time of vND introduction in Commercial 

Vaccinated Layer Flocks..................................................................................................................88

A. Overview ......................................................................................................................................................88

B. Estimating prior distributions.....................................................................................................................88

C. Goodness of Fit measure calculation .........................................................................................................89

D. Model Implementation and coding validation ..........................................................................................91

Results.......................................................................................................................................................92
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS iii

List of Figures and Tables

Figure 1. Counties with confirmed findings of vND from 17 May 2018 to 4 June 2019. .............................................10

Figure 2. California vND weekly case detection curve based upon the date the case definition was met for a 

presumptive positive flock, by day from 17 May 2018 to 25 February 2020........................................................11

Figure 3. Distribution of analyzed viruses by virus group and date of sample collection through November 

2019. ...........................................................................................................................................................................15

Figure 4. Distribution of the RV-a vNDV subgroup in California from 19 December 2018 to 11 May 2019.. ............16

Figure 5. Distribution of subgroup of vNDV-02 viruses which occurred after August 1, 2019.. .................................18

Figure 6. Phylogenetic analysis based on the full-length nucleotide sequence of the fusion gene of isolates 

representing Newcastle disease virus class II, genotype V.....................................................................................19

Figure 7. Comparison of predicted number of backyard poultry flocks (boxplots) with observed distribution of 

backyard poultry flocks (red). ...................................................................................................................................22

Figure 8. Predictive variables used in the generalized additive model. ......................................................................23

Figure 9. Smoothing splines describing the relationship between number of poultry flocks and non-linear 

predictor variables.....................................................................................................................................................23

Figure 10. Predicted geographic distribution of backyard poultry flocks in southern California. The map 

presents the density of flocks per km2.....................................................................................................................24

Figure 11. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

exposure in a 20000 vaccinated commercial cage free layer flock using baseline vND spread parameters......44

Figure 12. Predicted daily mortality on various days post exposure in a 20 000-bird vaccinated commercial 

cage free layer flock using baseline vND spread parameters.................................................................................44

Figure 13. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

exposure in a 400-bird unvaccinated backyard flock using baseline vND spread parameters. ...........................45

Figure 14. Predicted daily mortality on various days post exposure in a 400 bird unvaccinated backyard flock 

using baseline vND spread parameters....................................................................................................................46

Figure 15. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

vND exposure in a 400-bird vaccinated backyard flock. .........................................................................................47

Figure 16. Predicted daily mortality on various days post vND exposure in a 400-bird vaccinated backyard 

flock.............................................................................................................................................................................48

Figure 17. Model-fitted egg production rate curves from the approximate Bayesian computation and 

observed egg production rate for Barn A. ...............................................................................................................51

Figure 18. Model fitted disease plus normal mortality from the approximate Bayesian computation and the 

observed daily mortality for Barn A. ........................................................................................................................52

Figure 19. Posterior distribution for the adequate contact rate for Barn A. ................................................................53

Figure 20. Histogram of the Posterior distribution for the time of vND introduction for Barn A. ..............................53

Figure 21. Cumulative number of confirmed and presumptive positive vND premises detected in California 

from 16 May 2018 to 22 February 2020. .................................................................................................................56

Figure 22. Location of spatial (upper) and spatiotemporal (lower) clusters of vNDV-01 premises and the 

relative risk of cases occurring within census blocks in California from 16 May to 22 February 2020. ..............57

Figure 23. Location of spatial (upper) and spatiotemporal (lower) clusters of vNDV-02 premises and the 

relative risk of cases occurring within census blocks in California from 16 May to 22 February 2020. ..............58

Figure 24. Time period of occurrence of spatiotemporal clusters of vND-01 and vND-02 in California from 16 

May 2018 to 22 February 2020.................................................................................................................................60
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

iv USDA APHIS VS

Figure 25. Spatial dependence of vND infected premises and the percent of infected premises located within 

the specific distance and occurring within 21 days of each other. ........................................................................64

Figure 26. Spatial dependence of vND infected premises located within the specified distance and occurring 

within 21 and 120 days of each other.. ....................................................................................................................65

Table 1. Number of vND confirmed and presumptive positive premises, by county and dates of earliest 

confirmation in each county through 25 February 2020..........................................................................................9

Table 2. The number of distinct sampled infected commercial and independent premises, laboratory 

accessions, and samples collected from infected premises in the RQA as part of vNDV surveillance by 

production type. ........................................................................................................................................................12

Table 3. The number of distinct sampled uninfected commercial and independent premises, laboratory 

accessions, and samples collected from negative premises in the RCA as part of vNDV surveillance by 

production type. ........................................................................................................................................................13

Table 4. Detection timeline for the RV-a vNDV subgroup in California between 19 December 2018 to 11 May 

2019 by sample collection date. ...............................................................................................................................17

Table 5. Characteristics of backyard case premises (confirmed/presumptive positive for vND), dangerous 

contact (DC) premises, control premises (C), and odds ratios (OR) and p-values calculated by univariate 

logistic regression (dangerous contacts excluded)..................................................................................................28

Table 6. Adjusted odds ratios (OR) for significant risk factors identified in multivariate regression analyses. .........28

Table 7. Production types, counties, confirmation dates, and numbers of euthanized birds on ten vNDv 

infected commercial and backyard/non-commercial layer chicken premises......................................................32

Table 8. Numbers of birds, numbers of flocks, numbers of houses in use and numbers of employees reported 

by vND infected case premises (n=10) and control premises (n=28) located in the three-county regional 

quarantine area of southern California....................................................................................................................33

Table 9. Management characteristics of vND infected case premises (n=10) and control premises (n=28) in the 

three-county regional control area of southern California.....................................................................................34

Table 10. Qualitative summary comparison of the four alternative response options examined. ............................40

Table 11. Predicted days post onset of infectiousness to attain various cumulative mortality levels in a 

20,000-bird vaccinated commercial cage free layer flock using baseline vND spread parameters. ...................45

Table 12. Predicted days post onset of infectiousness to reach various cumulative mortality levels in a 400-

bird unvaccinated backyard flock using baseline vND spread parameters. ..........................................................46

Table 13. Predicted days post onset of infectiousness to reach various cumulative mortality levels in a 400-

bird vaccinated backyard flock using baseline vND spread parameters. ..............................................................48

Table 14. Estimated time of introduction and adequate contact rate for each of the four barns. ............................52

Table 15. Spatiotemporal clusters of vND cases in California from 16 May 16 2018 to 22 February 2020.a.............59

Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

2 USDA APHIS VS

EXECUTIVE SUMMARY

In May 2018, an owner brought several ill exhibition chickens to a veterinary clinic in southern 

California. The birds were displaying signs of virulent Newcastle disease (vND). Biological samples were 

collected from the chickens and sent the California Animal Health and Food Safety (CAHFS) Laboratory

where vND virus was detected. The U.S. Department of Agriculture’s (USDA) National Veterinary 

Services Laboratories (NVSL) confirmed vND in these birds on 17 May 2018. Between 17 May 2018 and 

31 May 2020, 476 premises were confirmed as infected with the virus. The last infected backyard noncommercial chickens were confirmed on 29 November 2019 and the last infected exhibition 

establishment was confirmed on 25 February 2020.

Once initial response efforts were in place, the USDA Animal and Plant Health Inspections Service’s 

(APHIS) Veterinary Services initiated a series of epidemiologic investigations and studies, which were

undertaken collaboratively with bird owners, State agriculture personnel, and the USDA’s Agricultural 

Research Service (ARS). This report provides a summary of the epidemiologic analyses conducted in 

support of this outbreak and is intended to provide a better understanding of how the vND virus was 

introduced and transmitted. 

The outbreak predominantly affected exhibition chickens in an area crossing three Southern California

counties: San Bernardino, Riverside, and Los Angeles. Additional isolated cases were detected in Ventura 

County, CA, Alameda County, CA, San Diego, CA, Utah County, UT, and Coconino County, AZ. Genetic 

analysis supports a single introduction followed by secondary spread. Lack of epidemiologic data 

regarding the index premises, and temporal and geographical gaps in available genetic data, contribute 

to the uncertainty surrounding the origin of the outbreak. Following introduction into CA, divergence of 

the virus into two sub-groups appeared early on and, where epidemiologic data is available, was useful 

to gain insights on virus spread. Although geospatial clustering of virus sub-groups was observed, the 

presence of different virus sub-groups in each of the major affected areas indicated virus movement 

within, and between, affected areas. 

The affected counties in CA have a high density of backyard or exhibition flocks, but such flocks are not 

typically registered, and their exact locations were unknown. Using a Bayesian hierarchical model, 

previously identified socioeconomic and demographic variables found to be associated with urban 

poultry ownership were used to estimate the probability of backyard flocks in this area. Results 

suggested that a single 10-km zone could have as many as 4,000 backyard flocks, and that the greater 

Los Angeles area might have more than 11,000. Modeled backyard ownership maps helped to inform

surveillance and response efforts.

Analyses of surveys conducted at case and control premises (including dangerous contacts)1identified 

flock size, ownership of exhibition birds, high proportions of roosters in flocks, and the use of housing 

that allows contact with wild birds asrisk factors for vND in this population. The percentage of premises 

reporting the use of Newcastle vaccine was low overall; however, its use was higher in case premises.

Improper vaccination of backyard birds is a concern due to improper administration leading to 

development of reservoirs of vND. An epidemiologic investigation into 10 vND infected commercial and 

1 Dangerous contact premises are defined as premises with backyard/exhibition birds that are high risk due to either an 

epidemiologic link or proximity to infected premises.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 3

backyard non-commercial laying chicken premises and 28 control premises found that some factors and 

management practices were shared across infected farms; however, the significance of these similarities 

was difficult to interpret given the small number of infected commercial and non-commercial laying 

chicken farms and the study design. All cases and controls reported vaccination of their flocks to protect 

against Newcastle disease. 

Initial results from disease-spread and control simulations suggested that local disease spread would

become increasingly important as the outbreak increased in size. This type of disease spread is distancedependent and represents mechanisms of spread that are difficult to trace, such as movement of free 

ranging birds, wildlife, or fence-line contact. Good biosecurity practices and measures are the best way

to reduce local spread, but completely preventing this type of spread is difficult. As the outbreak 

progressed, modeling scenarios were developed to compare alternative control options and resource 

levels for response. These scenarios found that minimal response levels (including low surveillance and 

depopulation capacities) were unlikely to prevent continued disease spread in backyard flocks. Rapid 

and targeted surveillance, depopulation, and disposal were most effective at minimizing outbreak size 

and severity. The largest and longest simulated outbreaks frequently involve significant disease spread 

within Los Angeles County, irrespective of the selected response option.

Using experimental data available from peer-reviewed literature and unpublished data provided by the 

USDA, ARS, Southeast Poultry Research Laboratory (SEPRL), analysts estimated the mean latent period 

for this virus was 0.40 days, and the mean infectious period was 4.33 days in unvaccinated birds. Using 

these values, analysts estimated the time to detect vND in an unvaccinated, 50-bird backyard flock 

based on observation of increased mortality (two or more dead birds within a 3-day period) to be from 4 

to 7 days. Building on this work, a stochastic within-flock vND transmission model was developed to 

predict the prevalence of infectious birds and cumulative mortality over time for both vaccinated and 

unvaccinated flocks. In large vaccinated flocks, it may take 14 to 22 days after the onset of 

infectiousness for the cumulative mortality to reach 2 percent of the starting flock size. In contrast, in an 

unvaccinated backyard flock, a 50 percent cumulative mortality may be seen within a week. This 

information was used to help guide on-farm surveillance and monitoring efforts. 

The identification of significant spatial and spatiotemporal clustering patterns of vND in California from

May 2018 to February 2020 supported control strategies of targeting high risk areas for disease spread 

with enhanced surveillance and depopulation activities. The primary spatial and spatiotemporal clusters 

were located within Riverside and San Bernardino Counties, identifying these areas as the location of 

the highest occurrence of vND cases detected from 16 May 2018 to 22 February 2020. These clusters 

occurred during the first seven months of the outbreak, corresponding to the increase in infected 

premises that were detected during this time as well as further disease spread over the next year within 

the Regional Quarantine Area (RQA)2. Examination of the spatial dependence of vND transmission risk 

from 342 cases from the start of the outbreak through 1 May 2019, found evidence for both local and 

long-distance spread of the virus. Most infected premises (75.6 percent) were found to be within 250 m 

of another infected premises, with over 95 percent of infected premises occurring within 1.5 km of 

another infected premises. However, the increased probability of premises being infected at longer 

2RQA was implemented on 27 February 2019 by the California Department of Food and Agriculture and encompassed all of Los 

Angeles County and most of Riverside and San Bernardino Counties.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

4 USDA APHIS VS

distances, from 2.5 to 6.0 km depending on virus sub-group, highlight the risk of spread by movement of 

infected poultry or fomites out of affected areas. Statistically significant spatial clustering over longer 

time periods (42 to 120 days apart in confirmation date) was also observed at distances between 5.0 

and 8.0 km. These results indicate longer-term disease transmission, which may occur due to 

undetected, infected premises or violations in the fallow period. The results of this analysis were used to 

guide surveillance and depopulations efforts for backyard/exhibition premises between July 2019 and 

the end of the outbreak.

On June 1, 2020, USDA APHIS certified that the United States of America (U.S.A.) satisfied the World 

Organisation for Animal Health (OIE) criteria for eradication of virulent Newcastle disease from poultry,

as defined by the OIE, and exhibition birds. Subsequently, CDFA announced an end to the vND 

quarantine in Southern California through release of the RQA, an area where millions of commercial and 

backyard poultry live. This action once again allowed poultry to move freely within California without a 

CDFA permit. All necessary actions and surveillance requirements were completed in accordance with 

the OIE Terrestrial Animal Health Code with no further detections of the disease. The USDA APHIS now 

considers the vND event officially closed and resolved. The total cost of indemnity approved by USDA 

during this outbreak was $6.7 million ($3.7 million to affected commercial producers and $3 million to 

backyard flock owners).

To guard against the risk of subsequent outbreaks, CDFA and USDA in partnership with many bird 

enthusiasts in Southern California are committed to on-going monitoring for disease and continual 

support for biosecurity training. All backyard poultry and exhibition bird owners and commercial 

operations are encouraged to practice biosecurity measures to help prevent the introduction of disease 

when people enter or depart the premises, to routinely check birds for signs of illness, and to report any 

incidence of suspected vND or other bird diseases.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 5

INTRODUCTION

California and USDA-APHIS initiated epidemiologic and genetic investigations in response to the vND 

outbreak in backyard/exhibition chickens in Southern California. These investigations provided a better 

understanding of factors associated with vND virus transmission among backyard chickens3and other 

susceptible species. These investigations included:

• Analysis of the phylogenetic characteristics of the virus,

• Estimation of the probability of homes in Southern California owning backyard birds,

• A field-based study of backyard case and control premises using data collected through site 

visits and interviews with backyard-chicken owners,

• A field-based study of commercial poultry case premises using data collected through site 

visits and interviews,

• An epidemiologic disease-spread simulation model of vND spread among bird-owning 

households in Southern California and comparison of alternative control options,

• An examination of within-flock disease transmission and the impact on the time to detection 

in small unvaccinated flocks,

• Prediction of disease mortality and infection prevalence in vND infected flocks of varying 

flock sizes and vaccination status,

• Estimation of the time of disease introduction in vND-infected commercial layer barns using 

egg production and mortality data,

• An analysis of spatial and spatiotemporal patterns of disease and the spatial dependence of 

vND transmission risk.

This report is a supplement to previous epidemiologic investigations of this outbreak reported 

previously. This report includes the results from these investigations, to provide producers, industry, and 

other stakeholders with epidemiologic information and to archive the analytical work performed to 

support future outbreak response. 

A. Disease Overview

Newcastle disease is the cause of regular, frequent poultry epizootics throughout Africa, Asia, Central 

America, and parts of South America. The disease is caused by strains of avian paramyxovirus-1, also 

known as Newcastle disease virus, which can be classified into three pathotypes based on their 

virulence in chickens. The World Organisation for Animal Health (OIE) defines Newcastle disease as 

infection caused by highly virulent strains of APMV-1 viruses. This virulent form of Newcastle disease

(vND) is considered a foreign animal disease in the United States.

3 For the purposes of this report, the term backyard flock may also refer to birds raised for exhibition.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

6 USDA APHIS VS

Clinical signs of vND vary and can include respiratory, neurological, reproductive, and intestinal signs. 

During this outbreak, clinical signs seen in chickens include loss of appetite, difficulty breathing, nasal 

discharge/ocular discharge, swelling around the eyes, diarrhea, blue combs, and death. Morbidity of 

unvaccinated chickens infected with vND virus strains can reach 100 percent, and mortality ranges from 

70 to 100 percent. The severity of disease produced varies with the host species and the strain of the 

virus. Many other avian diseases present with clinical signs similar to vND; therefore, laboratory testing 

is necessary to distinguish between diseases. 

Newcastle disease is transmitted by inhalation or ingestion, and birds shed the virus in both feces and 

respiratory secretions. The virus can infect many species of domestic and wild birds. Chickens are highly 

susceptible, and other gallinaceous birds such as turkey, quail, and guinea are also susceptible. There are 

two species-adapted viruses that are genetically distinguishable from those found in poultry in the 

absence of direct transmission: one is maintained in pigeons and doves, and another in double-crested 

cormorants (Brown and Bevins, 2017). Parrots have been reported to be infected with virulent viruses 

and have the potential to shed virus for long periods without showing clinical signs; however, data 

supporting virus maintenance in these species is lacking.

Vaccination of commercial poultry against Newcastle disease is common in the Americas, including the 

United States. The classical vaccine strains are distinguishable from other viruses by genome 

sequencing. Widespread vaccination of poultry was implemented in Mexico and several Central 

American countries in the early 2000s, and since this time divergence of subgenotypes circulating in 

vaccinated poultry has been documented (Susta et al., 2014; Garcia et al., 2013). Outbreaks of vND 

occurred in California, Nevada, and Arizona in 2002-2003 and in Texas in 2003. 

B. Description of Outbreak

16 May 2018 to 4 June 2020

On 16 May 2018, the California Department of Food and Agriculture (CDFA) reported vND in sick

exhibition chickens presented to a veterinary clinic in Los Angeles County (Figure 1). Biological samples 

were collected from the chickens and sent the California Animal Health and Food Safety (CAHFS) 

Laboratory where vND virus was detected. The National Veterinary Services Laboratories (NVSL) 

confirmed vND virus (vNDV) on 17 May 2018. This confirmation represented the first case of vND, 

(formerly referred to as exotic Newcastle disease) in the United States since 2003. Officials were first 

alerted to the possibility of a new finding of vND when an owner presented sick chickens to a California 

veterinary clinic. The CDFA responded to the incident by creating 3-km control areas around the 

premises associated with the index case and began targeted surveillance and outreach, including feed

stores and known exhibition bird premises. 

On 24 May 2018 NVSL confirmed vNDV in an exhibition premises in San Bernardino County. On 26 May 

2018, a USDA-APHIS incident management team joined the unified incident command in California. By 

this time, five premises had been confirmed in San Bernardino County and two in Los Angeles County. 

On 30 June 2018, a premises in Riverside County was confirmed. On 14 August 2018, vNDV was 

confirmed in Ventura County. 

On 25 September 2018, NVSL confirmed vNDV in a live bird market in Los Angeles County. The owner of 

the vND-infected live bird market in Los Angeles County reported first observing clinical signs 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 7

approximately two weeks prior to presumptive diagnosis. Over the four weeks prior to reporting 

disease, the market received 43 shipments of live birds from four suppliers: 37 shipments of broilers, 4 

shipments of spent hens, and 2 shipments of ducks. Bird shipment sizes ranged from 15 to 558 birds 

(mean=181 birds per shipment). Suppliers used dedicated cages that were washed and sanitized 

between shipments to transport birds. Suppliers typically made stops at more than one live-bird market 

on their routes. The market was visited by one renderer, typically three times per week. The owner of 

the market reported rarely receiving birds from the community, and no community birds were received 

in the 60 days prior to the onset of clinical signs. Active surveillance of other live bird markets resulted in 

an additional confirmed detection in a live bird market in March 2019.

On 14 December 2018, NVSL confirmed vNDV in a chicken pullet ranch in Riverside County representing 

the first detection in a commercial poultry operation. Three additional commercial premises in Riverside 

County (table egg layer facilities) were confirmed for vNDV in January and February 2019. On 24 

January 2019, a backyard non-commercial laying hen operation was confirmed as positive in San 

Bernardino County. Four additional backyard non-commercial laying hen operations were confirmed 

between February and March 2019. Of the 10 infected commercial and backyard non-commercial

premises, six were not reported to have had any clinical signs and were detected on routine mandatory 

surveillance, while the other four were reported to have clinical signs that included mild decreased egg 

production or increased mortality.

On 17 January 2019, vNDV was confirmed in Utah County, Utah, the first confirmed infection outside of 

southern California. Additional confirmations outside of southern California occurred in Alameda 

County, CA on 13 March 2019 and Coconino County, AZ on 1 April 2019. From 17 May 2018 to 25

February 2020, 496 confirmed or presumptive positive premises were identified in six California 

counties, one Utah county and one Arizona county (Figure 2, Table 1).

An infected exhibition flock premises with multiple bird owners was detected in Utah County, Utah in 

January 2019. A concerned individual contacted the Utah State Veterinarian’s office to report sick and 

dying birds with clinical signs consistent with vND. The owners were contacted, and samples submitted 

for testing on 15 January 2019. The ownersreported bringing birds from California in early January. 

NVSL confirmed vNDV in the flock on 17 January 2019. All but one of the owners depopulated their 

flocks themselves, while state/federal officials depopulated the remaining owner’s birds. Depopulation 

of the flock was completed on 19 January 2019. Construction vehicles, equipment, storage units, cages 

and pens were cleaned and disinfected, and the premises placed under extended fallow quarantine on 

20 January 2019. All commercial layer operations in the area were notified of the suspect case and 

advised to heighten biosecurity. Surveillance yielded no further positive cases.

A single infected pet chicken premises was identified in Flagstaff, Coconino County, AZ. The owner 

reported lethargy, upper respiratory signs and death in numerous birds starting on 22 March 

2019. Officials were first alerted to the possibility of vND on 27 March 2019 when the owner’s 

veterinarian reported that pathologic findings consistent with vND had been found on necropsy of one 

of the chickens. Oropharyngeal samples from remaining chickens on the premises were confirmed to be 

positive for vND on 1 April 2019. All remaining birds were depopulated, and the premises placed under 

extended fallow quarantine on 2 April 2019. Census, outreach, and surveillance testing of premises with 

poultry within 1 km of the index case was completed on 9 April 2019. All surveillance samples collected 

for premises with poultry within the 1 km zone and additional premises on border of 1 km zone (n=69) 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

8 USDA APHIS VS

tested negative by vNDV PCR at Arizona Veterinary Diagnostic laboratory. Samples from chicks at the 

local feed store where the owners’ chicks were sourced were found to be negative for vNDV. Although 

no epidemiologic links were identified, the virus genetic data connects this detection to other infected 

premises in California. No further cases in AZ were detected.

On 27 February 2019, the California State Veterinarian modified Southern California’s quarantine area to 

further restrict bird movement. The quarantine mandated the reporting of sick birds and prohibited 

poultry owners from moving birds in all of Los Angeles County, and in large areas of San Bernardino and 

Riverside counties. The quarantine required bird owners to allow diagnostic testing, to isolate poultry 

from other species, to cease exhibitions, to stop the shipping and receiving of birds, and to enhance 

biosecurity.

On 7 March 2019, the United State Postal Service issued an industry alert indicating that they would no 

longer allow shipments of poultry into or out of zip codes 90000-93599, which affected the San Diego, 

Los Angeles, Santa Ana and Sierra Coastal districts. The quarantine was updated on 21 March 2019 to 

include all birds as well as hatching and embryonated eggs. Reminders of the ban were also issued on 8 

November 2019 and 13 January 2020. This quarantine was officially lifted on 1 June 2020.

Beginning in June 2019, intensive control activities combined with diagnostic testing strategies allowed 

for the release of control areas to begin. Active work to identify and conduct outreach to all retail feed 

stores and their customers was on-going throughout the outbreak. On 14 August 2019 a retail feed 

store, previously located within a control area and identified through feed store outreach, had poultry 

which were confirmed positive for vND. Epidemiologic investigation revealed that the store was a 

location where unwanted poultry were left, often without any indication of their origin. Although tracing 

from the infected premises was challenging, the presence of positive birds was a valuable indicator of 

on-going viral circulation in the area. A new control area was established, and surveillance conducted in 

the surrounding area.

On 24 August 2019, an antibody production facility in San Diego County, which used chickens to produce 

eggs for the antibody production process, noted clinical signs consistent with vND, including diarrhea, 

depression, sudden death, discharge around eyes, coughing/gasping, paralysis, and swelling around the 

eyes and neck. The premises was confirmed infected with vND on 31 August 2019. The chickens at the 

facility were kept indoors, caged and in pens. Although other companies operated at the same location, 

no other companies housed any birds at this location. Trace-out investigations subsequently identified a

vND positive small exhibition flock. Poultry on the premises were housed outdoors in adjacent wire 

enclosures and included chickens, ducks, pigeons, and doves. This cluster of detections starting 14 

August 2019 all fell into the same vNDV-02 subgroup and did not represent a new introduction of the 

virus, based upon molecular studies and epidemiologic investigation. 

Release testing for all control areas was initially completed on 16 October 2019, and all control areas 

were closed. However, freedom from disease testing was suspended on 15 November 2019, after 

diagnostic testing of an exhibition chicken flock in San Bernardino County with high mortality and clinical 

signs compatible with vND. The flock was confirmed positive on 16 November 2019 and a new control 

area established. Additional surveillance and outreach activities resulted in an additional 26 detections, 

primarily in small exhibition chicken flocks on the border between San Bernardino and Riverside 

Counties. These detections were all epidemiologically linked, and investigations identified several risk 

factors for disease spread in this area. Many of the infected premises frequented a feed store that had a 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 9

drive-through arrangement for selling feed in bulk. November is also the beginning of many exhibition

activities, which while prohibited, were likely driven underground, resulting in illegal bird movements in 

the area. Twenty-three of the 27 cases detected in this cluster were in exhibition chickens. An additional 

detection of a pet chicken located in a retail pet store in Los Angeles County was also found to be linked 

to the San Bernardino cases, where the owner of the store lived and likely carried the virus from the

area to the pet store. A total of three control areas were established in Los Angeles, Riverside, and San 

Bernardino counties. The last detection in California occurred on 25 February 2020. The last control area 

was closed on 23 March 2020 after testing of all premises in the control area was completed with 

negative test results. 

Freedom from disease testing was completed, with ongoing outreach throughout the affected areas. On 

1 June 2020, USDA-APHIS certified that the U.S. had satisfied the World Organisation for Animal Health 

(OIE) criteria for eradication of virulent Newcastle disease (vND) from poultry as defined by the OIE and 

exhibition birds. All necessary actions and surveillance requirements were completed in accordance with 

the OIE Terrestrial Animal Health Code with no further detections of the disease. 

Over the course of two years, more than 8,700 premises were quarantined, and disease surveillance 

staff made more than 226,000 premises visits and coordinated more than 11,000 laboratory 

submissions. Approximately 2,400 premises with a total of more than 1.2 million birds were 

depopulated, either because they were infected with vNDV or because they were linked to an infected 

premises. At the peak of the outbreak, USDA had more than 150 personnel deployed, including rotating 

Incident Management Team staff to assist CDFA, for a total of more than 300 State and Federal 

personnel responding to this outbreak. To guard against the risk of subsequent outbreaks, CDFA and 

USDA in partnership with many bird enthusiasts in Southern California committed to on-going 

monitoring for disease and continual support for biosecurity training. All backyard and exhibition 

poultry owners and commercial operations are encouraged to practice biosecurity measures to help 

prevent the introduction of disease when people enter or depart the premises, to routinely check birds 

for signs of illness, and to report any incidence of suspected vND or other bird diseases.

Table 1. Number of vND confirmed and presumptive positive premises, by county and dates of earliest 

confirmation in each county through 25 February 2020.

County Confirmed/Presumptive

Premises Earliest Confirmation Date in County

Los Angeles, CA 50 17 May 2018

San Bernardino, CA 176 24 May 2018

Riverside, CA 269 30 June 2018

Ventura, CA 1 15 August 2018

San Diego, CA 1 31 August 2019

Alameda, CA 1 13 March 2019

Utah, UT 1 17 January 2019

Coconino, AZ 1 1 April 2019

Total 4964

4 Some premises were infected twice. The total number of confirmed and presumptive premises represents the total number of 

unique premises affected.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

10 USDA APHIS VS

Figure 1. Counties with confirmed findings of vND from 17 May 2018 to 25 February 2020.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 11

Figure 2. California vND weekly case detection curve based upon the date the case definition5 was met for a 

presumptive positive flock, by day from 17 May 2018 to 25 February 2020.

C. Surveillance Overview

Based on laboratory submission data, most premises sampled during the outbreak were small

operations. A small number of these premises had both pet birds as well as chickens and less than 50

premises had only pet birds. Approximately 25 percent of the premises had two or more poultry 

species6present at testing, with some having up to 9 different species present. Most infected, 

depopulated premises only had poultry species present (98 percent), with the number of species 

present ranging from 1 to 8 species. Thirty-six live bird markets were sampled during the outbreak. 

5 Case definitions 

• Suspect case: domesticated bird or flock having clinical signs compatible with vND; or detection of APMV-1 by 

rRT-PCR; or epidemiological information indicating exposure to vNDV

• Presumptive positive case: a suspect case with detection vNDV by the fusion-target rRT-PCR test at a laboratory 

designated by the Secretary of Agriculture

• Confirmed positive case: domesticated bird or flock from which vNDV has been identified at the NVSL as 

presumptive positive with confirmation of multiple basic amino acids (either directly via protein or by deduction 

through sequencing) in the fusion gene at the C-terminus of the F2 protein and phenylalanine at residue 117, 

which is the N-terminus of the F-1 protein. The term ’multiple basic amino acids’ refers to at least three arginine 

or lysine residues between residues 113 and 116; and/or the vNDV has an intracerebral pathogenicity index 

(ICPI) in day-old chicks (Gallus gallus) of 0.7 or greater.

6

Includes Chickens, Chukar, Doves, Duck, Emu, Geese, Guinea Fowl, Ostrich, Peafowl, Pheasant, Pigeons, Quail, Squab, Swans, 

and Turkeys
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

12 USDA APHIS VS

Forty-five commercial and independent (larger backyard non-commercial) poultry premises7 within the 

RQA had birds and were sampled during the outbreak as part of surveillance and permitted movement 

testing8. This included 10 infected commercial and larger non-commercial poultry premises and 35 

uninfected premises. An additional 15 commercial or independent (larger backyard non-commercial)

premises were sampled during the outbreak but not located within the RQA.

Table 2 provides an overview of the number of laboratory accessions and samples collected from 

infected commercial and independent premises in the RQA by production type through 8 June 2020.

Table 3 provides an overview of the number of laboratory accessions and samples collected from 

uninfected commercial and independent premises in the RQA by production type through 8 June 2020.

Table 2. The number of distinct sampled infected commercial and independent premises, laboratory 

accessions, and samples collected from infected premises in the RQA as part of vNDV surveillance by 

production type.

Production Type Premises Accessions1 Samples3

Commercial Table Egg Layer 3 136 803

Commercial Table Egg Pullets 1 1 4

Independent Table Egg Producer 6 288 1,694

Total2 10 425 2,501

1 LMS accessions were used as a proxy for the number of testing events that occurred at a given premises.

2 Does not include environmental testing performed after depopulation of infected commercial and independent premises.

3 LMS ID was used as a proxy for the number of tests conducted/ samples collected. Samples are assumed to be five bird pools.

7 Premises types included Commercial Broiler Production, Commercial Hatchery, Commercial Table Egg Layer, Commercial 

Table Egg Pullets, Commercial Turkey Meat Bird, Independent Table Egg Producer, Independent Table Egg Pullets, and Squab 

Producer

8 Commercial and backyard non-commercial poultry premises within the RQA were subject to routine, ongoing active 

surveillance testing throughout the duration of the outbreak. Commercial and larger non-commercial, backyard premises 

outside the RQA with links to premises within the RQA were tested as well.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 13

Table 3. The number of distinct sampled uninfected commercial and independent premises, laboratory 

accessions, and samples collected from negative premises in the RQA as part of vNDV surveillance by 

production type.

Production Type Premises Accessions1 Samples2

Commercial Broiler Production 7 116 690

Commercial Hatchery 1 65 393

Commercial Table Egg Layer 13 870 5,220

Commercial Table Egg Pullets 5 209 1,188

Commercial Turkey Meat Bird 2 19 114

Independent Table Egg Producer 29 1,642 9,332

Independent Table Egg Pullets 2 171 1,021

Squab Producer 1 1 6

Total 60 3,093 17,964

1 LMS accessions were used as a proxy for the number of testing events that occurred at a given premises.

2 LMS ID was used as a proxy for the number of tests conducted/ samples collected. Samples are assumed to be five bird pools.

D. References

USDA-APHIS (2018). “Epidemiologic Analysis of Virulent Newcastle Disease in Backyard Birds in 

California, December 2018.” USDA:APHIS:VS:STAS:Center for Epidemiology and Animal Health. 

Fort Collins, CO. December 2018. M&M Doc #447.0718. 41pgs.

Brown V.R., Bevins S.N., A review of virulent Newcastle disease viruses in the United States and the 

role of wild birds in viral persistence and spread. Vet Res. 2017; 48: 68. 

Freier, J. E., et al. "Spatially-targeted surveillance for Newcastle disease in southern California." Proc.

GISVET 4 (2004): 3-5.

Garcia S.C., Lopez R.N., Morales R., Olvera M. A., Marquez M. A., Merino R., Miller P. J., Afonso C.L., 

Molecular epidemiology of Newcastle disease in Mexico and the potential spillover of viruses 

from poultry into wild bird species. Appl. and Environ. Microbio. 2013; 79:4985-4992.

Susta L., Hamal K.R., Miller P.J., Cardenas-Garcia S., Brown C.C., Pedersen J.C., Gongora V., Afonso 

C.L., Separate evolution of virulent Newcastle disease viruses from Mexico and Central America. 

J Clin Micro. 2014; 52:1382-1390.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

14 USDA APHIS VS

II. PHYLOGENETIC ANALYSIS AND DIAGNOSTICS

A. Virulent Newcastle Disease Virus

This section describes viruses characterized from the 2018-2019 vND events in California (CA2018). The 

index case is chicken/California/18-016505-1/2018, which has an amino acid cleavage site of 

PGGRRQKR/FVGAII. The intracerebral pathogenicity index (ICPI) conducted on selected isolates in 

accordance with OIE guidelines confirms virulence9. Chickens have predominantly been affected; other 

species from which the virus has been recovered include turkey, peafowl (peacock), duck, goose, dove, 

and pigeon. Studies with the CA2018 index virus at the Southeast Poultry Research Laboratory suggest 

that it is highly adapted to and very infectious for chickens, and that knowledge from studies conducted 

on related viruses from California 2002 may be useful (Ferreira et al, 2019).

Methods

Genetic sequence data from the virus are used to determine the cleavage site, which serves as disease 

confirmation. Additionally, full genomic sequence data are generated and analyzed to monitor virus 

evolution and to inform epidemiologic investigations. Genetic data are also used to confirm that 

diagnostic assays are fit for purpose. 

Results

NOTE: The outcomes of phylogenetic analysis should be interpreted in context of all 

available virus and epidemiologic information and should not be used directly to infer 

transmission.

The CA2018 virus (genotype Vb) is related to older Mexican-lineage viruses from Central American 

village poultry (Belize 2008, Honduras 2007), and the U.S. (smuggled parrot 1996, CA2002), which 

represent viruses from birds with low or no vaccine coverage. The current genetic analysis based upon 

446 full genome sequences supports a recent, single introduction into California followed by secondary 

spread. Lack of epidemiologic data regarding the index premises, and of contemporary sequence data 

contribute to the uncertainty surrounding the origin of the outbreak. Evolutionary analysis of available 

sequences with the CA2018 and CA2002 viruses suggests that, although the viruses are related to one 

another, CA2018 is not directly descended from CA2002, and that the virus has likely been actively 

circulating and evolving at an expected rate; however, where and in what type of chicken population 

remains unclear.

There have been no changes in the amino acid profile at the cleavage site (RQKR/FVGAII) among 

sequenced viruses; however, synonymous nucleotide substitution within the cleavage site has been 

observed. The ICPI ranges between 1.6-1.8 for viruses tested (n=14). 

9 The World Organisation for Animal Health (OIE) defines Newcastle disease as an infection with a virulent APMV-1 virus (vNDV) 

characterized by either an intracerebral pathogenicity index (ICPI) of 0.7 or greater in day-old chickens, or the presence of 

multiple basic amino acids at positions 113- 116 of the C-terminus of the fusion (F2) protein (either arginine (R) or lysine (K)), 

plus phenylalanine (F) at residue 117 of the F1 protein.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 15

Divergence of the virus into two sub-groups appeared early on and, where epidemiologic data is 

available, has been useful to gain insights on virus spread. Two viruses that share the same nucleotides 

as a related reference virus at specific sites in the fusion gene represent the oldest viruses in terms of 

viral evolution (vNDV-00). The main sub-groups (vNDV-01 and vNDV-02) are defined by the presence of 

a sustained change (single nucleotide polymorphism [SNP]) in the fusion gene compared to a related 

reference sequence; both sub-groups have been detected in backyard, exhibition, and layer flocks 

(group vNDV-01 in San Bernardino, and vNDV-02 in Riverside, as well as exhibition flocks in Utah and 

Arizona). Further sub-clusters have also been defined by sustained SNPs along the genome. 

Although geospatial clustering of viruses has been observed, the presence of different virus sub-groups 

in each of the major affected areas indicates virus movement within, and between, affected areas 

(Figure 3). Virus from affected layer facilities in Riverside County (vNDV-01) are different from those in 

affected layer facilities in San Bernardino County (vNDV-02) representing separate events by county; the 

potential for limited lateral spread cannot be distinguished from common exposure within each county 

based upon available data.

Figure 3. Distribution of analyzed viruses by virus group and date of sample collection through November 

2019.

Further subgrouping within each group (vNDV-01 and vNDV-02) was observed as the outbreak 

continued. The presence of specific sustained nucleotide changes allows the ability to track specific 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

16 USDA APHIS VS

viruses (note this data should not be interpreted as a change in virulence or transmissibility). Based 

upon these sustained changes, the potential for epidemiologic links was further investigated for one 

vNDV-02 subgroup (henceforth “RV-a” for ease of reference). From 19 December 2018 to 11 May 2019, 

the RV-a subgroup was confirmed on 28 premises (Figure 4): 24 backyard producer premises in Riverside 

(n=10) and San Bernardino (n=14) counties; 2 independent table egg producer premises in San 

Bernardino County; 1 backyard producer premises in Compton, Los Angeles County; and 1 backyard 

producer premises in Flagstaff, Coconino County, AZ.

Figure 4. Distribution of the RV-a vNDV subgroup in California from 19 December 2018 to 11 May 2019.

Color changes from lighter blue to darker blue over time (i.e., lighter blue dots detected earlier). Not 

pictured: a backyard producer premises in Flagstaff, Coconino County, AZ, (collected on 28 March 2019), 

and a backyard producer premises in Compton, Los Angeles County, (collected on 15 February 2019).

The city location of premises and date sampled for the RV-a subgroup are listed in Table 4. The first virus 

from the RV-a subgroup was detected 19 December 2018 on the premises of a backyard producer with 

30 birds (21 laying hens and 7 roosters) in Riverside County. The owner called to report sick birds on 18 

December 2018 reporting mortality and sick birds in their flock. The flock was depopulated on 20 

December 2018. The next premises to be identified with this subgroup was a backyard producer with 

320 birds in Fontana, San Bernardino County who reported sick and dead birds on 16 January 2019. 

Epidemiologic links between these two premises were not identified, and no recent new birds or visitors 

with birds were reported on the second premises. Remaining live birds on the premises were 

depopulated on 19 January 2019.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 17

Table 4. Detection timeline for the RV-a vNDV subgroup in California between 19 December 2018 to 11 May 

2019 by sample collection date. RV = Riverside County, CA; SB = San Bernardino County, CA; LA = Los 

Angeles County, CA; CO = Coconino County, AZ.

During the month of February 2019, 4 additional background premises were identified in Fontana with 

the RV-a subgroup: 2 in Mira Loma, 1 in Highland, and 1 in Corona (all in Riverside and San Bernardino 

counties). The RV-a subgroup virus was also identified on a backyard bird premises in Los Angeles 

County. The owner made the sick call on 2 February 2019 after a 2-day history of bird illness, reporting 

signs consistent with vND. An epidemiological interview was not available for this premises at the time 

of this analysis. There have been no other detections of the RV-a subgroup in Los Angeles County as of 

23 July 2019.

The RV-a subgroup was detected in a sample from an independent table egg producer premises 

collected on 28 February 2019. The closest backyard premises infected with the RV-a subgroup at that 

time was about 2 km away. An interview was conducted with the owner of birds on the backyard 

premises on 24 February 2019, and no illness was reported in birds at that time. The birds were still 

reported to be without clinical signs on 4 March 2019 when follow-up targeted surveillance was 

performed, and positive results obtained. The RV-a subgroup was also confirmed in two additional 

backyard premises in Chino and one in Norco in early March. In early April, two additional premises 

were identified in Ontario (approximately 1.4 km from the premises sampled on 28 February 2019) and 

three additional premises were detected in Norco in Riverside County. 

A second independent table egg producer premises in San Bernardino County was identified with the 

RV-a subgroup from a sample collected on 12 March 2019. Surveillance in the area around this 

operation found several backyard premises in proximity that were also infected with the RV-a subgroup. 

Of these, one backyard premises had reported clinical signs consistent with vND within the previous 30 

days. In the epidemiologic report for this backyard premises, the interviewer noted that the birds were 

loose and known to wander onto the adjacent neighboring independent table egg producer premises. 

Two additional infected backyard premises were identified nearby during late March. 

Co. City

12/19/1801/16/1902/12/1902/13/1902/14/1902/15/1902/17/1902/19/1902/20/1902/28/1903/03/1903/04/1903/12/1903/13/1903/17/1903/27/1903/28/1903/31/1904/01/1904/03/1904/08/1904/13/1905/06/1905/11/19

Riverside 1 1 1

Mira Loma 1 1

Corona 1

Norco 1 1 1 1

Fontana 1 1 1 1 1 1 1 2

Highland 1

Ontario 1 1 1 1

Chino 1 1

LA Compton 1

CO Flagstaff 1

Date sample was collected (mm/dd/yy)

RV

SB
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

18 USDA APHIS VS

A single exhibition premises was identified with the RV-a subgroup in Flagstaff, AZ based on samples 

collected on 28 March 2019. Although no epidemiologic links were identified, the virus data connects 

this detection to other infected premises in California. No further cases in AZ have been detected. 

No presumptive or confirmed positive premises were reported between the weeks of 2 June 2019 and 

10 August 2019. On 14 August 2019, a new premises was confirmed in a feed store within a previously 

infected control zone through outreach testing. Further surveillance identified additional infected 

backyard premises within the control zone. Although there was a period of approximately 10 weeks 

where no virus was detected, genetic analysis of the new detections was closely related to a specific 

subgroup of vNDV-02 viruses that survived eradication attempts. This cluster of detections starting 

August 14 all fell into the same vNDV-02 subgroup and did not represent a new introduction of the virus,

based upon molecular studies and epidemiologic investigation (Figure 5). 

Examination of this subgroup of the vNDV-02 viruses provided valuable information on disease risks and 

linkages, while also revealing the complex and poorly understood pathways of transmission in these 

populations. Spatial and temporal patterns of this virus subgroup highlight the interconnected nature of 

these neighborhoods and populations, which can complicate disease control efforts. Phylogenetic 

analysis represents an important tool for understanding disease spread, and this understanding is 

further enhanced where epidemiologic data are available.

Figure 5. Distribution of subgroup of vNDV-02 viruses which occurred after 1 August 2019. The red circle 

indicates the location of an earlier detection of this virus subgroup prior to its resurgence in August.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 19

B. Comparison to Other Viruses/Lineages 

The CA2018 virus is not related to classic Newcastle disease vaccine strains, nor to available strains from 

vaccinated poultry in Mexico (2000-2010). CA2018 is also unrelated to viruses endemic to columbids 

(pigeons, doves; genotype VI), as well as genotype V from double-crested cormorants (Figure 6).

Figure 6. Phylogenetic analysis based on the full-length nucleotide sequence of the fusion gene of isolates 

representing Newcastle disease virus class II, genotype V (Dimitrov et al., 2019)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

20 USDA APHIS VS

C. Diagnostics

Testing avian swabs/tissues for APMV-1 involves screening assays (real time reverse transcription 

polymerase chain reaction [rRT-PCR]), virus isolation, and characterization of the virus (sequencing and 

in vivo tests). The National Animal Health Laboratory Network (NAHLN) tests swab/tissue first by the 

APMV-1 matrix-target rRT-PCR test,

10 best suited to detect Class II viruses that contain low and highly 

virulent pathotypes, including vaccine viruses. Detections by the matrix-target test are subsequently

tested by a fusion gene-target rRT-PCR test, which is designed to allow rapid identification of virulent 

viruses reportable in poultry. This approach does not provide the genetic or geographic lineage of the 

virus. Sequence analysis of the virus compared to the assay primers and probes confirmed high identity 

between the CA2018 virus sequences and the fusion gene-target rRT-PCR test. A negative fusion genetarget test in the face of clinical signs requires further testing including virus recovery, sequence, and/or 

ICPI testing.

Under normal surveillance, all poultry samples with a nonnegative test result by APMV-1 PCR or virus 

isolation are forwarded to NVSL for confirmatory testing; for the current CA vND event, the NAHLN 

laboratory is using the highly matched fusion-target assay. The NVSL uses Sanger sequencing protocols 

to generate partial fusion gene sequence directly from the sample for virulence determination, where 

sufficient viral RNA is present. Whole genome sequencing is conducted on all isolated viruses, and select 

viruses are further characterized by ICPI in specific pathogen-free chickens. 

The NVSL confirms the virus lineage and virulence through molecular sequencing. Where no virus can be 

recovered nor sequence obtained directly from sample(s), the virulence is determined by the clinical 

presentation of the flock compared to the USDA vNDV case definition.

D. References

Dimitrov KM, Ferreira HL, Pantin-Jackwood MJ, et al. Pathogenicity and transmission of virulent 

Newcastle disease virus from the 2018–2019 California outbreak and related viruses in young and 

adult chickens. Virology, 2019 Vol 531:203-218. https://doi.org/10.1016/j.virol.2019.03.010

Ferreira HL, Taylora TL, Dimitrov KM, et al. Virulent Newcastle disease viruses from chicken origin are 

more pathogenic and transmissible to chickens than viruses normally maintained in wild birds. 

Veterinary Microbiology 235 (2019) 25–34 (accepted). 

10 PCR results from the NVSL are reported as “detected” or “not detected” and include the cycle threshold (Ct) value. The lower 

the Ct value, the more viral nucleic acid was detected.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 21

III. POPULATION AT RISK

A. Predicting Areas of Backyard Bird Ownership

The distribution of backyard bird flocks in the United States is currently unknown. However, statistical 

modeling can be used to estimate the likely locations and densities of backyard flocks in a given 

geographic area using socio-economic and demographic variables that have been shown historically to 

be related to bird ownership. This approach was used to develop neighborhood-level risk maps to 

identify and prioritize areas for surveillance during the 2002-2003 outbreak of vND in the United States 

(Freier et al., 2004, Freier et al., 2007). Building on that historical work, statistical models were 

developed that identified areas with increased probability of backyard poultry ownership to inform 

surveillance and response efforts. The objectives of this analysis were two-fold, first to identify socioeconomic and demographic risk factors associated with poultry ownership. Second, to use these 

relationships to predict the number of backyard poultry flocks at the neighborhood-level.

Methods

Data 

Census block groups within 1.5km of positive premises were identified. These block groups, which can 

be conceptualized as neighborhoods, are assumed to have been completely surveyed for presence of 

poultry. The number of premises with poultry were tallied for each block group. These counts of homes 

with poultry were used as the response variable in models. The total number of households in each 

block group were extracted from the census data and assumed to represent all possible households that 

could have had poultry. Census variables previously identified as associated with backyard poultry 

ownership were considered in models determining associations among poultry ownership and sociodemographic and economic variables. 

Model 

Generalized additive models (GAMs) accounting for correlation in spatial areal units and non-linear 

effects of predictors were used to analyze vND outbreak response data and predict the number of 

backyard flocks present in census block groups. Three alternative model structures (Poisson, Binomial, 

and Negative Binomial) were evaluated based on predictive capacity as measured using adjusted R2and 

amount of deviance in the data the model explained, and Akaike information criterion (AIC). Because of 

non-linear distributions of predictors, a thin plate spline smoother was used for each predictor. The 

appropriate smoothness for each predictor was determined using likelihood-based methods with a 

smoothing penalty. The smoothing penalty, which includes a small shrinkage component, results in 

smoothing parameters that become identically zero when the predictor is not significant. This allows 

smoothing parameter selection to effectively remove the predictor from the model altogether without 

requiring formal model select methods which are CPU-intensive. Models were validated using k-fold 

cross validation consisting of 10 bins. Models where fit using the mgcv package in R (R Core Team, 

Vienna Austria, 2020). 

Results

The best predictive model was a generalized additive model (GAM) accounting for correlation in spatial 

areal units and non-linear effects of predictors. The model was used to predict the number of backyard 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

22 USDA APHIS VS

flocks present in each census block group. The GAM used a Negative Binomial error structure in the 

response variable (number of backyard flocks in each census block group). Because of non-linear 

distributions of predictors used in the GAM smoothing splines where used for predictors that 

demonstrated non-linear associations with the response variable. The appropriate smoothness for each 

predictor was determined using likelihood-based methods with a smoothing penalty. 

The final model explained 76.3 percent of the deviance. Out-of-sample cross validation using k-fold 

methods, had high correlation (0.75) among out-of-sample and predicted number of poultry flocks in 

census block groups (Figure 7). These results provide confidence in the predicted number of backyard 

flocks in census block groups. Despite this confidence there was large variation in the predictions thus 

predictions should be interpreted as relative measures of backyard poultry ownership with areas of high 

predicted backyard poultry flocks indicating relatively greater numbers of flocks.

Figure 7. Comparison of predicted number of backyard poultry flocks (boxplots) with observed distribution 

of backyard poultry flocks (red). The model tends to over-predict for very small numbers of poultry 

flocks (<5) in census block groups and under-predict for block groups with very large numbers of poultry 

flocks (>100).

Socio-demographic variables associated most closely with poultry ownership were the level of education 

of the population and the housing density (Figure 8 and Figure 9). Additionally, the number of 

nonfamily members living in homes and the degree of ethnic diversity in the neighborhood were also

associated with poultry ownership. Socio-economic factors of household income, home value, and 

receipt of public assistance were important but less so than other factors. Home density, total 

population, and the mean age of homes in years were also important predictors. 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 23

Figure 8. Predictive variables used in the generalized additive model. Panel A presents the significance of 

smoother (non-linear) predictors and Panel B presents the estimated effect size for the parametric 

predictive variables.

Figure 9. Smoothing splines describing the relationship between number of poultry flocks and non-linear 

predictor variables.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

24 USDA APHIS VS

The geographic distribution of poultry ownership (Figure 10) aligns well with the observed geographic 

distribution of poultry flocks. Additionally, this map identifies populations of backyard poultry that may 

be important for surveillance or at risk for vNDV transmission. These predictions can be used to inform 

surveillance activities, planning related to the number of vaccine doses that may be needed, or the 

number of poultry that may need to be culled to control transmission and spread. Additionally, these 

predictions also identify populations of poultry owners that may be important to target for education 

campaigns or other proactive prevention activities

Figure 10. Predicted geographic distribution of backyard poultry flocks in southern California. The map 

presents the density of flocks per km2.

Summary

The area impacted by the outbreak had a very dense population of backyard poultry. However, limited 

information was available prior to the outbreak to aid responders in locating and testing backyard 

poultry operations. Using sociodemographic variables to predict where backyard poultry are likely to be 

kept provided rapid information that served as a baseline for response planning. This work built upon

analyses that were performed during a previous outbreak of vND in 2002-2003. While many of the same 

predictors were found to be significant, the resurgence in popularity of keeping backyard chickens has 

led to the presence of backyard poultry in areas where it was historically uncommon. As a result, model 

outcomes should be interpreted as relative measures of backyard poultry ownership and supplemented 

with on the ground surveillance and neighborhood visits.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 25

IV. EPIDEMIOLOGIC RISK

A. Case Control Study

A case-control epidemiological analysis was performed on confirmed and presumptive 

positive virulent Newcastle disease (vND) backyard/exhibition premises, dangerous contact premises, 

and noninfected premises. Data were obtained from in-person interviews using the CDFA 

Non-Commercial Premises Virulent Newcastle Disease Epidemiology Questionnaire (Appendix A: 

Questionnaire). Questionnaire data were entered into the USDA’s Emergency Management Response 

System (EMRS).

Methods

Data were analyzed for 912 premises: 137 confirmed or presumptive positive premises, 68 dangerous 

contact premises, and 712 noninfected premises. The analysis included data from questionnaires that 

were completed from 16 May to 9 November 2018 and includes all confirmed and presumptive 

premises for which questionnaire data were entered into the EMRS as of 9 November 2018. The 

questionnaire form was updated in July 2018 with additional questions; 69 respondents completed the 

original questionnaire and 848 completed the updated questionnaire. Questionnaires were not 

complete for all premises, such as in cases in which the owners refused to provide answers to certain 

questions. The number (n) of responding premises is noted in Table 5. Odds ratios, p-values and 95-

percent confidence intervals (CI) for flock characteristics and other risk factors were estimated by 

univariate logistic regression, using confirmed/presumptive premises as cases and noninfected premises 

as controls. Dangerous contacts were excluded from the regression analysis. To identify significant risk 

factors, while controlling for possible confounding variables, two multivariable logistic regression 

analyses were performed. The first included questions found in both versions of the questionnaire, 

while the second included questions found only in the newer version of the questionnaire. All variables

that had a statistically significant (p-value < 0.1) predictive effect on being a case were included in the 

analysis, and backward stepwise elimination was used to obtain final models.

Results

Premises characteristics 

The reported flock sizes ranged from 1 to 853 birds (mean=51, median=18 birds). Thirty-three percent of 

all backyard/exhibition flock owners had multiple bird species on their premises. These premises 

primarily had backyard chickens (82.9 percent). Fewer premises had exhibition birds/game fowl (8.5 

percent), and ducks/geese (11.5 percent). Other types of birds were reported on 30 percent of 

premises; the most commonly reported species were pigeons, turkeys, peafowl, parrots, and cockatiels. 

Besides birds, 35 percent of owners had other livestock species on their backyard premises, 76 percent 

had dogs/cats, and 8.5 percent reported other non-bird species.

Housing types 

Most respondents (59.6 percent) reported housing birds outdoors in cages or coops, with 28 percent 

housing birds outdoors in open top pens or enclosures, and only 7 percent housing birds indoors. Only 5 

percent of respondents reported keeping birds individually tethered, and 35 percent reported having 

free-range birds.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

26 USDA APHIS VS

Illness and mortality 

Sixty-four percent of case premises reported bird illness, and 65.7 percent reported mortality. The mean 

time reported between onset of illness and presumptive detection was 9.6 days (median=6.0, range 1-

90 days). The mean time between onset of mortality and presumptive detection was 10.1 days 

(median=4.7 days, range 1 to 90 days). As an indicator of background morbidity and mortality, the 

percentage of control premises reporting illness was 10.5 percent and mortality was 17.6 percent. 

Risk factors – Univariate analysis 

• Flock size

Case premises reported larger flock sizes than control premises. The odds of being a case 

were significantly greater for flock sizes greater than 100 birds (OR = 11.6, 95 percent CI: 

6.4-21.0) or from 20 to 99 birds (OR = 5.0, 95 percent CI: 3.0 – 8.5) when compared with

flock sizes of fewer than 20 birds.

• Bird types

Case premises were more likely to report having flocks that included exhibition birds or 

other non-chicken bird species than control premises (OR = 7.7, 95 percent CI: 4.6-12.8). 

The odds of becoming a case premises were also higher when roosters comprised more 

than 50 percent of the adult birds in the flock (OR=4.3, 95 percent CI: 2.7-6.7).

• Contact with other domestic and wild birds 

Although only 8.8 percent of case premises reported keeping birds at other premises, the 

odds of being a case were higher (OR = 3.9, 95 percent CI: 1.8-8.2) when birds were kept 

at multiple locations.

A high percentage of both case and control premisesreported having neighbors with birds 

(75.9 percent and 55.0 percent, respectively); however, premises that reported that 

their birds visit neighboring properties or that their neighbors’ birds visit their property 

did not have increased odds of becoming a case. Contact with wild birds (OR = 3.5, 95

percent CI 2.0-6.2) was associated with greater odds of becoming a case premises.

• The use of Newcastle vaccine

The percentage of premises reporting the use of Newcastle vaccine was low overall (6.9 

percent). The percentage of case premises that reported using Newcastle vaccine was 

much higher than the percentage of controls that reported using Newcastle vaccine 

(18.9 percent vs 5.6 percent, respectively), and the risk of disease was greater among 

flocks that reported use of Newcastle vaccine (OR = 4.2, 95 percent CI: 2.4-7.5).

Risk factors – Multivariate analysis 

Many of the risk factors described previously are related. A multivariate analysis was performed in order 

to provide adjusted odds ratios for risk factors, while considering the interrelationships among these 

flock management characteristics and behaviors. For the multivariate analysis including both versions of 

the questionnaire, 103 cases and 579 controls were examined (Table 6). Larger flock sizes (OR = 3.9, 95
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 27

percent CI: 2.2-7.1 for 20-99 birds; and OR = 5.7 95 percent CI: 2.8-11.7 for flocks with more than 99 

birds), the presence of game fowl on the premises (OR = 4.6, 95 percent CI 2.5-8.6), and having greater 

than 50 percent of adult birds as roosters (OR = 2.4, 95 percent CI 1.4-4.1) significantly increased the 

odds of becoming infected. A nested analysis looking only at questions found in the newer version of the 

survey (84 cases and 622 controls) identified these same factors, as well as wild bird contact with 

domestic birds (OR = 3.1, 95 percent CI: 1.7-5.9), and having neighbors with birds (OR = 2.2, 95 percent

CI: 1.2-3.9) as significant risk factors. 

Summary

These results suggest that flock size, ownership of exhibition birds, a high proportion of roosters in the 

flock, and housing that facilitates contact with nearby domestic and wild birds are risk factors for vND 

infection in this population. Some of these practices have been shown to be risk factors in other studies 

or previous vND outbreaks in the United States, as summarized below. However, not all epidemiology 

questionnaires were complete, and it is likely there is misclassification bias for some of these results, 

such as the type and number of birds on premises, the number of owners, and use of Newcastle vaccine; 

therefore, results should be interpreted with caution. 

Summary of Historical Epidemiologic Risk Factors

An epidemiological study of backyard premises during the 2002-2003 California vND outbreak identified 

the following risk factors for vND infection on premises: presence of game fowl, presence of feral 

chickens, flock sizes larger than 40 birds, and multiple owners of a flock. Epidemiological descriptions of

infected backyard premises in the 1971-1974 outbreak identified contact with infected commercial layer 

farms as the primary source of infection, followed by active trading of birds among backyard flocks and 

purchases of infected exotic birds from dealers. The severity of infection among commercial premises 

during the 1971-1974 outbreak was attributed to the high density of egg-laying premises and extensive 

contact among those premises. In both the 1971-1974 and 2002-2003 California vND outbreaks, a 

suspected risk factor for vND infection in commercial premises was movement of contaminated 

equipment, such as egg carts.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

28 USDA APHIS VS

Table 5. Characteristics of backyard case premises (confirmed/presumptive positive for vND), dangerous 

contact (DC) premises, control premises (C), and odds ratios (OR) and p-values calculated by univariate 

logistic regression (dangerous contacts excluded).

Table 6. Adjusted odds ratios (OR) for significant risk factors identified in multivariate regression analyses.

Characteristic Level OR p-value

Number of birds1 1-19 Ref

20-99 5.4 0.04

100+ 9.0 0.001

Game fowl on premises1 4.8 0.001

Adult birds >50 percent roosters1 2.4 <0.001

Neighbors have birds2 2.2 0.007

Wild birds have contact with domestic birds2 2.6 0.003

1Results from analysis that included questions found on both versions of the survey (102 cases and 538 controls)

2Results from analysis that included questions found only on the newer version of the survey (84 cases and 604 controls)

Characteristic Level

n

Case DC Control OR p-value

Number of birds 1-19 20/125 8/43 385/698 Ref

20-99 64/125 9/43 245/698 5.0 <0.001

100+ 41/125 8/43 68/698 11.6 <0.001

Bird species on premises Backyard chickens 98/125 23/25 635/695 0.34 0.207

Exhibition birds 37/125 5/25 36/695 7.7 0.005

Ducks/geese 18/125 5/25 82/695 1.3 0.329

Other species 45/125 8/25 217/695 1.2 0.019

Adult birds >50 percent roosters 43/103 3/23 84/583 4.3 0.001

Owners keep birds on other 

premises

12/119 1/23 19/676 3.9 <0.001

Nonbird species or wildlife on 

premises

17/67 3/9 38/193 1.4 0.328

Housing Inside home

Outdoor open top

Outdoor cage/coop

Individual tether

Free range

3/93

34/93

76/93

6/93

46/93

0/19

10/19

13/19

0/19

10/19

52/671

217/671

458/671

43/671

266/671

0.4

1.2

2.1

1.0

1.5

0.126

0.417

0.009

NA

0.072

Movement of new birds onto the premises within 30 

days prior to the interview 12/121 2/24 44/674 1.7 0.123

Movement of birds off the premises within 30 days 

prior to the interview 8/119 0/23 30/651 1.5 0.33

Give/sell eggs 11/92 2/19 79/662 1.0 NA

Neighbors have birds 66/87 13/19 357/649 2.6 <0.001

Birds visit neighbors 16/88 2/18 392/624 1.8 0.063

Wild birds have contact with domestic birds 77/92 16/20 392/660 3.5 <0.001

Newcastle disease vaccine No 84/122 22/25 589/683 Ref

Yes 23/122 2/25 38/683 4.2 <0.001

Unsure 15/122 1/25 56/683 1.9 0.776
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 29

B. Epidemiologic Investigation of vNDv-Infected Commercial and Backyard NonCommercial Laying Chicken Premises

Between 14 December 2018 and 20 March 2019, one commercial table egg pullet, three commercial 

table egg layer, and six backyard/non-commercial layer chicken premises in Riverside County (n=5) and 

San Bernardino County (n=5) were confirmed positive for vND (Table 7)

11

.

Methods

A descriptive epidemiologic study was performed on 10 vNDv-infected commercial and backyard noncommercial layer chicken premises. Twenty-eight non-infected commercial and backyard noncommercial layer chicken premises located within the three-county regional quarantine area were 

included in the study as controls. CDFA personnel administered an in-person questionnaire to 

individual(s) on each premises most familiar with its management and operations. Questions focused 

on management practices, biosecurity, and potential epidemiologic contacts to generate hypotheses 

about potential risk factors for infection with vNDv. Questionnaires were not completed for all 

premises, such as in cases where the respondent declined to provide answers to certain questions. The 

numbers of responding premises for each question are noted in

11 Commercial table egg layer and commercial table egg pullet premises are defined as those with more than 75,000 birds. 

Table egg layer premises with fewer than 75,000 birds are referred to as backyard/non-commercial layer chicken premises.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

30 USDA APHIS VS

Table 9. Hypothesis testing for all yes/no questions was performed using Fisher’s exact test, given the 

small sample sizes; however, the resulting p-values for all questions were greater than 0.05. Therefore, 

odds ratios and statistical results are not provided.

Results

Case premises and control premises reported similar mean numbers of birds, numbers of flocks, 

numbers of houses in use, and numbers of employees (

Table 8). Transmission of vND virus in commercial flocks in previous US outbreaks has been attributed to 

movement of live birds, sharing of equipment, and contaminated service vehicles (Bulaga et al., 2004, 

Burridge et al., 1975, Utterbeck and Schwartz, 1973). Results of the questionnaire, focusing on risk 

factors identified in previous outbreaks, are summarized below and in
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 31

Table 9. Results showed that some factors and management practices were shared across infected 

farms; however, the significance of these similarities is difficult to interpret given the small number of 

infected farms and the study design. When considered in conjunction with knowledge of practices and 

risk factors from previous outbreaks, this information may provide insights into trends of management 

practices over time and elucidate opportunities to implement additional mitigations in the future.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

32 USDA APHIS VS

Table 7. Production types, counties, confirmation dates, and numbers of euthanized birds on 10 vNDv

infected commercial and backyard/non-commercial layer chicken premises.

Production Type County Confirmation Date Number of Birds

Euthanized

Commercial Table Egg Pullet Riverside 14 December 2018 103,000

Commercial Table Egg Layer Riverside 7 January 2019 140,732

Commercial Table Egg Layer Riverside 9 January 2019 172,187

Backyard Non-Commercial Laying 

Chickens San Bernardino 24 January 2019 46,953

Commercial Table Egg Layer Riverside 1 February 2019 406,402

Backyard Non-Commercial Laying 

Chickens San Bernardino 16 February 2019 71,955

Backyard Non-Commercial Laying 

Chickens San Bernardino 2 March 2019 63,000

Backyard Non-Commercial Laying 

Chickens San Bernardino 2 March 2019 28,000

Backyard Non-Commercial Laying 

Chickens San Bernardino 14 March 2019 42,282

Backyard Non-Commercial Laying 

Chickens Riverside 20 March 2019 40,542

Risk /Protective Factors 

• Ownership

One case premises and four control premises reported having at least two collocated flocks 

with different owners. Eight owners of case premises and nineteen owners of control 

premises reported owning multiple premises.

• Vaccination

All cases and controls that provided an answer (10/10 and 26/28, respectively) reported that 

their birds had been vaccinated for Newcastle virus. 

• Use of external poultry services

Four case premises and seven control premises reported using outside vaccination crews.

Four cases premises and seven control premises reported using outside beak trimming 

crews. Zero case premises and four control premises reported using outside layer catch 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 33

crews. Four case premises and ten control premises reported that non-employees 

hauled spent hens away.

• Dead bird disposal

Six case premises and seven control premises reported composting. Two case premises and 

four control premises reported incinerating. Two case premises and nine control 

premises reported disposing in a landfill. Zero case premises and two control premises

reported using a renderer. Six control premises reported other methods of disposal.

• Manure hauling

Nine cases reported using five different manure haulers. Twenty-three controls reported 

using ten different manure haulers.

• Sources of feed

One case reported supplying its own feed while the other nine used two different feed 

suppliers. Four controls reported supplying their own feed while twenty-four reported 

using five different feed suppliers. No cases and only two controls reported using more 

than one feed supplier.

• Physical biosecurity

All cases and most controls (25/26 responding) had a perimeter fence with a gate and 

disinfection station at the entrance. All cases and most controls (26/27 responding) 

restricted access to essential personnel.

Table 8. Numbers of birds, numbers of flocks, numbers of houses in use and numbers of employees 

reported by vND infected case premises (n=10) and control premises (n=28) located in the three-county

regional quarantine area of southern California.

Characteristic Case

mean (range)

Control

mean (range)

Reported number of birds 114,325 (24,000-420,000) 102,177 (740-1,500,000)

Number of flocks 4 (1-7) 3.4 (1-8)

Number of houses in use 10.4 (1-28) 7.9 (1-20)

Number of employees 10.5 (2-32) 8.3 (2-27)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

34 USDA APHIS VS

Table 9. Management characteristics of vND infected case premises (n=10) and control premises (n=28) in 

the three-county regional control area of southern California.

Characteristic Level or response N cases N controls

Production systems Inline layers 3/10 2/28

Offline layers 7/10 22/28

Brooders 0/10 2/28

Pullets 1/10 7/28

Housing type Open sided 3/10 12/28

Open sided with curtains 5/9 7/28

Closed house 1/10 7/28

Pasture raised 1/10 2/28

Raise own pullets Yes 5/10 16/28

Buy adult hens Yes 2/9 8/26

Live bird market supplier Yes 0/10 2/28

Eggs processed onsite Yes 5/10 13/25

Use processor that processes eggs for other 

premises

Yes 3/9 10/25

Repackage processed eggs from other 

premises

Yes 0/7 7/26

Equipment/vehicles shared with other 

premises

Feed truck 1/8 0/26

Egg truck 2/8 3/26

Live bird hauler 0/8 4/26

Unspecified vehicle 1/8 7/26

Egg flats/racks 3/8 8/26

Fertilizer machine 3/8 3/26

Employees shared between premises Yes 5/5 7/28

Use reusable egg flats Yes 9/9 21/26

Transport eggs for other producers Yes 0/9 4/24

Pullets delivered as split load for more than 

one premises

Yes 0/9 1/23

Consumers enter premises to purchase birds 

or eggs directly

Yes 4/10 9/28
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 35

Disposal of rejected eggs Breaker plant 0/9 3/26

Landfill 1/9 4/25

Rendering 1/9 6/25

Composted onsite 7/9 9/25

Buried onsite 0/9 1/25

Other 1/9 11/25

Perimeter fence with gate and disinfection 

stations

Yes 10/10 25/26

Garbage/dead bird pickup restricted to 

outside perimeter fence

Yes 3/9 12/26

Other species on premises Waterfowl 1/10 2/28

Gamefowl 0/10 0/28

Other birds 2/10 9/28

Hooved animals 3/10 6/28

Dogs 5/10 13/28

Cats 2/10 12/28

Rodents 4/10 13/26

Other non-birds 3/4 3/17

Free range poultry observed on premises Yes 2/10 3/28

Free range poultry observed nearby outside 

premises

Yes 5/10 7/28

Backyard poultry within 0.5 miles of 

premises

Yes 6/10 16/28

Employees wear dedicated shoes that stay 

on premises

Yes 9/10 22/28

Employees wear dedicated clothing that 

stay on premises

Yes 6/10 17/28

Employees Reside on premises Yes 5/10 19/27

Employees sign agreement not to own birds Yes 10/10 26/27

Downtime required after visiting other 

premises with birds 

Yes 10/10 26/27
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

36 USDA APHIS VS

C. References

Bulaga, L.L., Dargatz, D., Garber, L., Miller, R., Rhoads, G. (2004). Risk Factors for exotic Newcastle 

disease infection in non-commercial flocks, California. Unpublished Report

Burridge, M. J., Riemann, H. P., Utterback, W.W. (1975). Methods of spread of velogenic 

viscerotropic Newcastle disease virus in southern California. Avian Diseases, 19(4), 666-678.

Speers, R., Webb, M., Grund, M, Howell, B., Hughes, C., Myrus, E., and, Silverman, J. (2004).

Reconstruction of response operations to eradicate exotic Newcastle disease in 2002-2003. 

Technical report produced for USDA by the CNA Corporation. 

USDA-APHIS (1978). Eradication of exotic Newcastle disease in southern California 1971-1974. 

APHIS-91-34 Technical Report

Utterback WW, Schwartz, J.H. (1973) Epizootiology of velogenic viscerotropic Newcastle disease in 

southern California, 1971-1973. J Am Vet Med Assoc. 163(9), 1080-1088.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 37

V. ESTIMATING DISEASE SPREAD

A. Flock Disease Spread Model–Early Outbreak

Methods

An epidemiologic scenario was developed in InterSpread Plus®v. 6.01.44 (Stevenson et al., 2013) to 

model the introduction and spread of vND from confirmed premises in San Bernardino county, California 

following the first case detection. Commercial and backyard farm units from the Western United States

(17 states) were incorporated into the model. The Farm Location and Animal Population Simulator was 

used to generate likely farm locations based on geospatial characteristics, with backyard farm locations 

adapted from current and historic outbreak-related data. Model parameters were developed to reflect

the impact of sustained outreach activities, incorporate preliminary experimental data on viral 

pathogenesis in chickens, include current strategies for active surveillance of commercial operations, 

and describe the potential geographic extent of disease spread during the silent-spread period. The 

model was updated regularly in order to provide timely results to the response during the early phase of 

the outbreak. The results presented below were developed early in the outbreak in the absence of 

information on risk factors. The actual outbreak data has been used to better refine and improve the 

model for future applications. 

Results

Summary outcomes for a 300-iteration scenario were generated from ten seeded-sites. The seeded sites 

were based on the latitude/longitude of initial confirmed cases of vND in San Bernardino County. 

Simulations include control activities implemented in the vND response, including outreach, quarantine, 

euthanasia/depopulation of detected premises, movement controls, tracing, and active and passive 

surveillance. Note: These outcomes are based on a completely naïve poultry population. The variable 

levels of vaccination applied within backyard farms is not explicitly modeled in this scenario.

The summary of results and their potential implications for the current vND outbreak are as follows:

Initial disease spread commonly involves direct movements of infectious birds, but local spread 

becomes more prevalent as outbreaks become greater than 50 infected premises.

Direct contacts associated with live animal movements accounted for 36 percent of spread for 

simulated outbreaks that resulted in less than 50 infected premises, and 27 percent of spread 

for simulated outbreaks that resulted in 50 or more infected premises. 

Local area spread became more prevalent as simulated outbreaks became larger, being 

responsible for 56 percent of disease spread for simulated outbreaks that resulted in 50 or more 

infected premises.

Implications: As the number of detected premises continues to increase, outcomes from 

simulated outbreaks suggest that local spread of vND among premises might be 

responsible for additional infections. Local spread is associated with distance 

between infectious and susceptible premises and represents mechanisms of spread 

that are difficult to trace, such as movement of free ranging birds, wildlife, or fenceline contact. Good biosecurity practices and measures are the best way to prevent 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

38 USDA APHIS VS

local spread (e.g., keeping outside birds in cages, moving cages away from 

neighboring fence lines, repairing damaged/missing fences, rodent control,

covering/tarping cages to decrease wildlife/rodent/loose-chicken exposures, and 

the spread of vND viral particles into the environment).

Small backyard operations

12 are the primary premises involved in outbreaks; large backyard 

operations or commercial poultry farms have a lower likelihood of becoming infected.

Across all simulated outbreaks, large backyard operations represented slightly less than 1 

percent of all infected premises, and commercial poultry farms represented 0.14 percent of all 

infected premises. 

vND-infected small backyard operations in 100 percent of all simulated outbreaks, large 

backyard operations in 22 percent of all simulated outbreaks, and commercial poultry farms in 7 

percent of simulated outbreaks. 

All spread to commercial operations resulted from indirect contact (e.g., people or vehicles 

moving from operation to operation) with infected, primarily small backyard operations. 

Implications: Unless generated by indirect contacts with infected backyard operations, 

outcomes from simulated outbreaks suggest a low probability of spreading vND to 

commercial farms. 

The extent of spread for simulated outbreaks is primarily in San Bernardino, Los Angeles, and 

Riverside counties. 

When considering disease spread within the silent period of the outbreak (three days prior to 

the first observation of clinical signs to the day of first detection), spread from infected premises 

in San Bernardino County to backyard chicken premises in Riverside County occurred in 66 

percent of simulated outbreaks and to backyard chicken premises in Los Angeles County in 65 

percent of simulated outbreaks.

In the current modeling scenario, 42 percent of simulated outbreaks involved 50 or more 

infected premises, and 19 percent of outbreaks involved 100 or more infected premises. 

Implications: Simulated outbreaks suggest future detections in other Southern California

counties, most commonly Riverside and Los Angeles. In addition, some infected 

premises might not be detected due to natural viral elimination from these 

premises (i.e., birds die and go unreported) and/or no new, naïve birds being 

brought onto previously infected premises.

12 In the model operations are defined as follows:

1) Commercial poultry farms: more than 75,000 table egg laying chickens, or more than 100,000 meat-type 

chickens, or more than 30,000 meat-type turkeys

2) Large backyard operations: more than 1,000 birds but fewer than the number of birds described for commercial 

operations

3) Small backyard operations: fewer than 1,000 birds
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 39

B. Comparing Alternative Control Strategies–Mid-Outbreak

Methods

As the outbreak progressed, selected parameters were revised from preliminary scenarios described 

previously to compare the impact of alternative control strategies on the severity and duration of 

simulated vND outbreaks. This analysis was performed and supplied to the Incident Coordination Group 

approximately 3 months into the outbreak.

Summary outcomes for a series of four 250-iteration scenarios were generated from 57 selected sites. 

The initially infected sites in the model were based on the latitude/longitude of initial confirmed cases of 

vND in San Bernardino and Riverside counties and from premises frequently infected during the silent 

spread period identified in previous modeling analyses. Each simulated outbreak was allowed to run for

a maximum of 365 days from detection of the first infected premises. All disease spread was considered 

lateral spread between infected and susceptible farms. Simulations varied in the availability of resources 

for conducting disease control activities, including outreach, quarantine, euthanasia/depopulation of 

detected premises, movement controls, tracing, and active surveillance. We assumed a completely naïve 

population, and the variable levels of vaccination possibly applied within backyard farms was not 

modeled explicitly.

Four levels of response were evaluated. A specific combination of integrated control strategies was

associated with each response option, with a general increase in response intensity from response 1 to 4 

(see Appendix B for detailed information on specific activities modeled in each response option). 

Disease control activities are identical for the first 161 days of each scenario to reflect the actual 

outbreak response up to that point in time. Alternative disease control activities, based on resource 

level, were applied at day 162 of each iteration (75 days post first detection). The model was run for 

250-iterations for each of the four response options. 

A summary comparison of response options and associated control activities are described in Table 10. 

The ‘X’s are provided to estimate a qualitative comparison between control strategies. They are not 

intended to approximate a quantitative comparison between response options. 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

40 USDA APHIS VS

Table 10. Qualitative summary comparison of the four alternative response options examined.

Response 

Option

Surveillance 

Capacity

Surveillance 

Zones

Movement 

Restrictions

Depopulation 

Capacity

Depopulation 

Zones

1 X X X X X

2 XX X XX XX X

3 XX XX XX XX XX

4 XXX XX XXX XXX XXX

Results

The best response option was dependent on the desired outcome. If limiting disease spread, as 

expressed by the mean number of infected backyard premises, was the only goal, response option 4 

achieved the greatest reduction in the number of infected backyard premises. Reducing the total 

number of infected commercial premises was best achieved with response options 3 or 4.

Both response options 3 and 4 reduced the likelihood of extremely large outbreaks. However, any 

increase over response option 1 reduced the mean number of infected backyard premises, suggesting 

that minimal response is unlikely to achieve an adequate reduction in disease spread among backyard 

premises.

Outbreak duration, as expressed by the percentage of simulated outbreaks continuing into the months 

following the application of the response option was shortest, on average, for response options 3 or 4. 

Pronounced differences were observed when comparing response options 1 or 2 with response options 

3 or 4, with little difference observed between response options 3 and 4. 

Surveillance effectiveness, as expressed by the percentage of infected premises that were detected 

through passive and active surveillance activities, wassignificantly improved under response option 4, in 

comparison with any of the other response options. Little difference was observed in detection rates 

between response options 1 and 2, with some improvement observed with response option 3. 

With all response options, the predominant site of disease spread shifts from San Bernardino County to 

Los Angeles County shortly after applying the alternative response. This shift was most pronounced with 

response options 3 or 4. Surveillance surges within the first 30 days post-implementation of the 

response option generally increased the rates of detection in San Bernardino County and reduced 

further spread within the county, to the extent that the majority of future infections occurred in Los 

Angeles County.

The largest and longest simulated outbreaks frequently involve significant disease spread within Los 

Angeles County, irrespective of the selected response option. A relatively small number of simulated 

outbreaks became extremely large (greater than 1,000 infections) and persistent (remaining active for at 

least 3 months following the selection of a response strategy), irrespective of the selected response 

option.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 41

C. Estimating Within-Flock Transmission Parameters and Predicting the Time to Detect 

vND in Unvaccinated Flocks

Within-flock disease transmission models are used to evaluate surveillance options, support risk 

assessments, and assess different control measures. Statistical distributions for bird-level disease state 

durations are key inputs for within-flock disease transmission models. We estimated bird-level disease 

state durations and a lower bound on the rate of transmission (β) in unvaccinated flocks using 

experimental data available from the peer-reviewed literature and unpublished data. 

We used the estimated parameters to predict the time to detect vND in an unvaccinated, 50-bird flock,

based on observation of increased mortality (2 or more dead birds within a 3-day period).

Methods

Estimating the latent and infectious periods and time to death at the bird level 

For this analysis, we defined the latent period as the interval between when an individual bird is 

exposed to the virus and when it begins shedding virus in detectable concentrations. We estimated the 

distribution of the latent period from viral shedding data collected on various days post inoculation 

(DPI), as reported in experimental studies in the literature and from unpublished SEPRL data13. Data 

were available from 122 unvaccinated chickens. Oropharyngeal swabs were collected at specific 

sampling times post inoculation and starting on 1 or 2 DPI. These data points represented the CA 2018 

vND strain, CA 2002-2003 vND strain, and a mesogenic vND strain. An additional 73 data points (birds) 

were available for the time to death post inoculation (observed at daily intervals). These data included 

unvaccinated chickens inoculated with vND-CA 2002-2003, vND-CA 2018, vND-Peru 2008 or vND-India 

2012. Contact bird data from unvaccinated birds were not included for estimating the infectious period, 

as data was only available for five birds, and the first sampling time was 2 days post contact. The noninoculated birds in this experiment all died by day 6 post contact, indicating that the range of time to 

death is comparable to that for inoculated birds.

The infectious period was defined as the interval from when an individual bird begins shedding virus in 

detectable quantities to when it either recovers or dies. In several experimental studies, only the time to 

death was observed, and oropharyngeal swabs were not collected. We jointly fit the parameters of the 

latent and infectious periods given all the observed data, including instances in which only the time to 

death was observed.

We used the Metropolis MCMC algorithm implemented in R for parameter estimation. The three chains 

were run for 10,000 iterations with burn-in of 2,000 iterations. There was no significant autocorrelation 

beyond 60 lags. Uniform priors with wide limits that included the MLE estimate were used in the current 

analysis. 

Estimating the rate of transmission (β) 

The adequate contact rate is a key parameter that determines the rate of within-flock spread. In the 

Susceptible-Exposed-Infected-Recovered (SEIR) model, the adequate contact rate or the transmission 

parameter (β) is the average number of contacts that a bird has with other birds per unit time, such that 

13 Courtesy of Kiril M. Dimitrov, Helena L. Ferreira, Mary Pantin-Jackwood, Tonya L. Taylor, Iryna V. Goraichuk, Claudio L. 

Afonso, David L. Suarez
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

42 USDA APHIS VS

the contact can transmit infection. We estimated the adequate contact rate using data provided in 

Miller et al., 2003, in which the transmission to contact birds was studied. We used direct forward 

simulation to obtain the posterior distribution for the adequate contact rate, given the observed 

experimental data on viral shedding and the timing of death for the contact birds.

Estimating Time to Detection in Unvaccinated Flocks 

We estimated the time to detection in flocks of 50 unvaccinated birds using a stochastic within-flock 

simulation model (SEIR), applying the maximum likelihood estimates of the parameters (as described 

above) and a trigger criterion of observing 2 or more dead birds within a 3-day period.

Results

Latent and infectious periods and time to death at the bird level 

• Latent Period Parameters

The mean latent period was 0.40 days (95 percent CI: 0.30 – 0.51 days).

• Infectious Period

The mean infectious period was 4.33 days (95 percent CI: 4.03-4.98 days). The maximum 

likelihood estimate for the infectious period was shape parameter of 13.07 (95 percent

CI: 3.6-18.6) and a scale of 0.33196 (95 percent CI: 0.23-1.33).

• Time to Death

The maximum likelihood estimate for the bird-level mean time to death was 4.73 days (95

percent CI: 4.45-5.4 days).

Rate of transmission (β) 

There was considerable uncertainty for this parameter, given the limited amount of data available. 

However, based on the estimated posterior, a value of 1.7 contacts per day (95 percent CI: 1.69-9.79 

adequate contacts per day) may be used as a conservative estimate.

Time to detection in unvaccinated flocks 

Under the baseline scenario, the time to detection was 5.5 days (95 percent PI: 4-7 days) based on 

20,000 iterations of the model.

D. Predicted Disease Mortality and Infection Prevalence in vNDV Infected Flocks Using a

Disease Transmission Simulation Model

We used a stochastic within-flock vND transmission model to predict the prevalence of infectious birds 

and cumulative mortality over time in infected flocks (a flock in this analysis was defined as birds in a 

house or barn). The model results provide a general idea about the possible time elapsed since the 

onset of infectiousness based on the observed cumulative mortality levels in the flock.

We evaluated model scenarios for unvaccinated or vaccinated commercial and backyard flocks. Results 

for vaccinated commercial flocks (20,000 birds) and both vaccinated and unvaccinated backyard flocks 

(400 birds) are provided in the main text. The results for additional flock sizes and vaccination scenarios 

are included in Appendix C.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 43

Overall, the model results indicated low levels of mortality in vaccinated flocks due to a greater fraction 

of recovering birds; cumulative percent mortality over 4.5-5.0 percent was rarely noted in modeled 

outcomes for these flocks. Furthermore, disease spread was predicted to be slower in vaccinated flocks 

compared to unvaccinated flocks. Disease spread in unvaccinated flocks was predicted to be fairly rapid 

with extensive disease mortality (i.e. 50 percent mortality after 7-12 days of infectiousness in a backyard 

flock with 400 birds). The results also indicated that the time to attain specific percent cumulative 

mortality levels is longer for larger flocks. We note that the model results are approximate as there is 

considerable uncertainty in key parameters such as the adequate contact rate and the vaccine efficacy 

under field conditions.

Methods

We used a stochastic individual based transmission model to simulate vND spread in commercial and 

backyard flocks. The model simulates the number of birds in susceptible, latent, infectious and 

recovered or dead states in 0.01-day time steps. The model allowed for a fraction of the birds in a 

vaccinated flock to be immune. The predicted mortality and prevalence curves were based on 10,000 

model iterations.

Model parameters for unvaccinated flock scenarios were estimated from available experimental 

inoculation studies for the CA/2018 and other vND strains as described in Section V: Part C. (Dimitrov, 

2019 #3). The durations of latent and infectious periods for vaccinated flocks were estimated from 

experimental data presented in Miller et al. (2013) as described in Appendix C. The adequate contact 

rate and disease mortality in vaccinated flocks were based on estimates from outbreak data from 

commercial flocks as described in the Section V: Part E. Additional details of the model parameters are 

provided in Appendix C. Predicted Disease Mortality and Infection Prevalence Under Additional Flock 

Size And Vaccination Scenarios.

Results

Vaccinated commercial flocks 

The model results on the cumulative mortality percent14 and the prevalence of infectious birds on 

various days post infection for a vaccinated commercial flock of size 20,000 birds are provided in Figure 

11. The observed cumulative mortality percent at a time point can provide an approximate indication of 

the number of days post onset of infectiousness in the flock. 

14 Defined as the cumulative number of dead birds divided by the beginning flock size multiplied by 100.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

44 USDA APHIS VS

Table 11 provides the predicted days post the onset of infectiousness when various cumulative mortality 

levels were attained. For example, in the 20,000-bird vaccinated commercial flock, it took 17.4 (90

percent P.I. 13.8-22.0) days after the onset of infectiousness for the cumulative mortality to reach 2

percent of the starting flock size. In this analysis, the time to onset of infectiousness was defined as the 

earliest time point when one or more birds were infectious. Cumulative mortality in vaccinated 

commercial flocks remained relatively low. Cumulative mortality of at least 4.5 percent of the flock was 

observed in only 2.07 percent of the simulation iterations. Predicted daily mortality is shown in Figure 

12, which was predicted to peak about 17 days post exposure.

Figure 11. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

exposure in a 20,000 vaccinated commercial cage free layer flock using baseline vND spread 

parameters. Shaded area represents the 90 percent prediction interval for each variable. 

Figure 12. Predicted daily mortality on various days post exposure in a 20,000-bird vaccinated commercial 

cage free layer flock using baseline vND spread parameters. Shaded area represents the 90 percent

prediction interval.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 45

Table 11. Predicted days post onset of infectiousness to attain various cumulative mortality levels in a 

20,000-bird vaccinated commercial cage free layer flock using baseline vND spread parameters.

Cumulative Percent 

Mortality

Percent of simulation 

iterations in which this 

cumulative mortality is 

attained

Predicted number of days post onset of infectiousness to reach 

this cumulative mortality percent. median (90% Prediction 

Interval)

2 95.77 17.4 (13.8-22)

2.5 95.68 19.1 (15-24.2)

3 84.18 21.1 (16.5-27)

3.5 54.3 22.5 (17.8-28)

4 24.13 24.4 (19.8-28.8)

4.5 2.07 26.4 (22.5-29.5)

5 0 NA

Results for Unvaccinated backyard flocks 

Model results on the cumulative mortality percent and the prevalence of infectious birds on various 

days post infection for an unvaccinated backyard flock (400 birds) are provided in Figure 13. Table 12

provides the predicted days post the onset of infectiousness when various cumulative mortality levels 

were attained, and the predicted daily mortality is shown in Figure 14. Based on these results, 

unvaccinated backyard flocks are predicted to have rapid spread of disease with high levels of mortality.

Figure 13. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

exposure in a 400-bird unvaccinated backyard flock using baseline vND spread parameters. Shaded area 

represents the 90% prediction interval for each variable.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

46 USDA APHIS VS

Figure 14. Predicted daily mortality on various days post exposure in a 400-bird unvaccinated backyard flock 

using baseline vND spread parameters. Shaded area represents the 90% prediction interval.

Table 12. Predicted days post onset of infectiousness to reach various cumulative mortality levels in a 400-

bird unvaccinated backyard flock using baseline vND spread parameters.

Cumulative Percent Mortality Predicted number of days post onset of infectiousness to reach this cumulative mortality 

percent. median (90% Prediction Interval)

10 6.8 (5.2-9.5)

20 7.6 (6-10.5)

30 8.1 (6.5-11)

40 8.5 (6.8-11.8)

50 8.9 (7.2-12.2)

60 9.4 (7.5-12.8)

70 9.8 (8-13.2)

80 10.4 (8.5-14)

90 11.1 (9-15)

 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 47

Results for Vaccinated Backyard Flocks 

Model results on the cumulative mortality percent and the prevalence of infectious birds in vaccinated 

backyard birds on various days post infection are provided in Figure 15. The predicted days post the 

onset of infectiousness when various cumulative mortality levels were attained are provided in Table 13, 

and the predicted daily mortality is provided in Figure 16. As would be expected, disease spread is 

predicted to be slower in vaccinated backyard flocks with lower mortality, as compared to the results 

predicted for unvaccinated backyard flocks. The predicted time to reach certain cumulative mortality 

levels in the vaccinated backyard flocks was shorter than vaccinated commercial flocks, which are 

typically much larger.

Figure 15. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

vND exposure in a 400-bird vaccinated backyard flock. Shaded area represents the 90% prediction 

interval for each variable.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

48 USDA APHIS VS

Figure 16. Predicted daily mortality on various days post vND exposure in a 400-bird vaccinated backyard 

flock. Shaded area represents the 90% prediction interval.

Table 13. Predicted days post onset of infectiousness to reach various cumulative mortality levels in a 400-

bird vaccinated backyard flock using baseline vND spread parameters.

Cumulative Percent 

Mortality

Percent of simulation iterations 

in which this cumulative 

mortality is reached

Predicted number of days post onset of 

infectiousness to reach this cumulative 

mortality percent. Median (90% Prediction 

Interval)

2 91.23 13.5 (9-20.2)

2.5 84.72 14.8 (9.8-22.2)

3 73.26 16.1 (10.5-23.8)

3.5 57.17 17.1 (11.2-25.2)

4 39.57 18 (12.2-25.8)

4.5 23.53 18.8 (12.8-26.8)

5 12.64 19.5 (13.8-27.2)

Conclusions

We predicted the prevalence of infectious birds and the cumulative mortality percent in unvaccinated 

and vaccinated flocks using a stochastic within flock transmission model. The model results indicate a 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 49

fairly rapid disease spread in unvaccinated flocks with extensive disease mortality. The predicted time to 

attain specific percent cumulative mortality levels was longer for the larger commercial flocks. The 

transmission dynamics in vaccinated flocks were markedly different from those for unvaccinated flocks 

with a slower disease spread and lower disease mortality. We note that the model predictions are 

approximate and should be used cautiously as there is a significant uncertainty and variability in key 

parameters such as the adequate contact rate and vaccine efficacy in backyard and commercial flocks.

E. Estimating the Time of Disease Introduction in vNDv Infected Commercial Layer Barns 

Using Egg Production and Mortality Data

Determining the time of vND virus introduction in a flock is an important part of outbreak investigations. 

By narrowing the time window of possible virus introduction, we can better identify the potential routes 

of the virus introduction and enhance our understanding of the pattern of disease spread. In this 

analysis, egg production, diagnostic testing and daily mortality data were used to estimate the most 

likely date of virus introduction for four confirmed vNDv infected barns with vaccinated birds in a 

commercial layer premises in California.

Summary

The analysis was performed using a within-house disease transmission model along with approximate 

Bayesian computation (ABC) to estimate the distribution of the times of exposure that resulted in a 

smaller difference between the model predictions and the observed production and diagnostic testing 

data. Approximate Bayesian computation algorithms as described in Marjoram et al., 2003 were used to 

estimate the time of virus introduction into the barn, the adequate contact rate and other model 

parameters. 

The estimated time of introduction ranged from 28 November 2018 (95 percent C.I., 6 November - 10 

December 2018) for barn D to 25 December 2018 (95 percent C.I., 17 December -26 December 2018) for 

barn A. The adequate contact rate (a parameter that impacts the rate of disease transmission in a barn) 

was the highest in barn A with 1.42 (1.02-4.72) contacts per day for 102-week-old cage free birds and 

the lowest in barn D with 0.33 (0.26-0.58) contacts per day for 33 week old caged layers. The ABC 

estimation procedure is also useful to inform other model parameters such as the likelihood that an 

infected bird dies due to vND or the egg production rate among infected birds. The estimated 

parameters are beneficial in models used to inform risk analysis, surveillance design and developing 

scenarios for emergency preparedness exercises.

The results of this analysis are subject to considerable uncertainty due in part to a limited number of 

experimental studies with vaccinated layer birds, and uncertainties associated with vaccine efficacy in 

commercial flocks of different ages and breeds. Nevertheless, the results demonstrate the usefulness of 

production and testing data to understand the transmission dynamics of vND under field conditions.

Methods

Summary of production and diagnostic data 

The analysis was performed for four barns confirmed as vNDv infected in a commercial layer premises in 

California. The operation had a total of 21 occupied barns. Three barns (barns A, B, and C) housed cagefree laying hens, while barn D had caged layers. All 4 barns were positive for vNDv based on RRT-PCR 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

50 USDA APHIS VS

testing of dead bird samples collected on 3 January 2019. Five dead birds per barn were tested in each 

of the 4 positive barns on this sampling date. Barns B and C were also sampled on 17 December 2018 

and tested negative via RRT-PCR.

Barn level daily egg production data were provided for 12 days beginning 24 December 2018. The egg 

production drop was quite variable among different barns. A greater than 40 percent drop in egg 

production was observed in barn A, which housed birds of age 102 weeks, while a very mild drop in egg 

production was observed in the other barns, which housed birds of age 131 or 33 weeks. Approximately 

4 months of daily mortality data before detection were provided for barns A, B and C, while 12 days of 

daily mortality data were provided for barn D. Similar to the egg production, the daily mortality was also 

quite variable with doubling of mortality in some of the infected barns and milder elevations above 

baseline in others.

Overview of modeling approach 

We used ABC to estimate the likely time of virus introduction and the key model parameters such as the 

adequate contact rate (a parameter which regulates the rate of within flock disease spread) and the 

fraction of infected birds that die from the available production and test data. 

A stochastic individual based simulation model was first used to simulate the disease mortality, infection 

prevalence over time and egg production rate for a wide range of model parameters such as the 

adequate contact rate, times of disease introduction and disease mortality (i.e. prior distributions). In 

the next step, the sum of squared distance between the model predicted daily mortality and egg 

production and the observed data, and the difference between observed and simulated diagnostic test 

results was calculated as a measure of deviation between the model output and data (ψ). The ABC 

algorithm was then applied to simulate the model under input values. The parameters in model 

iterations where the metric ψ was sufficiently small, indicating a good fit to the data, were then 

accepted to estimate the distribution of the time of introduction and other model parameters. 

The transmission model parameters for vaccinated flocks were estimated from current outbreak data 

and experimental data presented in Miller et al. (2013) from vaccinated SPF chickens and contact birds. 

The mean latent period was 0.39 days while the mean infectious period in vaccinated birds was 4.6 days. 

Implementation details of the ABC procedure are provided in Appendix D.

Finally, the modeling methods were also validated by estimating the time of introduction using a gridbased simulation and Euclidian distance-based likelihood approach which gave comparable time of 

introduction estimates to the ABC procedure for barn A.

Results

Of the four barns included in the analysis, results for barn A produced the lowest uncertainty due to a 

marked increase in mortality and drop in egg production beyond the normal production range for that 

barn. The model fits of the egg production rate and daily mortality for barn A are shown in Figure 17 and 

Figure 18, respectively. Model fits for the other barns are provided in Appendix D. We observe that 

estimated egg production and daily mortality from the model closely matches the data, indicating a 

reasonable fit. The posterior distribution for the adequate contact rate and time of introduction for barn 

A is shown in Figure 19 and Figure 20, respectively. 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 51

The results for the estimated time of introduction and the adequate contact rate are summarized in 

Table 14. From Table 14, barn D, which housed caged layers, had the earliest date of introduction with a 

slower contact rate, while barn A had the latest estimated day of introduction. However, the intervals 

for the estimated day of introduction are overlapping for barns A, B and C. 

The results also indicate that the disease mortality in the vaccinated commercial flocks can be relatively 

low (2.7 percent, 95 percent C.I., 1.5 percent-4.7 percent for barn A) compared to the estimates from 

experimental studies (11 percent) (Miller, 2013). The drop in egg production due to vNDv infection was 

likely lower in barns B, C and D relative to barn A as model parameters representing smaller drops in egg 

production due to vNDv infection resulted in a better fit for these barns. The median egg production 

rate in infected birds from the model results was quite variable, for example 55 percent for barn C and 

24 percent for barn A. 

Figure 17. Model-fitted egg production rate curves from the approximate Bayesian computation and 

observed egg production rate for Barn A. The shaded region represents the 95 percent credibility 

interval for the fitted egg production.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

52 USDA APHIS VS

Figure 18. Model fitted disease plus normal mortality from the approximate Bayesian computation and the 

observed daily mortality for Barn A. The shaded region represents the 95 percent credibility interval for 

the fitted daily mortality.

Table 14. Estimated time of introduction and adequate contact rate for each of the four barns.

Barn

Estimated mode, median, (95% C.I.) of 

time of introduction

Estimated mode, median, (95% 

C.I.) of adequate contact rate 

(contacts per day)

A (cage free layers)

12/25/2018, 12/23/2018 

(12/17/2018 -12/26/2018)

1.42, 1.86 (1.02-4.72)

B (cage free layers) 12/8/2018, 12/6/2018 

(11/17/2018 -12/17/2018)

0.48, 0.53 (0.36-0.84)

C (cage free layers) 12/9/2018, 12/7/2018 

(11/24/2018 -12/20/2018)

0.5, 0.68 (0.34-2.35)

D (caged layers)*

11/28/2018, 11/24/2018 

(11/6/2018 -12/10/2018)

0.33, 0.36 (0.26-0.58)

*Results from barn D should be interpreted cautiously as the drop in egg production was mild to non-existent, increasing the 

uncertainty in the estimated results.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 53

Figure 19. Posterior distribution for the adequate contact rate for Barn A.

Figure 20. Histogram of the Posterior distribution for the time of vND introduction for Barn A.

Discussion

Flock daily mortality, egg production rate and available diagnostic test data can be used to estimate the 

time of virus introduction in a vND infected barn. By narrowing the time window of possible virus 

introduction, we can better identify the potential routes of virus introduction and enhance our 

understanding of the pattern of disease spread. We estimated the time of introduction for four 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

54 USDA APHIS VS

confirmed vND infected barns in a commercial layer premises in California using a stochastic simulation 

model together with approximate Bayesian computation (ABC). Approximate Bayesian computation is 

suitable for parameter estimation when explicit calculation of the likelihood is intractable. The ABC 

approach has been used to estimate the time of disease introduction using field mortality data for other 

diseases such as ASF (Guinat, 2018).

As can be observed in Table 14, the estimated likely time of vNDv introduction for barn A ranged from 

12/17/2018 -12/26/2018, 13-4 days before observing a considerable drop in egg production rate. Barn A 

was a cage free layer house with older birds (102 weeks) and showed a more than 40 percent drop in 

egg production over a two-week period along with increased mortality. The estimated adequate contact 

rate was the highest for this barn, indicating a faster rate of disease spread. 

Barn D, which housed 33-week-old caged layers, had the earliest estimated date of vNDv introduction of 

11/28/2018 (95 percent C.I., 11/6/2018, 12/10/2018). The estimated contact rate was lower for this 

barn, which could possibly be due to housing younger birds with a greater immunity or slower disease 

transmission among birds housed in cages. However, the results for this barn need to be interpreted 

cautiously as the drop in egg production was very mild resulting in a greater uncertainty in the 

estimates. Additional daily mortality and egg production data may help obtain more precise time of 

introduction estimates for this barn. 

The fall in egg production and increase in daily mortality were also fairly mild in barn B and barn C, 

leading to greater uncertainty in the estimate for the time of virus introduction as compared to the 

estimate for barn A. Lower contact rates, as were estimated for barns B and C, can also lead to greater 

uncertainty in the time of virus introduction estimates. In general, a significant deviation in the 

production parameters from baseline in the field data is required to estimate the time of virus 

introduction. 

The results suggest spread of vND in vaccinated commercial barns can be relatively slow (adequate 

contact rate estimate was less than 1 for barns B, C, and D). This can have important implications for 

surveillance design as slow spread can lead to a less pronounced presence of clinical signs in the flock, 

for example. The ABC estimation procedure is also useful to inform other model parameters such as the 

likelihood that an infected bird dies due to vND or impact on the egg production rate among infected 

birds. Our results indicated that the disease mortality in the vaccinated commercial flocks can be 

relatively low (2.7 percent, 95 percent C.I. 1.5 percent-4.7 percent based on barn A). The estimated egg 

production rate among diseased birds varied markedly between different barns. For example, the 

median estimated egg production rate in vNDv infected birds was 24 percent for barn A and 55 percent

for barn C. The adequate contact rate, disease mortality parameter and other parameter estimates are 

beneficial to inform risk assessment and active surveillance models and for developing scenarios in 

emergency preparedness tabletop exercises. 

There is considerable uncertainty in the estimated time of virus introduction and adequate contact rate 

due to limited data on key model input parameters such as level of immunity among vaccinated flocks of 

different ages and breeds, disease mortality in vaccinated birds, and the mild drop in egg production and 

mild elevation in mortality in some of the barns. Nonetheless, the analysis presented here demonstrates 

the value of production data and diagnostic testing data and its ability to provide information on disease 

dynamics within a poultry flock.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 55

F. Spatial and Spatiotemporal Patterns of the Outbreak

Knowledge of disease patterns in space and time can identify areas at higher risk for disease spread and 

allow disease control, prevention, and surveillance strategies to be implemented effectively (Ward, 

2007). We performed a spatiotemporal analysis on confirmed and presumptive positive vND in

backyard/exhibition premises in California. We obtained data on confirmed and presumptive positive 

premises from in-person interviews using the CDFA Non-Commercial Premises Virulent Newcastle 

Disease Epidemiology questionnaire, which were entered into the USDA’s Emergency Management 

Response System (EMRS). For population data, we used the results of a spatial analysis predicting the 

geographic area and density of backyard bird ownership in California at the census block level (see 

Section III, Part A: Predicting Areas of Backyard Bird Ownership).

Methods

We used spatial and spatiotemporal scan statistics to detect statistically significant high-risk clustering of 

vND cases (Kulldorff, 1997). For the analysis, we defined cases as confirmed or presumptive positive 

premises. Data from 435 cases detected from 16 May 2018 to 22 February 2020 located within the 

California Regional Quarantine Area (RQA) in Los Angeles, Riverside, and San Bernardino Counties were 

included in the analysis. Case information consisted of the location, reported date of onset of clinical 

disease, and presumptive and confirmed positive diagnosis date. Based on the phylogenetic analysis 

(see Section II, Part A: Phylogenetic Analysis and Diagnostics), spatial and spatiotemporal analyses were 

performed separately based on the two main vNDV sub-groups (vNDV-01 and vNDV-02) since premises 

within the same sub-group are genetically related, and premises between sub-groups are genetically 

unrelated. Sub-groups vNDV-01 and vNDV-02 contained a total of 147 and 288 premises, respectively. 

Cases were aggregated at the census block level within each county. Population information consisted 

of the estimated number of premises of predicted backyard bird ownership in each census block for the 

outbreak area. We used the centroid (latitude, longitude) of each census block as location information 

for the analysis. 

A Poisson model was used to estimate the number of cases that might be expected to occur in the 

absence of any clustering. For both the spatial and spatiotemporal cluster analyses, data were scanned 

with a 5-km radius spatial window. For the spatiotemporal cluster analysis, a temporal window of 21 

days was used, which is the World Organisation for Animal Health (OIE) reported incubation period for 

vND (OIE, 2012). We determined statistical significance (p-value < 0.05) of clusters using the likelihood 

ratio test and 999 iterations of Monte Carlo simulation implemented in SaTScan (version 9.6).

Results

The 435 detected cases from 16 May 2018 to 22 February 2020 were located within 26 control areas. 

The cases were located within 93 census blocks, with the number of cases ranging from 1 to 48 premises 

within an individual block. Riverside County had the highest number of reported cases, with 244 of the 

435 detected cases occurring in this area, followed by San Bernardino and Los Angeles Counties (148 

and 43 cases, respectively; Figure 21 and Table 15). 

The primary or most likely spatial and spatiotemporal statistically significant clusters (p-value < 0.001) of 

detected vNDV-01 and vNDV-02 cases occurred in Riverside and San Bernardino Counties, respectively 

(cluster 1 in Figure 22 and Figure 23). In the vNDV-01 primary spatiotemporal cluster, 38 cases occurred 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

56 USDA APHIS VS

out of an estimated population at risk of 249 backyard/exhibition premises from 3 – 13 December 2018 

(Table 15, Figure 24). In this cluster, the relative risk of cases occurring in this area and time period was 

1,220.63 times more likely, relative to outside this area. In the vNDV-02 primary spatiotemporal cluster, 

30 cases occurred out of an estimated population at risk of 440 backyard/exhibition premises from 18 

June – 8 July 2018 (Table 15 and Figure 24). In this cluster, cases were 230.35 times more likely to occur 

relative to outside this area. 

An additional two spatial and five spatiotemporal vNDV-01 clusters, and five spatial and 10 

spatiotemporal vNDV-02 clusters, were identified in the three-county area of the RQA (Figure 22 and 

Figure 23). The number of cases within the spatial clusters ranged from four to 94 cases, whereas the 

number of cases ranged from three to 38 in the spatiotemporal clusters. The relative risk for vNDV-01 

cases was highest in Riverside County, followed by San Bernardino County, whereas the relative risk for 

vNDV-02 cases was highest in San Bernardino County followed by Riverside County (Table 15). Figure 24

compares the temporal occurrence for vNDV-01 and vNDV-02 spatiotemporal clusters. Most statistically 

significant spatiotemporal clustering for the entire outbreak occurred during the months between 

December and March. 

Seventy-one of the 435 cases detected during the time period of this analysis did not occur in any spatial 

or spatiotemporal cluster.

Figure 21. Cumulative number of confirmed and presumptive positive vND premises detected in California 

from 16 May 2018 to 22 February 2020; data are aggregated at the census block level and the point 

location of the centroid of each census block is displayed.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 57

Figure 22. Location of spatial (upper) and spatiotemporal (lower) clusters of vNDV-01 premises and the 

relative risk of cases occurring within census blocks in California from 16 May to 22 February 2020. Data 

are aggregated at the census block level and the census block centroids are displayed. Clusters were 

statistically significant at the p<0.05 level.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

58 USDA APHIS VS

Figure 23. Location of spatial (upper) and spatiotemporal (lower) clusters of vNDV-02 premises and the 

relative risk of cases occurring within census blocks in California from 16 May to 22 February 2020. Data 

are aggregated at the census block level and the census block centroids are displayed. Clusters were 

statistically significant at the p<0.05 level.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 59

Table 15. Spatiotemporal clusters of vND cases in California from 16 May 16 2018 to 22 February 2020.a

No.: number; Exp.: expected

aAll clusters were statistically significant (p-value < 0.001) 

b1, primary cluster; 2–4, secondary clusters

cNumber of premises with predicted backyard bird ownership 

dRadius is zero as there is only one census block in the cluster

Genetic 

Subgroup ClusterbRadius 

(km) Time Period

Estimated 

Populationc

No. 

Case

s No. Exp.

Log 

Likelihood 

Ratio

Relative 

Risk

vNDV01

Riverside County

1 4.49 December 3 – 13, 2018 249 38 0.042 226.15 1,220.63

2 4.35 January 19 – February 7, 2019 98 11 0.017 60.95 719.66

4 4.98 January 7 – 25, 2019 185 8 0.028 37.43 299.80

Los Angeles County

3 0.60 July 16 – August 4, 2018 68 9 0.011 51.73 878.14

6 4.55 August 22 – September 11, 

2018

494 8 0.083 28.82 101.54

San Bernardino County

5 1.64 May 24 – 31, 2018 182 6 0.012 31.58 535.38

vNDV02

San Bernardino County

1 1.36 June 18 – July 8, 2018 440 30 0.15 131.65 230.35

3 0

d December 12 – 23, 2019 10 8 0.0017 59.63 4,756.71

6 0 January 3 – 7, 2020 2 3 0.0001

6

26.58 19,277.3

1

8 2.10 February 17 – 21, 2019 44 4 0.0035 24.24 1,172.42

11 0 February 16 – March 7, 2019 24 4 0.0075 21.13 537.35

Riverside County

2 2.99 January 7 – 23, 2019 778 22 0.21 81.60 114.44

4 4.49 January 17 – February 1, 2019 329 13 0.083 53.11 164.41

5 4.75 February 14 – March 5, 2019 289 8 0.091 28.02 90.50

7 1.01 January 28 – February 7, 2019 12 4 0.0021 26.28 1,954.05

10 3.27 December 5 – 18, 2019 268 6 0.059 21.85 103.83

Los Angeles County

9 0 July 31 – August 20, 2018 13 4 0.0043 23.38 944.81
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

60 USDA APHIS VS

Figure 24. Time period of occurrence of spatiotemporal clusters of vND-01 and vND-02 in California from 16 

May 2018 to 22 February 2020. All clusters were statistically significant at the p<0.05 level. Clusters are 

displayed in descending order of statistical significance, with cluster 1 representing the primary (or, 

most likely) cluster.

Conclusions

Results identified specific geographic areas at the census block level of statistically significant spatial and 

spatiotemporal disease clustering. The primary spatial and spatiotemporal clusters were located within 

Riverside and San Bernardino counties, identifying these areas as the location of the highest occurrence 

of vND cases detected from 16 May 2018 to 22 February 2020. Further, these clusters occurred during 

the first seven months of the outbreak, corresponding to the increase in infected premises that were 

detected during this time as well as further disease spread over the next year within the RQA. Of the 17 

statistically significant spatiotemporal clusters, 12 occurred during the months between December and 

March. This time period corresponds to when the fighting gamebird season occurs, as well as when 

resources to support the outbreak were decreased due to a federal government shutdown (December 

2018 – January 2019) and following a three month time period of no newly detected cases (August –

November 2019). 

This approach has some limitations. vND cases may be underreported, which can result in 

misclassification of cases and non-cases. In addition, actual data of true backyard bird ownership in the 

outbreak area remains limited. We used an estimated population at risk based on the predicted number 

of premises of backyard ownership using 2010 census block data. As such, the true number of premises 

with backyard/exhibition birds used in this analysis may be under- or overestimated, resulting in the 

number of detected clusters and estimated risk to be over or underestimated. 

In conclusion, the identification of significant spatial and spatiotemporal clustering patterns of vND in 

California from May 2018 to February 2020, support control strategies of targeting high risk areas for 

disease spread with increased response efforts in order to maximize the effectiveness of disease 

response strategies and control the outbreak.

G. Measuring the Spatial Dependence of Virulent Newcastle Disease Transmission Risk

Global spatial clustering methods can be used to evaluate the tendency of virulent Newcastle disease

(vND) positive premises to occur closer together in spatial distance and time than would be expected by 

chance. Evaluating the extent of spatial clustering provides insights into the spatial scale of disease 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 61

transmission and mechanisms of disease spread, thereby informing optimal disease response strategies. 

When these analyses are informed by genetic and temporal data to identify likely related and unrelated 

infected premises, the extent of spatial clustering can be evaluated even when knowledge of the 

underlying population distribution is unknown (Lessler et al., 2016). The analyses presented here aimed 

to measure the spatial dependence of vND transmission risk over different temporal scales to inform 

surveillance and control strategies for the current outbreak in California. 

Methods

In this analysis, data on vND infected premises from the current outbreak in California were obtained 

from USDA’s Emergency Response Management System (EMRS). Only confirmed vND positive premises 

that had full genomic sequence data from USDA’s National Veterinary Services Laboratories (NVSL) and 

were located within the Southern California vND Regional Quarantine Area, which encompasses Los 

Angeles County and parts of Riverside and San Bernardino Counties, were included in the analyses 

(CDFA, 2019). Results from the phylogenetic analysis of the genomic sequence data were used to 

determine the genetic relatedness between infected premises. Independent, commercial, and 

backyard/exhibition poultry operations were included in the analyses. 

The spatial clustering statistic, τ, was used to measure the spatial dependence of vND transmission risk 

(Lessler et al., 2016). The τ-statistic is interpreted as a relative risk of a premises at a specified spatial 

distance from a vND infected premises also being infected, versus the risk of a premises located 

anywhere within the Regional Quarantine Area being infected. It is calculated as:

τ̂(d1, d2

) =

π̂(d1, d2)

π̂(0, ∞)

where π̂(d1, d2) estimates the probability that a vND infected premises occurs within a certain distance 

range (i.e., between d1 and d2) of another infected premises. Where spatial clustering exists, τ will be 

greater than 1. Geographic coordinates of vND infected premises were used to determine their 

distances apart. Values of τ(d1, d2

) were calculated at 500-meter (m) wide windows centered from 250 

m to 10 km in 500 m increments.

The earliest date between the reported onset of clinical signs, diagnostic sample date, and presumptive 

positive date was used for estimating τ at different temporal scales. The time period of main interest 

was infected premises that occurred within 21 days of each other, which is the maximum length of the 

vND incubation period15 (OIE, 2012). The relative risk of infected premises within different distance 

ranges was also evaluated for 42 days, or double the incubation period, and 120 days, which is the 

minimum fallow period for vND virus elimination for outdoor premises (USDA, 2018). 

The significance of spatial clustering was assessed using bootstrapping simulation (1,000 iterations). The 

null distribution of the τ-statistic was obtained by randomly permuting the locations of vND infected 

premises and calculating the τ-statistic after each permutation. Similarly, confidence intervals for the τstatistic were obtained using bootstrapping simulation. No comparisons were made between an 

individual premises and itself for the simulations (Gatrell et al., 1996, Lessler et al., 2016). 

15 The incubation period is defined as the time period between when a flock becomes infected and when clinical signs appear.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

62 USDA APHIS VS

Direct local and long-distance vND spread between premises were evaluated by calculating the 

Euclidean distance between adjacent premises and infected zones16, respectively. Parcel data of all 

premises within the outbreak area were obtained from the Southern California Association of 

Governments (SCAG, 2016). Premises immediately adjacent to an infected premises (i.e., premises 

sharing a fence-line/border or immediately adjacent across a residential street) were identified and the 

distances between the centroid and edge of the resulting adjacent premises patches were calculated. 

The distances between infected zones were calculated based on the minimum distance between 

premises within different zones. All data analyses were performed in R (v.3.4.3) and ArcGIS (v. 10.5.1). 

Results

The analysis included 342 infected vND premises detected between 16 May 2018 and 1 May 2019 and 

located within the California Regional Quarantine Area. Based on the phylogenetic analysis (see Section 

II, Part A: Phylogenetic Analysis and Diagnostics), spatial clustering analyses were performed 

separately based on the two main vNDV sub-groups (vNDV-01 and vNDV-02) since premises within the 

same sub-group are genetically related, and premises between sub-groups are genetically unrelated. 

Sub-groups vNDV-01 and vNDV-02 contained a total of 129 and 213 premises, respectively. 

The mean (standard deviation) parcel size of a vND infected premises was 100.78 (52.31) m in length 

(range: 22.19 – 337.27 m) and 37.18 (28.18) m in width (range: 3.05 – 204.40 m). The mean (standard 

deviation) parcel patch size of premises adjacent to an infected premises was 206.94 (100.0) m in length 

(range: 34.13 – 615.35 m) and 114.29 (62.92) m in width (range: 12.96 – 387.04 m). The mean (standard 

deviation) infected zone size was 5.61 (4.73) km in length (range: 1.21 – 21.60 km) and 3.32 (2.79) km in 

width (range: 0.83 – 13.08 km). The mean (standard deviation) minimum distance between infected 

zones was 6.03 (4.31) km (range: 1.87 – 20.62 km). 

Strong and statistically significant spatial clustering was observed among adjacent premises, consistent 

with local vND spread between premises (Figure 25). The probability that a premises located within 250 

m (± 250 m) and 21 days of another infected vND premises was 3.99 (95 percent CI: 3.21 – 4.72) and 

2.78 (95 percent CI: 2.35 – 3.24) times greater for vNDV-01 (shown in blue, Figure 25) and vNDV-02 

premises (shown in brown, Figure 25), respectively, than the probability that any premises within the 

California Regional Quarantine Area was positive for the same vNDV sub-group. For vNDV-01 premises, 

there is an increased probability (τ>1) of premises being infected at distances up to 9.5 km (τ = 1.71, CI: 

0.50 – 3.17) from another infected premises, indicating vND spread over long distances and between 

zones.17 However, this probability is only statistically significant at distances up to 4.5 km (τ = 2.08, CI: 

1.12 – 3.19), which suggests that the majority of vND spread of this sub-group was within infected zones 

with less spread between zones. For vNDV-02 premises, there is an increased probability of premises 

being infected at distances up to 10 km (τ = 1.43, CI: 0.81 – 2.32); however, this probability is only 

16 An infected zone (IZ) is a zone immediately surrounding the Infected Premises. The IZ will initially encompass the perimeter 

of all presumptive or confirmed positive premises and include as many of the Contact Premises or contiguous premises as 

required epidemiologically or logistically. The size of the IZ depends upon the disease agent and circumstances of the outbreak

(USDA, 2018).

17 The τ-statistic is interpreted as the probability of a premises at the specified spatial distance from a vND infected 

premises also being infected, versus the probability of a premises located anywhere within the California Regional 

Quarantine Area being infected.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 63

statistically significant at distances up to 2.5 km (τ = 2.08, CI: 1.07 – 1.84) and at distances between 5.5 –

6.0 km (τ = 2.32, CI: 1.38 – 3.22). These results indicate both local and long-distance vND spread for this 

sub-group. Long distance spread may be due to the movement of infected poultry or fomites out of 

infected areas. Overall, 76.5 percent of infected premises were located within 250 m of another 

infected premises (black dashed line, Figure 25). This percent increased to 87.8 percent at 500 m and to 

over 95 percent at 1.5 km.

Spatial clustering over longer time periods was also evaluated. For vNDV-01 premises, statistically 

significant spatial clustering was observed at distances up to 6.0 km for infected premises that occurred 

at 42 and 120 days apart (τ = 2.39, CI: 1.58 – 2.98 and τ = 1.51, CI: 1.39 – 1.62, respectively; see also

Figure 26). For vNDV-02 premises, statistically significant spatial clustering was observed at distances up 

to 3.5 km for infected premises that occurred at 42 and 120 days apart (τ = 1.52, CI: 1.17 – 1.91 and τ = 

1.36, CI: 1.18 – 1.52, respectively; see also Figure 26). Statistically significant clustering was also 

observed at distances between 5.0 and 8.0 km for these same time periods. These results indicate 

longer-term disease transmission, which may occur due to undetected, infected premises that allow for 

sustained disease spread over time or violations in the fallow period. Fallow period violations, in which 

poultry are repopulated on premises before 120 days have passed, have been documented for the

current vND outbreak during inspections for fallow period compliance.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

64 USDA APHIS VS

Figure 25. Spatial dependence of vND infected premises and the percent of infected premises located within 

the specific distance and occurring within 21 days of each other. Spatial dependence analyses were 

performed on premises that are genetically related based on full genomic sequencing: A) vNDV-01 subgroup infected premises, and B) vNDV-02 sub-group infected premises. The shaded area represents 95% 

bootstrapped confidence intervals for the spatial clustering estimates. Estimates are plotted at the 

mid-point of the spatial range in 500 m increments.

A.

B.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 65

Figure 26. Spatial dependence of vND infected premises located within the specified distance and occurring 

within 21 and 120 days of each other. Spatial dependence analyses were performed on premises that 

are genetically related based on full genomic sequencing: A) and B) vNDV-01 sub-group infected 

premises with 95% bootstrapped confidence intervals for 42 and 120 days, respectively; C) and D) 

vNDV-02 sub-group infected premises with 95% bootstrapped confidence intervals for 42 and 120 days, 

respectively. Estimates were plotted at the mid-point of the spatial range in 500 m increments.

A. B.

C. D
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

66 USDA APHIS VS

Conclusions

This analysis measured the spatial dependence of vND transmission risk for the current vND outbreak in 

California. The results indicate the highest risk of disease transmission occurs in close proximity (250 m, 

± 250 m) of infected premises for both vNDV-01 and vNDV-02 sub-groups. This risk remains statistically 

significantly increased up to distances between 2.5 and 4.5 km, with over 95 percent of infected 

premises occurring within 1.5 km of another infected premises. The results also provide additional

evidence of long-distance disease spread between infected zones. 

Identification of the extent of spatial clustering support surveillance and control strategies that are 

targeted at areas in close proximity of infected premises and at longer distances but within the same 

infected zone. Disease tracing information would be needed to identify areas of likely long-distance 

disease to other infected zones; however, genomic sequence data provide critical information on 

infected zones that are genetically related and therefore, can also guide disease response efforts. Given 

statistically significant spatial clustering was identified at distances that encompass multiple infected 

zones and for genetically related, infected premises occurring in different zones, this analysis supports 

surveillance and control strategies aimed at multiple infected zones being performed in parallel. 

Implementation During Outbreak

After this analysis was completed in July 2019, the results were used to guide surveillance and 

depopulation efforts for backyard/exhibition premises during the vND outbreak. Mandatory 

depopulation of poultry was conducted within a 250 m area around infected backyard/exhibition

premises. Depending on the density of backyard premises, 1 to 1.5 km surveillance areas were 

established around the depopulation area with mandatory surveillance of all backyard/exhibition

premises conducted within a 500 m area immediately adjacent to the depopulation area. Depopulation 

activities prioritized backyard/exhibition premises closest to the infected premises and then worked 

outward (“inside-out strategy”), whereas surveillance activities prioritized backyard/exhibition premises 

at the outside perimeter of the mandatory surveillance area and worked inward (“outside-in strategy”). 

This allowed the depopulation area to be expanded if additional infected premises were found while 

minimizing the chance that a surveillance team would have required downtime from field activities due 

to testing infected, undetected premises. If additional infected premises were detected in the initial 

depopulation area, the area was expanded another 250 m or more, depending on the density of 

backyard/exhibition premises and field intelligence on sick bird observations in the area. 

Between July 2019 and the end of the vND outbreak, seven depopulation areas were formed around a 

total of 26 infected backyard/exhibition premises. Four (57.1 percent) of the seven depopulation areas 

did not expand beyond the initial 250 m area and included 10 infected premises. Three (42.9 percent) of 

the seven depopulation areas did expand beyond the initial 250 m area; two of these were expanded by 

250 m (500 m total depopulation area) and included six infected premises, whereas one was expanded 

by 750 m (1 km total depopulation area) and included 10 infected premises. The 1 km depopulation 

area was in a densely populated area of backyard/exhibition bird premises where residents had 

observed sick birds for several weeks.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 67

H. References

CDFA. 2019. Notice of Required Action Pursuant to Quarantine. California Department of Food and 

Agriculture. February 27, 2019. Accessed on 6/25/2019. 

https://www.cdfa.ca.gov/ahfss/animal_health/pdfs/VND_RegionalQuarantine_1.pdf

Burdett, C. L., Kraus, B. R., Garza, S. J., Miller, R. S., & Bjork, K. E. (2015). Simulating the distribution 

of individual livestock farms and their populations in the United States: An example using 

domestic swine (Sus scrofa domesticus) farms. PloS One, 10(11). doi: 

10.1371/journal.pone.0140338

Costa-Hurtado M, Afonso CL, Miller PJ, Shepherd E, Cha RM, Smith D, Spackman E, Kapczynski DR, 

Suarez DL, Swayne DE: Previous infection with virulent strains of Newcastle disease virus 

reduces highly pathogenic avian influenza virus replication, disease, and mortality in chickens. 

Veterinary research 2015, 46(1):97

Desingu P, Singh S, Dhama K, Kumar OV, Malik Y, Singh R: Clinicopathological characterization of 

experimental infection in chickens with sub-genotype VIIi Newcastle disease virus isolated from 

peafowl. Microbial pathogenesis 2017, 105:8-12

Diel DG, Susta L, Cardenas Garcia S, Killian ML, Brown CC, Miller PJ, Afonso CL: Complete genome 

and clinicopathological characterization of a virulent Newcastle disease virus isolate from South 

America. J Clin Microbiol 2012, 50(2):378-387

Guinat, C., Porphyre, T., Gogin, A., Dixon, L., Pfeiffer, D. U., & Gubbins, S. (2018). Inferring within‐

herd transmission parameters for African swine fever virus using mortality data from outbreaks 

in the Russian Federation. Transboundary and emerging diseases, 65(2), e264-e271.

Kapczynski DR, King DJ: Protection of chickens against overt clinical disease and determination of 

viral shedding following vaccination with commercially available Newcastle disease virus 

vaccines upon challenge with highly virulent virus from the California 2002-2003 exotic 

Newcastle disease outbreak. Vaccine 2005, 23(26):3424-3433

Kulldorff M. (1997). A spatial scan statistic. Communications in Statistics: Theory and Methods, 

26:1481-1496.

Kulldorff M. and Information Management Services, Inc. (2009). SaTScanTM v9.6: Software for the 

spatial and space-time scan statistics. http://www.satscan.org/.

Lessler, J., Salje, H., Grabowski, M.K., and Cummings, D.A.T. 2016. Measuring Spatial Dependence for 

Infectious Disease Epidemiology. PLoS ONE 11(5): e0155249. doi: 

10.1371/journal.pone.0155249.

Marjoram, P., Molitor, J., Plagnol, V., & Tavaré, S. (2003). Markov chain Monte Carlo without 

likelihoods. Proceedings of the National Academy of Sciences, 100(26), 15324-15328.

Miller PJ, Afonso CL, El Attrache J, Dorsey KM, Courtney SC, Guo Z, Kapczynski DR: Effects of 

Newcastle disease virus vaccine antibodies on the shedding and transmission of challenge 

viruses. Developmental & Comparative Immunology 2013, 41(4):505-513
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

68 USDA APHIS VS

OIE. 2012. World Organisation for Animal Health, Terrestrial Animal Health Code. OIE, Paris.

SCAG. 2016. GIS and Data Services, Southern California Association of Governments. 

http://www.scag.ca.gov/Pages/default.aspx. Accessed 5/13/19.

Spackman E, Pedersen JC, McKinley ET, Gelb J: Optimal specimen collection and transport methods 

for the detection of avian influenza virus and Newcastle disease virus. BMC veterinary research 

2013, 9(1):35

Stevenson, M.A., Sanson, R.L., Stern, M.W., O’Leary, B.D., Sujau, M., Moles-Benfell, N., Morris, R.S. 

(2013). Interspread plus: A spatial and stochastic simulation model of disease in animal 

populations. Preventive Veterinary Medicine, 109(1-2), 10-24. doi: 

10.1016/j.prevetmed.2012.08.015

USDA. 2018. vND Response 2018, Cleaning & Disinfection Basics (Virus Elimination). May 23, 2018. 

Accessed 6/25/19.

https://www.aphis.usda.gov/animal_health/emergency_management/downloads/vnd/cleaning

-disinfection.pdf

USDA. 2018. Foreign Animal Disease Response: Ready Reference Guide – Overview of Zones. May 

23, 2018. Accessed 6/25/19. 

https://www.aphis.usda.gov/animal_health/emergency_management/downloads/premises_an

d_zones.pdf

Ward, M. (2007). Spatiotemporal analysis of infectious disease outbreaks in veterinary medicine: 

clusters, hotspots, and foci. Vet Ital. 43(3), 559-570.

Wegmann, D., Leuenberger, C., & Excoffier, L. (2009). Efficient approximate Bayesian computation 

coupled with Markov chain Monte Carlo without likelihood. Genetics, 182(4), 1207-1218.

Wise MG, Suarez DL, Seal BS, Pedersen JC, Senne DA, King DJ, Kapczynski DR, Spackman E: 

Development of a real-time reverse-transcription PCR for detection of Newcastle disease virus 

RNA in clinical samples. Journal of Clinical Microbiology 2004, 42(1):329-338
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 69

VI. ACKNOWLEDGEMENTS

We greatly appreciate the cooperation and support of the poultry owners for allowing us access to their 

properties, providing information on their biosecurity and production practices, and for their 

cooperation with this report. 

We also appreciate the Federal and State animal health experts, as well as the many partners who 

assisted with these studies while serving in the incident command for this outbreak. 

This report would not have been possible without a large group of researchers, epidemiologists, 

laboratory staff, and data scientists who participated in the various analyses, and the drafting and 

review of this report. We appreciate their dedication and professionalism in providing the best 

information possible to help bird owners reduce the risk of Newcastle disease spread.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

70 USDA APHIS VS

APPENDIX A: QUESTIONNAIRE

California Department of Food and Agriculture

CA VND 2018

Non-Commercial Premises 

Virulent Newcastle Disease Epidemiology Questionnaire

Investigator name: ____________________Date of Investigation: _______/_____/_____

Investigator name: ____________________

Quarantine # ______________________ Date Quarantine Issued: _____/_____/_____

1. Name of Premises Owner:

___________________________________________

(First) (MI) (Last)

2. Premises Address (location of birds):

________________________________________________

________________________________________________

Latitude: ___________________ Longitude: ___________________

3. Premises Owner Telephone #: 

a. Mobile: ___________________

b. Home: ___________________

c. Other: ___________________

If Premises Owner is the Bird Owner skip to Question 7

4. Name of Bird Owner:

___________________________________________

(First) (MI) (Last)

5. Bird Owner Address: ________________________________________________

_______________________________________________

6. Bird Owner Telephone #: ______________________

7. Other than the interviewee, how many other owners with birds 

are on this premises: #_______
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 71

8. How many birds do you have on the premises today? # ______________

9. What percent of the adult chickens are: a) Roosters %____________________

b) Hens %_______________________

10. Which of the following birds are on the premises? Complete table below.

Type of Bird # Adults # Young birds Total

Backyard Poultry a b c

Exhibition Birds/gamefowl d e f

Ducks/Geese g h i

Other 

Specify j k l m

Other 

Specify n o p q

11. Which of the following animals are on the premises (potential fomites)? 

a) Livestock (Horses, Cattle, Swine, Sheep, Goats) 1 Yes 3 No

b) Dogs/Cats 1 Yes 3 No 

c) Other (specify _____________________) 1 Yes 3 No

12. Which of the following housing types are used to house birds? 

a) Inside the home 1 Yes 3 No

b) Outdoor open top poultry pen or enclosure 1 Yes 3 No

c) Outdoor cages or coops - fully enclosed 1 Yes 3 No

d) Individually tethered 1 Yes 3 No

e) Free range 1 Yes 3 No

f) Other (Specify__________________________) 1 Yes 3 No

13. Has there been an increase in illness in your birds 

on your premises? 1 Yes 3 No

a) If yes, how many days ago did the birds first show

signs of illness: ________days
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

72 USDA APHIS VS

Which of the following clinical signs of illness have you observed? 

Check all that apply.

b) Not eating 1 Yes 3 No

c) Coughing/gasping 1 Yes 3 No

d) Depressed 1 Yes 3 No

e) Twisting of the neck 1 Yes 3 No 

f) Paralysis 1 Yes 3 No

g) Diarrhea 1 Yes 3 No

h) Swellings around the eyes and neck 1 Yes 3 No

i) Sudden death 1 Yes 3 No

j) Other (specify___________________) 1 Yes 3 No

14. Have there been any deaths in your birds on this premises 

during the past 30 days? 1 Yes 3 No

a) If yes, when did the first bird die? _____/___/______

b) If yes, how many birds died in the first 7 days? # ______________

c) If yes, how many birds have died in the past 7 days? # ______________ 

15. Do you keep any birds at another premises? 1 Yes 3 No

a) If yes, where are the birds housed?

________________________________________________

________________________________________________

16. Have you brought new birds onto this premises 

during the past 30 days? 1 Yes 3 No 

If Yes, list date and name the source and location of the new birds: 

 Date Source/Location

 

___/___/___a _________________________________b

___/___/___c _________________________________d

___/___/___e _________________________________f
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 73

17. Have any of the following had contact with your birds, feed or water sources on your property in the 

last 30 days? 

a) Wild birds (e.g., pigeons, doves, sparrows) 1 Yes 3 No

b) Neighborhood/community chickens 1 Yes 3 No

c) Wild animals 1 Yes 3 No

18. Have any of your birds left these premises

during the last 30 days? 1 Yes 3 No 

If Yes, for what purposes listed below were the birds moved?

Purpose Date Destination (City/State) # of birds

Sale a b c

Show d e f

Competition g h i

Veterinary care j k l

Gift/trade m n o p

Other 

Specify q r s t

If Yes, did any birds leave and then return to these premises? 1 Yes 3 No

19. Do you give away or sell eggs from this premises? 1 Yes 3 No 

20. Do your neighbors have birds? 1 Yes 3 No

If No, skip to Question 23. 

If Yes, please note location(s) on the map at the end of the questionnaire.

21. When not cooped, do your birds ever visit the neighbor’s property? 1 Yes 3 No

22. Do your neighbor’s birds ever come onto your property? 1 Yes 3 No

a) If Yes, do the neighbors birds have contact with your birds? 1 Yes 3 No

23. Do you have family members or close friends 

who own/keep birds? 1 Yes 3 No

If Yes, do any of the following situations occur (evaluating direction of exposure): 

a) Your family or friends handle birds 

when they visit. 1 Yes 3 No

b) When visiting family/friends do 

you handle their birds. 1 Yes 3 No
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

74 USDA APHIS VS

24. What is the name and location of the store(s) where you get 

feed and supplies for your birds?

Name Location (City)

__________________________a _____________________________b

__________________________c _____________________________d

__________________________e _____________________________f

25. Have the birds on your premises today been vaccinated 

with Newcastle vaccine? 1 Yes 2 Unsure 3 No

Vaccine does not protect against disease!

a) If Yes, at what age(s) were your birds vaccinated with Newcastle 

 vaccine? 

26. Have you seen any dead wild birds on your premises 1 Yes 3 No

in the last 30 days?

If Yes, what type of wild bird(s)?

____________________________a _______________________________b

____________________________c_ _______________________________d

Additional comments, observations and leads:

Insert Google Maps Image of the premises or draw a map and specify bird 

locations. Please indicate which neighbors, if any, have birds.

I __________________________________certify that I have ________birds on / / @ __________

 (owner signature) (number) (date and time)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 75

APPENDIX B: MODELING SCENARIO DESIGN

Control Activities Associated with Respective Response Options

Scenario Design Overview

1

Day 1 through Day 161 

Identical response activities 

for all 4 scenarios

Day 162 

75 days postfirst detection

Scenario 1: Response Option 1 1, 2, 4, 6, 9, 11, 12, 14, 16, 

17, 19, 22, 24, 25, 26

Scenario 2: Response Option 

2 

Scenario 3: Response Option 

3 

Scenario 4: Response Option 

4 

1, 2, 4, 7, 9, 11, 13, 14, 16, 

17, 20, 22, 24, 25, 26

1, 2, 3, 4, 7, 9, 11, 13, 14, 16, 

17, 18, 20, 23, 24, 25, 26

1, 2, 3, 4, 5, 8, 10, 11, 13, 15, 

16, 17, 18, 21, 23, 24, 25, 26

Alternative Response Options Specific Activities From Table B.1 Initial Response 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

76 USDA APHIS VS

Table B1. Individual Control Activities Included in Response Options Response 

Options

Control Activity 1 2 3 4

1 Depopulation: detected backyard premises x x x x

2 Depopulation: backyard premises in proximity to detected backyard premises in Muscoy Zone x x x x

3 Depopulation: backyard premises in proximity to detected backyard premises in other high-risk 

zones (e.g.,Bloomington, Fontana, Riverside)

x x

4 Depopulation: detected commercial premises x x x x

5 Depopulation: backyard premises in proximity to all detected backyard premises x

6 Depopulation: capacity (low – maximum of 6 backyard premises per day) x

7 Depopulation: capacity (medium – maximum of 10 backyard premises per day) x x

8 Depopulation: capacity (high – maximum of 30 backyard premises per day) x

9 Movement restrictions for live animal movements originating from zoned backyard premises 

(low capacity – 30% of high capacity)

x x x

10 Movement restrictions enhanced for live animal movements originating from zoned backyard 

premises (high capacity)

x

11 Movement restrictions for live animal movements originating from zoned commercial premises x x x x

12 Movement restrictions for live animal movements originating from traced premises (low 

capacity – 50% of high capacity)

x

13 Movement restrictions for live animal movements originating from traced premises (high 

capacity)

x x x

14 Surveillance – Passive: Sick calls – initiates active surveillance visit (low public disease 

awareness)

x x x

15 Surveillance – Passive: Sick calls – initiates active surveillance visit (high public disease 

awareness – results in greater number of calls and surveillance visits) 

x

16 Surveillance – Active: 1-km radial zone around detected backyard premises x x x x

17 Surveillance – Active: Irregular zone surge (Muscoy) [enhanced surveillance for backyard 

premises]

x x x x

18 Surveillance – Active: Irregular zone surge (e.g., Bloomington, Fontana, Riverside) [enhanced 

surveillance for backyard premises]

x x

19 Surveillance – Active (post-irregular zone surge): Low capacity – fewest number of backyard 

premises eligible for surveillance (approx. 30% of high capacity)

x

20 Surveillance – Active (post-irregular zone surge): Medium capacity (approx. 67% of high 

capacity)

x x

21 Surveillance – Active (post-irregular zone surge): High capacity – greatest number of backyard 

premises eligible for surveillance

x

22 Surveillance – Active: baseline response time after zone formation (approx. 2X longer response 

time than for enhanced response)

x x

23 Surveillance – Active: enhanced response time after zone formation x x

24 Surveillance – Active: weekly to bi-weekly sampling of commercial premises x x x x

25 Tracing live animal movements originating from detected farms (movements occurred prior to 

detection)

x x x x

26 Tracing indirect contacts originating from detected commercial farms (movements occurred 

prior to detection)

x x x x
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 77

APPENDIX C. PREDICTED DISEASE MORTALITY AND INFECTION PREVALENCE UNDER 

ADDITIONAL FLOCK SIZE AND VACCINATION SCENARIOS

In this appendix, results are provided for unvaccinated and vaccinated backyard flocks housing 50 birds, 

unvaccinated and vaccinated commercial flocks housing 5000 birds, and unvaccinated commercial flocks 

housing 20,000 birds. The trends in the results for these additional scenarios are consistent with those 

noted in the main text, including slower spread and lower mortality in vaccinated flocks, and longer 

amounts of time required to reach specific cumulative mortality levels in larger flocks. 

Input parameters to the transmission model were estimated from inoculation study data and data from 

the current outbreak. A summary of the parameters is given in Table C1. Model parameters for the 

latent and infectious period distributions in unvaccinated flock scenarios were estimated using available 

experimental inoculation studies for the CA/2018 and other vND strains (Dimitrov et al., 2019) as 

described in Section V: Part C. The infectious period parameters for vaccinated flocks were estimated 

from experimental data presented in Miller et al. (2013) from vaccinated SPF chickens and contact birds. 

The latent period distribution from the unvaccinated flock scenario was also used in the vaccinated flock 

scenario due to a lack of adequate data on vaccinated birds. 

The contact rate in the vaccinated commercial flock scenario and the mortality proportion in vaccinated 

flocks were based on estimates from the time of introduction analysis in Section V: Part E. The contact 

rate in the unvaccinated commercial flock scenario was estimated as described in Section V: Part C. Due 

to greater uncertainty, the contact rate distributions were widened in the backyard flock scenarios. All 

birds infected in the unvaccinated bird scenarios were assumed to die from the disease. 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

78 USDA APHIS VS

Table C1.Transmission model input parameters used in the estimation of infection prevalence and disease 

mortality over time in vND infected vaccinated and unvaccinated flocks

 

Parameter Name Description Distribution

Adequate Contact Rate

Daily average number of contacts a bird 

has with other birds that are sufficient to 

transmit infection

Vaccinated commercial flocks: PERT (min = 0.90, 

mode = 1.20, max = 2.50)

Unvaccinated commercial flocks: Uniform (min = 

1.7, max = 4.0)

Vaccinated backyard flocks: PERT (min = 0.5, 

mode = 1.20, max = 2.50)

Unvaccinated backyard flocks: Uniform (min = 

1.00, max = 4.00) 

Latent Period Length 

Distribution Length of the latent period

Vaccinated and unvaccinated flocks: Gamma 

(shape = 1.00, scale = 0.39); mean = 0.39 days; 

variance = 0.15 days2

Infectious Period Length 

Distribution Length of the infectious period

Vaccinated flocks: Gamma (shape = 2.30, scale = 

2.48); mean = 5.68 days; variance = 14.07 days2

Unvaccinated flocks:: Gamma (shape = 13.07, 

scale = 0.33) mean = 4.34 days; variance = 1.44 

days2

Mortality Proportion Proportion of birds that die in a barn 

following exposure to vND

Vaccinated flocks: Uniform (min = 0.030, max = 

0.047)

Unvaccinated flocks: 100% mortality

Proportion Immune

Proportion of birds in a barn that are 

immune to vND following vaccination Uniform (min = 0.00, max = 0.04)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 79

Additional model scenarios for backyard flocks 

Predicted mortality and disease prevalence in a 50-bird unvaccinated backyard flock

Figure C1. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

exposure in a 50-bird unvaccinated backyard flock using baseline vND spread parameters. Shaded area 

represents the 90% prediction interval for each variable.

Figure C2. Predicted daily mortality on various days post exposure in a 50-bird unvaccinated backyard flock 

using baseline vND spread parameters. Shaded area represents the 90% prediction interval.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

80 USDA APHIS VS

Table C2. Predicted days post onset of infectiousness to reach various cumulative mortality levels in a 50-

bird unvaccinated backyard flock using baseline vND spread parameters

Cumulative 

Percent Mortality

Predicted number of days post onset of 

infectiousness to reach this cumulative 

mortality percent. median (90% Prediction 

Interval)

10 5.3 (4-7)

20 6 (4.8-8)

30 6.6 (5.2-8.8)

40 7 (5.5-9.2)

50 7.4 (6-9.8)

60 7.8 (6.2-10.2)

70 8.4 (6.8-11)

80 8.8 (7.2-11.5)

90 9.5 (7.8-12.5)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 81

Predicted mortality and disease prevalence in a 50-bird vaccinated backyard flock

Figure C3. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

vND exposure in a 50-bird vaccinated backyard flock. Shaded area represents the 90% prediction 

interval for each variable.

Figure C4. Predicted daily mortality on various days post vND exposure in a 50-bird vaccinated backyard 

flock. Shaded area represents the 90% prediction interval.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

82 USDA APHIS VS

Table C3. Predicted days post onset of infectiousness to reach various cumulative mortality levels in a 50-

bird vaccinated backyard flock using baseline vND spread parameters

Cumulative Percent 

Mortality

Percent of simulation iterations 

in which this cumulative 

mortality is reached

Predicted number of days post onset of 

infectiousness to reach this cumulative mortality 

percent. median (90% Prediction Interval)

2 80.32 8.8 (3.5-16.5)

4 53.13 11.6 (6-20)

6 27.63 13.2 (7.5-21.5)

8 10.8 14.1 (8.2-22.2)

Additional model scenarios for commercial flocks 

Predicted mortality and disease prevalence in a 5000-bird unvaccinated commercial flock

Figure C5. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

vND exposure in a 5000-bird unvaccinated commercial flock. Shaded area represents the 90% 

prediction interval for each variable. 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 83

Figure C6. Predicted daily mortality on various days post vND exposure in a 5000-bird unvaccinated 

commercial flock. Shaded area represents the 90% prediction interval.

Table C4. Predicted days post onset of infectiousness to reach various cumulative mortality levels in a 5000-

bird unvaccinated commercial flock using baseline vND spread parameters

Cumulative 

Percent Mortality

Predicted number of days post onset of infectiousness to reach this cumulative 

mortality percent. median (90% Prediction Interval)

10 7.9 (6.5-9.8)

20 8.6 (7.2-10.5)

30 9 (7.5-11)

40 9.4 (8-11.5)

50 9.8 (8.2-12)

60 10.2 (8.8-12.2)

70 10.6 (9.2-12.8)

80 11.2 (9.5-13.5)

90 11.9 (10.2-14.2)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

84 USDA APHIS VS

Predicted mortality and disease prevalence in a 20,000-bird unvaccinated commercial flock

Figure C7. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

vND exposure in a 20,000-bird unvaccinated commercial flock. Shaded area represents the 90% 

prediction interval for each variable. 

Figure C8. Predicted daily mortality on various days post vND exposure in a 20,000-bird unvaccinated 

commercial flock. Shaded area represents the 90% prediction interval.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 85

Table C5. Predicted days post onset of infectiousness to reach various cumulative mortality levels in a 

20,000-bird unvaccinated commercial flock using baseline vND spread parameters

Cumulative 

Percent 

Mortality

Predicted number of days post onset of infectiousness to reach this cumulative 

mortality percent. median (90% Prediction Interval)

10 8.8 (7.2-10.8)

20 9.4 (8-11.5)

30 9.9 (8.2-12.2)

40 10.3 (8.8-12.5)

50 10.7 (9-13)

60 11.1 (9.5-13.5)

70 11.5 (9.8-14)

80 12 (10.2-14.5)

90 12.8 (11-15.2)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

86 USDA APHIS VS

Predicted mortality and disease prevalence in a 5000-bird vaccinated commercial flock

Figure C9. Predicted cumulative mortality percent and prevalence of infectious birds on various days post 

exposure in a 5000-bird vaccinated commercial cage free layer flock using baseline vND spread 

parameters. Shaded area represents the 90% prediction interval for each variable. 

Figure C10. Predicted daily mortality on various days post exposure in a 5000-bird vaccinated commercial 

cage free layer flock using baseline vND spread parameters. Shaded area represents the 90% prediction 

interval.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 87

Table C6. Predicted days post onset of infectiousness to attain various cumulative mortality levels in a 5000-

bird vaccinated commercial cage free layer flock using baseline vND spread parameters

Cumulative 

Percent Mortality

Percent of simulation 

iterations in which this 

cumulative mortality is 

reached

Predicted number of days post onset of 

infectiousness to reach this cumulative 

mortality percent. median (90% Prediction 

Interval)

2 95.69 15.9 (12.2-20)

2.5 95.17 17.6 (13.5-22.8)

3 83.86 19.6 (15-25.8)

3.5 56.66 21.1 (16.2-27.2)

4 27.45 22.8 (18-28.2)

4.5 5.67 24.3 (19.2-28.8)

5 0 NA
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

88 USDA APHIS VS

APPENDIX D. TECHNICAL DETAILS FOR ESTIMATING THE TIME OF VND

INTRODUCTION IN COMMERCIAL VACCINATED LAYER FLOCKS

A. Overview

We used an approximate Bayesian computation (ABC) approach together with Monte Carlo simulation 

to estimate the time of vND introduction. Specifically, we used the ABC-MCMC function of the R 

package EasyABC in our estimation. This function implements the methods proposed by Marjoram et al., 

2003 where the parameter space is explored via a modified Metropolis-Hastings algorithm that does not 

involve likelihood calculation (Marjoram, 2003). The function also implements improvements proposed 

by Wegmann et al., (2009) to perform an automatic calibration step to determine a tolerance threshold 

for the goodness of fit metric representing the deviation between model predictions and the observed 

data. 

The algorithm begins with the calibration step where the goodness of fit measure is calculated for a 

specified number of model iterations simulated with the prior distributions. The threshold value for the 

goodness of fit metric ψmax is than set according to the input tolerance quantile (default 0.01). In the 

next step, the new values for parameters are generated according to a uniform proposal distribution 

and the iteration is accepted if ψ < ψmax. The model is then run until the required number of samples 

is collected. The approximate posterior distribution for the parameters is calculated from the parameter 

values in the selected iterations.

B. Estimating prior distributions

The prior distributions for the model parameters were based on estimates from experimental 

inoculation studies as well as the current outbreak data. A summary of the prior distributions used in the 

transmission model is given in Table D1. The distributions for the lengths of the infectious and latent 

periods in individual birds were estimated from data in Miller et al. 2013 consisting of vaccinated SPF 

chickens and contact birds (Miller, 2013). Parameters estimated for these distributions, assumed to be 

gamma distributed, were estimated using a maximum likelihood approach. Analysis of transmission data 

from Miller et al. 2013 indicated a contact rate in the range of 0.53 to 2.4 contacts per day for 

vaccinated flocks. Given the greater uncertainty regarding the transmission rate in commercial 

vaccinated poultry flocks, we used a uniform (0.2, 5) contacts per day as the prior distribution. 

The mortality among vaccinated birds in Miller et al. 2013 varied widely depending on the time between 

vaccination and challenge (from 40 percent to 0 percent mortality for birds challenged at days 3, 10 and 

21 post vaccination). We used a uniform (0, 0.12) prior for the probability that a vaccinated and infected 

bird dies from disease. The transmission model allows for a proportion of the birds to be completely 

immune due to vaccination. There is a considerable uncertainty regarding this model parameter in field 

flocks. Given that most of the infected barns in the premises had older aged birds, we used a uniform (0, 

0.04) distribution for the proportion of birds that are immune.

The input parameters for the mean and standard deviation of the normal mortality and egg production 

were estimated directly from the available production data for each barn. There is substantial 

uncertainty in the egg production parameters as only 12 days of data were available for each barn, while 

several weeks of mortality data were available. 
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 89

We used wide ranges for the egg production rates in healthy and vND infected hens to account for the 

uncertainty in these parameters. For example, for barn A, the egg production was fairly constant at 70

percent for a few days before dropping off. We used a prior of uniform (0.68, 0.72) for the egg 

production in healthy hens for barn A. The ending egg production on the last day of production data for 

barn A was 28 percent. We used a uniform (0.2, 0.3) distribution as the prior for the egg production rate 

in vND infected hens. The egg production drops in barns B and C were much milder compared to barn A. 

Egg production fell in these barns from about 70 percent to 50-60 percent. A uniform (0.64, 0.74) prior 

was used for egg production in healthy hens in barns B and C, while a uniform (0.4, 0.55) distribution 

was used for egg production in sick hens. There was almost no drop in egg production for barn D with 

the egg production around 90 percent on all days. A uniform (0.90, 0.94) distribution was used for egg 

production in healthy hens and a uniform (0.80, 0.90) distribution was used for egg production in sick 

hens in this barn.

More than 3 months of normal mortality data were available for barns A, B, and C. We estimated the 

normal mortality for these barns using a linear model for 30 days prior to 11/5/2018. The linear model is 

useful to account for the increasing trend in daily mortality with age under routine production. The 

normal mortality for barn D was estimated from other barns with similar ages of birds which tested 

negative on 1/3/2019 and had no pattern of drop in egg production or increased mortality. The input 

distributions related to mortality and egg production for the four barns are summarized in Table D2.

C. Goodness of Fit measure calculation

The goodness of fit measure metric ψ consisted of the sum of the mortality cost, the egg production 

cost and the diagnostic testing cost. The mortality cost Dm was calculated as the average sum of squared 

normalized residuals between the model’s predicted mortality and the data as shown in appendix 

Equation 1. Here Mobs and Msim are the observed and simulated mortalities, m is the standard deviation 

of normal mortality and N is the number of days of mortality data. Note that the residual sum of squares 

was also used for summary statistic calculation in other studies for parameter estimation from outbreak 

data (Guinat, 2018). Similarly, the egg production cost De was defined as the average sum of squared 

normalized differences between the model’s predicted egg production and the data.

Dm =

1

N

∑(

Mobs(t) − Msim(t)

σm

)

2

tm

ti

Appendix Equation 1

Table D1. Input prior distribution parameters used in the ABC approach to estimate the contact rate and time of 

virus introduction.

Parameter Name Description Distribution

Adequate Contact Rate

Daily average number of contacts a 

bird has with other birds that are 

sufficient to transmit infection

Uniform (min = 0.2, max = 5.0)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

90 USDA APHIS VS

Table D2. Input related to mortality and egg production in the ABC approach to estimate the contact rate and 

time of virus introduction.

Input parameter

Parameter values used for different barns

Barn A Barn B Barn C Barn D

Egg production in 

healthy hens

0.68 - 0.72 0.64 - 0.74 0.64 - 0.74 0.90 - 0.94

Egg production in vND 

infected hens 0.2 - 0.3 0.4 - 0.55 0.4 - 0.55 0.8 - 0.9

Normal mortality fraction 0.000638 0.000490 0.000463 0.000606

Standard deviation of normal 

mortality fraction 0.000373 0.000236 0.000214 0.000554

Latent Period Length 

Distribution Length of the latent period Gamma (shape = 1.00, scale = 0.39); mean = 0.39 days; variance = 0.15 days2

Infectious Period Length 

Distribution Length of the infectious period Gamma (shape = 2.30, scale = 2.48); mean = 5.68 days; variance = 14.07 days2

Mortality Proportion Proportion of birds that die in a barn 

following exposure to vND Uniform (min = 0, max = 0.11)

Proportion Immune

Proportion of birds in a barn that are 

immune to vND following 

vaccination

Uniform (min = 0.00, max = 0.04)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 91

The diagnostic testing cost was set to 0 if all the test results in an iteration matched the observed test 

results or to a large value (15) otherwise. Given this cost structure, only the iterations where the 

simulated and observed test results matched were selected in the Markov chain in the simulation 

results.

D. Model Implementation and coding validation

The disease transmission model was coded in the languages R and C. The R package EasyABC was used 

to estimate the posterior distribution. The number of iterations run for the distance threshold 

calibration was set to 20000. The model was run for 3000-6000 iterations with 1/50 thinning to account 

for the higher autocorrelation. For validation of the ABC approach, a forward simulation method was 

developed to estimate the time of virus introduction and adequate contact rate for barn 48. The 

forward simulation method consisted of comparing data simulated from the stochastic disease 

transmission model to the egg production, mortality, and diagnostic testing data from barn 48 for 

candidate virus introduction date and contact rate pairs evaluated across a grid. For each transmission 

model iteration an indicator variable for whether the simulated data fell within a certain distance of the 

egg production and mortality data was multiplied by the likelihood of observing the diagnostic test 

results given the simulated data. These values were averaged across 10 000 iterations performed for 

each contact rate and time of virus introduction pair to estimate a posterior likelihood. Table D3

compares the median and 95 percent C.I. time of virus introduction estimated from the forward 

simulation method with the estimates from the ABC method. The results suggest the two methods are 

in reasonable agreement, which is evidence that the ABC method was implemented accurately and run 

for a sufficient number of iterations to achieve convergence.

Table D3. The median and 95% C.I. for the time of virus introduction estimated from barn 48 egg production, 

mortality, and diagnostic testing data from two estimation approaches.

Estimation method

Time of introduction

Estimated median (95% C.I.)

ABC 12/23/2018 (12/17/2018 -12/26/2018)

Forward simulation 12/20/2018 (12/15/2018 – 12/23/2018)
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

92 USDA APHIS VS

Results

The results for the estimated day of vND introduction and the adequate contact rate for the four barns 

are shown in Table D4. The model fits to the observed egg production rate and daily mortality across 

different barns are shown in Figures D1-D8. The interval for the estimated time of introduction is the 

narrowest for barn A which had the highest drop in egg production and the most elevated mortality 

above baseline. There is a greater uncertainty in the times of introduction and the contact rate for other 

barns given the mild drops in egg production and mild elevation in mortality. These barns also have a 

lower adequate contact rate (which determines the rate of within barn disease spread) which leads to a 

greater uncertainty in the estimated time of introduction.

Table D4. Estimated time of introduction and adequate contact rate. 

Barn Time of introduction

Estimated mode, median, (95% C.I), 

(90% C.I)

Adequate contact rate

Estimated mode, median, (95% C.I.), 

(90% C.I)

A (cage free layers)

12/25/2018, 12/23/2018 

(12/17/2018 -12/26/2018)

(12/18/2018 -12/26/2018)

1.42, 1.86 (1.02-4.72)

(1.09-4.56)

B (cage free layers)

12/8/2018, 12/6/2018 

(11/17/2018 -12/17/2018)

(11/21/2018 -12/16/2018)

0.48, 0.53 (0.36-84)

(0.38-82)

C (cage free layers)

12/9/2018, 12/7/2018 

(11/24/2018 -12/20/2018)

(11/26/2018 -12/19/2018)

0.5, 0.68 (0.34-2.35)

(0.36-2.3)

D (caged layers)*

11/28/2018, 11/24/2018 

(11/6/2018 -12/10/2018) 

(11/72018 -12/8/2018)

0.33, 0.36 (0.26-0.58)

(0.28-0.55)

*Results from barn D should be interpreted cautiously as the drop in egg production was mild to nonexistent, increasing the 

uncertainty in the estimated results.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 93

Figure D1: Model fitted egg production rate curves from the approximate Bayesian computation and 

observed egg production rate for Barn A. The shaded region represents the 95 percent credibility 

interval for the fitted egg production.

Figure D2. Model fitted disease plus normal mortality from the approximate Bayesian computation and the 

observed daily mortality for Barn A. The shaded region represents the 95 percent credibility interval for 

the fitted daily mortality.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

94 USDA APHIS VS

Figure D3. Model fitted egg production rate curves from the approximate Bayesian computation and 

observed egg production rate for Barn B. The shaded region represents the 95 percent credibility 

interval for the fitted egg production.

Figure D4. Model fitted disease plus normal mortality from the approximate Bayesian computation and the 

observed daily mortality for Barn B. The shaded region represents the 95 percent credibility interval for 

the fitted daily mortality.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 95

Figure D5: Model fitted egg production rate curves from the approximate Bayesian computation and 

observed egg production rate for Barn C. The shaded region represents the 95 percent credibility 

interval for the fitted egg production.

Figure D6. Model fitted disease plus normal mortality from the approximate Bayesian computation and the 

observed daily mortality for Barn C. The shaded region represents the 95 percent credibility interval for 

the fitted daily mortality.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

96 USDA APHIS VS

Figure D7: Model fitted egg production rate curves from the approximate Bayesian computation and 

observed egg production rate for Barn D. The shaded region represents the 95 percent credibility 

interval for the fitted egg production.

Figure D8. Model fitted disease plus normal mortality from the approximate Bayesian computation and the 

observed daily mortality for Barn D. The shaded region represents the 95 percent credibility interval for 

the fitted daily mortality.
Epidemiologic Analyses of Virulent Newcastle Disease in Poultry in California March 2021

USDA APHIS VS 97

Epidemiologic Analyses of 

Virulent Newcastle Disease in 

Poultry in California

March 2021 Report

USDA  APHIS  VS

Center for Epidemiology and Animal Health

2150 Centre Avenue, Bldg. B, Fort Collins, CO, 80526-8117

Web: http://www.aphis.usda.gov/animal-health/ceah