bluuebunny/crossref_metadata_2025_split huggingface dataset:
376. Sensitivity and Specificity of the WHO Probable SARS-CoV-2 Case Definition Among Symptomatic Healthcare Personnel
Authors: Nguyen Han , Weber Sarah , Kataria Yachana , Cole Manisha , Duffy Elizabeth , Ragan Elizabeth , Turcinovic Jacquelyn , Miller Nancy , Hanage William P , Connor John , Pierre Cassandra , Jacobson Karen , Lodi Sara , Bouton Tara 
Published: December 2021

Abstract

Background
SARS-CoV-2 continues to spread globally, including in limited resource settings. It is therefore important to derive general case definitions that can be useful and accurate in the absence of timely test results. We aim to validate the World Health Organization (WHO) case definition, a symptom-screening tool currently used to identify SARS-CoV-2 cases in a cohort of symptomatic health care providers (HCP) who completed a symptom survey interview and received a PCR test at Boston Medical Center (BMC) between March 13, 2020 and May 5, 2020.

Methods
We classified each HCP as a probable or not probable case of SARS-CoV-2 based on the WHO case definition. Using PCR test as gold standard, we computed the sensitivity and specificity of the WHO case definition. We used a stepwise logistic regression model on all PCR-tested HCP to identify symptoms predictive of PCR positivity.

Results
Of 328 included HCP, 109 (33.2%) were PCR positive, 213 (64.9%) negative, and 6 (1.8%) had indeterminate test result. The sensitivity and specificity of the WHO case definition were 65.1% and 74.6%, respectively. The positive predictive value was 56.8% and the negative predictive value was 80.7%. Symptoms found to be predictive of PCR positivity were fever, headache, loss of smell and/or loss of taste, and muscle ache/joint pain. Sore throat was found to be predictive of PCR negativity. The area under the curve using the final model was 0.8412. All statistically significant symptoms included in the final model, were also included in the WHO case definition.

Conclusion
In our largely symptomatic HCP cohort, our model yielded similar symptoms to those identified in the WHO probable case definition. As seen in similar studies, it is unlikely that further adjustment will improve the performance of a SARS-CoV-2 case definition. However, it is concerning that 35% (38/109) of PCR positive SARS-CoV-2 HCP would have been classified as not probable cases by the WHO definition, given that this definition does not even include asymptomatic cases. This is further evidence for global building of laboratory capacity and development of affordable diagnostics to improve global pandemic control.

Disclosures
All Authors: No reported disclosures
377. SARS-CoV-2 Genomic Surveillance Reveals Little Spread Between a Large University Campus and the Surrounding Community
Authors: Valesano Andrew , Fitzsimmons William , Blair Christopher , Woods Robert , Gilbert Julie , Rudnik Dawn , Mortenson Lindsey , Petrie Joshua G , Martin Emily T , Lauring Adam 
Published: December 2021

Abstract

Background
Understanding SARS-CoV-2 transmission dynamics is critical for controlling and preventing outbreaks. The genomic epidemiology of SARS-CoV-2 on college campuses has not been comprehensively studied, and the extent to which campus-associated outbreaks lead to transmission in nearby communities is unclear. We used high-density genomic surveillance to track SARS-CoV-2 transmission across the University of Michigan-Ann Arbor campus and Washtenaw County during the Fall 2020 semester.

Methods
We retrieved all available residual diagnostic specimens from the Michigan Medicine Clinical Microbiology Laboratory and University Health Service that were positive for SARS-CoV-2 from August 16th – November 25th, 2020 (n = 2245). We extracted viral RNA, amplified the SARS-CoV-2 genome by multiplex RT-PCR, and sequenced these amplicons on an Illumina MiSeq. We applied maximum likelihood phylogenetic analysis to whole genome sequences to define and characterize transmission lineages.

Results
We assembled complete viral genomes from 1659 individual infections, representing roughly 25% of confirmed cases in Washtenaw County across the fall semester. Of these cases, 468 were University of Michigan students. Phylogenetic analysis revealed 203 genetically distinct introductions of SARS-CoV-2 into the student population, most of which were singletons (n = 171) or small clusters of 2 – 8 students. We identified two large SARS-CoV-2 transmission lineages (115 and 73 students, respectively), including individuals from multiple on-campus residences. Viral descendants of these student outbreaks were rare, constituting less than 4% of cases in the community.

Conclusion
We identified many SARS-CoV-2 transmission introductions into the University of Michigan campus in Fall 2020. While there was widespread transmission among students, there is little evidence that these outbreaks significantly contributed to the rise in COVID-19 cases that Washtenaw County experienced in November 2020.

Disclosures
Adam Lauring, MD, PhD, Roche (Advisor or Review Panel member) Sanofi (Consultant)
378. Descriptive Analysis of SARS-CoV-2 Infections Among Health System and University Employees
Authors: Seidelman Jessica , Akinboyo Ibukunoluwa , Rinehart Maya , Moehring Rebekah W , Anderson Deverick J , Said Kristen , Epling Carol A , Lewis Sarah S , Smith Becky , Stiegel Matthew 
Published: December 2021

Abstract

Background
We aimed to describe SARS-CoV-2 (COVID-19) infections among employees in a large, academic institution.
Table 1. COVID-19 Attribution Definitions

Table 2. Description of 3,140 COVID 19 Infections in Employees from 3/2020 to 4/2021

Methods
We prospectively tracked and traced COVID-19 infections among employees across our health system and university. Each employee with a confirmed positive test and 3 presumed positive cases were interviewed with a standard contact tracing template that included descriptive variables such as high-risk behaviors and contacts, dates worked while infectious, and initial symptoms. Using this information, the most likely location of infection acquisition was adjudicated (Table 1). We compared behavior frequency between community and unknown, likely community and community and unknown cases using descriptive statistics.
Table 3. Risk Factors for Community, Likely Community, and Unknown Cases

Number of SARS-CoV-2 cases among employees between 3/2020 and 4/2021 by month and stratified according to clinical employee working in the healthcare system, non-clinical employee employed by the healthcare system, and university employee

Results
From 3/2020 to 4/2021 we identified 3,140 COVID-19 infections in 3,119 employees out of a total of 34,562 employees (9.0%) (Figure 1). Of those 3,119 employees 1,685 (54.0%) were clinical employees working in the health system, 916 (29.4%) were non-clinical employees working in the health system, and 518 (16.6%) were university employees. Descriptive characteristics for the COVID-19 infections and adjudications are outlined in Table 2. Severe disease among employees was significantly less frequent compared to patients in the health system (15.3% vs 2.2%, p&lt; 0.01). The frequency of travel within 14 days, masked gatherings and unmasked gatherings/activities was not significantly different between the community and unknown, likely community groups or the community and unknown groups (Table 3).

Conclusion
The majority of COVID-19 infections were linked to acquisition in the community, and few were attributed to workplace exposures. Employees with unknown sources of COVID-19 participated in higher-risk activities at approximately the same frequency as employees with community sources of COVID-19. The most frequently reported initial symptoms were mild and non-specific and rarely included fever. Despite a comprehensive testing and benefit program, a large proportion of COVID-positive employees worked with symptoms, highlighting ongoing challenges with presenteeism in healthcare.

Disclosures
Rebekah W. Moehring, MD, MPH, UpToDate, Inc. (Other Financial or Material Support, Author Royalties)
379. Abstract For Comparison of Mandatory vs Non-Mandatory Compliance Rates For SARS-CoV-2 Testing in Grades K-12
Authors: Veltman Jennifer , Papayanis Philip , Dubov Alex 
Published: December 2021

Abstract

Background
Rapid testing to identify asymptomatically infected students with SARS-CoV-2 in elementary schools has been suggested as a possible method to reduce risk for in person instruction. As of August 3, 2020 (updated on January 25, 2021), California schools who obtained a waiver to conduct in-person instruction are not required to have mandatory testing for asymptomatic students, except for high contact sports which are required to undergo weekly testing. We explored the uptake of voluntary vs mandatory testing in a private waivered school.

Methods
Between the dates January 25, 2021 to April 16, 2021, the K-12 school superintendent sent an email to all parents outlining the voluntary testing program with a link to the on-line sign up and consent form. All students were offered weekly self-collected anterior nares BinaxNOW Rapid Antigen Test. Signed parental consent was required and tests were performed at the school. Students participating in contact sports were required to undergo testing the week a varsity game was played as a condition of participation. Data was gathered from the school administration and de-identified.

Results
K-5 Lower school had a school population of 448 students. Testing was offered on 8 weeks during the period of 2/15-2/19 to 4/5-4/9. 2 students (0.45%) receive screening on the week of 3/22-3/26. The other seven weeks when screening was offered 0 students received screening. 6-12 Upper school had a school population of 360 enrolled students. Testing was offered 3/8-3/12 and 3/15-3/19. The upper school had 22 students (6.11%) receive testing on the week of 3/8-3/12 and 21 students (5.83%) on the week of 3/15-3/19. Contact sports teams had 67 students on their roster. Weekly testing was offered from 3/22-3/26 to 4/12-4/16. Contact sports teams had 10 students (14.93%) receive testing on the week of 3/22-3/26, 33 students (52.24%) on the week of 4/5-4/9, and 32 students (49.25%) on the week of 4/12-4/16.
Figure 1. Percent of students from each campus and sports team screened per week offered.

Conclusion
Voluntary SARS-CoV-2 screening was not a feasible approach for detection of asymptomatically infected individuals due to low uptake, however in the same school, mandatory testing had high uptake and would be a feasible strategy.

Disclosures
All Authors: No reported disclosures
380. Environmental Contamination with SARS-CoV-2 in Nursing Homes
Authors: Mody Lona , Gibson Kristen , Bautista Liza , Neeb Karen , Montoya Ana , Jenq Grace , Mills John , Min Lillian , Mantey Julia , Kabeto Mohammed , Galecki Andrzej , Cassone Marco , Martin Emily T 
Published: December 2021

Abstract

Background
The COVID-19 pandemic has disproportionately affected nursing home (NH) patients, accounting for 5% of all cases and 32% of all COVID-19 deaths nationwide. Little is known about the frequency and persistence of SARS-CoV-2 environmental contamination in NHs. We characterize SARS-CoV-2 contamination in the rooms of COVID-19 patients and common areas in and around COVID-19 units.

Methods
A prospective cohort study was conducted at four NHs in Michigan between October 2020 and January 2021. Clinical research personnel obtained swab specimens from high-touch room surfaces of COVID-19 infected patients, up to three times per patient. Weekly swab specimens from six high-touch surfaces in common areas were also obtained. Demographic and clinical data were collected from patient clinical records. Our primary outcome of interest was the probability of SARS-CoV-2 detection from specific environmental surfaces in COVID-19 patient rooms.

Results
One hundred four patients with COVID-19 were enrolled and followed for 241 visits. Patient characteristics included: 61.5% over the age of 80; 67.3% female; 89.4% non-Hispanic white; 50.1% short-stay. The study population had significant disabilities in activities of daily living (ADL; 81.7% dependent in four or more ADLs) and comorbidities including dementia (55.8%), diabetes (40.4%) and heart failure (32.7) (Table 1). Over the 3-month study period, 2087 swab specimens were collected (1896 COVID-19 patient room surfaces, 191 common area swabs). Figure 1 shows contamination rates at sites proximate and distant to the patient bed. SARS-CoV-2 positivity was 28.4% (538/1896 swabs) on patient room surfaces and 3.7% (7/191 swabs) on common area surfaces. Over the course of follow-up, 89.4% (93/104) of patients had SARS-CoV-2 contamination in their room at least once (Figure 2). Environmental contamination detected on enrollment correlated with contamination of the same site during follow-up. Functional independence increased the odds of proximate contamination.
Table 1. Clinical and Demographic Characteristics of the Study Population Including Short- and Long-stay Patients

Figure 1. Contamination of Environmental Surfaces Relative to Distance from Patient Bed

Figure 2. SARS-CoV-2 on Swab Specimens Collected – Patient-level, Visit-level, and Swab-level

Conclusion
We conclude that environmental contamination of surfaces in the rooms of COVID-19 patients is nearly universal and persistent. Patients with greater independence are more likely than fully dependent patients to contaminate their immediate environment.

Disclosures
All Authors: No reported disclosures
382. Vitamin D Supplementation and Covid 19: Results from the U.S. N3C Data Enclave
Authors: Murray Kim , Fairfield Kathleen M , Rosen Clifford james , Hodder Sally L , Harper Jeremy 
Published: December 2021

Abstract

Background
It is estimated that 18% of adults in the U.S. take Vitamin D supplements. Some observational studies suggest that vitamin D supplementation activates the innate immune system and reduces the incidence and severity of viral infections. During the SARS-CoV-2 pandemic, vitamin D supplements were touted as a potential therapy to prevent the disease and/or complications. However, supportive evidence is lacking.

Methods
The National COVID Cohort Collaborative (N3C) enclave is the largest COVID-19 data base with nearly 1.4 million positive patients at 56 sites in the U.S. We performed a retrospective analysis of vitamin D supplementation, either prescribed before or during hospitalization for SARS-CoV-2.

Results
137,399 people took vitamin D supplements out of 1.4 million. Females prescribed vitamin D outnumbered males by almost 2:1, whereas in non-users there were no sex differences. Most supplement users were older than 50. African Americans constituted 13% of the non-users, but 23% of those prescribed vitamin D. Infected individuals with any vitamin D supplementation, pre-Covid, post-Covid or both, had a 6.66% mortality rate vs 2% mortality in non-users. Similarly, nearly a third of the supplement users were hospitalized compared to 11% in the non-users. The Charlson Co-Morbidity Index was 3.0±3 (SD) in users vs 1.0±2 (SD) in non-users.

Conclusion
10% of SARS-CoV-2 infected patients were taking vitamin D. They tended to be older, more likely to be African American and have significant co-morbidities. Hospitalization and mortality were higher among those taking Vitamin D in this cohort. Vitamin D is widely used to prevent and treat SARS-CoV-2 but without evidence of efficacy.

Disclosures
Sally L. Hodder, M.D., Gilead (Advisor or Review Panel member)Merck (Grant/Research Support, Advisor or Review Panel member)Viiv Healthcare (Grant/Research Support, Advisor or Review Panel member)
383. Feasibility of Specimen Self-collection in Young Children Undergoing SARS-CoV-2 Surveillance for In-person Learning
Authors: Altamirano Jonathan , Tam Grace , Lopez Marcela , Robinson India , Chun Leanne , Shaikh Nuzhat , Leary Sean , Carrington Yuan J , Jani Shilpa , Pulendran Uma , Ma Jasmin , Toomarian Elizabeth , Wang C Jason , Govindarajan Prasanthi , Blomkalns Andra , Robinson Makeda , Maldonado Yvonne A 
Published: December 2021

Abstract

Background
While pediatric cases of COVID-19 are at low risk for adverse events, schoolchildren should be considered for surveillance as they can become infected at school and serve as sources of household or community transmission. Our team assessed the feasibility of young children self-collecting SARS-CoV-2 samples for surveillance testing in an educational setting.

Methods
Students at a K-8 school were tested weekly for SARS-CoV-2 from September 2020 - June 2021. Error rates were collected from September 2020 - January 2021. Clinical staff provided all students with instructions for anterior nares specimen self-collection and then observed them to ensure proper technique. Instructions included holding the sterile swab while making sure not to touch the tip, inserting the swab into their nostril until they start to feel resistance, and rubbing the swab in four circles before repeating the process in their other nostril. An independent observer timed random sample self-collections from April - June 2021.

Results
2,590 samples were collected from 209 students during the study period when data on error rates were collected. Errors occurred in 3.3% of all student encounters (n=87). Error rates over time are shown in Figure 1, with the highest rate occurring on the first day of testing (n=20/197, 10.2%) and the lowest in January 2021 (n=1/202, 0.5%). 2,574 visits for sample self-collection occurred during the study period when independent timing data was collected (April - June 2021). Of those visits, 7.5% (n=193) were timed. The average duration of each visit was 70 seconds.
Figure 1. Swab Error Rates Over Time

Conclusion
Pediatric self-collected lower nasal swabs are a viable and easily tolerated specimen collection method for SARS-CoV-2 surveillance in school settings, as evidenced by the low error rate and short time window of sample self-collection during testing. School administrators should expect errors to drop quickly after implementing testing.

Disclosures
All Authors: No reported disclosures
384. SARS-CoV-2 Surveillance Testing Patterns among Hospitalized Pediatric Patients in a Single Academic Medical Center
Authors: Bukhari Areej , Seidelman Jessica , Smith Becky A , Lewis Sarah S , Smith Michael J , Moehring Rebekah W , Anderson Deverick J , Akinboyo Ibukunoluwa 
Published: December 2021

Abstract

Background
Children infected with SARS-CoV-2 often have mild or no symptoms, making symptom screening an ineffective tool for determining isolation precautions. As an infection control measure, universal pre-procedural and admission SARS-CoV-2 testing for pediatric patients was implemented in April and August 2020, respectively. Limited data exist on the utility screening programs in the pediatric population.

Methods
We performed a retrospective cohort study of pediatric patients (birth to 18 years) admitted to a tertiary care academic medical center from April 2020 to May 2021 that had one or more SARS-CoV-2 point-of-care or polymerase chain reaction tests performed. We describe demographic data, positivity rates and repeat testing trends observed in our cohort.

Results
A total of 2,579 SARS-CoV-2 tests were performed among 1,027 pediatric inpatients. Of these, 51 tests (2%) from 45 patients (4.3%) resulted positive. Community infection rates ranged from 4.5-60 cases/100,000 persons/day during the study period. Hispanic patients comprised 16% of the total children tested, but were disproportionately overrepresented (40%) among those testing positive (Figure1). Of 654 children with repeated tests, 7 (0.1%) converted to positive from a prior negative result. Median days between repeat tests was 12 (IQR 6-45), not necessarily performed during the same hospital stay. Five of these 7 patients had tests repeated &lt; 3 days from a negative result, of which only 2 had no history of recent infection by testing performed at an outside facility. Pre-procedural tests accounted for 35% of repeat testing, of which 0.9% were positive. Repeated tests were most frequently ordered for patients in hematology/oncology (35%) and solid organ transplant/surgical (33%) wards, each with &lt; 3% positive conversion rate. Notably, no hematopoietic stem cell transplant patients tested positive for SARS-CoV-2 during the study period.
Pediatric SARS-CoV-2 Testing Distributed by Race/Ethnicity

Conclusion
The positivity rate of universal pre-procedural and admission SARS-CoV-2 testing in pediatric patients was low in our inpatient cohort. Tests repeated &lt; 3 days from a negative result were especially low yield, suggesting limited utility of this practice. Diagnostic testing stewardship in certain populations may be useful, especially as community infection rates decline.

Disclosures
Michael J. Smith, MD, M.S.C.E, Merck (Grant/Research Support)Pfizer (Grant/Research Support) Rebekah W. Moehring, MD, MPH, UpToDate, Inc. (Other Financial or Material Support, Author Royalties)
385. SARS-CoV-2 Infections Among Military Personnel Deployed on the USNS COMFORT to New York City During the COVID-19 Pandemic and One-Year Follow-Up
Authors: Cooper Elizabeth , Lee Tida , Laing Eric , Ritter Andrew , Lee Melissa , Baker Matthew , Baldino Tyler , Mcadoo Terrance , Nguyen Huy , Broder Christopher C , Epsi Nusrat J , Richard Stephanie A , Warkentien Tyler , Millar Eugene , Burgess Timothy , Kronmann Karl , Lalani Tahaniyat 
Published: December 2021

Abstract

Background
The USNS COMFORT deployed to New York City to augment the inpatient health care capacity in March 2020. The aim of this study was to determine the prevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection among US Navy personnel upon return from deployment, and to identify incident cases of SARS-CoV-2 infection during 1 year of follow-up.

Methods
Crewmembers, the majority of whom were health care workers (HCW), were enrolled following deployment, in May 2020. PCR results from symptomatic crewmembers during deployment, and Day 0 and Day 14 post-deployment screening swabs conducted on all crewmembers, per military order, were abstracted. A questionnaire and serum were collected on Day 14 post-deployment. SARS-CoV-2 infection was defined as a positive SARS-CoV-2 spike glycoprotein immunoglobulin G antibody (IgG) or PCR. COVID-19 related medical encounters, PCR and antibody testing results within 1 year following deployment were abstracted from the Military Health System Data Repository (MDR). There was adequate provision of personal protective equipment (PPE) in the hospital and the COVID-19 vaccine roll-out for HCW began in December 2020.

Results
Of the 1200 crewmembers, 449 were enrolled and completed the questionnaire and screening swabs, and 432 (96.2%) completed the Day 14 blood draw (Table 1). The cumulative prevalence of SARS-CoV-2 infection was 3.01% (13/432; 95% CI, 1.61%–5.09%). One of 17 subjects did not complete the blood draw and was PCR positive on Day 14. 433/449 (96.4%) had a PCR performed during the follow-up period (i.e. after the Day 14 post-deployment visit until Feb 2021), for HCW screening or symptomatic illness (median number of tests: 2 [IQR: 1, 2; range: 1,6]). 25 of 433 (5.8%) were PCR positive (Fig 1). 19 (76.0%) occurred in corpsmen, 23 (92.0%) were symptomatic and none were hospitalized. One asymptomatic re-infection occurred in a crewmember who was PCR negative and IgG positive at Day 14 post-deployment.
Table 1. Characteristics of the overall cohort and by SARS-CoV-2 infection

Figure 1. Number of PCR tests (bar graph) and positivity rate (red line) by month in 449 USNS COMFORT crewmembers during 1-year follow-up after return from deployment

Conclusion
The post-deployment prevalence of SARS-CoV-2 infection was low. A high proportion of HCW underwent PCR testing during 1-year follow-up but a low incidence of infection was observed. This was likely from community transmission as nosocomial transmission was mitigated by adequate PPE and vaccine roll-out.

Disclosures
All Authors: No reported disclosures