bluuebunny/crossref_metadata_2025 huggingface dataset:
Delineation of Fusiform Rust Hazard Based on Estimated Volume Loss as a Guide to Rust Management Decisions in Slash Pine Plantations
Authors: Schmidt Robert A. , Klapproth Michael C.
Published: August 2019

Using published data, an empirical model is derived to approximate volume loss due to fusiform rust in slash pine plantations. Specifically, cumulative percentage volume loss at age 15 years is estimated as a function of percentage-rust-associated mortality at age 15 years, percentage stems infected at age 5 years and percentage trees infected at ages 5-10 years. Volume losses of <15, 15-35, and >35 percent at age 15 years are arbitrarily defined as low-, moderate-, and high-rust hazard, respectively. The corresponding percentages of trees with rust were <18, 18-43, and >43 at age 5 years, and <44, 44-77, and >77 at age 10 years. Using these approximations, a regional rust-hazard map for 10-year-old slash pine plantations is developed from rust survey data and potential rust management strategies are discussed for the region and for planatations.
Interim Models for Basal Area and Volume Projection of Uneven-Aged Loblolly-Shortleaf Pine Stands
Authors: Murphy Paul A. , Farrar Robert M.
Published: August 2019

Equations are presented for estimating current volume, projected basal area, and projected volume for stands of loblolly-shortleaf (Pinus taeda L.-Pinus echinata Mill.) pine managed under the selection system. The independent variables are initial stand basal area and elapsed time. The estimates should provide a guide to the cubic-foot volume production that might be expected from stands on average sites (site indices 80-90 ft.), medium basal areas (30 to 70 sq. ft.) and time periods of 10 years or less.
Portable Data Recorders in Forest Research
Authors: Rogerson Thomas L.
Published: August 2019

A small handheld data recorder has been a complete success during its first year of use in hydrologic and silviculture research studies. The recorder is user-programmed to operate in different data-entry and telecommunication formats so it can communicate with different terminals and computers. This new data-collection system eliminates both field forms and the keypunching and verifying process, reduces errors, and greatly reduces the time between data collection and analysis. The data recorder is simple to use. Anyone who can complete field-data forms should be able to use the recorder after one to two hours of instruction.
Detecting and Controlling the Southern Pine Beetle
Authors: Thatcher R. C. , Mason G. N. , Hertel G. D. , Searcy J. L.
Published: August 2019

This article summarizes four USDA agricultural handbooks dealing with detection, evaluation, suppression, and prevention of the southern pine beetle, Dendroctonus frontalis Zimmermann. Among topics covered are aerial location and evaluation of spots, techniques for assigning groundcheck and control priorities, and recommended direct-control techniques. Since the primary thrust of good pest management should be pest prevention by maintaining tree vigor, preventative silviculture guidelines are also presented.
Cubic-Foot Volume for Yellow-Poplar in the Hilly Coastal Plain of Alabama
Authors: Golden Michael S. , Knowe Steven A. , Tuttle Charles L.
Published: August 2019

Volume equations of the form V = b0 + b1 D²H were developed to estimate total volume inside and outside bark for yellow-poplar (Liriodendron tulipfera L.) in the hilly Coastal Plain of Alabama. Volumes predicted using the outside-bark equation were determined to be different from those predicted by the comparable volume equation developed for southern Appalachian yellow-poplar. A nonlinear ratio model was developed to estimate the volume to any specified top diameter.
Smoke Management on the Okefenokee National Wildlife Refuge
Authors: Johansen Ragnar W. , Phernetton Ronald A.
Published: August 2019

Prescribed burns on the Okefenokee National Wildlife Refuge demonstrate the effectiveness of smoke-management guidelines in planning prescribed fires. Procedures for preventing smoke incidents and methods used to predict concentrations of downwind particulate matter in the smoke are described.
The Recurring Option Contract
Authors: Shaffer Robert M.
Published: August 2019

Long-term timber management contracts can be an attractive option to both the nonindustrial private landowner and the forest industry firm. However, many such contracts incorporate inequities or operational problems which may lead to eventual dissatisfaction by one or both parties. The recurring option contract presented is both equitable and operationally sound. Using a modified version of the Black-Scholes Option Pricing Model, an option premium is calculated for each year of the contract in which timber is sold. Through this premium, the firm retains control over the stumpage and the landowner is compensated for relinquishing the right to market his timber independently. The considerable flexibility of the contract permits adaptation to a variety of management objectives.
Early Growth and Survival of Loblolly, Shortleaf, and Putative Hybrid Pines on Littleleaf Sites in the Piedmont of South Carolina
Authors: Benson J. D. , Schoenike R. E. , Van Lear D. H.
Published: August 2019

Progeny of presumed natural hybrids of shortleaf (Pinus echinata Mill.) and loblolly pine (Pinus taeda L.) growing in the Piedmont of South Carolina were found to have height and diameter growth rates between that of the two species. Survival of these trees was less than loblolly but no differences were found between them and shortleaf pine. Incidence of fusiform rust was low with the putalive hybrid having a infection rate 3 to 11 percent lower than loblolly pine. These putative hybrids, perhaps natural hybrids of loblolly and shortleaf pines, also offer potential resistance to littleleaf disease and would be a planting alternative to shortleaf pine in certain areas.
Predicting Mortality After Thinning in Old-field Loblolly Pine Plantations
Authors: Lemin Ronald C. , Burkhart Harold E.
Published: August 2019

Four equations were compared for predicting mortality after thinning in old-field loblolly pine (Pinus taeda L.) plantations. The model selected is of the form: N2 = [N1a1 + a2(A2a3 - A1a3)] 1/a1 where N1 and N2 denote trees per acre at ages A1 and A2. Survival curves for thinned, old-field loblolly pine plantations in Coastal Plain and Piedmont Virginia are given.
Optimum Paraquat Treatments for Inducing Resin-Soaking in Slash and Loblolly Pines
Authors: Roberts Donald R. , Outcalt Kenneth W.
Published: August 2019

Slash pine (Pinus elliottii Engelm. var elliottii) trees near Olustee, Florida, and loblolly pine (Pinus taeda L.) trees on the Savannah River Plant near Aiken, South Carolina, were treated with five concentrations of paraquat solution at three application volumes and by two methods to determine the optimum combination of concentration and volume for lightwood production in each species. Tree mortality was considerably higher with the tree injector method than with the bark-streak method. When tree mortality and yield are both considered, the optimum treatment for loblolly pine is 0.8 ml per injection with 6-percent paraquat or 0.5 ml of 7-percent paraquat per 25 mm of bark-streak wound. In slash pine trees, injections of 0.6 to 1 ml of 2-percent paraquat should give acceptable yields.
Paraffin Grafting Techniques for Loblolly Pine
Authors: White Gordon , Lowe William J. , Wright Jeff
Published: August 2019

Paraffin can be used instead of plastic and kraft bags to protect new loblolly pine (Pinus taeda L.) grafts. Prior to grafting, all of the needles should be removed from the scion. After the graft is made by the standard technique, it should be completely covered with paraffin which has been heated to 175-200° F to obtain a proper seal. Graft aftercare is reduced to loosening the graft rubber, which deteriorates slowly because of the paraffin coating. Records indicate an approximate 77-percent cost reduction in grafting using the paraffin technique.
KUDZU: Where Did It Come From? and How Can We Stop It?
Authors: Miller James H. , Edwards Boyd
Published: August 2019

Kudzu is spreading in the South and control measures are required on large acreages. Control can be accomplished by persistent applications of effective herbicides or by overgrazing for two to three years. Soil-active herbicides containing the active ingredients picloram or dicamba are presently most effective. Herbicide sprays should be applied in a mixture with 60 to 100 gallons of water per acre; complete coverage is best achieved with double application and right-angle spray passes when using ground equipment. Repeated applications are usually required to kill every root crown. The tender nature of kudzu leaves and the large tuber roots make kudzu difficult to control.
Timber Mart-South
How Good Is It?
Authors: Franklin E. C. , Hazel Dennis
Published: August 2019

Based on a sampling of 238 sealed-bid and 166 negotiated timber sales from December 1976 to September 1981, Timber Mart-South does a credible job of representing the ranges and trends of timber prices in the North Carolina Piedmont and Coastal Plain.
Fusiform Rust Resistance of Select Loblolly Pine Seedlots in the Laboratory, Nursery, and Field
Authors: Skoller Deborah L. , Bridgewater Floyd E. , Lambeth Clements C.
Published: August 2019

Twenty-three seedlots exhibited consistency in relative resistance to fusiform rust whether testing was in the Resistance Screening Center, nursery, or in long-term field tests. Results indicate that family screening for rust resistance can be conducted on one-year-old trees at less cost, and perhaps more accurately, than that of long-term field testing. In a nursery where some seedlings were left unprotected from infection while others were chemically protected, both lots were culled to produce rust-free seedlings for field planting. After four years both protected and unprotected trees had the same level of infection. As nursery screening of moderately infected trees does not significantly increase field resistance of the remaining noninfected trees, we suggest that nursery seedlings be chemically protected.
The Soil Survey and Its Value in the
Ad Valorem Taxation of Privately Owned Timberland
Authors: Harding R. Bruce , Baker Robert D.
Published: August 2019

The use of detailed county soil surveys for predicting site productivity was evaluated for taxation purposes. One hundred and thirty permanent forest inventory plots containing suitable site index trees for loblolly pine (Pinus teada L.) were located on 11 different soil mapping units in the Sam Houston National Forest in Texas. The correlation between the field site indices for the mapping units and the site indexes projected by the Soil Conservation Service (SCS) was extremely low (r = .10). Analysis of variance for the soil mapping units suggested that the actual average site index between mapping units was significantly different. Duncan's multiple range test, however, showed that these differences were limited to those soils having extreme site index values, with the majority of the mapping units showing no significant difference in productivity. Detailed county soil surveys provided an inadequate basis for determination of productivity as defined by site index for taxation purposes.
Snag Densities in Managed Stands of the South Carolina Coastal Plain
Authors: Harlow Richard F. , Guynn David C.
Published: August 2019

The availability of pine and hardwood snags was determined in managed pine and nonpine stands on the Francis Marion National Forest in the Coastal Plain of South Carolina. An estimate was made of snags required for nesting by avian cavity nesters indigenous to the region and of the density of cavity nesters currently provided for on the forest. Avian species that use snags 5 to 9 in. d.b.h. were apparently provided with more than 100 percent of the minimum number of suitable-size snags for average bird populations in the nonpine stands, which encompassed about 30 percent of the area. In pine stands, by contrast, there were enough snags of this size for only 20 percent of the average avian populations. For species using larger snags (≥10 in. d.b.h.), nonpine stands provided enough for approximately 27 percent of average bird populations, while pine stands provided snags for only about 6 percent of average population densities.
Distribution of Gum Spots by Causal Agent in Black Cherry and Effects On Log and Tree Quality
Authors: Rexrode C. O. , Baumgras J. E.
Published: August 2019

Gum spots were studied in 116 black cherry (Prunus serotina Ehrh.) trees in West Virginia. Bark beetles are the major cause of gum spots in both black cherry poletimber and sawtimber trees. Approximately 90 percent of all gum spots in the bole sections are caused by bark beetles. Cambium miners cause few gum spots in the lower 6 m of the trees and virtually none in the quality zone. Bark beetle-caused gum spots are grade defects in both veneer and factory grade sawlogs. Cambium miner-caused gum spots cause little degrade in veneer logs and none in factory grade 1 and 2 sawlogs.
Dimension Lumber Grade and Yield Estimates for Yellow-Poplar
Authors: Denig Joseph , Wengert Eugene M. , Brisbin Robert , Schroeder James
Published: August 2019

Equations that predict the dimension lumber grade yield from yellow-poplar trees (Liriodendron tulipfera L.) and sawlogs that are manufactured into 2 x 4's using the Saw-Dry-Rip system are presented. These equations require the measurement of dbh and merchantable height measured to an 8-in. top diameter. To predict the dimension lumber yield from yellow-poplar logs, a grading system that incorporates limiting defects with the clear-face concept used in southern pine log grading is utilized to stratify the logs. Once the logs have been graded, scaling diameter is used to predict the dimension lumber yield.
Converting Rhododendron-Laurel Thickets to White Pine with Picloram and Mycorrhizae-Inoculated Seedlings
Authors: Neary Daniel G. , Douglass James E. , Ruehle John L. , Fox Walter
Published: August 2019

A ridge site in the Appalachian highlands of North Carolina was prepared for planting container-grown white pine (Pinus strobus L.) seedlings by treatment with herbicide. A pellet formulation of picloram (4-amino-3,5,6-trichloropicolinic acid) containing 10% acid equivalent was applied in May 1978. Control of rhododendron (Rhododendron maximum L.), laurel (Kalmia latifolia L.), and other hardwood vegetation was sufficient to allow pine establishment. White pine survival was 96% 18 months after planting. Inoculation of seedlings while still in the greenhouse with the mycorrhizal fungus Pisolithus tinctorius (Pers.) Coker and Couch did not significantly affect seedling survival, total height, seasonal height growth, or basal diameter in the field. Height growth the second growing season after planting 6-month, container-grown stock averaged 5.1 to 7.5 inches. Eighteen months after planting, total seedling height averaged 13.3 inches, with the tallest exceeding 29.1 inches. Both height and diameter growth of white pine seedlings were inversely related to the degree of shading from remaining vegetation.
Relation between Early- and Late-Season Loblolly Pine Seedling Mortality from Pales and Pitcheating Weevil Attack in Southeast Oklahoma¹
Authors: Lynch A. M. , Hedden R. L.
Published: August 2019

Impact of the pales weevil (Hylobius pales (Herbst)) and the pitcheating weevil (Pachylobius picivorus (Germar)) was assessed during the 1979 growing season on 15 newly established loblolly pine (Pinus taeda L.) plantations in southeast Oklahoma. Early-season seedling mortality was directly related to total-season seedling mortality attributed to weevils. A linear regression model, ML = 4.04 + 1.44 M20, is used to predict cumulative late-season (late October) seedling mortality (ML) as a function of mortality accumulated by the twentieth calendar week (mid-May) (M20). This model has been used in southeast Oklahoma to establish threshold levels of weevil impact on which to base decisions regarding remedial chemical treatments.
Should Small Infestations of Southern Pine Beetle Receive Control Priority?
Authors: Lorio Peter L.
Published: August 2019

Southern pine beetle, Dendrotonus frontalis Zimm., infestations were endemic on 480,000 of national forest in central Louisiana for 3 years from July 1977 through June 1980. Study of 137 spots that varied in size from 3 to 57 trees showed that spots of less than 10 trees were in large-diameter stands, that large sawtimber comprised 80% of the infested volume per acre, and that the cumulative losses of large sawtimber were almost 9 times the losses in 30- to 57-tree spots. Based on these results, small spots in sawtimber stands should receive as high, or higher, control priority as large spots in small diameter stands during endemic periods.¹
Soil Losses from Roadbeds and Cut and Fill Slopes in the Southern Appalachian Mountains
Authors: Swift Lloyed W.
Published: August 2019

Soil losses were measured on the cut, fill, and roadbed surfaces of a forest road at Coweeta Hydrologic Laboratory. Before grass was planted or gravel spread, roadbed surfaces had the least loss per unit area and loss was primarily waterborne fine particles. A large part of the soil loss from fill slopes was due to slippage of wet soils in early spring. Surface erosion of fills was negligible because storm water from the roadbed was not spilled across loose soil. The cut slopes eroded most, principally because soils were loosened by diurnal cycles of freezing and thawing in winter. This study shows that inclined surfaces of cut and fill slopes are potential sources of large soil loss but these losses can be mitigated by early establishment of grass cover and by design features to control storm water. Soil loss from roadbeds was greatly reduced by gravel surfacing.¹
Efficacy of Morning vs. Afternoon Applications of Triadimefon for Controlling Fusiform Rust
Authors: Kelley Walter D.
Published: August 2019

No differences were found between mornings (0800-1000 h) and afternoon (1600-1800 h) applications of triadimefon on loblolly pine (Pinus taeda L.) seedlings for control of fusiform rust in nursery beds. Also, rates of 4, 6, 8, and 12 oz/ac were equally effective in protecting seedlings. Results indicate that a lesser rate than the standard 8 oz/ac/application can be used and that time of application is not important.¹
Effects of Air Drying on Survival, Height, and Root Growth Potential of Loblolly Pine Seedlings
Authors: Feret Peter P. , Kreh Richard E. , Mulligan Carolyn
Published: August 2019

Loblolly pine (Pinus taeda) seedlings were dried by exposure to ambient conditions and their subsequent quality evaluated for both field performance and root-growth potential. Seedling survival after one growing season was diminished 6.9% and first-year height growth 17% for each 10 minutes of exposure out-doors. Root-growth potential was significantly diminished by air drying with the half-life of a seedling ranging from 15 to 35 minutes depending on ambient conditions. A strong relationship between field performance and root-growth potential was shown. Results support earlier research concluding that seedling desiccation must be avoided if seedling quality is to be maintained at the planting site.1
Yield Relationships in Unthinned Loblolly Pine Plantations on Cutover, Site-Prepared Lands
Authors: Burkhart Harold E. , Cloeren Deborah C. , Amateis Ralph L.
Published: August 2019

Data were collected in unthinned loblolly pine (Pinus taeda) plantations on cutover, site-prepared lands across much of the southern United States. Initial measurement data from these permanent plots were used to (1) develop regression relationships between yield of the planted loblolly pine and measurements of the planted pine and competing vegetation, and (2) assess relationships between yield and site preparation methods and physiographic regions (Coastal Plain and Piedmont). These analyses showed that yield of the planted pine component could be predicted adequately from age, average height of dominant and codominant trees, and number of surviving planted trees per unit area. Measurements on the competing vegetation did not significantly reduce the error sum of squares after accounting for the planted-pine variables. An analysis of covariance showed that mean yields (after adjusting for the effects of plantation age, site index, and number of surviving trees) were not significantly different for site preparation classes or physiographic regions. Further analyses showed that survival relationships were similar for the physiographic regions and site preparation classes included. Although the height-age relationships for anamorphic site index curve construction were significantly different for the Coastal Plain and Piedmont, there were no significant differences between site preparation classes within the regions.1
Residential Property Values Improved by Landscaping with Trees
Authors: Anderson L. M. , Cordell H. K.
Published: August 2019

A 3 to 5% increase in the sales prices of-single-family houses in Athens, Georgia, was associated with the presence of trees in their landscaping, according to data from real estate records on over 800 house sales from 1978 to 1980. The average house sold for about $47,000 and had five front-yard trees visible in its Multiple Listing Service photographs. An average sales price increase of $1,700 to $2,100 was associated with the presence of these trees. This increase in property value represents an income of over $200,000 a year to the city in property tax revenues.
Preliminary Performance of the Computerized Inventory-Monitoring System for Pine Seed Orchards
Authors: Merkle Scott A. , Feret Peter P. , Bramlett David L.
Published: August 2019

A seed orchard Inventory-Monitoring System (IMS) and companion computer program were tested for predictive accuracy and monitoring effectiveness in an operational loblolly pine (Pinus taeda) seed orchard. The IMS was used to predict 1980 and 1981 cone harvests by tracking the survival of strobili on sample trees representing each producing clone in the orchard. The 1980 cone harvest was substantially overestimated, possibly due to the use of generalized cone efficiency estimates. Predictions for the 1981 cone harvest, made with the benefit of clonal cone efficiency estimates from the 1980 crop, were much more accurate, under-estimating the actual harvest by as little as 5%.Predictive performance of the IMS is expected to improve with accumulation of productivity data for each clone and with the reduction of nonclonal sources of variation resulting from improved orchard management practices. Seed orchard-to-nursery efficiency (SO-NE) data from the system's monitoring function showed that low SO-NE values for the orchard of 22 % in 1980 and 24 % in 1981 were due mainly to low cone efficiency and low seed efficiency.2
Use of Livingston Parish, Louisiana Loblolly Pine by Forest Products Industries in the Southeast
Authors: Wells O. O.
Published: August 2019

Southern forest products industries planted 329,000 acres of loblolly pine (Pinus taeda)from fusiform rust-resistant geographic seed sources during the period 1971-1980, according to a survey conducted in 1981. This amounted to about 20% of the total acreage planted to loblolly by the reporting industries. Of the rust-resistant stock, 93% came from Livingston Parish, Louisiana. Two experiments indicate that the Livingston Parish trees will have about 50% less rust than would have been the case had susceptible local seed sources been used. Livingston Parish loblolly appears to be adapted as far north as Dooly County in the coastal plain of Georgia, and Coosa County in central Alabama. Less than 100 miles farther north, however, its form has been noticeably poorer and late mortality has been excessive.
Development of Direct-Seeded and Planted Loblolly and Slash Pines Through Age 20
Authors: Campbell T. E.
Published: August 2019

After 20 years in the field, planted loblolly pine (Pinus taeda) yielded volumes that were not significantly higher than volumes on three of six direct-seeding treatments. However, planted trees were fewer in number, larger in diameter, and more uniformly spaced than seeded trees. Slash pine (P. elliottii) volumes were not influenced by regeneration method.
Speed of Germination Affects Diameter at Lifting of Nursery-Grown Loblolly Pine Seedlings
Authors: Boyer James N. , South David B. , Muller Carl , Vanderveer Harry , Chapman Walter , Rayfield William
Published: August 2019

Speed of germination affects seedling quantity and quality. This study investigated the effect of germination speed on loblolly pine (Pinus taeda) seedling diameter at lifting. Studies were installed at three forest nurseries in Alabama to test the effects of stratification treatments on speed of germination and of seedling emergence date on final seedling diameter. Results varied with the length of stratification employed. However, in all cases, seedlings which emerged earliest (first 40%) attained significantly larger diameters than seedlings from seeds which germinated later.¹
The absence of choice of law in commercial contracts: problems and solutions
Authors: Beheshti Reza
Published: August 2019

In a commercial contract with an arbitration clause, the parties may fail to determine any applicable law, in which case the arbitral tribunal is expected to identify the rules applicable to the merits of the dispute. A modern approach suggests that localizing legal issues originated from an international contract is inappropriate and that the tribunal should conduct an assessment to identify international or non-national rules or practices appropriate to the issues at hand. This approach, which grants the tribunal maximum freedom in choosing the applicable law with no reference to any choice-of-law rules, is adopted in a few institutional rules such as the Article 21(1) of the ICC Rules. This article seeks to introduce an evaluative framework informing the tribunal’s methodical task in identifying the most suitable legal regimes. The evaluative framework seeks to assess the relationship of legal doctrines to commercial considerations and expectations regarded by businesses. A significant issue that befalls the arbitrators is that of pleading, proving, and measuring monetary damages. Yet, damages have remained an issue that is inaccurately dealt with by arbitral tribunals. This article aims to examine the principles governing damages available to an innocent commercial party under significant legal regimes widely applied in international commercial arbitration in an attempt to offer guidance on which legal regime has provided the most appropriate set of principles reflecting the essential needs and interests of commercial parties.
A6 Does treatment cause virulence changes in HIV-1?
Authors: Hodgson David , Hué Stéphane , Panovska-Griffiths Jasmina , Iamarino Atila , Atkins Katherine E
Published: August 2019

Antiretroviral treatment (ART) has provided substantial benefits for HIV-1-infected patients and has reduced incidence in areas with high uptake since its introduction in the late 1980s. As ART has led to shifts in the worldwide epidemiology of HIV-1, it may also have the potential to cause concomitant selective pressure on the virus population. Evidence for changes in HIV-1 virulence since the introduction of ART appears to be inconsistent. As well as reviewing both empirical and theoretical studies on the likely impact of ART on HIV-1 virulence, we developed a mathematical framework to evaluate the likely impact of ART on virulence selection under the widespread treatment programs and the future impact of recent test-and-treat recommendations. By quantifying both the relationship between virulence changes with the transmissibility through disease progression and the speed of diagnosis and treatment, we reconcile observational studies on virulence changes with the mathematical model predictions. On adoption of new test-and-treat programs—synonymous with early detection and immediate treatment—it is likely that increased virulence will be observed. Our findings highlight the potential public health consequences of mass treatment and the ensuing requirement for greater access and adherence to nullify the public health effect of these virulence changes.
A12 Modeling residual HIV replication and the emergence of drug resistance on ART
Authors: Michael Bale J , Valerie Boltz F , Mellors John W , Coffin John M , Hughes Stephen H , Kearney Mary F
Published: August 2019

There are conflicting reports regarding the presence of low-level HIV replication during suppressive antiretroviral therapy (ART). We simulated varying levels of replication and estimated the number of generations needed to obtain linked, drug resistance mutations to explore the effects of replication during ART. HIV replication was simulated with varying population sizes (10 to 3,000,000). Each population size was modeled ten times. Each genome was given a Poisson-distributed number of mutations according to its length and the average replication error rate (3.4 × 10−5 sub/nt/cycle). Simulations were run a maximum of 20,000 generations with endpoints defined as detection of a variant with resistance mutations to at least two ARVs. In all simulations, variants that were resistant to all three ARVs emerged in less than 20,000 generations. The time to emergence ranged from 148–16,156 generations in the various simulations, depending on the replicating population size (4.8 months to 44.3 years if the generation time is 1 day). Clinically detectable virologic failure can result from linkage of two mutations conferring resistance to two ARVs in a regimen. In our simulations, two linked mutations emerged in from 9 to 6,429 generations (9 days to 17.6 years). Our simulations suggest that in patients continually suppressed on ART for at least 10 years, the replicating population size would have to be less than ten, or virologic failure would have occurred from emergence of two ARV-resistant variants. Because most patients on ART do not experience virologic failure, our simulations suggest that any residual replicating population on ART is very small and thus not likely to either sustain or significantly contribute to the HIV reservoir.
A19 The origin of acute HCV in HIV-infected men who have sex with men in the Netherlands
Authors: Popping S , Boucher C , Verjans G , Rijnders B , van de Vijver D
Published: August 2019

In recent years, several outbreaks of hepatitis C virus (HCV) infections have been observed among HIV-infected men who have sex with men (MSM) in Europe. In the Netherlands, high incidence rates of 10/1,000 person-years are reported. In this analysis, we describe whether acute HCV is linked to specific transmission networks. A total of 50 Dutch HIV-infected MSM, diagnosed with acute HCV genotype 1a between 2013 and 2014, were included. Target enrichment for viral nucleic acid separation and deep sequencing were used to recover whole HCV genomes. Phylogenetic trees were constructed by use of the maximum likelihood method. Pairwise distance matrices were generated by use of the Kimura-2 parameter distance estimation method. The consistency of the phylogenetic clustering was tested by bootstrap analysis with 1,000 replicates. A cluster was defined as having a genetic distance of at most 1.5 per cent and bootstrap values of 100 per cent. The most recent common ancestor was estimated with a coalescent-based model with a Bayesian statistical framework. Four transmission clusters were identified that included a total of 38 patients (76% of the total). The clusters were indicative of recent outbreaks, as highlighted by small genetic distances and a most recent common ancestor after the year 2000, when the first cases of HCV infection in HIV-infected MSM were reported. The HCV epidemic among HIV-infected MSM is a young epidemic, with most of the acute infections linked within the four major transmission networks. Prevention strategies identifying and targeting these transmission networks can potentially curb the epidemic.
A30 Avian influenza viruses in wild birds: Virus evolution in a multi-host ecosystem
Authors: Venkatesh Divya , Poen Marjolein J , Bestebroer Theo M , Scheuer Rachel D , Vuong Oanh , Chkhaidze Mzia , Machablishvili Anna , Mamuchadze Jimsher , Ninua Levan , Fedorova Nadia B , Halpin Rebecca A , Lin Xudong , Ransier Amy , Stockwell Timothy B , Wentworth David E , Kriti Divya , Dutta Jayeeta , van Bakel Harm , Puranik Anita , Slomka Marek J , Essen Steve , Brown Ian H , Fouchier Ron A M , Lewis Nicola S
Published: August 2019

Wild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter, or stage. The Republic of Georgia is located at the intersection of three migratory flyways: the Central Asian Flyway, East Asian/East African Flyway, and Black Sea/Mediterranean Flyway. For six consecutive years (2010–6), we collected AIV samples from various duck and gull species that breed, migrate, and overwinter in Georgia. We found substantial subtype diversity of viruses that varied in prevalence from year to year. Low pathogenic (LP)AIV subtypes included H1N1, H2N3, H2N5, H2N7, H3N8, H4N2, H6N2, H7N3, H7N7, H9N1, H9N3, H10N4, H10N7, H11N1, H13N2, H13N6, H13N8, and H16N3, plus two H5N5 and H5N8 highly pathogenic (HP)AIVs belonging to clade 2.3.4.4. Whole-genome phylogenetic trees showed significant host species lineage restriction for nearly all gene segments and significant differences for LPAIVs among different host species in observed reassortment rates, as defined by quantification of phylogenetic incongruence, and in nucleotide diversity. Hemagglutinin clade 2.3.4.4 H5N8 viruses, circulated in Eurasia during 2014–5 did not reassort, but analysis after its subsequent dissemination during 2016–7 revealed reassortment in all gene segments except NP and NS. Some virus lineages appeared to be unrelated to AIVs in wild bird populations in other regions with maintenance of local AIV viruses in Georgia, whereas other lineages showed considerable genetic inter-relationship with viruses circulating in other parts of Eurasia and Africa, despite relative under-sampling in the area.
A34 Molecular characterization of Zika virus in Cuba
Authors: Martínez P A , Díaz G , Castillo E M , Álvarez M , Santana E , Serrano S , Mederos D , Guzmán M G
Published: August 2019

Until now, three genotypes of Zika virus (ZIKV) have been detected (two African lineages and one Asian lineage). After the declaration of Public Health Emergency of International Concern issued by The Pan American Health Organization and the World Health Organization authors from some Latin American countries have identified the Asian genotype as the lineage responsible for the Zika epidemic in the western hemisphere. However, data from the Caribbean are sparse, and there is no published data regarding the genotypes that produced isolated outbreaks in Cuba. Aiming to realize the molecular characterization of ZIKV in Cuba, we will sequence by next-generation sequencing the full genome of the ZIKV identified in samples from Cuban patients of different provinces in which ZIKV produced outbreaks. All samples required for this study have been collected during the molecular surveillance of Arboviral diseases conducted at the National Reference Laboratory at Pedro Kourí Tropical Medicine Institute. Viral RNA will be purified from urine and serum samples collected from patients with confirmed ZIKV infection by real time PCR. Using evolutionary dynamics studies, we will map the spread of a virus or of particular variants in time and space in order to understand how frequently ZIKV has been introduced into Cuba. Moreover, we will evaluate the amino acid diversity of each ZIKV proteins. Further, we will evaluate the population dynamics of ZIKV in samples from patients with varying clinical outcomes. The results will allow us to characterize the ZIKV genome and its evolution into the Cuban population that would also have impact for vaccine development, diagnosis, and pathogenesis studies.
A43 Translational research: NGS metagenomics into clinical diagnostics
Authors: Schmitz D , Nooij S , Janssens T , Cremer J , Vennema H , Kroneman A , Koopmans M
Published: August 2019

As research next-generation sequencing (NGS) metagenomic pipelines transition to clinical diagnostics, the user-base changes from bioinformaticians to biologists, medical doctors, and lab-technicians. Besides the obvious need for benchmarking and assessment of diagnostic outcomes of the pipelines and tools, other focus points remain: reproducibility, data immutability, user-friendliness, portability/scalability, privacy, and a clear audit trail. We have a research metagenomics pipeline that takes raw fastq files and produces annotated contigs, but it is too complicated for non-bioinformaticians. Here, we present preliminary findings in adapting this pipeline for clinical diagnostics. We used information available on relevant fora (www.bioinfo-core.org) and experiences and publications from colleague bioinformaticians in other institutes (COMPARE, UBC, and LUMC). From this information, a robust and user-friendly storage and analysis workflow was designed for non-bioinformaticians in a clinical setting. Via Conda [https://conda.io] and Docker containers [http://www.docker.com], we made our disparate pipeline processes self-contained and reproducible. Furthermore, we moved all pipeline settings into a separate JSON file. After every analysis, the pipeline settings and virtual-environment recipes will be archived (immutably) under a persistent unique identifier. This allows long-term precise reproducibility. Likewise, after every run the raw data and final products will be automatically archived, complying with data retention laws/guidelines. All the disparate processes in the pipeline are parallelized and automated via Snakemake1 (i.e. end-users need no coding skills). In addition, interactive web-reports such as MultiQC [http://multiqc.info] and Krona2 are generated automatically. By combining Snakemake, Conda, and containers, our pipeline is highly portable and easily scaled up for outbreak situations, or scaled down to reduce costs. Since patient privacy is a concern, our pipeline automatically removes human genetic data. Moreover, all source code will be stored on an internal Gitlab server, and, combined with the archived data, ensures a clear audit trail. Nevertheless, challenges remain: (1) reproducible reference databases, e.g. being able to revert to an older version to reproduce old analyses. (2) A user-friendly GUI. (3) Connecting the pipeline and NGS data to in-house LIMS. (4) Efficient long-term storage, e.g. lossless compression algorithms. Nevertheless, this work represents a step forward in making user-friendly clinical diagnostic workflows.
A50 Whole-genome sequencing of African swine fever isolates from Sardinia
Authors: Torresi C , Granberg F , Bertolotti L , Oggiano A , Colitti B , Giammarioli M , De Mia G M
Published: August 2019

In order to assess the molecular epidemiology of African swine fever (ASF) in Sardinia, we analyzed a wide range of isolates from wild and domestic pigs over a 31-year period (1978–2009) by genotyping sequence data from the genes encoding the p54 and the p72 proteins and the CVR. On this basis, the analysis of the B602L gene revealed a minor difference, placing the Sardinian isolates into two clusters according to their temporal distribution. As an extension of this study, in order to achieve a higher level of discrimination, three further variable genome regions, namely p30, CD2v, and I73R/I329L, of a large number of isolates collected from outbreaks in the years 2002–14 have been investigated. Sequence analysis of the CD2v region revealed a temporal subdivision of the viruses into two subgroups. These data, together with those from the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72/genotype I, but since 1990 have undergone minor genetic variations in respect to its ancestor, thus making it impossible to trace isolates, enabling a more accurate assessment of the origin of outbreaks, and extending knowledge of virus evolution. To solve this problem, we have sequenced and annotated the complete genome of nine ASF isolates collected in Sardinia between 1978 and 2012. This was achieved using sequence data determined by next-generation sequencing. The results showed a very high identity with range of nucleotide similarity among isolates of 99.5 per cent to 99.9 per cent. The ASF virus (ASFV) genomes were composed of terminal inverted repeats and conserved and non-conserved ORFs. Among the conserved ORFs, B385R, H339R, and O61R-p12 showed 100 per cent amino acid identity. The same was true for the hypervariable ORFs, with regard to X69R, DP96R, DP60R, EP153R, B407L, I10L, and L60L genes. The EP402R and B602L genes showed, as expected, an amino acid identity range of 98.5 per cent to 100 per cent and 91 per cent to 100 per cent, respectively. In addition, all of the isolates displayed variable intergenic sequences. As a whole, the results from our studies confirmed a remarkable genetic stability of the ASFV/p72 genotype I viruses circulating in Sardinia.
A51 Genetic variability of small ruminant lentiviruses in sheep and goats from single-species flocks from Poland
Authors: Olech Monika , Kuźmak Jacek
Published: August 2019

Previous phylogenetic analyses of small ruminant lentivirus (SRLV) sequences found in Poland revealed the circulation of subtype A1 in both sheep and goats, subtypes B1 in goats, and subtypes B2, A12, and A13 in sheep only. This study aimed to analyze the genetic nature of SRLV circulating in sheep and goats from single-species flocks. In order to analyze the degree of genetic variability, the fragments of gag and env genes of 24 SRLV strains were amplified by PCR, cloned into plasmid vectors, sequenced, and consensus sequences were aligned to each other and to reference sequences available from GenBank. Phylogenetic analysis was performed using the Geneious tree-builder tool, and phylogenetic trees were constructed using Mr Bayes (using the general time reversible substitution model) within Geneious Pro 5.3. Pairwise genetic distances were calculated in MEGA 6. Phylogenetic analysis revealed that the strains were highly heterogeneous and represented ovine strains belonging to subtypes A12 and B2 and caprine strains grouped in subtypes B1, B2, A1, and A12. In addition, two novel subtypes, A16 and A17, were found in goats. The mean pairwise genetic distances of gag and env sequences of both clusters were above 15 per cent nucleotide divergence when compared to all other subtypes within group A, which is a criterion required to distinguish a new subtype. Additionally, the existence of two separated clusters was confirmed by high bootstrap values. Co-infections with strains belonging to different subtypes within A and B groups were detected in one sheep and four goats originating from four flocks. Since the co-infection with more than one lentivirus genotype offers an opportunity for viral recombination, the possible recombination events were tested based on RDP analysis. For all co-infected animals, no evidence of recombination was found within the gag gene; however, env sequences showed some recombination patterns in three samples. In conclusion, we have demonstrated extended genetic variability of SRLV in sheep and goats from Poland with the existence of co-infection and recombination events.
A54 Genomic analysis of camel-HKU23 in Nigeria dromedary camels reveals strain-specific cross-species recombination
Authors: So R T Y , Oladipo J O , Chu D K W , Peiris M
Published: August 2019

Coronaviruses (CoVs) are enveloped, single stranded, positive-sense RNA viruses with a large genomic size of 26–32 kilobases. The first human CoV identified in the 1960s was isolated from patients presenting with common cold symptoms. Subsequent epidemic outbreaks of novel zoonotic CoV transmission were reported, examples including HCoV-229E (229E), HCoV-OC43 (OC43), severe acute respiratory syndrome, and Middle East respiratory syndrome (MERS). The ongoing outbreak of MERS in the Middle East is originating from a zoonotic source of dromedary camels. Surveillance later revealed that three CoV species—HCoV-229E (229E), camel-HKU23, and MERS-CoV—were co-circulating in Saudi Arabia dromedary camels. Camel-HKU23 belongs to Group 2a CoV, which also includes human coronavirus OC43, bovine coronavirus, and porcine hemagglutinating encephalomyelitis virus. Recombination, resulting in the generation of different novel genotypes, has been reported previously among these CoVs. Our surveillance of dromedary camels slaughtered in a major abattoir in Nigeria identified camel-HKU23 from nasal swab samples with a prevalence of 2.2 per cent. Phylogenetic analysis showed Nigeria camel-HKU23 is distinct from those previously identified in Saudi Arabia, while still genetically similar, as they share a monophyletic origin. Recombination analysis of Nigeria camel-HKU23 revealed two recombination breakpoints at positions of 22774–24100 base pairs (bp) and 28224–29362 bp. Recombination breakpoint at position 22774, encoding the Group 2a CoV-specific hemagglutinin esterase gene, exhibited high bootstrap support for clustering with RbCoV HKU14, which was previously detected in domestic rabbits in China. The recombination signal is only observed in Nigeria camel-HKU23, suggesting a regional varied evolutionary history of camel-HKU23. Our findings extended the knowledge of the evolutionary relationship among Group 2a CoVs. Further surveillance in other African camels will be important to elucidate the evolution of camel-HKU23.
A56 Visualization of recombination in deformed wing virus infecting bees
Authors: Bigot Diane , Gogol-Döring Andreas , Koch Peter , Paxton Robert J
Published: August 2019

Honey bees suffer increasing colony mortality worldwide, partially caused by the spread of viral pathogens. Among these pathogens, deformed wing virus (DWV) is one of the major, widespread viruses of honey bees resulting in wing deformities and weakening colonies. DWV can be found in honey bees, bumble bees, and other wild bees as three major genotypes named DWV-A, -B (also named Varroa destructor virus 1), and -C. Various recombinants of DWV-A and -B have been previously found in honey bees, some of which have been suggested to have higher virulence over non-recombinant, parental virus. In most of these cases, recombinants were only shown as consensus sequences from previous assemblies and alignments and may not reflect the biological reality of all variants present within a host bee. It is therefore important to build a method of recombinant detection and quantification within mixed infections in single-host individuals, including both parental and various recombinant genomes, so as to evaluate the relevance of recombinants for viral genome evolution and the impact on hosts. Here, we propose to visualize and quantify these recombinants using next-generation sequencing data to better understand how these genomes evolve within bees. Our method will be performed directly from raw sequence reads from various datasets (including field and lab experiments as well as screening of public databases) in order to obtain an overview of DWV recombination in various in vivo and in vitro conditions. Recombination of viral genomes is a key point for virus evolution. The detection and quantification of recombination will facilitate analysis of the determinants of recombination and help in understanding the routes by which new viral variants emerge. The emergence of new (more virulent) recombinant viruses can result from acquisition of new capabilities, such as escape from host immunity or increased transmission rates. Recombination can also lead to adaptation to new environments and new hosts by a change in cell tropism, allowing cross-species transmission, which may be particularly relevant for bumble bees and wild bees infected by honey bee-derived DWV.