bluuebunny/crossref_metadata_2025_split huggingface dataset:
A40 Estimation of Lassa virus emergence in Upper Guinea through a time-calibrated phylogeny
Authors: Fichet-Calvet Elisabeth , Magassouba N’Faly , Günther Stephan 
Published: August 2019

Abstract
Lassa fever is a hemorrhagic fever caused by an arenavirus, the Lassa virus (LASV), and can affect 150–200,000 persons per year in West Africa. The virus is hosted by several rodents, Mastomys natalensis and M. erythroleucus, Hylomyscus pamfi, and Mus baoulei. People can be contaminated at home or in the farms, by touching contaminated surfaces, eating contaminated food, or breathing aerosolized viral particles. Human-to-human transmission is occurring as well through infected bodily fluids. In Upper Guinea in particular, M. natalensis is the main host, with LASV prevalence of 14 per cent and IgG prevalence of 27 per cent. In humans, IgG prevalence is 40 per cent. This is, therefore, a hot spot for LASV transmission. In a previous phylogenetic study including 132 partial nucleoprotein (NP) sequences isolated from rodents, we showed that LASV could have emerged 90 years ago in the area. Here, we aim to revise the time of emergence upon analyzing the complete NP and polymerase genes of two strains coming from Upper Guinea: ‘Bantou 366’, a strain isolated from M. natalensis in 2003, and ‘Faranah’, a strain isolated from a human in 1996. They were aligned with 22 other LASV sequences belonging to all lineages and dated by their day of collection. In BEAST (v1.10) tree reconstruction, the following settings were used: GTR+gamma distributed rate variation (four discrete categories) across each codon position and constant population size demographic model. Four clock models were tested: strict, uncorrelated relaxed, random local, and fixed local. The best model was determined by comparing the resulting likelihoods using AICM model testing. Markov chain Monte Carlo (MCMC) sampling was performed for a total of 20 million states (sampling every 10,000 states) to obtain an effective sample size above 200 for all parameters. Results of MCMC sampling were examined in Tracer 1.6. The results showed that the Upper Guinea clade emerged 153 years ago when the phylogeny was reconstructed for partial NP (nt = 754, better model fit with strict clock), 208 years ago with complete NP (nt = 1,707, better model fit with random local clock), and 350 years ago with complete polymerase (nt = 6,681, better model fit with strict clock). The difference of emergence 1, 2, or 3 centuries ago, can be explained by the inclusion of some parts of the genome evolving slower than the partial NP. Therefore, the longer the sequence, the greater the divergence time. In order to have an accurate time of divergence, we suggest to use complete genes to perform a time-calibrated phylogeny.
A44 Genome analysis of bovine enterovirus variants isolated from cattle in Thailand
Authors: Kosoltanapiwat N , Income N , Cadar D , Schmidt-Chanasit J , Tongshoob J 
Published: August 2019

Abstract
Bovine enteroviruses (BEV) are non-enveloped RNA viruses of the genus Enterovirus, family Picornaviridae, which are commonly found in cattle. They have been classified into two species, enterovirus E (EV-E) and enterovirus F (EV-F). The viruses were previously considered non-pathogenic, but recent evidences suggest their association with pathogenesis in cattle. BEV-like enteroviruses have also been increasingly isolated from a wide range of animals, such as sheep, goats, horses, geese, possum, and deer, from many countries. The isolation and characterization of novel enteroviruses expands the range of the genus. Our data show that both EV-E and EV-F are circulating in cattle in Thailand. The viruses have been detected in 35–67 per cent of dairy and meat cattle feces in Kanchanaburi Province. Recently, we retrieved EV-E isolates from cattle feces by virus isolation in Madin-Darby Bovine Kidney cells. Four virus isolates were subjected to whole-genome sequencing using Illumina next-generation sequencing. A phylogenetic analysis of VP1 capsid protein, which is used for virus genotyping, suggested that there are at least two EV-E genotypes circulating in cattle in the area of study. Two virus strains, closely related to EV-E1 with amino acid sequence identities >88 per cent were identified as EV-E1. The other two strains, closely related to EV-E2 with amino acid sequence identities < 85 per cent, were likely to constitute a new EV-E genotype separate from the existing EV-E2.
A45 Genetic diversity of anelloviruses in the blood virome
Authors: Thijssen Marijn , Beller Leen , Yinda Kwe Claude , Deboutte Ward , Maes Piet , Matthijnssen Jelle , Van Ranst Marc , Pourkarim Mahmoudreza 
Published: August 2019

Abstract
The microbiome has an important impact on human health. The microbiome is a complex ecosystem that contains of a wide variety of microorganisms shaped by the immune system, host genetic factors, and the environment. Studies of the human virome have identified a diverse group of viruses in different compartments of the body, including viruses of the Anelloviridae family. These viruses are widespread among the general population. In various clinical conditions an association has been found between the Anelloviridae abundance and the patient’s immune status. However, no pathological consequences have been identified for this viral family. In this study, we analyzed the Anelloviridae diversity in plasma samples of liver transplant recipients. The virome contents of plasma samples from liver transplant recipients were sequenced by next-generation sequencing techniques on an Illumina platform (NextSeq). Complete Anelloviridae ORF1 contigs were extracted from metagenomic data and aligned with 66 RefSeq anellovirus sequences for phylogenetic analysis. The study included 144 plasma samples of 24 liver transplant recipients who had been infected by the hepatitis B virus and developed end-stage liver disease. The identified Anelloviridae viruses belong to the Alphatorquevirus, Betatorquevirus, and Gammatorquevirus genera. In total, we were able to retrieve 142 unique anellovirus contigs that were less than 95 per cent identical on the nucleotide level. A phylogenetic tree was constructed from these contigs with 65 RefSeq sequences retrieved from GenBank. The majority of the identified Anelloviridae sequences were assigned to the Alphatorquevirus genus, which represents the largest group of anelloviruses. We were able to identify a high diversity of Anelloviridae viruses in serum samples of liver transplant recipients. Phylogenetic analysis showed that the majority of anelloviruses belonged to the Alphatorque genus. Future research should focus at elucidating the role of these commensal viruses in both immunocompromised and healthy individuals.
A46 Hand, foot, and mouth disease in Vietnam
Authors: Nhu Le Nguyen Truc , Van Hoang Minh Tu , Nhan Le Nguyen Thanh , Anh Nguyen To , Thanh Tran Tan , Hang Vu Thi Ty , Ny Nguyen Thi Han , Hong Nguyen Thi Thu , Hung Nguyen Thanh , Khanh Truong Huu , Quy Du Tuan , Tuan Ha Manh , Viet Ho Lu , Viet Do Chau , Nam Nguyen Tran , Thanh Nguyen Thi My , Sabanathan Saraswathy , Qui Phan Tu , Chau Nguyen Van Vinh , Thwaites Guy E , Wills Bridget , Thwaites C Louise , van Doorn H Rogier , Van Tan Le 
Published: August 2019

Abstract
Hand, Foot, and Mouth Disease (HFMD) is a major public health issue in the Asia-Pacific region. Our research program aims to address unanswered questions about clinical, epidemiology, pathogen evolution, cost of illness, and host-genetic makers associated with severe HFMD in Vietnam. A multi-hospital-based observational study has been conducted at three referral hospitals in Ho Chi Minh City, Vietnam since 2013. Demographic, clinical data, and cost of illness were collected alongside clinical specimens. Multiplex PCR and next-generation sequencing were employed to identify enterovirus serotypes and to study pathogen evolution, respectively. A genome-wide association-based approach was used to explore genetic markers of disease severity. From 2013 to 2017, 2,191 HFMD patients were enrolled. More than twenty enterovirus serotypes were detected in 84.3 per cent of patients. EV-A71 was the major cause, accounting for 22 per cent of total number of cases, followed by CV-A6 (21%), CV-A16 (13%), and CV-A10 (8%). Interestingly, these four common enteroviruses replaced each other during the study period. EV-A71 and CV-A6 were the two most predominant viruses detected in 2013 and 2014. However, CV-A6 was replaced by CV-A16 and CV-A10 in 2015 and 2016, respectively. A total of 396 whole-genome sequences (EV-A71 (n = 200), CV-A6 (n = 98), CV-A10 (n = 66), and CV-A16 (n = 32)) were obtained. Phylogenetic analysis showed that EV-A71 subgenogroup B5 has replaced C4 in 2012, and, since then, B5 has continued to circulate predominantly, while C4 has been sporadically detected. All Vietnamese CV-A6 isolates belonged to genogroup A, which has caused large outbreaks of HFMD worldwide. Costs of illness varied between disease severities, ranging from $USD 244 [95% confidence interval (95% CI): 230–258] per patient for grade 2A (mild) to $USD 1984 (95% CI: 1,752–2,227) for grade 3 (severe). The genome-wide association study identified two genetic markers potentially associated with severe HFMD. The results highlight that active surveillance and understanding pathogen evolution are essential to inform public health in prioritizing the development of intervention strategies. Efforts to unravel the evolutionary process of Vietnamese CV-A10 and CV-A16 in relation to global strains are ongoing. An independent cohort is needed to replicate the preliminary findings of the genome-wide association study.
A52 MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity
Authors: Chu D K W , Hui K P Y , Perera R A P M , Miguel E , Oladipo J O , Traore A , Fassi-Fihri O , Chan M C W , Zhou Z , So R T Y , Chevalier V , Peiris J S M 
Published: August 2019

Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes a zoonotic respiratory disease of global public health concern, and dromedary camels are the only proven source of this zoonotic infection. Although MERS-CoV infection is ubiquitous in dromedaries across Africa and the Arabian Peninsula, the continuous appearance of zoonotic MERS cases in humans is confined to the Arabian Peninsula. MERS-CoV from Africa has hitherto been poorly studied. Here, we report the genetic and phenotypic characterization of MERS-CoV from dromedaries in African countries. Phylogenetically, viruses from dromedaries in Africa formed a monophyletic clade, which we have provisionally designated as virus clade C. Molecular dating analyses of MERS-CoV, including clade C viruses, suggests that the ancestral MERS-CoV in dromedaries could have spread to the two continents within a short timeframe. Camel MERS-CoVs from west and north African countries form a subclade (C1) that shares genetic signatures of a major deletion in the accessory gene ORF4b. Compared with human and camel MERS-CoV from Saudi Arabia, virus isolates from Burkina Faso (BF785) and Nigeria (Nig1657) had lower virus replication competence in Calu-3 cells and in ex vivo cultures of human bronchus and lung, and BF785 replicated to lower titer in lungs of human DPP4-transduced mice. However, it is still inconclusive whether ORF4b deletions may lead to the reduced replication competence of BF785 and Nig1657. Genetic and phenotypic differences in West African viruses may be relevant to the zoonotic potential of MERS-CoV.
A55 Molecular systematics of sturgeon nucleocytoplasmic large DNA viruses
Authors: Clouthier S , Anderson E , Kurath G , Breyta R 
Published: August 2019

Abstract
Namao virus (NV) is a sturgeon nucleocytoplasmic large DNA virus (sNCLDV) that can cause a lethal disease of the integumentary system in lake sturgeon Acipenser fulvescens. As a group, the sNCLDV have not been assigned to any currently recognized taxonomic family of viruses. In this study, a dataset of NV DNA sequences was generated and assembled as two non-overlapping contigs of 306 and 448 base pairs (bp) and then used to conduct a comprehensive systematics analysis using Bayesian phylogenetic inference for NV, other sNCLDV, and representative members of six families of the NCLDV superfamily. The phylogeny of NV was reconstructed using protein homologues encoded by nine nucleocytoplasmic virus orthologous genes (NCVOGs): NCVOG0022—mcp, NCVOG0038—DNA polymerase B elongation subunit, NCVOG0076—VV A18-type helicase, NCVOG0249—VV A32-type ATPase, NCVOG0262—AL2 VLTF3-like transcription factor, NCVOG0271—RNA polymerase II subunit II, NCVOG0274—RNA polymerase II subunit I, NCVOG0276—ribonucleotide reductase small subunit, and NCVOG1117—mRNA capping enzyme. The accuracy of our phylogenetic method was evaluated using a combination of Bayesian statistical analysis and congruence analysis. Stable tree topologies were obtained with datasets differing in target molecule(s), sequence length, and taxa. Congruent topologies were obtained in phylogenies constructed using individual protein datasets and when four proteins were used in a concatenated approach. The major capsid protein phylogeny indicated that ten representative sNCLDV form a monophyletic group comprised of four lineages within a polyphyletic Mimi-Phycodnaviridae group of taxa. Overall, the analyses revealed that Namao virus is a member of the Mimiviridae family with strong and consistent support for a clade containing NV and CroV as sister taxa.
A63 Quantifying the dynamics of evolutionary rates through time
Authors: Membrebe J V , Baele G , Suchard M A , Lemey P 
Published: August 2019

Abstract
The availability of evolutionary rate estimates in recent years led to the observation that they may depend on the time-scale on which they are measured. Specifically, RNA virus evolutionary rates are frequently estimated to be low towards the past and high towards the present. This time-dependent rate phenomenon (TDRP) has important implications for evolutionary studies as it could severely bias divergence time estimates. While recent studies are providing insights into the relationship between viral evolutionary rate and time, formal probabilistic models to draw inference under TDRP scenarios remain lacking. Here, we adopt epoch-modelling to develop a Bayesian model of discrete rate changes through time in an unknown evolutionary history and combine this with a log-linear parameterization of rates as a function of times in the past. We provide an implementation for nucleotide substitution rates as well as for nonsynonymous rates change in a codon substitution model. Using a foamy virus dataset for which internal node calibrations can be applied based on host-virus co-divergence, we estimate a significant decline in evolutionary rates as a function of time into the past for nucleotide substitutions as well as for non-synonymous substitutions in a codon model. We also estimate a deep evolutionary history for primate Lentiviruses by combining an HIV-1 group M node calibration and a biogeographic calibration for viruses in drill monkeys in the TDRP model. Our analyses lead to the conclusion that studies of evolutionary timescales require a reconsideration of substitution rates, in either codon and nucleotide substitution model, as a dynamic feature of molecular evolution.
A67 Bloodstream infections by carbapenem-resistant Klebsiella pneumoniae subsp. pneumoniae: Bayesian phylogenetic analysis of whole genomes
Authors: Cella Eleonora , Leoni Davide , Mirandola Walter , Fontana Carla , Sarmati Loredana , Andreoni Massimo , Angeletti Silvia , Ciccozzi Massimo 
Published: August 2019

Abstract
Bloodstream infection (BSI) caused by carbapenemase-producing Enterobacteriaceae (CPE) is a major public health concern, particularly in the hospital setting. The rapid detection of resistance patterns is of paramount importance for establishing the proper antibiotic regime. In addition, in countries where CPE are endemic, it is also important to evaluate genetic relationship among the isolates in order to trace pathogen circulation and to improve the infection control programs. This study is an application of a rapid blood culture (BC) workflow consisting of fast reporting of Gram stain results, rapid pathogen identification (using MALDI TOF technology), and a molecular assay for the detection of the major genes conferring resistance, all of them performed directly from positive BCs. The application of phylogenetic and phylodynamic analyses to bacterial whole-genome sequencing (WGS) data have become essential in the epidemiological surveillance of multidrug-resistant nosocomial pathogens. We analyzed 40 strains of Klebsiella pneumoniae subsp. pneumoniae (KP) carrying blaKPC (KP-KPC), randomly selected among 147 CPE identified from BCs collected from consecutive patients from 2013 to 2016. The number of BSIs-related CPE were 23, 31, 43, and 50 in 2013, 2014, 2015, and 2016, respectively. Among 147 CPE isolates, 143 were KP and four were Escherichia coli (EC). The gene blaKPC was detected in 117 strains of KP and in four strains of EC. Other carbapenemase genes, such as blaVIM and blaOXA-48, were detected in four and nine different isolates of KP, respectively. Moreover, 13 KP strains carried two resistance genes: twelve vehicled blaKPC plus blaVIM and one blaKPC plus blaOXA-48. Phylogenetic analysis of bacterial WGS data was used to investigate the evolution and spatial dispersion of KP in support of hospital infection control. The maximum likelihood tree showed two main clades statistically supported, with statistical support for several subclusters within as well. The minimum spanning tree showed mixing between sequences from different years and wards with only few specific groups. Bayesian analyses are ongoing, as the aid of Bayesian genomic epidemiology in combination with active microbial surveillance is highly informative regarding the development of effective infection prevention in healthcare settings or constant strain reintroduction.
Stump-to-Truck Cable Logging Cost Equations for Young-Growth Douglas-fir
Authors: LeDoux Chris B. , Fight Roger D. , Ortman Tom L. 
Published: August 2019

Abstract
Logging cost simulators and data from logging cost studies have been assembled and converted into a series of equations that can be used to estimate the cost of logging young-growth coastal Douglas-fir. (Pseudotsuga menziesii [Mirb.] Franco var. menziesii) in mountainous terrain of the Pacific Northwest. These equations were developed for two small cable yarders and one medium-sized yarder and are applicable for harvests of timber from 6 to 24 inches in diameter on slopes of 10 to 50%. Cost components can be easily Calculated on a hand calculator. A computer program that can be adapted to many desktop computers and that will calculate the total stump-to-truck logging cost for a specified set of logging conditions is also available. West. J. Appl. For. 1:19-21, Jan. 1986.
Production Analysis of the Bitterroot Yarder in Colorado
Authors: Lynch Dennis L. 
Published: August 2019

Abstract
The Bitterroot Miniyarder was analyzed for productivity during demonstrations on Colorado's Front Range. The yarder was operated in both single-span and multi-span configurations and averaged 13.25 cords/day and 12.21 cords/day, respectively. Environmental damage was minimal, and areas not accessible to ground skidding were logged. The yarder lost horsepower at higher elevations, which reduced its potential effectiveness. Estimated productive hourly cost was $34.43, which translates to a cost of $28.42 per cord at an average production rate of 12.7 cords per day. West. J. Appl. For. 1:22-25, Jan. 1986.
Can Income Tax Rules Affect Management Strategies for Forest Roads?
Authors: Sessions John 
Published: August 2019

Abstract
Income tax rules on capital investments in forest roads affect strategies for managing forest land. Costs of roads plus harvesting are divided into expensable, depreciable, and nondepreciable components. Tax rules that differentiate among types of costs can influence investments in both the number and standard of roads. The marginal tax rate of the landowner is an important variable. Income tax rules may lead landowners with similar management objectives but different marginal tax rates to adopt different strategies of road management. West. J. Appl. For. 1:26-28, Jan. 1986.
Silvicultural Value of Chemical Brush Control in the Management of Douglas-fir
Authors: Walstad J. D. , Brodie J. D. , McGinley B. C. , Roberts C. A. 
Published: August 2019

Abstract
Retrospective analyses of three conifer sites in western Oregon and Washington were conducted to determine the long-term silvicultural impact and economic value of chemical brush control treatments performed 10 to 25 years earher. Comparisons between areas treated with phenoxy herbicides and untreated areas of the sites revealed significant differences in stocking and growth of Douglas-fir (Pseudotsuga menziesii). On two sites, invading red alder (Alnus rubra) virtually excluded conifers in the absence of brush control. On the untreated area of the third site, dense growth of varnishleaf ceanothus (Ceanothus velutinus var. laevigatus) reduced Douglas-fir stocking and diameter growth. On all three sites, projections of mature yield and economic returns based on current stand conditions indicated substantial benefits for areas where brush control treatments were applied. West. J. Appl. For. 1:69-73, July 1986.
The Impact of Logging on Red Squirrels in an Idaho Conifer Forest
Authors: Medin Dean E. 
Published: August 2019

Abstract
Red squirrel (Tamiasciurus hudsonicus) population densities were studied on logged and unlogged plots in an Idaho Douglas-fir (Pseudotsuga menziesii) forest. Squirrel population densities were estimated before and after logging by using spot-mapping methods. In the unlogged forest, we estimated 0.75 to 1.25 individuals/ac, but in the second year after logging there were only 0.05 to 0.08 squirrels/ac. Red squirrel densities on logged study plots were less than one-fifth those on unlogged plots. West. J. Appl. For. 1:73-76 July 1986.
Sampling Aerial Photographs for Estimation of Pest-Caused Tree Mortality
Authors: Waters William E. , Graebner Robert W. 
Published: August 2019

Abstract
Six methods of estimating pest-caused tree mortality were evaluated by computer-based sampling of the aerial photo and numerical database of a 9,320 ha area of ponderosa pine (Pinus ponderosa) in the central Sierra Nevada, California. Two sampling universes were defined, one comprising 9 X 9 in photo units, the other 70 mm photo units. Of the sampling designs simulated, 2-stage designs involving subsampling of photo strips with either equal or variable probability provided estimates with the lowest standard deviations, and hence would require smaller sample sizes (and less photo-interpretation time) for a specified precision. The findings of this study have application to operational surveys of pest damage for which complete aerial photo coverage is available, or to the design of surveys for which only sample aerial photo coverage is feasible. West J. Appl. For. 1:84-89, July 1986.
Productivity of Nonindustrial Private Forests in Western Washington: Alternative Futures
Authors: Alig Ralph J. , Adams Darius M. 
Published: August 2019

Abstract
Nonindustrial private timberlands in western Washington have high productive potential and contribute harvest amounts somewhat more than proportional to their area. Of all private ownerships they are influenced the most by land use shifts and are affected in important ways by forest practice regulations. About 1 million acres of nonindustrial private timberland contain opportunities for timber management intensification that would increase net growth, in many cases offering attractive financial returns. Significant increases in timber growing investments could double softwood harvest levels in the long term. A combination of forest practice regulations to lengthen rotations by 10 yr and a 15% setaside of other timberland with older timber could reduce short-term softwood harvest levels by one-third. West. J. Appl. For. 10(1):29-35.