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  • Adintoviruses: A Proposed Animal-Tropic Family of Midsize Eukaryotic Linear dsDNA (MELD) Viruses
    Virus Evol. (IF 5.549) Pub Date : 2020-10-01
    Gabriel J Starrett; Michael J Tisza; Nicole L Welch; Anna K Belford; Alberto Peretti; Diana V Pastrana; Christopher B Buck

    Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA (dsDNA) viruses. This supports the

  • Determinants of dengue virus dispersal in the Americas
    Virus Evol. (IF 5.549) Pub Date : 2020-10-01
    Orchid M Allicock; Nikita Sahadeo; Philippe Lemey; Albert J Auguste; Marc A Suchard; Andrew Rambaut; Christine V F Carrington

    Dengue viruses (DENV) are classified into four serotypes, each of which contains multiple genotypes. DENV genotypes introduced into the Americas over the past five decades have exhibited different rates and patterns of spatial dispersal. In order to understand factors underlying these patterns we utilized a statistical framework that allows for the integration of ecological, socioeconomic and air transport

  • Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation
    Virus Evol. (IF 5.549) Pub Date : 2020-09-29
    Jiangbin Fan; Johannes A Jehle; Jörg T Wennmann

    Genetic diversity of viruses is driven by genomic mutations and selection through its host, resulting in differences in virulence as well as host responses. For baculoviruses, which are naturally occurring pathogens of insects and which are frequently sprayed on hundred thousands to millions of hectares as biocontrol agents of insect pests, the phenomenon of virus-host co-evolution is of particular

  • Multi-host dispersal of known and novel carnivore amdoparvoviruses
    Virus Evol. (IF 5.549) Pub Date : 2020-09-29
    Marta Canuti; Emily McDonald; Stephanie M Graham; Bruce Rodrigues; Émilie Bouchard; Richard Neville; Mac Pitcher; Hugh G Whitney; H Dawn Marshall; Andrew S Lang

    Amdoparvoviruses (family Parvoviridae) are ssDNA viruses that cause an immune complex-mediated wasting syndrome in carnivores. They are multi-host pathogens and cross-species infection is facilitated by the fact that viral entry is mediated by cellular Fc receptors recognizing antibody-coated viruses. We developed a pan-amdoparvovirus PCR and screened tissue samples from 666 wild carnivores (families

  • Large-scale survey reveals pervasiveness and potential function of endogenous geminiviral sequences in plants
    Virus Evol. (IF 5.549) Pub Date : 2020-09-21
    Vikas Sharma; Pierre Lefeuvre; Philippe Roumagnac; Denis Filloux; Pierre-Yves Teycheney; Darren P Martin; Florian Maumus

    The family Geminiviridae contains viruses with single-stranded DNA genomes that have been found infecting a wide variety of angiosperm species. The discovery within the last 25 years of endogenous geminivirus-like (EGV) elements within the nuclear genomes of several angiosperms has raised questions relating to the pervasiveness of EGVs and their impacts on host biology. Only a few EGVs have currently

  • Newly emerged resistance-breaking variants of cucumber mosaic virus represent ongoing host-interactive evolution of an RNA virus
    Virus Evol. (IF 5.549) Pub Date : 2020-09-10
    Kyeong-Jae Heo; Sun-Jung Kwon; Mi-Kyeong Kim; Hae-Ryun Kwak; Soo-Jung Han; Min-Jun Kwon; A L N Rao; Jang-Kyun Seo

    Understanding the evolutionary history of a virus and the mechanisms influencing the direction of its evolution is essential for the development of more durable strategies to control the virus in crop fields. While the deployment of host resistance in crops is the most efficient means to control various viruses, host resistance itself can act as strong selective pressure and thus play a critical role

  • Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics and high-throughput RT-PCR
    Virus Evol. (IF 5.549) Pub Date : 2020-09-01
    Gideon J Mordecai; Emiliano Di Cicco; Oliver P Günther; Angela D Schulze; Karia H Kaukinen; Shaorong Li; Amy Tabata; Tobi J Ming; Hugh W Ferguson; Curtis A Suttle; Kristina M Miller

    The emergence of infectious agents poses a continual economic and environmental challenge to aquaculture production, yet the diversity, abundance and epidemiology of aquatic viruses are poorly characterised. In this study, we applied salmon host transcriptional biomarkers to identify and select fish in a viral disease state, but only those that were negative for known viruses based on RT-PCR screening

  • PuMA: a papillomavirus genome annotation tool
    Virus Evol. (IF 5.549) Pub Date : 2020-08-26
    Josh Pace; Ken Youens-Clark; Cordell Freeman; Bonnie Hurwitz; Koenraad Van Doorslaer

    High-throughput sequencing technologies provide unprecedented power to identify novel viruses from a wide variety of (environmental) samples. The field of ‘viral metagenomics’ has dramatically expanded our understanding of viral diversity. Viral metagenomic approaches imply that many novel viruses will not be described by researchers who are experts on (the genomic organization of) that virus family

  • Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence
    Virus Evol. (IF 5.549) Pub Date : 2020-08-25
    Christopher Ruis; Lisa C Lindesmith; Michael L Mallory; Paul D Brewer-Jensen; Josephine M Bryant; Veronica Costantini; Christopher Monit; Jan Vinjé; Ralph S Baric; Richard A Goldstein; Judith Breuer

    The control of re-occurring pandemic pathogens requires understanding the origins of new pandemic variants and the factors that drive their global spread. This is especially important for GII.4 norovirus, where vaccines under development offer promise to prevent hundreds of millions of annual gastroenteritis cases. Previous studies have hypothesised that new GII.4 pandemic viruses arise when previously

  • Red fox viromes in urban and rural landscapes
    Virus Evol. (IF 5.549) Pub Date : 2020-08-25
    Sarah J Campbell; Wilbur Ashley; Margarita Gil-Fernandez; Thomas M Newsome; Francesca Di Giallonardo; Ayda Susana Ortiz-Baez; Jackie E Mahar; Alison L Towerton; Michael Gillings; Edward C Holmes; Alexandra J R Carthey; Jemma L Geoghegan

    The Red fox (Vulpes vulpes) has established large populations in Australia’s urban and rural areas since its introduction following European settlement. The cryptic and highly adaptable nature of foxes allows them to invade cities and live among humans while remaining largely unnoticed. Urban living and access to anthropogenic food resources also influence fox ecology. Urban foxes grow larger, live

  • Estimating hepatitis B virus cccDNA persistence in chronic infection
    Virus Evol. (IF 5.549) Pub Date : 2020-08-25
    Katrina A Lythgoe; Sheila F Lumley; Lorenzo Pellis; Jane A McKeating; Philippa C Matthews

    Hepatitis B virus (HBV) infection is a major global health problem with over 240 million infected individuals at risk of developing progressive liver disease and hepatocellular carcinoma. HBV is an enveloped DNA virus that establishes its genome as an episomal, covalently closed circular DNA (cccDNA) in the nucleus of infected hepatocytes. Currently available standard-of-care treatments for chronic

  • Broadscale phage therapy is unlikely to select for widespread evolution of bacterial resistance to virus infection
    Virus Evol. (IF 5.549) Pub Date : 2020-08-25
    Frederick M Cohan; Matthew Zandi; Paul E Turner

    Multi-drug resistant bacterial pathogens are alarmingly on the rise, signaling that the golden age of antibiotics may be over. Phage therapy is a classic approach that often employs strictly lytic bacteriophages (bacteria-specific viruses that kill cells) to combat infections. Recent success in using phages in patient treatment stimulates greater interest in phage therapy among Western physicians.

  • Efficient inference, potential, and limitations of site-specific substitution models
    Virus Evol. (IF 5.549) Pub Date : 2020-08-20
    Vadim Puller; Pavel Sagulenko; Richard A Neher

    Natural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states, or only change in concert with other sites. One one hand, such constraints on sequence evolution can be to infer biological function, one the other

  • Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates
    Virus Evol. (IF 5.549) Pub Date : 2020-08-20
    Ashleigh F Porter; John H-O Pettersson; Wei-Shan Chang; Erin Harvey; Karrie Rose; Mang Shi; John-Sebastian Eden; Jan Buchmann; Craig Moritz; Edward C Holmes

    The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus and Flavivirus – each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including

  • Inference of Nipah virus Evolution, 1999-2015
    Virus Evol. (IF 5.549) Pub Date : 2020-08-19
    Shannon L M Whitmer; Michael K Lo; Hossain M S Sazzad; Sara Zufan; Emily S Gurley; Sharmin Sultana; Brian Amman; Jason T Ladner; Mohammed Ziaur Rahman; Stephanie Doan; Syed M Satter; Meerjady S Flora; Joel M Montgomery; Stuart T Nichol; Christina F Spiropoulou; John D Klena

    Despite near-annual human outbreaks of Nipah virus (NiV) disease in Bangladesh, typically due to individual spillover events from the local bat population, only 20 whole genome NiV sequences exist from humans and 10 from bats. NiV whole genome sequences (WGS) from annual outbreaks have been challenging to generate, primarily due to the low viral load in human throat swab and serum specimens. Here,

  • Temporal signal and the phylodynamic threshold of SARS-CoV-2
    Virus Evol. (IF 5.549) Pub Date : 2020-08-19
    Sebastian Duchene; Leo Featherstone; Melina Haritopoulou-Sinanidou; Andrew Rambaut; Philippe Lemey; Guy Baele

    The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publicly available in near real-time. Early analyses of these data revealed low sequence variation, a finding that is consistent with a recently emerging outbreak, but which raises the question of whether such data are sufficiently informative for phylogenetic inferences of evolutionary

  • Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase
    Virus Evol. (IF 5.549) Pub Date : 2020-08-17
    Mart Krupovic; Natalya Yutin; Eugene Koonin

    The diverse viruses in the phylum Nucleocytoviricota (also known as NLCDV, Nucleo-cytoplasmic Large DNA Viruses) typically possess large icosahedral virions. However, in several families of Nucleocytoviricota, the icosahedral capsid was replaced by irregular particle shapes, most notably, the amphora-like virions of Pandoraviruses and Pithoviruses, the largest known virus particles in the entire virosphere

  • Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season
    Virus Evol. (IF 5.549) Pub Date : 2020-08-16
    Festus M Nyasimi; David Collins Owuor; Joyce M Ngoi; Alexander G Mwihuri; Grieven P Otieno; James R Otieno; George Githinji; Joyce U Nyiro; David James Nokes; Charles N Agoti

    The genomic epidemiology of influenza B virus (IBV) remains understudied in Africa despite significance to design of effective local and global control strategies. We undertook surveillance throughout 2016 in coastal Kenya, recruiting individuals presenting with acute respiratory illness at nine outpatient health facilities (any age) or admitted to the Kilifi County Hospital (<5 years old). Whole genomes

  • Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages
    Virus Evol. (IF 5.549) Pub Date : 2020-08-14
    M Chiapello; J Rodríguez-Romero; M A Ayllón; M Turina

    The obligatory biotrophic oomycetes Plasmopara viticola is the causal agent of downy mildew, a destructive disease of grapevine worldwide. So far, chemical fungicides are widely employed to limit this pathogen, but their adverse effects are stimulating the quest for environmentally friendly alternative approaches. Here we report on the search for mycoviruses that might be later developed as biocontrol

  • Intra-genome variability in the dinucleotide composition of SARS-CoV-2
    Virus Evol. (IF 5.549) Pub Date : 2020-08-13
    Paul Digard; Hui Min Lee; Colin Sharp; Finn Grey; Eleanor Gaunt

    CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and SARS-CoV-2 is no exception to this. Artificial modification of CpG frequency is a valid approach for live attenuated vaccine development; if this is to be applied to SARS-CoV-2, we must first understand the role CpG motifs play in regulating SARS-CoV-2 replication. Accordingly, the CpG composition of the SARS-CoV-2

  • The evolutionary history and global spatio-temporal dynamics of potato virus Y
    Virus Evol. (IF 5.549) Pub Date : 2020-08-06
    Fangluan Gao; Shusuke Kawakubo; Simon Y W Ho; Kazusato Ohshima

    Potato virus Y (PVY) is a destructive plant pathogen that causes considerable losses to global potato and tobacco production. Although the molecular structure of PVY is well characterized, the evolutionary and global transmission dynamics of this virus remain poorly understood. We investigated the phylodynamics of the virus by analysing 253 nucleotide sequences of the genes encoding the third protein

  • Genomes Reveal Genetic Diversity of Piscine Orthoreovirus in Farmed and Free-ranging Salmonids from Canada and USA
    Virus Evol. (IF 5.549) Pub Date : 2020-07-31
    A Siah; B R Breyta; K I Warheit; N Gagne; M K Purcell; D Morrison; J F F Powell; S C Johnson

    Piscine orthoreovirus (PRV-1) is a segmented RNA virus which is commonly found in salmonids in the Atlantic and Pacific Oceans. PRV-1 causes the Heart and Skeletal Muscle Inflammation (HSMI) disease in Atlantic salmon and is associated with several other disease conditions. Previous phylogenetic studies of genome segment 1 (S1) identified four main genogroups of PRV-1 (S1 genogroups I – IV). The goal

  • Diversity and circulation of Jingmen tick virus in ticks and mammals
    Virus Evol. (IF 5.549) Pub Date : 2020-07-27
    Jing-Jing Guo; Xian-Dan Lin; Yan-Mei Chen; Zong-Yu Hao; Zhao-Xiao Wang; Zhu-Mei Yu; Miao Lu; Kun Li; Xin-Cheng Qin; Wen Wang; Edward C Holmes; Wei Hou; Yong-Zhen Zhang

    Since its initial identification in ticks in 2010, Jingmen tick virus (JMTV) has been described in cattle, rodents and primates. To better understand the diversity, evolution and transmission of JMTV, we sampled 215 ticks, 104 cattle bloods, 216 bats and 119 rodents in Wenzhou city, Zhejiang province, China, as well as 240 bats from Guizhou and Henan provinces. JMTV was identified in 107 ticks (from

  • HTLV in South America: origins of a silent ancient human infection
    Virus Evol. (IF 5.549) Pub Date : 2020-07-24
    Ricardo Ishak; Marluísa de Oliveira Guimarães Ishak; Vânia Nakauth Azevedo; Luiz Fernando Almeida Machado; Izaura Maria Cayres Vallinoto; Maria Alice Freitas Queiroz; Greice de Lemos Cardoso Costa; João Farias Guerreiro; Antonio Carlos Rosário Vallinoto

    The description of the first human retrovirus, Human T-lymphotropic virus 1 (HTLV-1), was soon associated with an aggressive lymphoma and a chronic inflammatory neurodegenerative disease. Later, other associated clinical manifestations were described, affecting diverse target organs in the human body and showing the enormous burden carried by the virus and the associated diseases. The epidemiology

  • Towards a unified classification for human respiratory syncytial virus genotypes
    Virus Evol. (IF 5.549) Pub Date : 2020-07-24
    Kaat Ramaekers; Annabel Rector; Lize Cuypers; Philippe Lemey; Els Keyaerts; Marc Van Ranst

    Since the first human respiratory syncytial virus (HRSV) genotype classification in 1998, inconsistent conclusions have been drawn regarding the criteria that define HRSV genotypes and their nomenclature, challenging data comparisons between research groups. ‬‬‬‬‬‬‬‬‬In this study, we aim to unify the field of HRSV genotype classification by reviewing the different methods that have been used in the

  • Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17.
    Virus Evol. (IF 5.549) Pub Date : 2020-07-15
    Everlyn Kamau,James R Otieno,Nickson Murunga,John W Oketch,Joyce M Ngoi,Zaydah R de Laurent,Anthony Mwema,Joyce U Nyiro,Charles N Agoti,D James Nokes

    Respiratory syncytial virus (RSV) circulates worldwide, occurring seasonally in communities, and is a leading cause of acute respiratory illness in young children. There is paucity of genomic data from purposively sampled populations by which to investigate evolutionary dynamics and transmission patterns of RSV. Here we present an analysis of 295 RSV group B (RSVB) genomes from Kilifi, coastal Kenya

  • Emergence and evolution of highly pathogenic porcine epidemic diarrhea virus by natural recombination of a low pathogenic vaccine isolate and a highly pathogenic strain in the spike gene.
    Virus Evol. (IF 5.549) Pub Date : 2020-07-10
    Huinan Wang,Libo Zhang,Yuanbin Shang,Rongrong Tan,Mingxiang Ji,Xinliang Yue,Nannan Wang,Jun Liu,Chunhua Wang,Yonggang Li,Tiezhong Zhou

    Outbreaks of a new variant of porcine epidemic diarrhea virus (PEDV) at the end of 2010 have raised interest in the mutation and recombination of PEDV. A PEDV strain (CN/Liaoning25/2018) isolated from a clinical outbreak of piglet diarrhea contained a 49 bp deletion in the ORF3 gene. This deletion is considered a genetic characteristic of low pathogenic attenuated vaccine strains. However, CN/Liaoning25/2018

  • Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity
    Virus Evol. (IF 5.549) Pub Date : 2020-07-08
    Yang Song; Yong Zhang; Zhenzhi Han; Wen Xu; Jinbo Xiao; Xianjun Wang; Jianxing Wang; Jianfang Yang; Qiuli Yu; Deshan Yu; Jianhua Chen; Wei Huang; Jie Li; Tong Xie; Huanhuan Lu; Tianjiao Ji; Qian Yang; Dongmei Yan; Shuangli Zhu; Wenbo Xu

    Hand, foot and mouth disease (HFMD) is a common global epidemic. From 2008 onwards, many HFMD outbreaks caused by coxsackievirus A6 (CV-A6) have been reported worldwide. Since 2013, with a dramatically increasing number of CV-A6-related HFMD cases, CV-A6 has become the predominant HFMD pathogen in mainland China. Phylogenetic analysis based on the VP1 capsid gene revealed that subtype D3 dominated

  • Dual infection and recombination of Kaposi sarcoma herpesvirus revealed by whole-genome sequence analysis of effusion samples
    Virus Evol. (IF 5.549) Pub Date : 2020-06-30
    Elena M Cornejo Castro; Vickie Marshall; Justin Lack; Kathryn Lurain; Taina Immonen; Nazzarena Labo; Nicholas C Fisher; Ramya Ramaswami; Mark N Polizzotto; Brandon F Keele; Robert Yarchoan; Thomas S Uldrick; Denise Whitby

    Kaposi sarcoma herpesvirus (KSHV) is the etiological agent of three malignancies, Kaposi sarcoma, primary effusion lymphoma and KSHV-associated multicentric Castelman disease. KSHV infected patients may also have an interleukin six-related KSHV-associated inflammatory cytokine syndrome. KSHV-associated diseases occur in only a minority of chronically KSHV-infected individuals and often in the setting

  • Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event.
    Virus Evol. (IF 5.549) Pub Date : 2020-06-30
    Fanni Borvető,Ignacio G Bravo,Anouk Willemsen

    Papillomaviruses (PVs) have evolved through a complex evolutionary scenario where virus–host co-evolution alone is not enough to explain the phenotypic and genotypic PV diversity observed today. Other evolutionary processes, such as host switch and recombination, also appear to play an important role in PV evolution. In this study, we have examined the genomic impact of a recombination event between

  • Co-circulation of both low and highly pathogenic avian influenza H5 viruses in current poultry epidemics in Taiwan.
    Virus Evol. (IF 5.549) Pub Date : 2020-06-30
    Yao-Tsun Li,Chen-Chih Chen,Ai-Mei Chang,Day-Yu Chao,Gavin J D Smith

    Highly pathogenic avian influenza (HPAI) A(H5) viruses belonging to clade of the A/goose/Guangdong/1/96-like (Gs/GD) lineage caused severe global outbreaks in domestic birds from 2014 to 2015, that also represented the first incursions of Gs/GD viruses into Taiwan and the USA. However, few studies have investigated the circulation of clade viruses after 2015. Here, we describe Gs/GD

  • The characterization of two novel neotropical primate papillomaviruses supports the ancient within-species diversity model.
    Virus Evol. (IF 5.549) Pub Date : 2020-06-30
    Mirela D'arc,Filipe R R Moreira,Cecilia A Dias,Antonizete R Souza,Héctor N Seuánez,Marcelo A Soares,Maria C H Tavares,André F A Santos

    Papillomaviruses (PVs) are non-enveloped icosahedral viruses with a circular double-stranded DNA genome of ∼8,000 base pairs (bp). More than 200 different PV types have been identified to date in humans, which are distributed in five genera, with several strains associated with cancer development. Although widely distributed in vertebrates, Neotropical Primates (NP) PV infection was described for the

  • UPΦ phages, a new group of filamentous phages found in several members of Enterobacteriales.
    Virus Evol. (IF 5.549) Pub Date : 2020-06-22
    Jason W Shapiro,Catherine Putonti

    Filamentous phages establish chronic infections in their bacterial hosts, and new phages are secreted by infected bacteria for multiple generations, typically without causing host death. Often, these viruses integrate in their host’s genome by co-opting the host’s XerCD recombinase system. In several cases, these viruses also encode genes that increase bacterial virulence in plants and animals. Here

  • Evolutionary analysis of exogenous and integrated HHV-6A/HHV-6B populations.
    Virus Evol. (IF 5.549) Pub Date : 2020-04-30
    Diego Forni,Rachele Cagliani,Mario Clerici,Uberto Pozzoli,Manuela Sironi

    Human betaherpesviruses 6A and 6B (HHV-6A and HHV-6B) are highly prevalent in human populations. The genomes of these viruses can be stably integrated at the telomeres of human chromosomes and be vertically transmitted (inherited chromosomally integrated HHV-6A/HHV-6B, iciHHV-6A/iciHHV-6B). We reconstructed the population structures of HHV-6A and HHV-6B, showing that HHV-6A diverged less than HHV-6B

  • Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains.
    Virus Evol. (IF 5.549) Pub Date : 2020-06-19
    Charles Masembe,My V T Phan,David L Robertson,Matthew Cotten

    African Swine Fever Virus (ASFV), belonging to the Asfarviridae family, was originally described in Africa almost 100 years ago and is now spreading uncontrolled across Europe and Asia and threatening to destroy the domestic pork industry. Neither effective antiviral drugs nor protective vaccines are currently available. Efforts to understand the basis for viral pathogenicity and the development of

  • Genetic Evolution and Transmission Dynamics of Clade Highly Pathogenic Avian Influenza A/H5N1 Viruses in Bangladesh
    Virus Evol. (IF 5.549) Pub Date : 2020-06-13
    Jung-Hoon Kwon; Dong-Hun Lee; Miria Ferreira Criado; Lindsay Killmaster; Md Zulfekar Ali; Mohammad Giasuddin; David E Swayne

    Asian lineage A/H5N1 highly pathogenic avian influenza viruses (HPAIVs) have been responsible for continuous outbreaks in Bangladesh since 2007. While clades 2.2.2 and HPAIVs have disappeared since poultry vaccination was introduced in 2012, clade viruses have continued to be detected in Bangladesh. In this study, we identified A/H9N2 (n = 15), A/H5N1 (n = 19) and A/H5N1-A/H9N2 (n = 18)

  • Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015-16.
    Virus Evol. (IF 5.549) Pub Date : 2020-06-02
    Carol A Abidha,Joyce Nyiro,Everlyn Kamau,Osman Abdullahi,David James Nokes,Charles N Agoti

    Human coronavirus OC43 (HCoV-OC43) is a major contributor to seasonal outbreaks of acute respiratory illness (ARI). The origins of locally circulating HCoV-OC43 strains and characteristics of their genetic diversity are unknown for most settings despite significance to effective HCoV control strategies. Between December 2015 and June 2016, we undertook ARI surveillance in coastal Kenya in nine outpatients

  • Origin and evolution of dengue virus type 2 causing outbreaks in Kenya: Evidence of circulation of two cosmopolitan genotype lineages.
    Virus Evol. (IF 5.549) Pub Date : 2020-06-02
    Solomon K Langat,Fredrick Lunyagi Eyase,Irina Maljkovic Berry,Albert Nyunja,Wallace Bulimo,Samuel Owaka,Victor Ofula,Samson Limbaso,Joel Lutomiah,Richard Jarman,John Distelhorst,Rosemary C Sang

    Dengue fever (DF) is an arboviral disease caused by dengue virus serotypes 1-4 (DENV 1-4). Globally, DF incidence and disease burden have increased in the recent past. Initially implicated in a 1982 outbreak, DENV-2 recently reemerged in Kenya causing outbreaks between 2011 and 2014 and more recently 2017–8. The origin and the evolutionary patterns that may explain the epidemiological expansion and

  • Evolution of dependoparvoviruses across geological timescales-implications for design of AAV-based gene therapy vectors.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-22
    Evin Hildebrandt,Judit J Penzes,Robert J Gifford,Mavis Agbandje-Mckenna,Robert M Kotin

    Endogenous viral elements (EVEs) are genetic remnants of viruses that have integrated into host genomes millions of years ago and retained as heritable elements passed on to offspring until present-day. As a result, EVEs provide an opportunity to analyze the genomes of extinct viruses utilizing these genomic viral fossils to study evolution of viruses over large timescales. Analysis of sequences from

  • When to be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny
    Virus Evol. (IF 5.549) Pub Date : 2020-05-22
    Guanlin Li; Michael H Cortez; Jonathan Dushoff; Joshua S Weitz

    Bacterial viruses, i.e., ‘bacteriophage’ or ‘phage’, can infect and lyse their bacterial hosts, releasing new viral progeny. In addition to the lytic pathway, certain bacteriophage (i.e., ‘temperate’ bacteriophage) can also initiate lysogeny, a latent mode of infection in which the viral genome is integrated into and replicated with the bacterial chromosome. Subsequently, the integrated viral genome

  • Adaptation of turnip mosaic potyvirus to a specific niche reduces its genetic and environmental robustness.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-20
    Anamarija Butković,Rubén González,Inés Cobo,Santiago F Elena

    Robustness is the preservation of the phenotype in the face of genetic and environmental perturbations. It has been argued that robustness must be an essential fitness component of RNA viruses owed to their small and compacted genomes, high mutation rates and living in ever-changing environmental conditions. Given that genetic robustness might hamper possible beneficial mutations, it has been suggested

  • The role of genetic sequencing and analysis in the polio eradication programme.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-20
    David Jorgensen,Margarita Pons-Salort,Alexander G Shaw,Nicholas C Grassly

    Genetic sequencing of polioviruses detected through clinical and environmental surveillance is used to confirm detection, identify their likely origin, track geographic patterns of spread, and determine the appropriate vaccination response. The critical importance of genetic sequencing and analysis to the Global Polio Eradication Initiative has grown with the increasing incidence of vaccine-derived

  • Three arenaviruses in three subspecific Natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure?
    Virus Evol. (IF 5.549) Pub Date : 2020-05-19
    Laura N Cuypers; Stuart J E Baird; Alexandra Hánová; Tatjana Locus; Abdul S Katakweba; Sophie Gryseels; Josef Bryja; Herwig Leirs; Joëlle Goüy de Bellocq

    Mastomys natalensis is widespread in sub-Saharan Africa and hosts several arenavirus species, including the pathogenic zoonotic Lassa virus in West Africa. Mitochondrial lineages sub-divide the range of M. natalensis and have been associated with cryptic structure within the species. To test specificity of arenaviruses to hosts carrying these lineages, we screened 1772 M. natalensis in a large area

  • Multivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-14
    Haogao Gu,Daniel K W Chu,Malik Peiris,Leo L M Poon

    Coronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genus Betacoronavirus, which also includes severe acute respiratory syndrome-related coronavirus (SARSr-CoV) and Middle East respiratory syndrome-related coronavirus (MERSr-CoV)

  • No evidence for distinct types in the evolution of SARS-CoV-2.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-14
    Oscar A MacLean,Richard J Orton,Joshua B Singer,David L Robertson

    A recent study by Tang et al. claimed that two major types of severe acute respiratory syndrome-coronavirus-2 (CoV-2) had evolved in the ongoing CoV disease-2019 pandemic and that one of these types was more ‘aggressive’ than the other. Given the repercussions of these claims and the intense media coverage of these types of articles, we have examined in detail the data presented by Tang et al., and

  • Tracking echovirus eleven outbreaks in Guangdong, China: a metatranscriptomic, phylogenetic, and epidemiological study.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-10
    Jing Lu,Min Kang,Hanri Zeng,Yuwen Zhong,Ling Fang,Xiaoling Zheng,Leng Liu,Lina Yi,Huifang Lin,Jingju Peng,Caixia Li,Yingtao Zhang,Limei Sun,Shuhua Luo,Jianpeng Xiao,Bas B Oude Munnink,Marion P G Koopmans,Jie Wu,Yong Zhang,Yonghui Zhang,Tie Song,Hui Li,Huanying Zheng

    In April 2019, a suspect cluster of enterovirus cases was reported in a neonatology department in Guangdong, China, resulting in five deaths. We aimed to investigate the pathogen profiles in fatal cases, the circulation and transmission pattern of the viruses by combining metatranscriptomic, phylogenetic, and epidemiological analyses. Metatranscriptomic sequencing was used to characterize the enteroviruses

  • Opportunistic sampling of wild native and invasive birds reveals a rich diversity of adenoviruses in Australia.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-10
    Frederico F Vaz,Tânia F Raso,Jessica E Agius,Tony Hunt,Alan Leishman,John-Sebastian Eden,David N Phalen

    Little is known about the diversity of adenoviruses in wild birds and how they have evolved and are maintained in complex ecosystems. In this study, 409 samples were collected from woodland birds caught for banding (droppings), birds submitted to a wildlife hospital (droppings and tissues), silver gulls (droppings or tissues), and feral pigeons (Columbia livia; oral, cloacal swabs, or tissues) from

  • The dynamics of molecular evolution of emerging avian reoviruses through accumulation of point mutations and genetic re-assortment.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-10
    Lisanework E Ayalew,Khawaja Ashfaque Ahmed,Zelalem H Mekuria,Betty Lockerbie,Shelly Popowich,Suresh K Tikoo,Davor Ojkic,Susantha Gomis

    In the last decade, the emergence of variant strains of avian reovirus (ARV) has caused enormous economic impact in the poultry industry across Canada and USA. ARVs are non-enveloped viruses with ten segments of double-stranded RNA genome. So far, only six genotyping cluster groups are identified worldwide based on sequence analysis of the σC protein encoded by the S1 segment. In this study, we performed

  • Intrinsically disordered regions are abundant in simplexvirus proteomes and display signatures of positive selection.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-10
    Alessandra Mozzi,Diego Forni,Rachele Cagliani,Mario Clerici,Uberto Pozzoli,Manuela Sironi

    Whereas the majority of herpesviruses co-speciated with their mammalian hosts, human herpes simplex virus 2 (HSV-2, genus Simplexvirus) most likely originated from the cross-species transmission of chimpanzee herpesvirus 1 to an ancestor of modern humans. We exploited the peculiar evolutionary history of HSV-2 to investigate the selective events that drove herpesvirus adaptation to a new host. We show

  • Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments†.
    Virus Evol. (IF 5.549) Pub Date : 2020-05-08
    Mark P Zwart,Santiago F Elena

    Multipartite viruses have two or more genome segments, and package different segments into different particle types. Although multipartition is thought to have a cost for virus transmission, its benefits are not clear. Recent experimental work has shown that the equilibrium frequency of viral genome segments, the setpoint genome formula (SGF), can be unbalanced and host-species dependent. These observations

  • Structure of a filamentous virus uncovers familial ties within the archaeal virosphere.
    Virus Evol. (IF 5.549) Pub Date : 2020-04-29
    Fengbin Wang,Diana P Baquero,Zhangli Su,Tomasz Osinski,David Prangishvili,Edward H Egelman,Mart Krupovic

    Viruses infecting hyperthermophilic archaea represent one of the most enigmatic parts of the global virome, with viruses from different families showing no genomic relatedness to each other or to viruses of bacteria and eukaryotes. Tristromaviruses, which build enveloped filamentous virions and infect hyperthermophilic neutrophiles of the order Thermoproteales, represent one such enigmatic virus families

  • Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations.
    Virus Evol. (IF 5.549) Pub Date : 2020-04-29
    Artem Baidaliuk,Sébastian Lequime,Isabelle Moltini-Conclois,Stéphanie Dabo,Laura B Dickson,Matthieu Prot,Veasna Duong,Philippe Dussart,Sébastien Boyer,Chenyan Shi,Jelle Matthijnssens,Julien Guglielmini,Andrea Gloria-Soria,Etienne Simon-Lorière,Louis Lambrechts

    Flaviviruses encompass not only medically relevant arthropod-borne viruses (arboviruses) but also insect-specific flaviviruses (ISFs) that are presumably maintained primarily through vertical transmission in the insect host. Interestingly, ISFs are commonly found infecting important arbovirus vectors such as the mosquito Aedes aegypti. Cell-fusing agent virus (CFAV) was the first described ISF of mosquitoes

  • Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host.
    Virus Evol. (IF 5.549) Pub Date : 2020-04-27
    Brittany RifeMagalis,Samantha L Strickland,Stephen D Shank,Patrick Autissier,Alexandra Schuetz,Pasiri Sithinamsuwan,Sukalaya Lerdlum,James L K Fletcher,Mark de Souza,Jintanat Ananworanich,Victor Valcour,,Kenneth C Williams,Sergei L Kosakovsky Pond,Silvia RattoKim,Marco Salemi

    Human immunodeficiency virus (HIV) is a rapidly evolving virus, allowing its genetic sequence to act as a fingerprint for epidemiological processes among, as well as within, individual infected hosts. Though primarily infecting the CD4+ T-cell population, HIV can also be found in monocytes, an immune cell population that differs in several aspects from the canonical T-cell viral target. Using single

  • Cross-order host switches of hepatitis C-related viruses illustrated by a novel hepacivirus from sloths.
    Virus Evol. (IF 5.549) Pub Date : 2020-04-25
    Andres Moreira-Soto,Francisco Arroyo-Murillo,Anna-Lena Sander,Andrea Rasche,Victor Corman,Birthe Tegtmeyer,Eike Steinmann,Eugenia Corrales-Aguilar,Nicolas Wieseke,Judy Avey-Arroyo,Jan Felix Drexler

    The genealogy of the hepatitis C virus (HCV) and the genus Hepacivirus remains elusive despite numerous recently discovered animal hepaciviruses (HVs). Viruses from evolutionarily ancient mammals might elucidate the HV macro-evolutionary patterns. Here, we investigated sixty-seven two-toed and nine three-toed sloths from Costa Rica for HVs using molecular and serological tools. A novel sloth HV was

  • New hemagglutinin dual-receptor-binding pattern of a human-infecting influenza A (H7N9) virus isolated after fifth epidemic wave.
    Virus Evol. (IF 5.549) Pub Date : 2020-04-20
    Lei Guo,Nan Li,Wenlong Li,Jienan Zhou,Ruotong Ning,Min Hou,Longding Liu

    Since 2013, influenza H7N9 virus has caused five epidemic waves of human infection. The virus evolved from low pathogenic to highly pathogenic in wave 5, 2017, while the prevalence of host receptor-binding tropism in human-infecting viruses maintained dual-receptor-binding property with preference for avian receptor. A human-infecting H7N9 virus was isolated after the fifth epidemic wave and possessed

  • Evolution of a wild-plant tobamovirus passaged through an exotic host: Fixation of mutations and increased replication.
    Virus Evol. (IF 5.549) Pub Date : 2017-03-02
    Shu Hui Koh,Hua Li,Krishnapillai Sivasithamparam,Ryan Admiraal,Michael G K Jones,Stephen J Wylie

    Tobamovirus is a group of viruses that have become serious pathogens of crop plants. As part of a study informing risk of wild plant virus spill over to crops, we investigated the capacity of a solanaceous-infecting tobamovirus from an isolated indigenous flora to adapt to new exotic hosts. Yellow tailflower mild mottle virus (YTMMV) (genus Tobamovirus, family Virgaviridae) was isolated from a wild

  • The phylogenetics of the global population of potato virus Y and its necrogenic recombinants.
    Virus Evol. (IF 5.549) Pub Date : 2017-03-02
    Adrian J Gibbs,Kazusato Ohshima,Ryosuke Yasaka,Musa Mohammadi,Mark J Gibbs,Roger A C Jones

    Potato virus Y (PVY) is a major pathogen of potatoes and other solanaceous crops worldwide. It is most closely related to potyviruses first or only found in the Americas, and it almost certainly originated in the Andes, where its hosts were domesticated. We have inferred the phylogeny of the published genomic sequences of 240 PVY isolates collected since 1938 worldwide, but not the Andes. All fall

  • In vivo mutation rates and the landscape of fitness costs of HIV-1.
    Virus Evol. (IF 5.549) Pub Date : 2017-03-02
    Fabio Zanini,Vadim Puller,Johanna Brodin,Jan Albert,Richard A Neher

    Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1 infection, we estimated mutation rates and fitness costs in HIV-1 from the dynamics of genetic variation. At approximately neutral sites, mutations accumulate with

  • Two sides of the same coin: A population genetics perspective on lethal mutagenesis and mutational meltdown.
    Virus Evol. (IF 5.549) Pub Date : 2017-03-02
    Sebastian Matuszewski,Louise Ormond,Claudia Bank,Jeffrey D Jensen

    The extinction of RNA virus populations upon application of a mutagenic drug is frequently referred to as evidence for the existence of an error threshold, above which the population cannot sustain the mutational load. To explain the extinction process after reaching this threshold, models of lethal mutagenesis have been proposed, in which extinction is described as a deterministic (and thus population

  • The diversification of begomovirus populations is predominantly driven by mutational dynamics.
    Virus Evol. (IF 5.549) Pub Date : 2017-03-02
    Alison T M Lima,José C F Silva,Fábio N Silva,Gloria P Castillo-Urquiza,Fabyano F Silva,Yee M Seah,Eduardo S G Mizubuti,Siobain Duffy,F Murilo Zerbini

    Begomoviruses (single-stranded DNA plant viruses) are responsible for serious agricultural threats. Begomovirus populations exhibit a high degree of within-host genetic variation and evolve as quickly as RNA viruses. Although the recombination-prone nature of begomoviruses has been extensively demonstrated, the relative contribution of recombination and mutation to the genetic variation of begomovirus

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