Sustained Wolbachia-mediated blocking of dengue virus isolates following serial passage in Aedes aegypti cell culture

Cassandra Koh,Edward C Holmes,Elizabeth A McGraw,Emily J Kerton,Francesca Di Giallonardo,Michelle D Audsley,Paul R Young

Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes

Alice G Russo,Andrew G Kelly,Daniel Enosi Tuipulotu,Mark M Tanaka,Peter A White

Evidence for a recombinant origin of HIV-1 Group M from genomic variation

Abayomi S Olabode,Art F Y Poon,David W Dick,Faisal Abu-Sardanah,Garway T Ng,Mariano Avino

Gut virome of mammals and birds reveals high genetic diversity of the family Microviridae

Eric Delwart,Hao Wang,Hui Xu,Shixing Yang,Tongling Shan,Wen Zhang,Xutao Deng,Yu Ling

Why viruses sometimes disperse in groups?

Contrasting selective patterns across the segmented genome of bluetongue virus in a global reassortment hotspot

Divakar Hemadri,Kalyani Putty,Karam P Singh,Kyriaki Nomikou,Maude Jacquot,Nagendra R Hegde,Narasimha Reddy,Narender Singh Maan,Pavuluri P Rao,Peter Mertens,Roman Biek,Sarita Yadav,Sushila Maan,Y Krishna Jyothi

Changes on the viral capsid surface during the evolution of porcine circovirus type 2 (PCV2) from 2009 till 2018 may lead to a better receptor binding

Hans J Nauwynck,Jiexiong Xie,Ruifang Wei,Sebastiaan Theuns

DISSEQT—DIStribution-based modeling of SEQuence space Time dynamics

A V Bordería,G Moratorio,M Fontes,M Vignuzzi,R Henningsson

Conserved structural RNA domains in regions coding for cleavage site motifs in hemagglutinin genes of influenza viruses

Alexander P Gultyaev,Mathilde Richard,Monique I Spronken,René C L Olsthoorn,Ron A M Fouchier

Evolutionary dynamics and molecular epidemiology of West Nile virus in New York State: 1999–2015

Alexander T Ciota,Brett Pickett,Cheri A Koetzner,Emmi A Mueller,Joseph G Maffei,Laura D Kramer,Mark Novotny,Meghan Shilts,Nadia B Fedorova,Paolo Amedeo,Rebecca A Halpin,Sean M Bialosuknia,Steven D Zink,Suman R Das,Yi Tan

Novel hepatitis D-like agents in vertebrates and invertebrates

Callum Le Lay,Edward C Holmes,John H-O Pettersson,John-Sebastian Eden,Mang Shi,Michelle Wille,Nathan Lo,Wei-Shan Chang

Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa

Agnès Pinel-Galzi,Bram Vrancken,Denis Fargette,Eugénie Hébrard,Jean Stéphan Randrianangaly,Mbolarinosy Rakotomalala,Perle Ramavovololona,Philippe Lemey,Simon Dellicour

Within-host infectious disease models accommodating cellular coinfection, with an application to influenza

Alex P Farrell,Christopher B Brooke,Katia Koelle,Ruian Ke

Influenza passaging annotations: what they tell us and why we should listen

Catherine B Smith,Claire D McWhite,Claus O Wilke,Cory D DuPai,Rebecca Garten,Sebastian Maurer-Stroh

Why viruses sometimes disperse in groups

María-Isabel Thoulouze,Rafael Sanjuán

Evolutionary dynamics and molecular epidemiology of West Nile virus in New York State: 1999–2015

Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

Gytis Dudas,Nicola F Müller,Tanja Stadler

Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes

Art F Y Poon,John Palmer

Modelling and in vitro testing of the HIV-1 Nef fitness landscape

Arup K Chakraborty,Dariusz K Murakowski,Erasha Rajkoomar,Jaclyn K Mann,John P Barton,Macdonald Mahiti,Mako Toyoda,Phillip Mwimanzi,Takamasa Ueno,Thumbi Ndung’u

The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus

Edward C Holmes,Jackie E Mahar,Mang Shi,Nina Huang,Robyn N Hall,Roslyn Mourant,Tanja Strive

Co-circulation of genetically distinct highly pathogenic avian influenza A clade 2.3.4.4 (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017–18

Adam Dan,Anne Pohlmann,Bas B Oude Munnink,Benedicte Lambrecht,Dennis de Meulder,Divya Venkatesh,Ian H Brown,Leon Kelder,Marion P G Koopmans,Marjolein J Poen,Martin Beer,Mathilde Richard,Mieke Steensels,Nicola S Lewis,Oanh Vuong,Rachel D Scheuer,Ron A M Fouchier,Theo M Bestebroer,Thijs Kuiken,Vladimir Savic,Yong-Joo Kim,Youn-Jeong Lee

Gauging genetic diversity of generalists: A test of genetic and ecological generalism with RNA virus experimental evolution

Lele Zhao,Siobain Duffy

Identifying the patterns and drivers of Puumala hantavirus enzootic dynamics using reservoir sampling

Bert Vanmechelen,Bram Vrancken,Guy Baele,Herwig Leirs,Katrien Tersago,Lies Laenen,Philippe Lemey,Piet Maes,Simon Dellicour,Valentijn Vergote

Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection

Ali B Abbasi,Christopher J R Illingworth,Lei Zhao

Viral invasion fitness across a continuum from lysis to latency

Guanlin Li,Hayriye Gulbudak,Joshua S Weitz,Michael H Cortez,Rachel J Whitaker

Molecular epidemiology of Marek’s disease virus in central Pennsylvania, USA

Andrew F Read,Andrew S Bell,Christopher L Cairns,David A Kennedy,Matthew J Jones,Moriah L Szpara,Patricia A Dunn,Utsav Pandey

Measurements of intrahost viral diversity require an unbiased diversity metric

Christopher J R Illingworth,Lei Zhao

Evolutionary effects of the AID/APOBEC family of mutagenic enzymes on human gamma-herpesviruses

Maxwell Shapiro,Sumita Bhaduri-McIntosh,Teresa Martinez,Thomas MacCarthy

Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission

Chris Wymant,Christophe Fraser,Jayna Raghwani,Katrina A Lythgoe,Rebecca A Spriggs,Robin N Thompson

Evolutionary persistence of insect bunyavirus infection despite host acquisition and expression of the viral nucleoprotein gene

Derek J Taylor,Matthew J Ballinger

Cytomegalovirus distribution and evolution in hominines

Andrew J Plumptre,Angelique Todd,Anthony Agbor,Barbara Fruth,Bernhard Ehlers,Deo Kujirakwinja,Emma Bailey,Emmanuel Ayuk Ayimisin,Emmanuel Muhindo,Erin Wessling,Fabian H Leendertz,Gregory Brazzola,Guillain Mitamba,Henk Eshuis,Hjalmar Kühl,Ilka Herbinger,Kathryn O’Brien,Kevin Lee,Klara J Petrzelkova,Laura Kehoe,Lucy J Ormsby,Manasseh Eno-Nku,Martha M Robbins,Martijn Ter Heegde,Maryke Gray,Michael A Jarvis,Mimi Arandjelovic,Nadège F Madinda,Paula Dieguez,Radar Nishuli,Raymond Tokunda,Richard A Bergl,Samuel Angedakin,Sorrel Jones,Sripriya Murthy,Sébastien Calvignac-Spencer,Thomas R Gillespie,Volker Sommer,Yisa Ginath

Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography

Arjun Magge,Davy Weissenbacher,Graciela Gonzalez-Hernandez,Karen O’Connor,Marc A Suchard,Matteo Vaiente,Matthew Scotch,Tasnia Tahsin

Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing

Emma B Hodcroft,Jan Albert,Monika Mastafa,Richard A Neher,Robert Dyrdak

Inferring population genetics parameters of evolving viruses using time-series data

Adi Stern,Danielle Miller,Maoz Gelbart,Pleuni S Pennings,Tal Zinger

A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses

Edward C Holmes,Guangqian Duan,Jie Cui,Xiaoman Wei,Yicong Chen

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination

Abbas Jariani,Alexei J Drummond,Andrew Rambaut,Christopher Warth,Frederick A Matsen IV,Koen Deforche,Kristof Theys,Pieter Libin

Selective constraint and adaptive potential of West Nile virus within and among naturally infected avian hosts and mosquito vectors

Chase W Nelson,Christina M Newman,Edward D Walker,Gabriel L Hamer,Jeffrey D Brawn,Marilyn O Ruiz,Samuel D Sibley,Sergios-Orestis Kolokotronis,Tavis K Anderson,Tony L Goldberg,Uriel D Kitron

Inter- and intracontinental migrations and local differentiation have shaped the contemporary epidemiological landscape of canine parvovirus in South America

Alice Alfieri,Amauri Alfieri,Ana Marandino,Ana Paula da Silva,Daniela Name,Gonzalo Tomás,Gregorio Iraola,Jaime Aldaz,Leticia Maya,Lourdes Francia,Lucía Calleros,Marina Gallo Calderón,Nicola Decaro,Ruben Pérez,Sofía Grecco,Yanina Panzera

Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts

Brittany Rife Magalis,Marco Salemi,Michael F Summers,Sergei L Kosakovsky Pond

Private collection: high correlation of sample collection and patient admission date in clinical microbiological testing complicates sharing of phylodynamic metadata

Alexander L Greninger,Ryan C Shean

Estimating evolutionary rates in giant viruses using ancient genomes

Edward C Holmes,Sebastián Duchêne

The global origins of resistance-associated variants in the non-structural proteins 5A and 5B of the hepatitis C virus

Anita Y M Howe,Bradley R Jones,Jeffrey B Joy,P Richard Harrigan

Discovery of Culex pipiens associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family

Célestine M Atyame,Diane Bigot,Elisabeth A Herniou,Fabienne Justy,Mylène Weill,Philippe Gayral

Viral attenuation by engineered protein fragmentation

Andrew D Ellington,Daniel J Garry,Ian J Molineux,James J Bull

TreeTime: Maximum-likelihood phylodynamic analysis

Pavel Sagulenko,Richard A Neher,Vadim Puller

The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic

Carsten Magnus,Tanja Stadler,Veronika Boskova

A3？Brazilian network for HIV drug resistance surveillance: An investigation of pre-treatment drug resistance transmission chains

A39？Genetic diversity of the hepatitis C virus NS5B gene during HIV/HCV co-infection

A37？Genome sequencing, genetic characterization, and vaccine-match analysis of influenza B virus detected in hematopoietic stem cell transplant recipients (HSCT), an overview from 2010 to 2017

A36？Circulating strains of human respiratory syncytial virus in Belgium during six consecutive respiratory seasons (2011–2017)