Virus Evolution

Article	Citations
The spatial-temporal dynamics of respiratory syncytial virus infections across the east–west coasts of Australia during 2016–17	903
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal	112
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China	100
Evolution of a novel engineered tripartite viral genome of a torradovirus	78
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary	78
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	70
Phycova — a tool for exploring covariates of pathogen spread	67
High pathogenic avian influenza A(H5) viruses of clade 2.3.4.4b in Europe—Why trends of virus evolution are more difficult to predict	56
Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito	54
Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates	52
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	49
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history	42
Genome sizes of animal RNA viruses reflect phylogenetic constraints	39
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	38
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	37
Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe	36
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	36
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	36
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	35
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic	34
Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids	31
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness	30
Effects of host and pathogenicity on mutation rates in avian influenza A viruses	29
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	29
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	28

The coevolutionary mosaic of bat betacoronavirus emergence risk	28
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development	28
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals	27
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut	27
Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine	27
Evolution of exploitation and replication of giant viruses and virophages	27
EvoLaps 2: Advanced phylogeographic visualization	26
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza	25
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria	25
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters	25
Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations	24
The successive emergence of ERVL-MaLRs in primates	24
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation	24
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host	24
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance	24
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	24
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny	23
Virome release of an invasive exotic plant species in southern France	23
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	22
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	22
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia	22
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia	21
Evolutionary characterization of the establishment of H6 influenza viruses in domestic geese in China: implications for the position of the host in the ecosystem	21
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	21
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time	20
Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host	20
Revealing RNA virus diversity and evolution in unicellular algae transcriptomes	19
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites	19
Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids)	19
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak	19
Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021	18
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations	18
Genomic surveillance and evolution of Getah virus	18
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	17
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii	17
Known phyla dominate the Tara Oceans RNA virome	16
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	16
Accommodating sampling location uncertainty in continuous phylogeography	16
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges	16
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations	16
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals	16
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes	15
Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites	15
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa	15
Prospects for a sequence-based taxonomy of influenza A virus subtypes	15
A biophysical model of viral escape from polyclonal antibodies	14
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks	14
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda	13
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	13
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh	13

Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure	13
Mathematical comparison of protocols for adapting a bacteriophage to a new host	13
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	13
Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing	13
Emergence and pandemic spread of small ruminant lentiviruses	12
Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes	12
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies	12
Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study	12
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China	12
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia	12
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies	12
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications	12
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples	12
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	12
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	11
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: Phylogeography and evolutionary insights	11
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York	11
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia	11
A critique of the use of species and below-species taxonomic terms for viruses—time for change?	11
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation	11
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	11
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	11
Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status	11
Recombinant SARS-CoV-2 genomes circulated at low levels over the first year of the pandemic	11
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	11
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	11
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes	11
Long-read transcriptomics of Ostreid herpesvirus 1 uncovers a conserved expression strategy for the capsid maturation module and pinpoints a mechanism for evasion of the ADAR-based antiviral defence	11
Human genomics of the humoral immune response against polyomaviruses	10
Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains	10
Variation within major internal repeats of KSHV in vivo	10
Heat adaptation of phage T7 under an extended genetic code	10
Global spatiotemporal transmission patterns of human enterovirus 71 from 1963 to 2019	10
Heptad stereotypy, S/Q layering, and remote origin of the SARS-CoV-2 fusion core	10
The early SARS-CoV-2 epidemic in Senegal was driven by the local emergence of B.1.416 and the introduction of B.1.1.420 from Europe	10
The impact of global lineage dynamics, border restrictions, and emergence of the B.1.1.7 lineage on the SARS-CoV-2 epidemic in Norway	10
Evolution and diversity of inherited viruses in the Nearctic phantom midge, Chaoborus americanus	10
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak	10
Integrating animal movements with phylogeography to model the spread of PRRSV in the USA	9
Twenty years of evolution and diversification of digitaria streak virus in Digitaria setigera	9
Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization	9
Independent epidemic patterns of HIV-1 CRF01_AE lineages driven by mobile population in Shenzhen, an immigrant city of China	9
Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system	9
Correction to: The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK	9
The evolution of the HIV-1 protease folding stability	9
Sequencing SARS-CoV-2 genomes from saliva	9
Lytic/Lysogenic Transition as a Life-History Switch	9
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection	9
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression	9
Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons	9
H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks	9
Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals	9
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics	9
Exploration of the Ixodes ricinus virosphere unveils an extensive virus diversity including novel coltiviruses and other reoviruses	9
Selection of viral variants with enhanced transmission and reduced neutralization susceptibility alongside lateral introductions may explain the persistence of porcine reproductive and respiratory syn	9
Identification of a novel mycovirus belonging to the “flexivirus”-related family with icosahedral virion	9
Co-infection of mammarenaviruses in a wild mouse, Tanzania	9
Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	8
Monotreme-specific conserved putative proteins derived from retroviral reverse transcriptase	8
Genomic epidemiology reveals the variation and transmission properties of SARS-CoV-2 in a single-source community outbreak	8
Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans	8
Evolutionary dynamics of respiratory syncytial virus in Buenos Aires: Viral diversity, migration, and subgroup replacement	8
A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains	8
Polerovirus genomic variation	8
Haplotype assignment of longitudinal viral deep sequencing data using covariation of variant frequencies	8
Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark	8
Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago	8
A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon	8
Genomic analysis of human noroviruses using combined Illumina–Nanopore data	7
Formal recognition and classification of gene transfer agents as viriforms	7
Eco-evolutionary dynamics of temperate phages in periodic environments	7
Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic	7
Fitness effects of mutations to SARS-CoV-2 proteins	7
Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived	7
On the importance of assessing topological convergence in Bayesian phylogenetic inference	7
Unraveling gene content variation across eukaryotic giant viruses based on network analyses and host associations	7
Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus	7
Evolution of influenza A virus in intensive and free-range swine farms in Spain	7
Origin, spread, and interspecies transmission of a dominant genotype of BJ/94 lineage H9N2 avian influenza viruses with increased threat	7
Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology	7

Corrigendum to: Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020	6
The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses	6
HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies	6
Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat	6
Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012–8	6
Tick virome diversity in Hubei Province, China, and the influence of host ecology	6
The untapped potential of phage model systems as therapeutic agents	6
Viromes of Antarctic fish resemble the diversity found at lower latitudes	6
High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA	6
A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data	6
Viral community composition of hypersaline lakes	6
Virome analysis of New Zealand’s bats reveals cross-species viral transmission among the Coronaviridae	6
Transmission dynamics of low pathogenicity avian influenza (H2N2) viruses in live bird markets of the Northeast United States of America, 2013–2019	6
Conserved recombination patterns across coronavirus subgenera	6
Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates	6
Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts	6
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha	6
Modeling the therapeutic potential of defective interfering particles in the presence of immunity	6
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana	6
GALV-KoRV-related retroviruses in diverse Australian and African rodent species	6
Evolutionary analyses of emerging GII.2[P16] and GII.4 Sydney [P16] noroviruses	6
Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales	5
Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections	5
Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway	5
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes	5
Molecular epidemiological features of SARS-CoV-2 in Japan, 2020–1	5
Cell type-specific adaptation of the SARS-CoV-2 spike	5
Widespread interspecific phylogenetic tree incongruence between mosquito-borne and insect-specific flaviviruses at hotspots originally identified in Zika virus	5
The virome of the invasive Asian bush mosquito Aedes japonicus in Europe	5
Correction to: Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation	5
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions	5
Integrated viral elements suggest the dual lifestyle of Tetraselmis spp. Polinton-like viruses	5
Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation	5
Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens	5
Evolution of virulence in emerging epidemics: from theory to experimental evolution and back	5
A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways	5
Viral origin of eukaryotic type IIA DNA topoisomerases	4
Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations	4
Contemporary and historical human migration patterns shape hepatitis B virus diversity	4
Everglades virus evolution: Genome sequence analysis of the envelope 1 protein reveals recent mutation and divergence in South Florida wetlands	4
Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020	4
Evolution of Zika virus in Rag1-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication fitness	4
Molecular phylogeny of human adenovirus type 41 lineages	4
Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae	4
Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections?	4
Expanding the RNA virome of nematodes and other soil-inhabiting organisms	4
Phylodynamic analysis and spike protein mutations in porcine deltacoronavirus with a new variant introduction in Taiwan	4
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2	4
Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing	4
Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market	4
Correction to: Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	4
A new perspective on the evolution and diversity of the genus Amdoparvovirus (family Parvoviridae) through genetic characterization, structural homology modeling, and phylogenetics	4
Evolution of the Cytomegalovirus RL11 gene family in Old World monkeys and Great Apes	4
Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages	4
Coronaviruses in wild animals sampled in and around Wuhan at the beginning of COVID-19 emergence	4
Increased virulence of Italian infectious hematopoietic necrosis virus (IHNV) associated with the emergence of new strains	4
Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021	4
Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants	4
Coordinating SARS-CoV-2 genomic surveillance in the United States	4
Correction to: Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil	4
Bacteriophage Φ21’s receptor-binding protein evolves new functions through destabilizing mutations that generate non-genetic phenotypic heterogeneity	4
Unraveling the genomic landscape of piscine myocarditis virus: mutation frequencies, viral diversity and evolutionary dynamics in Atlantic salmon	4
Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines	4
Defining virus-carrier networks that shape the composition of the mosquito core virome of a local ecosystem	4
Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses	4
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae)	4
Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron	4
Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of (RNA) viruses	4
Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a	4
Strong selection and high mutation supply characterize experimental Chlorovirus evolution	4
Long-term evolution of human seasonal influenza virus A(H3N2) is associated with an increase in polymerase complex activity	4