Virus Evolution

Article	Citations
Evolution of a novel engineered tripartite viral genome of a torradovirus	133
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary	123
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China	94
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	93
Phycova — a tool for exploring covariates of pathogen spread	84
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	81
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal	77
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	63
Host replacement dynamics shape virulence and genome evolution in a plant RNA virus	62
Effects of host and pathogenicity on mutation rates in avian influenza A viruses	54
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic	52
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history	50
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients	46
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development	46
Plant biosecurity threats detected using metatranscriptomic sequencing of animal gut contents	46
Phylogeographic evaluation of the effectiveness of Canadian travel restrictions in reducing SARS-CoV-2 variant importations and burden	40
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	38
Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya	37
Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe	36
Genome sizes of animal RNA viruses reflect phylogenetic constraints	36
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	34
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	34
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	31
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	31
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	30

Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	30
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny	28
Evolution of exploitation and replication of giant viruses and virophages	28
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut	27
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance	27
Phylogenetic analysis of pigeon paramyxovirus type 1 detected in the British Isles between 1983 and 2023	27
Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics	26
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals	26
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation	26
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	25
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza	24
EvoLaps 2: Advanced phylogeographic visualization	24
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	23
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters	23
Virome release of an invasive exotic plant species in southern France	22
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	22
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	22
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA p	21
The coevolutionary mosaic of bat betacoronavirus emergence risk	21
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host	21
The successive emergence of ERVL-MaLRs in primates	20
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia	19
Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021	19
Hantavirus co-circulation in common shrews (Sorex araneus) in Sweden	19
Evolutionary characterization of the establishment of H6 influenza viruses in domestic geese in China: implications for the position of the host in the ecosystem	18
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites	18
Divergent hepaciviruses, delta-like viruses and a chu-like virus in Australian marsupial carnivores (dasyurids)	17
Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host	17
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak	17
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time	17
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations	16
Intra-host GI.1 norovirus evolution is shaped by genetic drift and purifying selection	16
Genomic surveillance and evolution of Getah virus	16
Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil	16
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia	16
Viral Diversity Influences T Cell Responses to Enteric Human Adenoviruses F40 and F41	16
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	16
A biophysical model of viral escape from polyclonal antibodies	15
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks	15
Accommodating sampling location uncertainty in continuous phylogeography	15
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii	15
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes	15
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals	15
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa	15
Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans	15
Prospects for a sequence-based taxonomy of influenza A virus subtypes	15
Known phyla dominate the Tara Oceans RNA virome	15
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges	15
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	15
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations	15

Emergence and pandemic spread of small ruminant lentiviruses	14
Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections	14
Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes	14
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	14
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh	14
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies	14
Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure	14
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	14
Mathematical comparison of protocols for adapting a bacteriophage to a new host	14
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda	14
Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing	14
Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage	13
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	13
Constraint in West Nile virus envelope protein across mosquito, human, and avian host cell environments	13
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples	13
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications	13
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia	13
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China	13
Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study	13
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	13
Experimental evidence of vaccine-driven evolution of porcine reproductive and respiratory syndrome virus type 2	13
Correction to: Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load	13
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes	13
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights	12
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	12
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies	12
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York	12
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation	12
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	11
Variation within major internal repeats of KSHV in vivo	11
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia	11
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	11
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	11
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak	11
The emergence of NY10: insights into the 2012 West Nile Virus outbreak in the United States	11
Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains	11
Focal persistence and phylodynamics of Heartland virus in Georgia	11
Sequencing SARS-CoV-2 genomes from saliva	10
Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals	10
Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization	10
Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system	10
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics	10
Lytic/Lysogenic Transition as a Life-History Switch	10
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection	10
Correction to: The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK	10
Evolution and diversity of inherited viruses in the Nearctic phantom midge, Chaoborus americanus	10
Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status	10
A critique of the use of species and below-species taxonomic terms for viruses—time for change?	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
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	10
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression	9
Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	9
H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks	9
The evolution of the HIV-1 protease folding stability	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
Monotreme-specific conserved putative proteins derived from retroviral reverse transcriptase	9
Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons	9
Genomic epidemiology reveals the variation and transmission properties of SARS-CoV-2 in a single-source community outbreak	8
Co-infection of mammarenaviruses in a wild mouse, Tanzania	8
Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans	8
Phylogenetic insights into the early spread of the SARS-CoV-2 Alpha variant across Europe	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
Fitness effects of mutations to SARS-CoV-2 proteins	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
Haplotype assignment of longitudinal viral deep sequencing data using covariation of variant frequencies	8
Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction	8
Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark	8
Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus	7
Beyond the Amazon: vector surveillance and emerging Oropouche virus in South America	7
Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic	7
The untapped potential of phage model systems as therapeutic agents	7
Viral community composition of hypersaline lakes	7
Eco-evolutionary dynamics of temperate phages in periodic environments	7
Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology	7
Formal recognition and classification of gene transfer agents as viriforms	7
Viromes of Antarctic fish resemble the diversity found at lower latitudes	7
Conserved recombination patterns across coronavirus subgenera	7

Evolutionary analyses of emerging GII.2[P16] and GII.4 Sydney [P16] noroviruses	7
Transmission dynamics of low pathogenicity avian influenza (H2N2) viruses in live bird markets of the Northeast United States of America, 2013–2019	7
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana	7
Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived	7
Origin, spread, and interspecies transmission of a dominant genotype of BJ/94 lineage H9N2 avian influenza viruses with increased threat	7
Within- and between-host evolutionary effects on viral oncogenicity	7
GALV-KoRV-related retroviruses in diverse Australian and African rodent species	7
Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012–8	7
Virome analysis of New Zealand’s bats reveals cross-species viral transmission among the Coronaviridae	7
On the importance of assessing topological convergence in Bayesian phylogenetic inference	7
Correction to: Increase of niche filling with increase of host richness for plant-infecting mastreviruses	7
Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat	6
Sustained cross-species transmission of gammacoronavirus in wild birds revealed by viral characterization in China	6
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes	6
ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods	6
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha	6
HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies	6
Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts	6
Evolution of virulence in emerging epidemics: from theory to experimental evolution and back	6
A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways	6
The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses	6
A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data	6
High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA	6
Correction to: Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation	6
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions	6
Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates	6
Modeling the therapeutic potential of defective interfering particles in the presence of immunity	6
The virome of the invasive Asian bush mosquito Aedes japonicus in Europe	5
Correction to: Coevolutionary phage training and Joint application delays the emergence of phage resistance in Pseudomonas aeruginosa	5
Molecular epidemiological features of SARS-CoV-2 in Japan, 2020–1	5
Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025	5
Bacteriophage Φ21’s receptor-binding protein evolves new functions through destabilizing mutations that generate non-genetic phenotypic heterogeneity	5
Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment	5
Correction to: Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil	5
Emergence of the BA.2.87.1 lineage of SARS-CoV-2 in South Africa, a highly diverged BA.2-related lineage	5
Viral origin of eukaryotic type IIA DNA topoisomerases	5
Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation	5
Intra-host evolution of cell-fusing agent virus following acute infection in Aedes aegypti mosquito	5
Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway	5
Persistence, spillover, and evolution of co-occurring lineages of lymphocytic choriomeningitis virus	5
Widespread interspecific phylogenetic tree incongruence between mosquito-borne and insect-specific flaviviruses at hotspots originally identified in Zika virus	5
Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing	5
Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations	5
Long-term evolution of human seasonal influenza virus A(H3N2) is associated with an increase in polymerase complex activity	5
Decoding VZV’s evolutionary arsenal: how Beijing strains use recombination and adaptive mutations to thrive	5
Changes in intra-host mycovirus population diversity after vertical and horizontal transmission	5
Rapid glycoprotein evolution enables variant interactions in herpes simplex virus type 1	5
Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales	5
Cell type-specific adaptation of the SARS-CoV-2 spike	5
Integrated viral elements suggest the dual lifestyle of Tetraselmis spp. Polinton-like viruses	5
Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections?	5
Strong selection and high mutation supply characterize experimentalChlorovirusevolution	5
Unraveling the genomic landscape of piscine myocarditis virus: mutation frequencies, viral diversity and evolutionary dynamics in Atlantic salmon	5
Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens	5
Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market	4
Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021	4
Coronaviruses in wild animals sampled in and around Wuhan at the beginning of COVID-19 emergence	4
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2	4
Evolution of the Cytomegalovirus RL11 gene family in Old World monkeys and Great Apes	4
A new perspective on the evolution and diversity of the genus Amdoparvovirus (family Parvoviridae) through genetic characterization, structural homology modeling, and phylogenetics	4
Computational multigene interactions in virus growth and infection spread	4
Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts	4
Molecular phylogeny of human adenovirus type 41 lineages	4
Everglades virus evolution: Genome sequence analysis of the envelope 1 protein reveals recent mutation and divergence in South Florida wetlands	4
Expanding the RNA virome of nematodes and other soil-inhabiting organisms	4
Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines	4
Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants	4
Correction to: Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	4
Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron	4
Evolution of Zika virus in Rag1-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication fitness	4
Recurrent SARS-CoV-2 mutations in immunodeficient patients	4
SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period	4
Geographic origin and evolution of dengue virus serotypes 1 and 3 circulating in Africa	4
Fast-forwarding evolution—Accelerated adaptation in a proofreading-deficient hypermutator herpesvirus	4
Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages	4
Biosurveillance of coronaviruses in Rhinolophus bats from South Africa	4
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae )	4
Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses	4
Ecology and evolution of influenza A viruses in wild waterfowl in Argentina reveals novel viral genotypes	4
Diverse viral pathogens in Australian canines: limited geographic structure and the first detection of an RNA virus in dingoes	4
Coxsackievirus A6 was the Predominant Pathogen of Hand, Foot, and Mouth Disease with Frequent Recombination and Mutations in Shandong Province, 2023	4
Rabbit haemorrhagic disease virus 2 from Singapore 2020 outbreak revealed an Australian recombinant variant	4
Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages	4
Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases	4
What makes a host a good reservoir? Determinants of the reservoir potential of Nicotiana glauca for tobacco mild green mosaic virus	4
Defining virus-carrier networks that shape the composition of the mosquito core virome of a local ecosystem	4
Contemporary and historical human migration patterns shape hepatitis B virus diversity	4