Virus Evolution

Article	Citations
Unveiling the RNA virus landscape of Cotesia chilonis : geographic distribution, diversity, and potential roles in parasitoid–host interactions	131
Experimental evolution of the host range dynamics in two isolates of potato virus Y	108
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary	104
Evolution of a novel engineered tripartite viral genome of a torradovirus	103
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	97
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	91
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	72
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history	64
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	61
Genome sizes of animal RNA viruses reflect phylogenetic constraints	59
Plant biosecurity threats detected using metatranscriptomic sequencing of animal gut contents	51
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	48
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic	47
Phylogeographic evaluation of the effectiveness of Canadian travel restrictions in reducing SARS-CoV-2 variant importations and burden	44
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	38
Host replacement dynamics shape virulence and genome evolution in a plant RNA virus	37
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	35
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	32
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development	32
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients	30
Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe	30
Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya	29
EvoLaps 2: Advanced phylogeographic visualization	29
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	29
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia	29

Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	29
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny	29
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	27
The successive emergence of ERVL-MaLRs in primates	26
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	25
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	25
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals	25
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA p	23
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut	23
Phylogenetic analysis of pigeon paramyxovirus type 1 detected in the British Isles between 1983 and 2023	22
Virome release of an invasive exotic plant species in southern France	22
Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics	22
Evolution of exploitation and replication of giant viruses and virophages	21
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance	21
The coevolutionary mosaic of bat betacoronavirus emergence risk	21
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza	20
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host	20
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites	19
Sequence based virus host prediction: a curated dataset and generalizable framework for training artificial intelligence to identify viruses of humans	19
Viral diversity influences T-cell responses to enteric human adenoviruses F40 and F41	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
Genomic surveillance and evolution of Getah virus	18
Intra-host GI.1 norovirus evolution is shaped by genetic drift and purifying selection	18
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak	17
Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021	17
Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant	17
Divergent hepaciviruses, delta-like viruses and a chu-like virus in Australian marsupial carnivores (dasyurids)	17
Metaviromics reveals a high diversity of viruses belonging to the Caliciviridae family in seal feces	17
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges	16
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia	16
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks	16
Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans	16
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
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals	16
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	16
Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil	15
Getting to the root of HIV transmitted founder virus sequences	15
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii	15
Known phyla dominate the Tara Oceans RNA virome	15
Prospects for a sequence-based taxonomy of influenza A virus subtypes	15
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies	14
A biophysical model of viral escape from polyclonal antibodies	14
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa	14
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations	14
Mapping the global distribution and spread of the Plasmodium vivax -associated virus MaRNAV-1	14
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh	13
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	13
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda	13
Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections	13

Mathematical comparison of protocols for adapting a bacteriophage to a new host	13
Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing	12
Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes	12
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	12
Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage	12
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	12
Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure	12
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York	12
The whole genome analysis of four Orf virus strains from Europe and South America	12
Emergence and pandemic spread of small ruminant lentiviruses	12
Constraint in West Nile virus envelope protein across mosquito, human, and avian host cell environments	11
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	11
Experimental evidence of vaccine-driven evolution of porcine reproductive and respiratory syndrome virus type 2	11
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	11
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	11
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	11
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes	11
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia	11
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	11
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples	11
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation	11
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights	11
Correction to: Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load	11
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies	11
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection	10
The emergence of NY10: insights into the 2012 West Nile Virus outbreak in the United States	10
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics	10
Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals	10
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak	10
A critique of the use of species and below-species taxonomic terms for viruses—time for change?	10
Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization	10
Focal persistence and phylodynamics of Heartland virus in Georgia	10
Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status	10
Variation within major internal repeats of KSHV in vivo	10
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia	10
Identification and genomic characterization of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa	10
Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system	9
Identification of a novel mycovirus belonging to the “flexivirus”-related family with icosahedral virion	9
Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	9
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	9
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression	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
Correction to: The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK	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
Lytic/Lysogenic Transition as a Life-History Switch	9
A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains	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
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
Co-infection of mammarenaviruses in a wild mouse, Tanzania	8
Single capsid mutations modulating phage adsorption, persistence, and plaque morphology shape evolutionary trajectories in ΦX174	8
Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark	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
Monotreme-specific conserved putative proteins derived from retroviral reverse transcriptase	8
Formal recognition and classification of gene transfer agents as viriforms	7
Within- and between-host evolutionary effects on viral oncogenicity	7
Begomovirus species demarcation based on genome-sequence identity yields non-monophyletic species: a case study of sweet potato-infecting begomoviruses	7
HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies	7
Anthropozoonotic spillovers reveal sustained long-term cryptic circulation of SARS-CoV-2 within and between Lithuanian mink farms	7
The untapped potential of phage model systems as therapeutic agents	7
Conserved recombination patterns across coronavirus subgenera	7
Beyond the Amazon: vector surveillance and emerging Oropouche virus in South America	7
Eco-evolutionary dynamics of temperate phages in periodic environments	7
Virome analysis of New Zealand’s bats reveals cross-species viral transmission among the Coronaviridae	7
GALV-KoRV-related retroviruses in diverse Australian and African rodent species	7
Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates	7
Origin, spread, and interspecies transmission of a dominant genotype of BJ/94 lineage H9N2 avian influenza viruses with increased threat	7
Viromes of Antarctic fish resemble the diversity found at lower latitudes	7
Fitness effects of mutations to SARS-CoV-2 proteins	7
On the importance of assessing topological convergence in Bayesian phylogenetic inference	7
Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived	7
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana	7
Correction to: Increase of niche filling with increase of host richness for plant-infecting mastreviruses	7
Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts	7
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha	7

Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012–8	7
Phylogenetic insights into the early spread of the SARS-CoV-2 Alpha variant across Europe	7
Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus	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
Viral community composition of hypersaline lakes	6
Correction to: Coevolutionary phage training and Joint application delays the emergence of phage resistance in Pseudomonas aeruginosa	6
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes	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
High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA	6
Extreme GC3 codon bias in a novel brown seaweed virus results in pseudoambigrammatic characteristics	6
Correction to: Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation	6
Cell type-specific adaptation of the SARS-CoV-2 spike	6
Rapid glycoprotein evolution enables variant interactions in herpes simplex virus type 1	6
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions	6
Persistence, spillover, and evolution of co-occurring lineages of lymphocytic choriomeningitis virus	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
ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods	6
Intra-host evolution of cell-fusing agent virus following acute infection in Aedes aegypti mosquito	6
Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales	6
Evolution of virulence in emerging epidemics: from theory to experimental evolution and back	6
Modeling the therapeutic potential of defective interfering particles in the presence of immunity	6
Long-term evolution of human seasonal influenza virus A(H3N2) is associated with an increase in polymerase complex activity	5
Comprehensive hallmark gene sequence, genomic and structural analysis clarifies new and established taxa within the Picornavirales	5
Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation	5
Decoding VZV’s evolutionary arsenal: how Beijing strains use recombination and adaptive mutations to thrive	5
Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis	5
Viral origin of eukaryotic type IIA DNA topoisomerases	5
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2	5
Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants	5
Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment	5
Genetic and antigenic diversity of rotavirus A in faeces from Danish pigs	5
Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations	5
The virome of the invasive Asian bush mosquito Aedes japonicus in Europe	5
Integrated viral elements suggest the dual lifestyle of Tetraselmis spp. Polinton-like viruses	5
Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025	5
Correction to: Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil	5
Biosurveillance of coronaviruses in Rhinolophus bats from South Africa	5
Unraveling the genomic landscape of piscine myocarditis virus: mutation frequencies, viral diversity and evolutionary dynamics in Atlantic salmon	5
Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections?	5
Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens	5
Emergence of the BA.2.87.1 lineage of SARS-CoV-2 in South Africa, a highly diverged BA.2-related lineage	5
Changes in intra-host mycovirus population diversity after vertical and horizontal transmission	5
Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway	5
Bacteriophage Φ21’s receptor-binding protein evolves new functions through destabilizing mutations that generate non-genetic phenotypic heterogeneity	5
Coxsackievirus A6 was the predominant pathogen of hand, foot, and mouth disease with frequent recombination and mutations in Shandong Province, 2023	5
Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market	5
Correction to: Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	5
Ecology and evolution of influenza A viruses in wild waterfowl in Argentina reveals novel viral genotypes	5
Fast-forwarding evolution—Accelerated adaptation in a proofreading-deficient hypermutator herpesvirus	4
Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines	4
Contemporary and historical human migration patterns shape hepatitis B virus diversity	4
Evolution of Zika virus in Rag1-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication fitness	4
Rabbit haemorrhagic disease virus 2 from Singapore 2020 outbreak revealed an Australian recombinant variant	4
Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae)	4
Visualizing and deciphering influenza A(H1N1) pdm09 reassortment in the 2019–23 seasons	4
Viral intra-host evolutionary dynamics revealed via serial passage of Japanese encephalitis virus in vitro	4
Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: Implications for bird–mammal transmission in South America	4
Recurrent SARS-CoV-2 mutations in immunodeficient patients	4
What makes a host a good reservoir? Determinants of the reservoir potential of Nicotiana glauca for tobacco mild green mosaic virus	4
Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages	4
Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021	4
Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron	4
Everglades virus evolution: Genome sequence analysis of the envelope 1 protein reveals recent mutation and divergence in South Florida wetlands	4
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae )	4
Computational multigene interactions in virus growth and infection spread	4
Human outbreak detection and best practice MPXV analysis and interpretation with squirrel	4
The genetic architecture of HIV-1 virulence	4
SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period	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
Diverse viral pathogens in Australian canines: limited geographic structure and the first detection of an RNA virus in dingoes	4
Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses	4
Molecular phylogeny of human adenovirus type 41 lineages	4
Evolution of the Cytomegalovirus RL11 gene family in Old World monkeys and Great Apes	4
Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies	4
The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus	4
Correction to: Contemporary and historical human migration patterns shape hepatitis B virus diversity	4
Geographic origin and evolution of dengue virus serotypes 1 and 3 circulating in Africa	4
Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes	4
Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts	4
The adaptive plasticity of temperate phage λ	4