Virus Evolution

Article	Citations
Unveiling the RNA virus landscape of Cotesia chilonis : geographic distribution, diversity, and potential roles in parasitoid–host interactions	114
Experimental evolution of the host range dynamics in two isolates of potato virus Y	92
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	79
Evolution of a novel engineered tripartite viral genome of a torradovirus	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
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	47
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history	39
Plant biosecurity threats detected using metatranscriptomic sequencing of animal gut contents	34
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic	33
Host replacement dynamics shape virulence and genome evolution in a plant RNA virus	31
Phylogeographic evaluation of the effectiveness of Canadian travel restrictions in reducing SARS-CoV-2 variant importations and burden	31
Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya	30
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	30
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients	30
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	30
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	27
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	26
Genome sizes of animal RNA viruses reflect phylogenetic constraints	24
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	23
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development	23
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	23
EvoLaps 2: Advanced phylogeographic visualization	22
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut	22
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance	21
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals	21

An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	20
The successive emergence of ERVL-MaLRs in primates	20
Phylogenetic analysis of pigeon paramyxovirus type 1 detected in the British Isles between 1983 and 2023	20
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny	20
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia	19
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host	19
Virome release of an invasive exotic plant species in southern France	19
Evolution of exploitation and replication of giant viruses and virophages	19
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	18
The coevolutionary mosaic of bat betacoronavirus emergence risk	18
Hantavirus co-circulation in common shrews (Sorex araneus) in Sweden	17
Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics	17
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza	17
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	17
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	17
Sequence based virus host prediction: a curated dataset and generalizable framework for training artificial intelligence to identify viruses of humans	16
Viral diversity influences T-cell responses to enteric human adenoviruses F40 and F41	15
Divergent hepaciviruses, delta-like viruses and a chu-like virus in Australian marsupial carnivores (dasyurids)	15
Evolutionary characterization of the establishment of H6 influenza viruses in domestic geese in China: implications for the position of the host in the ecosystem	15
Metaviromics reveals a high diversity of viruses belonging to the Caliciviridae family in seal feces	14
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations	14
Intra-host GI.1 norovirus evolution is shaped by genetic drift and purifying selection	14
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia	14
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak	14
Known phyla dominate the Tara Oceans RNA virome	13
Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil	13
Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant	13
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii	13
Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans	13
Genomic surveillance and evolution of Getah virus	13
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks	13
Mapping the global distribution and spread of the Plasmodium vivax -associated virus MaRNAV-1	12
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations	12
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies	12
Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections	12
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	12
Emergence and pandemic spread of small ruminant lentiviruses	12
Prospects for a sequence-based taxonomy of influenza A virus subtypes	12
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa	12
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	12
Mathematical comparison of protocols for adapting a bacteriophage to a new host	12
Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage	12
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh	12
Getting to the root of HIV transmitted founder virus sequences	12
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals	12
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
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda	12
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York	11
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	11

Constraint in West Nile virus envelope protein across mosquito, human, and avian host cell environments	11
Antagonistic Co-Evolution Throughout the Herpesvirus Life Cycle	11
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	11
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies	11
Correction to: Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load	11
The whole genome analysis of four Orf virus strains from Europe and South America	11
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia	11
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	11
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia	10
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	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
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation	10
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights	10
The emergence of NY10: insights into the 2012 West Nile Virus outbreak in the United States	10
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes	10
Experimental evidence of vaccine-driven evolution of porcine reproductive and respiratory syndrome virus type 2	10
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection	9
Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status	9
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics	9
Variation within major internal repeats of KSHV in vivo	9
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak	9
Focal persistence and phylodynamics of Heartland virus in Georgia	9
Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization	9
Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals	9
H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks	8
A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains	8
Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago	8
Selection of viral variants with enhanced transmission and reduced neutralization susceptibility alongside lateral introductions may explain the persistence of porcine reproductive and respiratory syn	8
Lytic/Lysogenic Transition as a Life-History Switch	8
Identification of a novel mycovirus belonging to the “flexivirus”-related family with icosahedral virion	8
Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system	8
Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction	8
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression	8
Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons	8
Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	8
Identification and genomic characterization of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa	8
A critique of the use of species and below-species taxonomic terms for viruses—time for change?	8
Single capsid mutations modulating phage adsorption, persistence, and plaque morphology shape evolutionary trajectories in ΦX174	7
Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark	7
Characterizing the parvovirome of Swazi bats: novel species, highly divergent lineages, endogenous viral elements, and taxonomic challenges	7
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
A single-stranded DNA virus replicates in the mitochondria of a marine oomycete	7
Evolutionary dynamics of respiratory syncytial virus in Buenos Aires: Viral diversity, migration, and subgroup replacement	7
A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon	7
Phylogenetic insights into the early spread of the SARS-CoV-2 Alpha variant across Europe	7
Dynamic evolution of retroviral envelope-derived sequences in primates	7
Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived	7
Correction to: Increase of niche filling with increase of host richness for plant-infecting mastreviruses	7
Genomic epidemiology reveals the variation and transmission properties of SARS-CoV-2 in a single-source community outbreak	7
Fitness effects of mutations to SARS-CoV-2 proteins	7
Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans	7
Experimental evolution of Rc-o319 sarbecovirus spike protein reveals limited ACE2 adaptability	7
On the importance of assessing topological convergence in Bayesian phylogenetic inference	7
Eco-evolutionary dynamics of temperate phages in periodic environments	6
Viromes of Antarctic fish resemble the diversity found at lower latitudes	6
Viral community composition of hypersaline lakes	6
Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts	6
Origin, spread, and interspecies transmission of a dominant genotype of BJ/94 lineage H9N2 avian influenza viruses with increased threat	6
Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012–8	6
GALV-KoRV-related retroviruses in diverse Australian and African rodent species	6
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha	6
The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses	6
Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates	6
Within- and between-host evolutionary effects on viral oncogenicity	6
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana	6
The untapped potential of phage model systems as therapeutic agents	6
HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies	6
Extreme GC3 codon bias in a novel brown seaweed virus results in pseudoambigrammatic characteristics	6
Differences in codon usage between host-species-specific rabies virus clades are driven by non-GC3 nucleotide composition	6
Virome analysis of New Zealand’s bats reveals cross-species viral transmission among the Coronaviridae	6
Begomovirus species demarcation based on genome-sequence identity yields non-monophyletic species: a case study of sweet potato-infecting begomoviruses	6
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes	5
Sustained cross-species transmission of gammacoronavirus in wild birds revealed by viral characterization in China	5
High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA	5
Cell type-specific adaptation of the SARS-CoV-2 spike	5
Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens	5
Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation	5
Comprehensive hallmark gene sequence, genomic and structural analysis clarifies new and established taxa within the Picornavirales	5
Intra-host evolution of cell-fusing agent virus following acute infection in Aedes aegypti mosquito	5

Evolution of virulence in emerging epidemics: from theory to experimental evolution and back	5
Persistence, spillover, and evolution of co-occurring lineages of lymphocytic choriomeningitis virus	5
A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data	5
Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025	5
Changes in intra-host mycovirus population diversity after vertical and horizontal transmission	5
Emergence of the BA.2.87.1 lineage of SARS-CoV-2 in South Africa, a highly diverged BA.2-related lineage	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
Correction to: Coevolutionary phage training and Joint application delays the emergence of phage resistance in Pseudomonas aeruginosa	5
ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods	5
Anthropozoonotic spillovers reveal sustained long-term cryptic circulation of SARS-CoV-2 within and between Lithuanian mink farms	5
Rapid glycoprotein evolution enables variant interactions in herpes simplex virus type 1	5
Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway	5
The virome of the invasive Asian bush mosquito Aedes japonicus in Europe	5
Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations	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	4
The adaptive plasticity of temperate phage λ	4
Genetic and antigenic diversity of rotavirus A in faeces from Danish pigs	4
Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021	4
Geographic origin and evolution of dengue virus serotypes 1 and 3 circulating in Africa	4
Computational multigene interactions in virus growth and infection spread	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
Ecology and evolution of influenza A viruses in wild waterfowl in Argentina reveals novel viral genotypes	4
Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections?	4
Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses	4
Coxsackievirus A6 was the predominant pathogen of hand, foot, and mouth disease with frequent recombination and mutations in Shandong Province, 2023	4
Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market	4
Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes	4
Rabbit haemorrhagic disease virus 2 from Singapore 2020 outbreak revealed an Australian recombinant variant	4
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2	4
Correction to: Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	4
Correction to: Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil	4
Diverse viral pathogens in Australian canines: limited geographic structure and the first detection of an RNA virus in dingoes	4
Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis	4
Unraveling the genomic landscape of piscine myocarditis virus: mutation frequencies, viral diversity and evolutionary dynamics in Atlantic salmon	4
Biosurveillance of coronaviruses in Rhinolophus bats from South Africa	4
Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies	4
Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts	4
Evolution of Zika virus in Rag1-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication fitness	4
Contemporary and historical human migration patterns shape hepatitis B virus diversity	4
Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants	4