Virus Evolution

Article	Citations
Evolution of a novel engineered tripartite viral genome of a torradovirus	132
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary	120
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal	92
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China	90
Phycova — a tool for exploring covariates of pathogen spread	80
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	79
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	72
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	61
Effects of host and pathogenicity on mutation rates in avian influenza A viruses	51
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	49
Plant biosecurity threats detected using metatranscriptomic sequencing of animal gut contents	48
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic	46
Phylogeographic evaluation of the effectiveness of Canadian travel restrictions in reducing SARS-CoV-2 variant importations and burden	46
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness	46
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history	44
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development	36
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	35
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients	35
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	34
Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya	34
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	33
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	33
Genome sizes of animal RNA viruses reflect phylogenetic constraints	33
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	30

Evolution of exploitation and replication of giant viruses and virophages	30
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	30
Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe	30
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host	28
The successive emergence of ERVL-MaLRs in primates	27
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut	27
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny	26
Phylogenetic analysis of pigeon paramyxovirus type 1 detected in the British Isles between 1983 and 2023	25
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation	24
EvoLaps 2: Advanced phylogeographic visualization	24
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance	24
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia	24
Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics	24
The coevolutionary mosaic of bat betacoronavirus emergence risk	24
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza	22
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	22
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA p	22
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters	22
Virome release of an invasive exotic plant species in southern France	21
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals	21
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	21
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	20
Evolutionary characterization of the establishment of H6 influenza viruses in domestic geese in China: implications for the position of the host in the ecosystem	19
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	19
Hantavirus co-circulation in common shrews (Sorex araneus) in Sweden	19
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites	18
Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021	18
Genomic surveillance and evolution of Getah virus	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	17
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak	17
Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host	17
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	16
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time	16
Divergent hepaciviruses, delta-like viruses and a chu-like virus in Australian marsupial carnivores (dasyurids)	16
Accommodating sampling location uncertainty in continuous phylogeography	16
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia	16
Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil	15
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	15
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa	15
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes	15
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations	15
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges	15
Prospects for a sequence-based taxonomy of influenza A virus subtypes	15
Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans	15
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals	15
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks	15
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies	14
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda	14
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	14
Mathematical comparison of protocols for adapting a bacteriophage to a new host	14

A biophysical model of viral escape from polyclonal antibodies	14
Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study	14
Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes	14
Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage	14
Known phyla dominate the Tara Oceans RNA virome	14
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii	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
Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing	14
Emergence and pandemic spread of small ruminant lentiviruses	14
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh	13
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China	13
Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections	13
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	13
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia	13
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples	13
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	13
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications	13
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	13
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	12
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	12
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	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
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes	12
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation	12
Correction to: Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load	12
Heptad stereotypy, S/Q layering, and remote origin of the SARS-CoV-2 fusion core	11
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	11
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia	11
Variation within major internal repeats of KSHV in vivo	11
Constraint in West Nile virus envelope protein across mosquito, human, and avian host cell environments	11
Experimental evidence of vaccine-driven evolution of porcine reproductive and respiratory syndrome virus type 2	11
Focal persistence and phylodynamics of Heartland virus in Georgia	11
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights	11
The emergence of NY10: insights into the 2012 West Nile Virus outbreak in the United States	11
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak	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
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
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
A critique of the use of species and below-species taxonomic terms for viruses—time for change?	10
Evolution and diversity of inherited viruses in the Nearctic phantom midge, Chaoborus americanus	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
Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains	10
H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks	10
Heat adaptation of phage T7 under an extended genetic code	10
Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status	10
Sequencing SARS-CoV-2 genomes from saliva	10
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection	10
Lytic/Lysogenic Transition as a Life-History Switch	10
The evolution of the HIV-1 protease folding stability	10
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression	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
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
Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction	8
Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	8
Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans	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
Monotreme-specific conserved putative proteins derived from retroviral reverse transcriptase	8
A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon	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 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
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
Fitness effects of mutations to SARS-CoV-2 proteins	7
Formal recognition and classification of gene transfer agents as viriforms	7
Conserved recombination patterns across coronavirus subgenera	7
Virome analysis of New Zealand’s bats reveals cross-species viral transmission among the Coronaviridae	7
Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012–8	7
GALV-KoRV-related retroviruses in diverse Australian and African rodent species	7
Beyond the Amazon: vector surveillance and emerging Oropouche virus in South America	7
Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus	7
Polerovirus genomic variation	7
Phylogenetic insights into the early spread of the SARS-CoV-2 Alpha variant across Europe	7

Within- and between-host evolutionary effects on viral oncogenicity	7
Evolutionary analyses of emerging GII.2[P16] and GII.4 Sydney [P16] noroviruses	7
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana	7
Viromes of Antarctic fish resemble the diversity found at lower latitudes	7
Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology	7
Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived	7
Co-infection of mammarenaviruses in a wild mouse, Tanzania	7
Eco-evolutionary dynamics of temperate phages in periodic environments	7
Origin, spread, and interspecies transmission of a dominant genotype of BJ/94 lineage H9N2 avian influenza viruses with increased threat	7
The untapped potential of phage model systems as therapeutic agents	7
Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic	7
Transmission dynamics of low pathogenicity avian influenza (H2N2) viruses in live bird markets of the Northeast United States of America, 2013–2019	7
HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies	6
Viral community composition of hypersaline lakes	6
The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses	6
Sustained cross-species transmission of gammacoronavirus in wild birds revealed by viral characterization in China	6
A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data	6
Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat	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
High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA	6
Modeling the therapeutic potential of defective interfering particles in the presence of immunity	6
ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods	5
Evolution of virulence in emerging epidemics: from theory to experimental evolution and back	5
Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway	5
Cell type-specific adaptation of the SARS-CoV-2 spike	5
Intra-host evolution of cell-fusing agent virus following acute infection in Aedes aegypti mosquito	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
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes	5
Persistence, spillover, and evolution of co-occurring lineages of lymphocytic choriomeningitis virus	5
Molecular epidemiological features of SARS-CoV-2 in Japan, 2020–1	5
Correction to: Coevolutionary phage training and Joint application delays the emergence of phage resistance in Pseudomonas aeruginosa	5
The virome of the invasive Asian bush mosquito Aedes japonicus in Europe	5
Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025	5
Widespread interspecific phylogenetic tree incongruence between mosquito-borne and insect-specific flaviviruses at hotspots originally identified in Zika virus	5
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions	5
Correction to: Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation	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
Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales	5
Rapid glycoprotein evolution enables variant interactions in herpes simplex virus type 1	5
Changes in intra-host mycovirus population diversity after vertical and horizontal transmission	5
Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections	5
Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021	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
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
Correction to: Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil	4
Emergence of the BA.2.87.1 lineage of SARS-CoV-2 in South Africa, a highly diverged BA.2-related lineage	4
Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens	4
Long-term evolution of human seasonal influenza virus A(H3N2) is associated with an increase in polymerase complex activity	4
Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market	4
Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases	4
Everglades virus evolution: Genome sequence analysis of the envelope 1 protein reveals recent mutation and divergence in South Florida wetlands	4
Molecular phylogeny of human adenovirus type 41 lineages	4
Strong selection and high mutation supply characterize experimentalChlorovirusevolution	4
Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages	4
Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants	4
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae )	4
Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment	4
Contemporary and historical human migration patterns shape hepatitis B virus diversity	4
Bacteriophage Φ21’s receptor-binding protein evolves new functions through destabilizing mutations that generate non-genetic phenotypic heterogeneity	4
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
Evolution of the Cytomegalovirus RL11 gene family in Old World monkeys and Great Apes	4
Defining virus-carrier networks that shape the composition of the mosquito core virome of a local ecosystem	4
Fast-forwarding evolution—Accelerated adaptation in a proofreading-deficient hypermutator herpesvirus	4
Biosurveillance of coronaviruses in Rhinolophus bats from South Africa	4
Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts	4
Correction to: Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	4
Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines	4
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2	4
Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron	4
Unraveling the genomic landscape of piscine myocarditis virus: mutation frequencies, viral diversity and evolutionary dynamics in Atlantic salmon	4
Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing	4
Decoding VZV’s evolutionary arsenal: how Beijing strains use recombination and adaptive mutations to thrive	4
Evolution of Zika virus in Rag1-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication fitness	4
Coronaviruses in wild animals sampled in and around Wuhan at the beginning of COVID-19 emergence	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
Expanding the RNA virome of nematodes and other soil-inhabiting organisms	4