Virus Evolution

Article	Citations
Evolution of a novel engineered tripartite viral genome of a torradovirus	124
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	114
Phycova — a tool for exploring covariates of pathogen spread	86
Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito	84
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary	81
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal	76
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China	65
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	62
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development	56
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients	55
Effects of host and pathogenicity on mutation rates in avian influenza A viruses	46
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	45
Host replacement dynamics shape virulence and genome evolution in a plant RNA virus	43
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	42
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	42
Genome sizes of animal RNA viruses reflect phylogenetic constraints	40
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness	36
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history	32
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	32
Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya	32
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	32
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	31
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	31
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	31
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic	31

Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe	30
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	29
Evolution of exploitation and replication of giant viruses and virophages	27
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host	27
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance	27
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals	27
The coevolutionary mosaic of bat betacoronavirus emergence risk	27
Virome release of an invasive exotic plant species in southern France	27
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut	25
The successive emergence of ERVL-MaLRs in primates	25
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza	24
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters	24
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	24
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny	24
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria	24
EvoLaps 2: Advanced phylogeographic visualization	24
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	23
Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine	23
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	23
Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics	22
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation	22
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia	21
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time	20
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites	20
Divergent hepaciviruses, delta-like viruses and a chu-like virus in Australian marsupial carnivores (dasyurids)	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
Hantavirus co-circulation in common shrews (Sorex araneus) in Sweden	19
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia	18
Genomic surveillance and evolution of Getah virus	18
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
Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021	17
Known phyla dominate the Tara Oceans RNA virome	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
Accommodating sampling location uncertainty in continuous phylogeography	16
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals	16
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges	15
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks	15
Prospects for a sequence-based taxonomy of influenza A virus subtypes	15
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations	15
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	15
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes	15
Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil	15
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa	14
A biophysical model of viral escape from polyclonal antibodies	14
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	14
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii	14
Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans	14
Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections	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	13

Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study	13
Mathematical comparison of protocols for adapting a bacteriophage to a new host	13
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh	13
Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes	13
Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing	13
Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage	13
Emergence and pandemic spread of small ruminant lentiviruses	12
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	12
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples	12
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies	12
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	12
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	12
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda	12
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications	12
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	12
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	12
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies	12
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	12
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	12
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	12
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
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China	11
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation	11
Experimental evidence of vaccine-driven evolution of respiratory syndrome virus type 2	11
Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals	11
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights	11
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York	11
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics	10
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak	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
Sequencing SARS-CoV-2 genomes from saliva	10
Heat adaptation of phage T7 under an extended genetic code	10
The impact of global lineage dynamics, border restrictions, and emergence of the B.1.1.7 lineage on the SARS-CoV-2 epidemic in Norway	10
Twenty years of evolution and diversification of digitaria streak virus in Digitaria setigera	10
A critique of the use of species and below-species taxonomic terms for viruses—time for change?	10
Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains	10
Evolution and diversity of inherited viruses in the Nearctic phantom midge, Chaoborus americanus	10
Variation within major internal repeats of KSHV in vivo	10
The emergence of NY10: insights into the 2012 West Nile Virus outbreak in the United States	10
Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization	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
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection	10
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
Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons	9
Focal persistence and phylodynamics of Heartland virus in Georgia	9
Independent epidemic patterns of HIV-1 CRF01_AE lineages driven by mobile population in Shenzhen, an immigrant city of China	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
Monotreme-specific conserved putative proteins derived from retroviral reverse transcriptase	9
Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status	9
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia	9
Correction to: The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK	9
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression	9
H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks	9
Haplotype assignment of longitudinal viral deep sequencing data using covariation of variant frequencies	9
Heptad stereotypy, S/Q layering, and remote origin of the SARS-CoV-2 fusion core	9
Lytic/Lysogenic Transition as a Life-History Switch	9
Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system	9
Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark	8
A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains	8
Co-infection of mammarenaviruses in a wild mouse, Tanzania	8
Polerovirus genomic variation	8
Genomic epidemiology reveals the variation and transmission properties of SARS-CoV-2 in a single-source community outbreak	8
A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon	8
Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago	8
Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans	8
Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction	8
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
Formal recognition and classification of gene transfer agents as viriforms	7
Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology	7
Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus	7
Evolutionary dynamics of respiratory syncytial virus in Buenos Aires: Viral diversity, migration, and subgroup replacement	7
Phylogenetic insights into the early spread of the SARS-CoV-2 Alpha variant across Europe	7
Evolution of influenza A virus in intensive and free-range swine farms in Spain	7
Virome analysis of New Zealand’s bats reveals cross-species viral transmission among the Coronaviridae	7
Fitness effects of mutations to SARS-CoV-2 proteins	7
Genomic analysis of human noroviruses using combined Illumina–Nanopore data	7

Eco-evolutionary dynamics of temperate phages in periodic environments	7
Correction to: Increase of niche filling with increase of host richness for plant-infecting mastreviruses	7
Within- and between-host evolutionary effects on viral oncogenicity	7
Evolutionary analyses of emerging GII.2[P16] and GII.4 Sydney [P16] noroviruses	6
Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic	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
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes	6
HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies	6
Viral community composition of hypersaline lakes	6
Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts	6
The untapped potential of phage model systems as therapeutic agents	6
Origin, spread, and interspecies transmission of a dominant genotype of BJ/94 lineage H9N2 avian influenza viruses with increased threat	6
Viromes of Antarctic fish resemble the diversity found at lower latitudes	6
Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates	6
Tick virome diversity in Hubei Province, China, and the influence of host ecology	6
The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses	6
Cell type-specific adaptation of the SARS-CoV-2 spike	6
Sustained cross-species transmission of gammacoronavirus in wild birds revealed by viral characterization in China	6
Corrigendum to: Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020	6
Conserved recombination patterns across coronavirus subgenera	6
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana	6
Unraveling gene content variation across eukaryotic giant viruses based on network analyses and host associations	6
Transmission dynamics of low pathogenicity avian influenza (H2N2) viruses in live bird markets of the Northeast United States of America, 2013–2019	6
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha	6
Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat	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
Modeling the therapeutic potential of defective interfering particles in the presence of immunity	6
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
Correction to: Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation	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
Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections	5
Bacteriophage Φ21’s receptor-binding protein evolves new functions through destabilizing mutations that generate non-genetic phenotypic heterogeneity	5
Evolution of virulence in emerging epidemics: from theory to experimental evolution and back	5
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions	5
Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway	5
Widespread interspecific phylogenetic tree incongruence between mosquito-borne and insect-specific flaviviruses at hotspots originally identified in Zika virus	5
Long-term evolution of human seasonal influenza virus A(H3N2) is associated with an increase in polymerase complex activity	5
Viral origin of eukaryotic type IIA DNA topoisomerases	5
Molecular epidemiological features of SARS-CoV-2 in Japan, 2020–1	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
Integrated viral elements suggest the dual lifestyle of Tetraselmis spp. Polinton-like viruses	5
Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations	5
Phylodynamic analysis and spike protein mutations in porcine deltacoronavirus with a new variant introduction in Taiwan	4
Diverse viral pathogens in Australian canines: limited geographic structure and the first detection of an RNA virus in dingoes	4
Coronaviruses in wild animals sampled in and around Wuhan at the beginning of COVID-19 emergence	4
Rabbit haemorrhagic disease virus 2 from Singapore 2020 outbreak revealed an Australian recombinant variant	4
Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron	4
Strong selection and high mutation supply characterize experimentalChlorovirusevolution	4
Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment	4
Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market	4
Unraveling the genomic landscape of piscine myocarditis virus: mutation frequencies, viral diversity and evolutionary dynamics in Atlantic salmon	4
Correction to: Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	4
Fast-forwarding evolution—Accelerated adaptation in a proofreading-deficient hypermutator herpesvirus	4
Evolution of the Cytomegalovirus RL11 gene family in Old World monkeys and Great Apes	4
Molecular phylogeny of human adenovirus type 41 lineages	4
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae)	4
Contemporary and historical human migration patterns shape hepatitis B virus diversity	4
Correction to: Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil	4
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2	4
Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing	4
Evolution of Zika virus in Rag1-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication fitness	4
Expanding the RNA virome of nematodes and other soil-inhabiting organisms	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
Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines	4
Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses	4
Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants	4
Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections?	4