Virus Evolution

Article	Citations
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool	810
Cenote-Taker 2 democratizes virus discovery and sequence annotation	103
An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain	101
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK	80
Intra-host evolution during SARS-CoV-2 prolonged infection	73
Virome composition in marine fish revealed by meta-transcriptomics	70
Interannual dynamics, diversity and evolution of the virome in Sclerotinia sclerotiorum from a single crop field	64
Recurrent SARS-CoV-2 mutations in immunodeficient patients	61
The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus	52
A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways	50
Possible host-adaptation of SARS-CoV-2 due to improved ACE2 receptor binding in mink	47
Recombinant SARS-CoV-2 genomes circulated at low levels over the first year of the pandemic	45
RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data	45
Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic	44
The history of foot-and-mouth disease virus serotype C: the first known extinct serotype?	43
Evolution of DNA packaging in gene transfer agents	42
Synonymous mutations and the molecular evolution of SARS-CoV-2 origins	42
The evolutionary dynamics of endemic human coronaviruses	41
Fitness effects of mutations to SARS-CoV-2 proteins	41
Contributions of adaptation and purifying selection to SARS-CoV-2 evolution	41
Viromics of extant insect orders unveil the evolution of the flavi-like superfamily	40
Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray–Darling Basin, Australia	37
Adintoviruses: a proposed animal-tropic family of midsize eukaryotic linear dsDNA (MELD) viruses	37
Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations	33
Revealing RNA virus diversity and evolution in unicellular algae transcriptomes	32

Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses	32
The discovery, distribution, and diversity of DNA viruses associated withDrosophila melanogasterin Europe	32
Polerovirus genomic variation	31
Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution	31
Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae	30
The characterization of multiple novel paramyxoviruses highlights the diverse nature of the subfamilyOrthoparamyxovirinae	30
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	29
The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein	29
Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis	29
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes	28
Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa	27
Identification of a novel SARS-CoV-2 P.1 sub-lineage in Brazil provides new insights about the mechanisms of emergence of variants of concern	27
The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia	26
Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes	26
Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000–18	26
Divergent RNA viruses in Macrophomina phaseolina exhibit potential as virocontrol agents	26
Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses	25
SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity	25
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil	25
Tick virome diversity in Hubei Province, China, and the influence of host ecology	24
Alternate primers for whole-genome SARS-CoV-2 sequencing	24
Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host	22
A biophysical model of viral escape from polyclonal antibodies	22
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	21
Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians	21
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	21
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	20
Defects in plant immunity modulate the rates and patterns of RNA virus evolution	20
Genomic evolution, transmission dynamics, and pathogenicity of avian influenza A (H5N8) viruses emerging in China, 2020	20
A genome-wide association study identifies Arabidopsis thaliana genes that contribute to differences in the outcome of infection with two Turnip mosaic potyvirus strains that differ in t	20
Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites	19
Coronaviruses in wild animals sampled in and around Wuhan at the beginning of COVID-19 emergence	19
Endogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii	19
Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene	18
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	18
Genomic epidemiology of a densely sampled COVID-19 outbreak in China	18
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae)	18
Conserved recombination patterns across coronavirus subgenera	17
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	17
Two distant helicases in one mycovirus: evidence of horizontal gene transfer between mycoviruses, coronaviruses and other nidoviruses	17
Unification and extensive diversification of M/Orf3-related ion channel proteins in coronaviruses and other nidoviruses	17
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications	17
Decomposing the sources of SARS-CoV-2 fitness variation in the United States	17
Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2	16
Three new clades of putative viral RNA-dependent RNA polymerases with rare or unique catalytic triads discovered in libraries of ORFans from powdery mildews and the yeast of oenological interest St	16
Limited cross-species virus transmission in a spatially restricted coral reef fish community	16
Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution	16
Increasing temperature alters the within-host competition of viral strains and influences virus genetic variability	15
Genetic diversity of avian leukosis virus subgroup J (ALV-J): toward a unified phylogenetic classification and nomenclature system	15
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	15

Comparative genomic analysis of genogroup 1 and genogroup 2 rotaviruses circulating in seven US cities, 2014–2016	15
Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota	15
Gene copy number variations at the within-host population level modulate gene expression in a multipartite virus	15
A scenario for the emergence of protoviroids in the RNA world and for their further evolution into viroids and viroid-like RNAs by modular recombinations and mutations	15
Adaptation of the endemic coronaviruses HCoV-OC43 and HCoV-229E to the human host	15
A comprehensive analysis of genetic diversity of EBV reveals potential high-risk subtypes associated with nasopharyngeal carcinoma in China	15
Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices	15
Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine	15
Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains	14
Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito	14
The central role of Italy in the spatial spread of USUTU virus in Europe	14
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions	14
Defining virus-carrier networks that shape the composition of the mosquito core virome of a local ecosystem	14
Viral origin of eukaryotic type IIA DNA topoisomerases	14
Integrating animal movements with phylogeography to model the spread of PRRSV in the USA	14
The spatial-temporal dynamics of respiratory syncytial virus infections across the east–west coasts of Australia during 2016–17	14
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time	14
Cross-scale dynamics and the evolutionary emergence of infectious diseases	13
Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates	13
Human land use impacts viral diversity and abundance in a New Zealand river	13
Phenotypic flux: The role of physiology in explaining the conundrum of bacterial persistence amid phage attack	13
Emergence and spread of a sub-lineage of SARS-CoV-2 Alpha variant B.1.1.7 in Europe, and with further evolution of spike mutation accumulations shared with the Beta and Gamma variants	12
Timescales modulate optimal lysis–lysogeny decision switches and near-term phage reproduction	12
Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes	12
Host prediction for disease-associated gastrointestinal cressdnaviruses	12
Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status	12
Exploration of the Ixodes ricinus virosphere unveils an extensive virus diversity including novel coltiviruses and other reoviruses	12
Splitting of RNA-dependent RNA polymerase is common in Narnaviridae: Identification of a type II divided RdRp from deep-sea fungal isolates	12
Molecular detection and genomic characterization of diverse hepaciviruses in African rodents	11
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters	11
Human genomics of the humoral immune response against polyomaviruses	11
Emergence and characterization of a putative novel human adenovirus recombinant HAdV-C104 causing pneumonia in Southern China	11
Intrahost speciations and host switches played an important role in the evolution of herpesviruses	11
Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections	11
Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador	11
Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology	11
Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley	11
Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E	11
The virome of the invasive Asian bush mosquito Aedes japonicus in Europe	10
Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020	10
Evolutionary analyses of emerging GII.2[P16] and GII.4 Sydney [P16] noroviruses	10
Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: Implications for bird–mammal transmission in South America	10
Evolutionary history and introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan through international travelers	10
Crossroads of highly pathogenic H5N1: overlap between wild and domestic birds in the Black Sea-Mediterranean impacts global transmission	10
Intra-host analysis of hepaciviral glycoprotein evolution reveals signatures associated with viral persistence and clearance	10
Molecular phylogeny of human adenovirus type 41 lineages	9
Genetic and biological characteristics of species A rotaviruses detected in common shrews suggest a distinct evolutionary trajectory	9
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	9
Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study	9
Accommodating sampling location uncertainty in continuous phylogeography	9
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation	9
Ancient viral integrations in marsupials: a potential antiviral defence	9
Intra- and inter-host evolution of H9N2 influenza A virus in Japanese quail	9
A comprehensive evolutionary and epidemiological characterization of insertion and deletion mutations in SARS-CoV-2 genomes	9
Molecular epidemiological features of SARS-CoV-2 in Japan, 2020–1	9
Expanding the RNA virome of nematodes and other soil-inhabiting organisms	8
The emergence and transmission dynamics of HIV-1 CRF07_BC in Mainland China	8
Genetic diversity and connectivity of the Ostreid herpesvirus 1 populations in France: A first attempt to phylogeographic inference for a marine mollusc disease	8
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China	8
Genomic analysis of human noroviruses using combined Illumina–Nanopore data	8
Genome evolution of dengue virus serotype 1 under selection by Wolbachia pipientis in Aedes aegypti mosquitoes	8
Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon,Cucumis melo, crops, and adjacent wild communities	8
Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron	8
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations	8
Phylodynamic study of the conserved RNA structure encompassing the hemagglutinin cleavage site encoding region of H5 and H7 low pathogenic avian influenza viruses	8
Mammalian birnaviruses identified in pigs infected by classical swine fever virus	8
Identification of diverse viruses associated with grasshoppers unveils the parallel relationship between host phylogeny and virome composition	7
Redondoviridae and periodontitis: a case–control study and identification of five novel redondoviruses from periodontal tissues	7
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	7
Accumulation of copy-back viral genomes during respiratory syncytial virus infection is preceded by diversification of the copy-back viral genome population followed by selection	7
Formal recognition and classification of gene transfer agents as viriforms	7
Correction to: The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK	7
Integrated viral elements suggest the dual lifestyle of Tetraselmis spp. Polinton-like viruses	7
Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids	7
Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages	7
Strong selection and high mutation supply characterize experimental Chlorovirus evolution	7
Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection	7
HIV-2 diversity displays two clades within group A with distinct geographical distribution and evolution	7
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	7
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	7

Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl	7
Evolution of influenza A virus in intensive and free-range swine farms in Spain	7
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	7
Emergence and pandemic spread of small ruminant lentiviruses	6
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria	6
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	6
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness	6
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal	6
Differential disease severity and whole-genome sequence analysis for human influenza A/H1N1pdm virus in 2015–2016 influenza season	6
Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons	6
MutaGAN: A sequence-to-sequence GAN framework to predict mutations of evolving protein populations	6
Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency	6
Viral community composition of hypersaline lakes	6
Evolutionary dynamics of respiratory syncytial virus in Buenos Aires: Viral diversity, migration, and subgroup replacement	6
Genomic epidemiology of human adenovirus F40 and F41 in coastal Kenya: A retrospective hospital-based surveillance study (2013–2022)	6
CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes	6
Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area	6
Increased virulence of Italian infectious hematopoietic necrosis virus (IHNV) associated with the emergence of new strains	5
Multiple introductions and country-wide spread of DENV-2 genotype II (Cosmopolitan) in Brazil	5
Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants	5
SARS-CoV-2 intra-host single-nucleotide variants associated with disease severity	5
Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens	5
covSampler: A subsampling method with balanced genetic diversity for large-scale SARS-CoV-2 genome data sets	5
Conserved untranslated regions of multipartite viruses: Natural markers of novel viral genomic components and tags of viral evolution	5
Heat adaptation of phage T7 under an extended genetic code	5
Evolution and diversity of inherited viruses in the Nearctic phantom midge, Chaoborus americanus	5
Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014–15 influenza season	5
Erratum: Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses	5
Whole-genome analysis to determine the rate and patterns of intra-subtype reassortment among influenza type-A viruses in Africa	5
A new perspective on the evolution and diversity of the genus Amdoparvovirus (family Parvoviridae) through genetic characterization, structural homology modeling, and phylogenetics	5
Polymorphism of genetic ambigrams	5
Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections	5
Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals	5
Phylodynamics of deer tick virus in North America	5
Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates	5
Pirahy virus: Identification of a new and potential emerging arbovirus in South Brazil	5
Unraveling gene content variation across eukaryotic giant viruses based on network analyses and host associations	5
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	5
Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes	5
A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains	5
Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat	5
Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing	5
The recombinogenic history of turnip mosaic potyvirus reveals its introduction to Japan in the 19th century	5
Erratum: Virome composition in marine fish revealed by meta-transcriptomics	5
Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe	5
Origin, genomic diversity and evolution of African swine fever virus in East Asia	4
Genome Evolution and Early Introductions of the SARS-CoV-2 Omicron Variant in Mexico	4
The evolutionary dynamics of viruses: virion release strategies, time delays and fitness minima	4
Reconstruction of the origin and dispersal of the worldwide dominant Hepatitis B Virus subgenotype D1	4
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	4
Virus-induced interference as a means for accelerating fitness-based selection of cyprinid herpesvirus 3 single-nucleotide variantsin vitroandin vivo	4
Identification of a novel polyomavirus from a marsupial host	4
Effects of host and pathogenicity on mutation rates in avian influenza A viruses	4
Quantifying the clonality and dynamics of the within-host HIV-1 latent reservoir	4
Unresolved advantages of multipartitism in spatially structured environments	4
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	4
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges	4
GRACy: A tool for analysing human cytomegalovirus sequence data	4
Haplotype assignment of longitudinal viral deep sequencing data using covariation of variant frequencies	4
Multiple waves of viral invasions in Symbiodiniaceae algal genomes	4
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression	4
Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions	4
Twenty years of evolution and diversification of digitaria streak virus in Digitaria setigera	4
Modeling the therapeutic potential of defective interfering particles in the presence of immunity	4
Phycova — a tool for exploring covariates of pathogen spread	4
The untapped potential of phage model systems as therapeutic agents	4
Anellovirus evolution during long-term chronic infection	4
Monotreme-specific conserved putative proteins derived from retroviral reverse transcriptase	4
Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans	4
In action—an early warning system for the detection of unexpected or novel pathogens	4
H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks	4
Rapid evolution of SARS-CoV-2 in domestic cats	4
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes	4
Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype	4
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes	4