Virus Evolution

Article	Citations
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool	725
Temporal signal and the phylodynamic threshold of SARS-CoV-2	300
RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets	256
Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation	121
Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages	101
An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain	87
Cenote-Taker 2 democratizes virus discovery and sequence annotation	83
The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization	79
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK	67
Intra-host evolution during SARS-CoV-2 prolonged infection	64
Interannual dynamics, diversity and evolution of the virome in Sclerotinia sclerotiorum from a single crop field	55
The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus	51
Virome composition in marine fish revealed by meta-transcriptomics	51
Recurrent SARS-CoV-2 mutations in immunodeficient patients	50
Possible host-adaptation of SARS-CoV-2 due to improved ACE2 receptor binding in mink	47
Synonymous mutations and the molecular evolution of SARS-CoV-2 origins	39
Recombinant SARS-CoV-2 genomes circulated at low levels over the first year of the pandemic	39
The evolutionary dynamics of endemic human coronaviruses	38
Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic	37
Evolution of DNA packaging in gene transfer agents	36
Diversity and circulation of Jingmen tick virus in ticks and mammals	36
The history of foot-and-mouth disease virus serotype C: the first known extinct serotype?	35
A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways	34
Viromics of extant insect orders unveil the evolution of the flavi-like superfamily	34
Towards a unified classification for human respiratory syncytial virus genotypes	33

Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations	33
Intra-genome variability in the dinucleotide composition of SARS-CoV-2	32
Contributions of adaptation and purifying selection to SARS-CoV-2 evolution	31
Revealing RNA virus diversity and evolution in unicellular algae transcriptomes	29
Extensive genetic diversity and host range of rodent-borne coronaviruses	29
Adintoviruses: a proposed animal-tropic family of midsize eukaryotic linear dsDNA (MELD) viruses	29
Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution	27
Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray–Darling Basin, Australia	27
The discovery, distribution, and diversity of DNA viruses associated withDrosophila melanogasterin Europe	27
When to be temperate: on the fitness benefits of lysis vs. lysogeny	27
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types	27
Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses	27
Red fox viromes in urban and rural landscapes	27
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	26
Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa	26
Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses	25
RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data	25
Divergent RNA viruses in Macrophomina phaseolina exhibit potential as virocontrol agents	25
Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae	24
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	24
Polerovirus genomic variation	23
Alternate primers for whole-genome SARS-CoV-2 sequencing	23
Genetic diversity, phylogeography, and evolutionary dynamics of highly pathogenic avian influenza A (H5N6) viruses	23
SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity	22
Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes	22
Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host	22
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil	22
The characterization of multiple novel paramyxoviruses highlights the diverse nature of the subfamilyOrthoparamyxovirinae	21
Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence	21
The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia	21
Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates	21
Tick virome diversity in Hubei Province, China, and the influence of host ecology	21
Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis	21
Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase	21
Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000–18	21
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes	21
Fitness effects of mutations to SARS-CoV-2 proteins	21
Emergence and evolution of highly pathogenic porcine epidemic diarrhea virus by natural recombination of a low pathogenic vaccine isolate and a highly pathogenic strain in the spike gene	19
Genomic evolution, transmission dynamics, and pathogenicity of avian influenza A (H5N8) viruses emerging in China, 2020	19
Emerging phylogenetic structure of the SARS-CoV-2 pandemic	19
Inference of Nipah virus evolution, 1999–2015	19
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	19
Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure?	18
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	18
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	18
Full-genome sequencing of German rabbit haemorrhagic disease virus uncovers recombination between RHDV (GI.2) and EBHSV (GII.1)	18
The role of genetic sequencing and analysis in the polio eradication programme	18
Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites	17
Estimating hepatitis B virus cccDNA persistence in chronic infection†	17
A biophysical model of viral escape from polyclonal antibodies	17

Genomic epidemiology of a densely sampled COVID-19 outbreak in China	17
Coronaviruses in wild animals sampled in and around Wuhan at the beginning of COVID-19 emergence	16
Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene	16
HTLV in South America: Origins of a silent ancient human infection	16
Unification and extensive diversification of M/Orf3-related ion channel proteins in coronaviruses and other nidoviruses	16
Two distant helicases in one mycovirus: evidence of horizontal gene transfer between mycoviruses, coronaviruses and other nidoviruses	16
Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians	16
Newly emerged resistance-breaking variants of cucumber mosaic virus represent ongoing host-interactive evolution of an RNA virus	15
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	15
Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution	15
The evolutionary history and global spatio-temporal dynamics of potato virus Y	15
Large-scale survey reveals pervasiveness and potential function of endogenous geminiviral sequences in plants	15
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	14
The central role of Italy in the spatial spread of USUTU virus in Europe	14
Multi-host dispersal of known and novel carnivore amdoparvoviruses	14
Increasing temperature alters the within-host competition of viral strains and influences virus genetic variability	14
Broadscale phage therapy is unlikely to select for widespread evolution of bacterial resistance to virus infection	14
Integrating animal movements with phylogeography to model the spread of PRRSV in the USA	14
Comparative genomic analysis of genogroup 1 and genogroup 2 rotaviruses circulating in seven US cities, 2014–2016	14
Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA	14
Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2	14
Adaptation of turnip mosaic potyvirus to a specific niche reduces its genetic and environmental robustness	14
Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito	14
Human land use impacts viral diversity and abundance in a New Zealand river	13
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	13
Cross-scale dynamics and the evolutionary emergence of infectious diseases	13
A comprehensive analysis of genetic diversity of EBV reveals potential high-risk subtypes associated with nasopharyngeal carcinoma in China	13
Gene copy number variations at the within-host population level modulate gene expression in a multipartite virus	13
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions	13
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae)	13
Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR	13
Phenotypic flux: The role of physiology in explaining the conundrum of bacterial persistence amid phage attack	13
Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine	13
Defects in plant immunity modulate the rates and patterns of RNA virus evolution	13
Conserved recombination patterns across coronavirus subgenera	13
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	12
Endogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii	12
Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota	12
PuMA: A papillomavirus genome annotation tool	12
Adaptation of the endemic coronaviruses HCoV-OC43 and HCoV-229E to the human host	12
Genetic diversity of avian leukosis virus subgroup J (ALV-J): toward a unified phylogenetic classification and nomenclature system	12
Decomposing the sources of SARS-CoV-2 fitness variation in the United States	12
Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity	12
Cross-order host switches of hepatitis C-related viruses illustrated by a novel hepacivirus from sloths	12
Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices	12
Defining virus-carrier networks that shape the composition of the mosquito core virome of a local ecosystem	11
Molecular detection and genomic characterization of diverse hepaciviruses in African rodents	11
The spatial-temporal dynamics of respiratory syncytial virus infections across the east–west coasts of Australia during 2016–17	11
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	11
Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates	11
Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status	10
Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E	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
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time	10
Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains	10
Emergence and characterization of a putative novel human adenovirus recombinant HAdV-C104 causing pneumonia in Southern China	10
Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections	10
Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador	10
Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020	9
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications	9
Evolution of dependoparvoviruses across geological timescales—implications for design of AAV-based gene therapy vectors	9
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters	9
Mapping the evolutionary landscape of Zika virus infection in immunocompromised mice	9
Viral origin of eukaryotic type IIA DNA topoisomerases	9
Intrahost speciations and host switches played an important role in the evolution of herpesviruses	9
Molecular epidemiological features of SARS-CoV-2 in Japan, 2020–1	9
Human genomics of the humoral immune response against polyomaviruses	9
A comprehensive evolutionary and epidemiological characterization of insertion and deletion mutations in SARS-CoV-2 genomes	9
Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley	9
Exploration of the Ixodes ricinus virosphere unveils an extensive virus diversity including novel coltiviruses and other reoviruses	9
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	8
Genetic and biological characteristics of species A rotaviruses detected in common shrews suggest a distinct evolutionary trajectory	8
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	8
Intra- and inter-host evolution of H9N2 influenza A virus in Japanese quail	8
Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology	8
Genetic evolution and transmission dynamics of clade 2.3.2.1a highly pathogenic avian influenza A/H5N1 viruses in Bangladesh	8
Host prediction for disease-associated gastrointestinal cressdnaviruses	8
Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation	8
Evolutionary history and introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan through international travelers	8

Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	8
Splitting of RNA-dependent RNA polymerase is common in Narnaviridae: Identification of a type II divided RdRp from deep-sea fungal isolates	8
Phylodynamic study of the conserved RNA structure encompassing the hemagglutinin cleavage site encoding region of H5 and H7 low pathogenic avian influenza viruses	7
Timescales modulate optimal lysis–lysogeny decision switches and near-term phage reproduction	7
Simulating within host human immunodeficiency virus 1 genome evolution in the persistent reservoir	7
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	7
Genomic analysis of human noroviruses using combined Illumina–Nanopore data	7
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation	7
Genetic incompatibilities and reduced transmission in chickens may limit the evolution of reassortants between H9N2 and panzootic H5N8 clade 2.3.4.4 avian influenza virus showing high virulence for ma	7
Ancient viral integrations in marsupials: a potential antiviral defence	7
Bottleneck, Isolate, Amplify, Select (BIAS) as a mechanistic framework for intracellular population dynamics of positive-sense RNA viruses	7
Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes	7
Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon,Cucumis melo, crops, and adjacent wild communities	7
Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids	7
HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification	7
Accommodating sampling location uncertainty in continuous phylogeography	7
Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains	6
Strong selection and high mutation supply characterize experimental Chlorovirus evolution	6
Genome evolution of dengue virus serotype 1 under selection by Wolbachia pipientis in Aedes aegypti mosquitoes	6
Integrated viral elements suggest the dual lifestyle of Tetraselmis spp. Polinton-like viruses	6
Exploring utility of genomic epidemiology to trace origins of highly pathogenic influenza A/H7N9 in Guangdong	6
Mammalian birnaviruses identified in pigs infected by classical swine fever virus	6
Molecular phylogeny of human adenovirus type 41 lineages	6
Differential disease severity and whole-genome sequence analysis for human influenza A/H1N1pdm virus in 2015–2016 influenza season	6
HIV-2 diversity displays two clades within group A with distinct geographical distribution and evolution	6
Genetic diversity and connectivity of the Ostreid herpesvirus 1 populations in France: A first attempt to phylogeographic inference for a marine mollusc disease	6
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	6
Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl	6
Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study	6
Formal recognition and classification of gene transfer agents as viriforms	6
Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons	6
Redondoviridae and periodontitis: a case–control study and identification of five novel redondoviruses from periodontal tissues	6
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness	6
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China	6
Determinants of dengue virus dispersal in the Americas	5
Evolutionary analyses of emerging GII.2[P16] and GII.4 Sydney [P16] noroviruses	5
Unraveling gene content variation across eukaryotic giant viruses based on network analyses and host associations	5
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations	5
Polymorphism of genetic ambigrams	5
Correction to: The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK	5
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	5
Limited cross-species virus transmission in a spatially restricted coral reef fish community	5
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal	5
Emergence and pandemic spread of small ruminant lentiviruses	5
Erratum: Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses	5
The emergence and transmission dynamics of HIV-1 CRF07_BC in Mainland China	5
The virome of the invasive Asian bush mosquito Aedes japonicus in Europe	5
Identification of diverse viruses associated with grasshoppers unveils the parallel relationship between host phylogeny and virome composition	5
Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency	5
Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages	5
Increased virulence of Italian infectious hematopoietic necrosis virus (IHNV) associated with the emergence of new strains	5
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	5
Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection	5
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria	5
Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area	5
CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes	5