Virus Evolution

Papers
(The TQCC of Virus Evolution is 10. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-05-01 to 2025-05-01.)
ArticleCitations
The spatial-temporal dynamics of respiratory syncytial virus infections across the east–west coasts of Australia during 2016–17903
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal112
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China100
Evolution of a novel engineered tripartite viral genome of a torradovirus78
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary78
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants70
Phycova — a tool for exploring covariates of pathogen spread67
High pathogenic avian influenza A(H5) viruses of clade 2.3.4.4b in Europe—Why trends of virus evolution are more difficult to predict56
Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito54
Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates52
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea49
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history42
Genome sizes of animal RNA viruses reflect phylogenetic constraints39
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia38
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-2137
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein36
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink36
Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe36
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection35
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic34
Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids31
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness30
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations29
Effects of host and pathogenicity on mutation rates in avian influenza A viruses29
The coevolutionary mosaic of bat betacoronavirus emergence risk28
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development28
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant28
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut27
Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine27
Evolution of exploitation and replication of giant viruses and virophages27
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals27
EvoLaps 2: Advanced phylogeographic visualization26
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza25
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria25
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters25
Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations24
The successive emergence of ERVL-MaLRs in primates24
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation24
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host24
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance24
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine24
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny23
Virome release of an invasive exotic plant species in southern France23
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany22
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia22
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual22
Evolutionary characterization of the establishment of H6 influenza viruses in domestic geese in China: implications for the position of the host in the ecosystem21
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis21
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia21
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time20
Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host20
Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids)19
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak19
Revealing RNA virus diversity and evolution in unicellular algae transcriptomes19
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites19
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations18
Genomic surveillance and evolution of Getah virus18
Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 202118
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer17
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii17
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years16
Accommodating sampling location uncertainty in continuous phylogeography16
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges16
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations16
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals16
Known phyla dominate the Tara Oceans RNA virome16
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes15
Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites15
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa15
Prospects for a sequence-based taxonomy of influenza A virus subtypes15
A biophysical model of viral escape from polyclonal antibodies14
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks14
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe13
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh13
Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure13
Mathematical comparison of protocols for adapting a bacteriophage to a new host13
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin13
Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing13
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda13
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE212
Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study12
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China12
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia12
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies12
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications12
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples12
Emergence and pandemic spread of small ruminant lentiviruses12
Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes12
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies12
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes11
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)11
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes11
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 defence11
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster11
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: Phylogeography and evolutionary insights11
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York11
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia11
A critique of the use of species and below-species taxonomic terms for viruses—time for change?11
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation11
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis11
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region11
Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status11
Recombinant SARS-CoV-2 genomes circulated at low levels over the first year of the pandemic11
Heptad stereotypy, S/Q layering, and remote origin of the SARS-CoV-2 fusion core10
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 Europe10
The impact of global lineage dynamics, border restrictions, and emergence of the B.1.1.7 lineage on the SARS-CoV-2 epidemic in Norway10
Evolution and diversity of inherited viruses in the Nearctic phantom midge, Chaoborus americanus10
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak10
Human genomics of the humoral immune response against polyomaviruses10
Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains10
Variation within major internal repeats of KSHV in vivo10
Heat adaptation of phage T7 under an extended genetic code10
Global spatiotemporal transmission patterns of human enterovirus 71 from 1963 to 201910
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