OOIR: Observatory of International Research

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 2021-04-01 to 2025-04-01.)

Article	Citations
Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic	892
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China	106
Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda	96
Computational multigene interactions in virus growth and infection spread	78
Viral community composition of hypersaline lakes	74
SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method	69
A novel and diverse family of filamentous DNA viruses associated with parasitic wasps	66
Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts	55
Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito	51
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia	51
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	46
Defining virus-carrier networks that shape the composition of the mosquito core virome of a local ecosystem	41
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal	38
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China	37
Modeling the therapeutic potential of defective interfering particles in the presence of immunity	36
A new perspective on the evolution and diversity of the genus Amdoparvovirus (family Parvoviridae) through genetic characterization, structural homology modeling, and phylogenetics	36
The spatial-temporal dynamics of respiratory syncytial virus infections across the east–west coasts of Australia during 2016–17	35
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples	34
Polymorphisms predicting phylogeny in hepatitis B virus	34
Rabbit haemorrhagic disease virus 2 from Singapore 2020 outbreak revealed an Australian recombinant variant	32
SARS-CoV-2 intra-host single-nucleotide variants associated with disease severity	29
Fast-forwarding evolution—Accelerated adaptation in a proofreading-deficient hypermutator herpesvirus	29
Everglades virus evolution: Genome sequence analysis of the envelope 1 protein reveals recent mutation and divergence in South Florida wetlands	29
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	28
Genome analyses of species A rotavirus isolated from various mammalian hosts in Northern Ireland during 2013−2016	27

Mammalian birnaviruses identified in pigs infected by classical swine fever virus	27
Phycova — a tool for exploring covariates of pathogen spread	27
Ancient viral integrations in marsupials: a potential antiviral defence	27
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation	26
Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships	26
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary	26
Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes	26
Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat	25
High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA	24
Molecular epidemiology of HIV-1 in Oryol Oblast, Russia	23
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha	23
VIPERA: Viral Intra-Patient Evolution Reporting and Analysis	23
Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype	22
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies	22
Enhanced detection and molecular modeling of adaptive mutations in SARS-CoV-2 coding and non-coding regions using the c/µ test	22
Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage	21
Swine influenza A virus infection dynamics and evolution in intensive pig production systems	21
The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses	21
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	21
Evolution of a novel engineered tripartite viral genome of a torradovirus	20
Independent repeated mutations within the alphaviruses Ross River virus and Barmah Forest virus indicates convergent evolution and past positive selection in ancestral populations despite ongoing puri	20
HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies	19
Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts	19
Splitting of RNA-dependent RNA polymerase is common in Narnaviridae: Identification of a type II divided RdRp from deep-sea fungal isolates	19
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York	18
Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates	18
Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020	18
Recurrent SARS-CoV-2 mutations in immunodeficient patients	17
Increase of niche filling with increase of host richness for plant-infecting mastreviruses	17
Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages	17
Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates	17
Recurring incursions and dissemination of novel Eurasian-origin H5Nx avian influenza viruses in Atlantic Canada	16
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	16
Recombinant SARS-CoV-2 genomes circulated at low levels over the first year of the pandemic	16
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	16
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	16
A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data	16
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	15
Geographic origin and evolution of dengue virus serotypes 1 and 3 circulating in Africa	15
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	15
SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period	14
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes	14
An orphan viral genome with unclear evolutionary status sheds light on a distinct lineage of flavi-like viruses infecting plants	14
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: Phylogeography and evolutionary insights	14
Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: Implications for bird–mammal transmission in South America	13
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	13
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	13
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	12
Correction to: Contemporary and historical human migration patterns shape hepatitis B virus diversity	12
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	12

Correction to: Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation	12
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	12
Evaluation of recombination detection methods for viral sequencing	12
Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein	12
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load	11
RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection	11
Timescales modulate optimal lysis–lysogeny decision switches and near-term phage reproduction	11
Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador	11
A critique of the use of species and below-species taxonomic terms for viruses—time for change?	11
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	11
Twenty years of evolution and diversification of digitaria streak virus in Digitaria setigera	11
Genetic diversity and connectivity of the Ostreid herpesvirus 1 populations in France: A first attempt to phylogeographic inference for a marine mollusc disease	11
Heat adaptation of phage T7 under an extended genetic code	11
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil	11
Integrating animal movements with phylogeography to model the spread of PRRSV in the USA	11
Sequencing SARS-CoV-2 genomes from saliva	11
Importation and circulation of rubella virus lineages 1E-L2 and 2B-L2c between 2018 and 2021 in China: Virus evolution and spatial–temporal transmission characteristics	11
Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae)	10
Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area	10
Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon,Cucumis melo, crops, and adjacent wild communities	10
Variation within major internal repeats of KSHV in vivo	10
Diving deep into fish bornaviruses: Uncovering hidden diversity and transcriptional strategies through comprehensive data mining	10
An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain	10
Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids	10
Global spatiotemporal transmission patterns of human enterovirus 71 from 1963 to 2019	10
Effects of host and pathogenicity on mutation rates in avian influenza A viruses	10
Exploration of the Ixodes ricinus virosphere unveils an extensive virus diversity including novel coltiviruses and other reoviruses	10
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness	10