OOIR: Observatory of International Research

Papers

(The TQCC of Virus Evolution is 11. 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 2020-11-01 to 2024-11-01.)

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
RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data	45
Recombinant SARS-CoV-2 genomes circulated at low levels over the first year of the pandemic	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
Fitness effects of mutations to SARS-CoV-2 proteins	41
Contributions of adaptation and purifying selection to SARS-CoV-2 evolution	41
The evolutionary dynamics of endemic human coronaviruses	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
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
Revealing RNA virus diversity and evolution in unicellular algae transcriptomes	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
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
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	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
Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000–18	26
Divergent RNA viruses in Macrophomina phaseolina exhibit potential as virocontrol agents	26
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
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
Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses	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
A biophysical model of viral escape from polyclonal antibodies	22
Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host	22
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
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	21
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
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	20
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
Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites	19
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
Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene	18
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
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
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
Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2	16
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
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
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
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
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
Cross-scale dynamics and the evolutionary emergence of infectious diseases	13
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
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
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
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