OOIR: Observatory of International Research

Papers

(The TQCC of Virus Evolution is 13. 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 2020-05-01 to 2024-05-01.)

Article	Citations
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool	739
Temporal signal and the phylodynamic threshold of SARS-CoV-2	301
Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation	122
Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages	101
Cenote-Taker 2 democratizes virus discovery and sequence annotation	90
An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain	88
The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization	82
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK	69
Intra-host evolution during SARS-CoV-2 prolonged infection	65
Interannual dynamics, diversity and evolution of the virome in Sclerotinia sclerotiorum from a single crop field	57
Virome composition in marine fish revealed by meta-transcriptomics	53
The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus	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	40
Recombinant SARS-CoV-2 genomes circulated at low levels over the first year of the pandemic	39
Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic	39
The evolutionary dynamics of endemic human coronaviruses	38
Diversity and circulation of Jingmen tick virus in ticks and mammals	37
Evolution of DNA packaging in gene transfer agents	36
Viromics of extant insect orders unveil the evolution of the flavi-like superfamily	36
A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways	36
The history of foot-and-mouth disease virus serotype C: the first known extinct serotype?	35
Intra-genome variability in the dinucleotide composition of SARS-CoV-2	33
Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations	33

Towards a unified classification for human respiratory syncytial virus genotypes	33
Contributions of adaptation and purifying selection to SARS-CoV-2 evolution	32
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
Revealing RNA virus diversity and evolution in unicellular algae transcriptomes	29
Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray–Darling Basin, Australia	28
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types	28
When to be temperate: on the fitness benefits of lysis vs. lysogeny	28
The discovery, distribution, and diversity of DNA viruses associated withDrosophila melanogasterin Europe	28
Red fox viromes in urban and rural landscapes	27
Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa	27
RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data	27
Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses	27
Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution	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
Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae	25
Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses	25
Divergent RNA viruses in Macrophomina phaseolina exhibit potential as virocontrol agents	25
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
Alternate primers for whole-genome SARS-CoV-2 sequencing	23
Polerovirus genomic variation	23
Genetic diversity, phylogeography, and evolutionary dynamics of highly pathogenic avian influenza A (H5N6) viruses	23
Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes	23
Fitness effects of mutations to SARS-CoV-2 proteins	23
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes	22
Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates	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
SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity	22
The characterization of multiple novel paramyxoviruses highlights the diverse nature of the subfamilyOrthoparamyxovirinae	22
Tick virome diversity in Hubei Province, China, and the influence of host ecology	21
The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia	21
Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence	21
Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase	21
Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis	21
Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000–18	21
Emerging phylogenetic structure of the SARS-CoV-2 pandemic	20
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	20
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	20
Genomic evolution, transmission dynamics, and pathogenicity of avian influenza A (H5N8) viruses emerging in China, 2020	20
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	19
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	19
Inference of Nipah virus evolution, 1999–2015	19
Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure?	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
A biophysical model of viral escape from polyclonal antibodies	18
Estimating hepatitis B virus cccDNA persistence in chronic infection†	18
Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites	17
Genomic epidemiology of a densely sampled COVID-19 outbreak in China	17

HTLV in South America: Origins of a silent ancient human infection	17
Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene	17
Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians	17
Coronaviruses in wild animals sampled in and around Wuhan at the beginning of COVID-19 emergence	16
Newly emerged resistance-breaking variants of cucumber mosaic virus represent ongoing host-interactive evolution of an RNA virus	16
Two distant helicases in one mycovirus: evidence of horizontal gene transfer between mycoviruses, coronaviruses and other nidoviruses	16
Unification and extensive diversification of M/Orf3-related ion channel proteins in coronaviruses and other nidoviruses	16
Conserved recombination patterns across coronavirus subgenera	15
The evolutionary history and global spatio-temporal dynamics of potato virus Y	15
Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution	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 survey reveals pervasiveness and potential function of endogenous geminiviral sequences in plants	15
Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA	14
Increasing temperature alters the within-host competition of viral strains and influences virus genetic variability	14
Adaptation of turnip mosaic potyvirus to a specific niche reduces its genetic and environmental robustness	14
Multi-host dispersal of known and novel carnivore amdoparvoviruses	14
Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity	14
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae)	14
Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2	14
The central role of Italy in the spatial spread of USUTU virus in Europe	14
Integrating animal movements with phylogeography to model the spread of PRRSV in the USA	14
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	14
Defects in plant immunity modulate the rates and patterns of RNA virus evolution	14
Comparative genomic analysis of genogroup 1 and genogroup 2 rotaviruses circulating in seven US cities, 2014–2016	14
Broadscale phage therapy is unlikely to select for widespread evolution of bacterial resistance to virus infection	14
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	14
Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito	14
A comprehensive analysis of genetic diversity of EBV reveals potential high-risk subtypes associated with nasopharyngeal carcinoma in China	13
Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices	13
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions	13
Cross-scale dynamics and the evolutionary emergence of infectious diseases	13
Endogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii	13
Phenotypic flux: The role of physiology in explaining the conundrum of bacterial persistence amid phage attack	13
Gene copy number variations at the within-host population level modulate gene expression in a multipartite virus	13
Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR	13
Human land use impacts viral diversity and abundance in a New Zealand river	13
Decomposing the sources of SARS-CoV-2 fitness variation in the United States	13
Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine	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	13