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 2022-05-01 to 2026-05-01.)

Article	Citations
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary	131
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	103
Evolution of a novel engineered tripartite viral genome of a torradovirus	103
Unveiling the RNA virus landscape of Cotesia chilonis : geographic distribution, diversity, and potential roles in parasitoid–host interactions	100
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	94
Experimental evolution of the host range dynamics in two isolates of potato virus Y	90
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	70
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	64
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	58
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	58
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic	50
Genome sizes of animal RNA viruses reflect phylogenetic constraints	45
Phylogeographic evaluation of the effectiveness of Canadian travel restrictions in reducing SARS-CoV-2 variant importations and burden	45
Host replacement dynamics shape virulence and genome evolution in a plant RNA virus	44
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	37
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	37
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history	34
Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya	32
Plant biosecurity threats detected using metatranscriptomic sequencing of animal gut contents	32
Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe	29
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients	29
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development	28
The successive emergence of ERVL-MaLRs in primates	28
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	28
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia	28

Phylogenetic analysis of pigeon paramyxovirus type 1 detected in the British Isles between 1983 and 2023	27
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny	26
EvoLaps 2: Advanced phylogeographic visualization	26
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	25
The coevolutionary mosaic of bat betacoronavirus emergence risk	25
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	24
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	23
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals	23
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA p	22
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host	22
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut	22
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	21
Virome release of an invasive exotic plant species in southern France	20
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance	20
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza	20
Hantavirus co-circulation in common shrews (Sorex araneus) in Sweden	19
Evolution of exploitation and replication of giant viruses and virophages	19
Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics	19
Sequence based virus host prediction: a curated dataset and generalizable framework for training artificial intelligence to identify viruses of humans	19
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites	18
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations	18
Genomic surveillance and evolution of Getah virus	17
Evolutionary characterization of the establishment of H6 influenza viruses in domestic geese in China: implications for the position of the host in the ecosystem	17
Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant	17
Intra-host GI.1 norovirus evolution is shaped by genetic drift and purifying selection	17
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia	17
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak	17
Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021	17
Viral diversity influences T-cell responses to enteric human adenoviruses F40 and F41	17
Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil	16
Divergent hepaciviruses, delta-like viruses and a chu-like virus in Australian marsupial carnivores (dasyurids)	16
Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans	16
Prospects for a sequence-based taxonomy of influenza A virus subtypes	15
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals	15
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations	15
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	15
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges	15
A biophysical model of viral escape from polyclonal antibodies	15
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii	14
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks	14
Getting to the root of HIV transmitted founder virus sequences	14
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa	14
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies	14
Known phyla dominate the Tara Oceans RNA virome	14
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda	14
Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes	13
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	13
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	13
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh	13
Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure	13

Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections	12
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	12
Mathematical comparison of protocols for adapting a bacteriophage to a new host	12
Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage	12
The whole genome analysis of four Orf virus strains from Europe and South America	12
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	11
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	11
Experimental evidence of vaccine-driven evolution of porcine reproductive and respiratory syndrome virus type 2	11
Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing	11
Correction to: Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load	11
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation	11
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples	11
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York	11
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights	11
Emergence and pandemic spread of small ruminant lentiviruses	11
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	11
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia	11
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies	11
Constraint in West Nile virus envelope protein across mosquito, human, and avian host cell environments	11
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	11
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	10
Identification and genomic characterization of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa	10
Focal persistence and phylodynamics of Heartland virus in Georgia	10
Variation within major internal repeats of KSHV in vivo	10
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 defence	10
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia	10
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes	10
The emergence of NY10: insights into the 2012 West Nile Virus outbreak in the United States	10
Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization	10