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 2021-12-01 to 2025-12-01.)

Article	Citations
Evolution of a novel engineered tripartite viral genome of a torradovirus	132
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary	120
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal	92
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China	90
Phycova — a tool for exploring covariates of pathogen spread	80
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	79
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	72
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	63
Host replacement dynamics shape virulence and genome evolution in a plant RNA virus	61
Effects of host and pathogenicity on mutation rates in avian influenza A viruses	51
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	49
Plant biosecurity threats detected using metatranscriptomic sequencing of animal gut contents	48
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness	46
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic	46
Phylogeographic evaluation of the effectiveness of Canadian travel restrictions in reducing SARS-CoV-2 variant importations and burden	46
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history	44
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development	36
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients	35
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	35
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	34
Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya	34
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	33
Genome sizes of animal RNA viruses reflect phylogenetic constraints	33
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	33
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	30

Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe	30
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	30
Evolution of exploitation and replication of giant viruses and virophages	30
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host	28
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut	27
The successive emergence of ERVL-MaLRs in primates	27
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny	26
Phylogenetic analysis of pigeon paramyxovirus type 1 detected in the British Isles between 1983 and 2023	25
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance	24
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia	24
Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics	24
The coevolutionary mosaic of bat betacoronavirus emergence risk	24
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation	24
EvoLaps 2: Advanced phylogeographic visualization	24
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters	22
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza	22
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	22
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA p	22
Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual	21
Virome release of an invasive exotic plant species in southern France	21
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals	21
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	20
Hantavirus co-circulation in common shrews (Sorex araneus) in Sweden	19
Evolutionary characterization of the establishment of H6 influenza viruses in domestic geese in China: implications for the position of the host in the ecosystem	19
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	19
Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021	18
Genomic surveillance and evolution of Getah virus	18
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites	18
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak	17
Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host	17
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations	17
Divergent hepaciviruses, delta-like viruses and a chu-like virus in Australian marsupial carnivores (dasyurids)	16
Accommodating sampling location uncertainty in continuous phylogeography	16
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia	16
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	16
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time	16
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes	15
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations	15
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges	15
Prospects for a sequence-based taxonomy of influenza A virus subtypes	15
Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans	15
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals	15
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks	15
Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil	15
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	15
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa	15
Known phyla dominate the Tara Oceans RNA virome	14
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii	14
Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure	14
Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing	14

Emergence and pandemic spread of small ruminant lentiviruses	14
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies	14
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda	14
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	14
Mathematical comparison of protocols for adapting a bacteriophage to a new host	14
A biophysical model of viral escape from polyclonal antibodies	14
Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study	14
Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes	14
Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage	14
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia	13
Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections	13
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples	13
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	13
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	13
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	13
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications	13
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China	13
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh	13
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies	12
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York	12
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes	12
Comparative analysis of multiple consensus genomes of the same strain of Marek’s disease virus reveals intrastrain variation	12
Correction to: Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load	12
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	12
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	12
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	12
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	11
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia	11
Variation within major internal repeats of KSHV in vivo	11
Constraint in West Nile virus envelope protein across mosquito, human, and avian host cell environments	11
Experimental evidence of vaccine-driven evolution of porcine reproductive and respiratory syndrome virus type 2	11
Focal persistence and phylodynamics of Heartland virus in Georgia	11
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights	11
The emergence of NY10: insights into the 2012 West Nile Virus outbreak in the United States	11
Heptad stereotypy, S/Q layering, and remote origin of the SARS-CoV-2 fusion core	11