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 2021-10-01 to 2025-10-01.)

Article	Citations
Evolution of a novel engineered tripartite viral genome of a torradovirus	125
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants	117
A single early introduction governed viral diversity in the second wave of SARS-CoV-2 epidemic in Hungary	88
Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal	83
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China	78
Phycova — a tool for exploring covariates of pathogen spread	69
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	66
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients	62
Genome sizes of animal RNA viruses reflect phylogenetic constraints	56
Correction to: Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea	47
Analyses of HIV proteases variants at the threshold of viability reveals relationships between processing efficiency and fitness	47
Effects of host and pathogenicity on mutation rates in avian influenza A viruses	44
Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya	44
Host replacement dynamics shape virulence and genome evolution in a plant RNA virus	44
A systematic review on Nipah virus: global molecular epidemiology and medical countermeasures development	43
Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations	39
Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia	33
Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21	33
Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant	32
Plant biosecurity threats detected using metatranscriptomic sequencing of animal gut contents	32
Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection	32
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink	32
Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe	32
Discovery of novel Mamastroviruses in Bactrian camels and dromedaries reveals complex recombination history	31
Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic	30

Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein	29
Evolution of exploitation and replication of giant viruses and virophages	29
Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals	28
Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host	28
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters	27
The successive emergence of ERVL-MaLRs in primates	27
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria	27
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut	27
Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia	25
Phylogenetic analysis of pigeon paramyxovirus type 1 (PPMV-1) detected in the British Isles between 1983 – 2023	24
Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics	24
EvoLaps 2: Advanced phylogeographic visualization	24
The coevolutionary mosaic of bat betacoronavirus emergence risk	24
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza	24
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance	24
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny	24
A 1.5-Mb continuous endogenous viral region in the arbuscular mycorrhizal fungus Rhizophagus irregularis	23
Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine	22
Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine	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
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation	21
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany	20
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
Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia	19
Identifying SARS-CoV-2 regional introductions and transmission clusters in real time	18
Hantavirus co-circulation in common shrews (Sorex araneus) in Sweden	17
Genomic surveillance and evolution of Getah virus	17
Divergent hepaciviruses, delta-like viruses and a chu-like virus in Australian marsupial carnivores (dasyurids)	16
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak	16
A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations	16
Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host	16
Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites	16
Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021	16
A biophysical model of viral escape from polyclonal antibodies	15
Accommodating sampling location uncertainty in continuous phylogeography	15
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges	15
Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks	15
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations	15
Known phyla dominate the Tara Oceans RNA virome	15
Prospects for a sequence-based taxonomy of influenza A virus subtypes	14
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa	14
Avian H7N9 influenza viruses are evolutionarily constrained by stochastic processes during replication and transmission in mammals	14
Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans	14
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes	14
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies	13
Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda	13
Mathematical comparison of protocols for adapting a bacteriophage to a new host	13
Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections	13
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii	13

Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing	13
Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin	13
From vaccine to pathogen: Modeling Sabin 2 vaccine virus reversion and evolutionary epidemiology in Matlab, Bangladesh	13
Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil	13
Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer	13
Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes	13
Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage	13
Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study	13
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years	13
The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia	12
Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region	12
Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe	12
Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2	12
Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China	12
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples	12
Emergence and pandemic spread of small ruminant lentiviruses	12
The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights	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
Experimental evidence of vaccine-driven evolution of respiratory syndrome virus type 2	12
Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure	12
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications	12
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies	11
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster	11
Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status	11
Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York	11
Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009–22)	11
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak	11
Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis	11
Evolution of transient RNA structure–RNA polymerase interactions in respiratory RNA virus genomes	11
Twenty years of evolution and diversification of digitaria streak virus in Digitaria setigera	10
Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization	10
A critique of the use of species and below-species taxonomic terms for viruses—time for change?	10
Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains	10
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	10
The emergence of NY10: insights into the 2012 West Nile Virus outbreak in the United States	10
Heat adaptation of phage T7 under an extended genetic code	10
Sequencing SARS-CoV-2 genomes from saliva	10
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics	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
Evolution and diversity of inherited viruses in the Nearctic phantom midge, Chaoborus americanus	10
A new genus of alphasatellites associated with banana bunchy top virus in Southeast Asia	10