Research Papers

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Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates.
Druelle V; Neher RA.
Virus Evol (Unknown)
Published: 2022
2/6 Transparent
Funding Declared
Long-term host-pathogen evolution of endogenous beta- and gammaretroviruses in mouse lemurs with little evidence of rec…
Kessler SE; Tsangaras K; Rasoloharijaona S; Radespiel U; Greenwood AD.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression.
Ferreira RC; Wong E; Poon AFY.
Virus Evol (Unknown)
Published: 2022
3/6 Transparent
Data Code
Polymorphisms predicting phylogeny in hepatitis B virus.
Lourenço J; McNaughton AL; Pley C; Obolski U; Gupta S; Matthews PC.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
Everglades virus evolution: Genome sequence analysis of the envelope 1 protein reveals recent mutation and divergence i…
Valente MC; Prakoso D; Vittor AY; Blosser EM; Abid N; Pu R; Beachboard SE; Long MT; Burkett-Cadena ND; Mavian CN.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
Genome Evolution and Early Introductions of the SARS-CoV-2 Omicron Variant in Mexico.
Castelán-Sánchez HG; Martínez-Castilla LP; Sganzerla-Martínez G; Torres-Flores J; López-Leal G.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Code
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK.
Hill V; Du Plessis L; Peacock TP; Aggarwal D; Colquhoun R; Carabelli AM; Ellaby N; Gallagher E; Groves N; Jackson B; McCrone JT; O'Toole Á; Price A; Sanderson T; Scher E; Southgate J; Volz E; Barclay WS; Barrett JC; Chand M; Connor T; Goodfellow I; Gupta RK; Harrison EM; Loman N; Myers R; Robertson DL; Pybus OG; Rambaut A.
Virus Evol (Unknown)
Published: 2022
3/6 Transparent
Funding Declared
High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years.
Götting J; Baier C; Panagiota V; Maecker-Kolhoff B; Dhingra A; Heim A.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS.
Boswell MT; Nazziwa J; Kuroki K; Palm A; Karlson S; Månsson F; Biague A; da Silva ZJ; Onyango CO; de Silva TI; Jaye A; Norrgren H; Medstrand P; Jansson M; Maenaka K; Rowland-Jones SL; Esbjörnsson J.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
Importation and circulation of rubella virus lineages 1E-L2 and 2B-L2c between 2018 and 2021 in China: Virus evolution …
Liu Y; Han Z; Kang C; Cui A; Zhang Y; Liu L; Chen Y; Deng L; Zhao H; Zhou J; Li F; Zhou S; Feng D; Tian X; Feng Y; Cui X; Lei Y; Wang Y; Yuan F; Fan L; Tang X; Chen M; Peng X; Guo Y; Gao H; Wang S; Li L; Zhang T; Deng X; Chen H; Wang S; Ma Y; Zhu Z; Xu W.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family <i>Flavi…
Bamford CGG; de Souza WM; Parry R; Gifford RJ.
Virus Evol (Unknown)
Published: 2022
5/6 Transparent
Data Code Funding Declared
covSampler: A subsampling method with balanced genetic diversity for large-scale SARS-CoV-2 genome data sets.
Cheng Y; Ji C; Han N; Li J; Xu L; Chen Z; Yang R; Zhou HY; Wu A.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Code Funding Declared
New <i>Microviridae</i> isolated from <i>Sulfitobacter</i> reveals two cosmopolitan subfamilies of single-stranded DNA …
Zucker F; Bischoff V; Olo Ndela E; Heyerhoff B; Poehlein A; Freese HM; Roux S; Simon M; Enault F; Moraru C.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
SARS-CoV-2 intra-host single-nucleotide variants associated with disease severity.
Zhang Y; Jiang N; Qi W; Li T; Zhang Y; Wu J; Zhang H; Zhou M; Cui P; Yu T; Fu Z; Zhou Y; Lin K; Wang H; Wei T; Zhu Z; Ai J; Qiu C; Zhang W.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
Haplotype assignment of longitudinal viral deep sequencing data using covariation of variant frequencies.
Venturini C; Pang J; Tamuri AU; Roy S; Atkinson C; Griffiths P; Breuer J; Goldstein RA.
Virus Evol (Unknown)
Published: 2022
5/6 Transparent
Data Code Funding Declared
Fast-forwarding evolution-Accelerated adaptation in a proofreading-deficient hypermutator herpesvirus.
Xing N; Höfler T; Hearn CJ; Nascimento M; Camps Paradell G; McMahon DP; Kunec D; Osterrieder N; Cheng HH; Trimpert J.
Virus Evol (Unknown)
Published: 2022
5/6 Transparent
Data Code Funding Declared
Modeling cellular co-infection and reassortment of bluetongue virus in <i>Culicoides</i> midges.
Cavany SM; Barbera C; Carpenter M; Rodgers C; Sherman T; Stenglein M; Mayo C; Perkins TA.
Virus Evol (Unknown)
Published: 2022
5/6 Transparent
Data Code Funding Declared
Molecular phylogeny of human adenovirus type 41 lineages.
Götting J; Cordes AK; Steinbrück L; Heim A.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions.
Nahata KD; Bielejec F; Monetta J; Dellicour S; Rambaut A; Suchard MA; Baele G; Lemey P.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Code Funding Declared
Accumulation of copy-back viral genomes during respiratory syncytial virus infection is preceded by diversification of …
Felt SA; Achouri E; Faber SR; López CB.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
Host prediction for disease-associated gastrointestinal cressdnaviruses.
Kinsella CM; Deijs M; Becker C; Broekhuizen P; van Gool T; Bart A; Schaefer AS; van der Hoek L.
Virus Evol (Unknown)
Published: 2022
3/6 Transparent
Funding Declared
Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron.
van Dorp C; Goldberg E; Ke R; Hengartner N; Romero-Severson E.
Virus Evol (Unknown)
Published: 2022
3/6 Transparent
Funding Declared
Monotreme-specific conserved putative proteins derived from retroviral reverse transcriptase.
Kitao K; Miyazawa T; Nakagawa S.
Virus Evol (Unknown)
Published: 2022
3/6 Transparent
Funding Declared
Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation.
Külekci B; Schwarz S; Brait N; Perkmann-Nagele N; Jaksch P; Hoetzenecker K; Puchhammer-Stöckl E; Goerzer I.
Virus Evol (Unknown)
Published: 2022
4/6 Transparent
Data Funding Declared
Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination sta…
Fonseca PLC; Moreira FRR; de Souza RM; Guimarães NR; Carvalho NO; Adelino TER; Alves HJ; Alvim LB; Candido DS; Coelho HP; Costa AVB; Costa WC; de Carvalho AF; de Faria BWF; de Lima AB; de Oliveira ES; de Souza CSA; de Souza FG; Dias RC; Geddes VEV; Godinho IP; Gonçalves AL; Lourenço KL; Magalhães RDM; Malta FSV; Medeiros ELA; Mendes FS; Mendes PHBP; Mendonça CPTB; Menezes AL; Menezes D; Menezes MT; Miguita L; Moreira RG; Peixoto RB; Queiroz DC; Ribeiro AA; Ribeiro APB; Saliba JW; Sato HI; Silva JDP; Silva NP; Faria NR; Teixeira SMR; da Fonseca FG; Fernandes APSM; Zauli DAG; Januario JN; de Oliveira JS; Iani FCM; de Aguiar RS; de Souza RP.
Virus Evol (Unknown)
Published: 2022
5/6 Transparent
Data Code Funding Declared