Litvin, U., Wang, E. C.Y., Stanton, R. J., Fielding, C. A. and Hughes, J. (2024) Evolution of the cytomegalovirus RL11 gene family in Old World monkeys and great apes. Virus Evolution, (doi: 10.1093/ve/veae066) (Early Online Publication)

Illingworth, C. J.R. , Guerra-Assuncao, J. A., Gregg, S., Charles, O., Pang, J., Roy, S., Abdelnabi, R., Neyts, J. and Breuer, J. (2024) Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus Evolution, (doi: 10.1093/ve/veae001) (Early Online Publication)

Carrozza, M.-L., Niewiadomska, A.-M., Mazzei, M., Abi-Said, M. R., Hue, S., Hughes, J. , Gatseva, A. and Gifford, R. J. (2023) Emergence and pandemic spread of small ruminant lentiviruses. Virus Evolution, 9(1), vead005. (doi: 10.1093/ve/vead005) (PMID:36793939) (PMCID:PMC9924038)

Makori, T. O. et al. (2023) Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012–8. Virus Evolution, 9(1), vead025. (doi: 10.1093/ve/vead025) (PMID:37207000) (PMCID:PMC10190042)

Gao, Y. et al. (2023) Virus-induced interference as a means for accelerating fitness-based selection of cyprinid herpesvirus 3 single nucleotide variants in vitro and in vivo. Virus Evolution, 9(1), vead003. (doi: 10.1093/ve/vead003) (PMID:36816049) (PMCID:PMC9936792)

Bamford, C. G.G., de Souza, W. M., Parry, R. and Gifford, R. J. (2022) Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae). Virus Evolution, 8(2), veac085. (doi: 10.1093/ve/veac085) (PMID:36533146) (PMCID:PMC9752770)

de Klerk, A. et al. (2022) Conserved recombination patterns across coronavirus subgenera. Virus Evolution, 8(2), veac054. (doi: 10.1093/ve/veac054) (PMID:35814334) (PMCID:PMC9261289)

Xu, R. et al. (2022) The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China. Virus Evolution, 8(1), veac012. (doi: 10.1093/ve/veac012) (PMID:35600095) (PMCID:PMC9115904)

Camiolo, S. et al. (2022) Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples. Virus Evolution, 8(2), veac114. (doi: 10.1093/ve/veac114) (PMID:37091479) (PMCID:PMC10120596)

Gömer, A. et al. (2022) Intra-host analysis of hepaciviral glycoprotein evolution reveals signatures associated with viral persistence and clearance. Virus Evolution, 8(1), veac007. (doi: 10.1093/ve/veac007) (PMID:35242360) (PMCID:PMC8887644)

Li, Y.-T. et al. (2022) Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines. Virus Evolution, 8(2), veac078. (doi: 10.1093/ve/veac078) (PMID:36090771) (PMCID:PMC9452094)

Hill, V. et al. (2022) The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evolution, 8(2), veac080. (doi: 10.1093/ve/veac080) (PMID:36533153) (PMCID:PMC9752794)

Wright, D. W. et al. (2022) Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus Evolution, 8(1), veac023. (doi: 10.1093/ve/veac023) (PMID:35502202) (PMCID:PMC9037374)

Benfield, C. T.O., Hill, S., Shatar, M., Shiilegdamba, E., Damdinjav, B., Fine, A., Willett, B. , Kock, R. and Bataille, A. (2021) Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates. Virus Evolution, 7(2), veab062. (doi: 10.1093/ve/veab062) (PMID:34754511) (PMCID:PMC8570150)

Cotten, M. , Robertson, D. L. and Phan, M. V.T. (2021) Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses. Virus Evolution, 7(2), veab067. (doi: 10.1093/ve/veab067) (PMID:34527286) (PMCID:PMC8385934)

Cotten, M. , Bugembe, D. L., Kaleebu, P. and Phan, M. V.T. (2021) Alternate primers for whole-genome SARS-CoV-2 sequencing. Virus Evolution, 7(1), veab006. (doi: 10.1093/ve/veab006) (PMID:33841912) (PMCID:PMC7928614)

Lytras, S., Arriagada, G. and Gifford, R. J. (2021) Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes. Virus Evolution, 7(1), veab012. (doi: 10.1093/ve/veab012) (PMID:33747544) (PMCID:PMC7955980)

Camiolo, S. , Suárez, N. M., Chalka, A., Venturini, C., Breuer, J. and Davison, A. J. (2021) GRACy: a tool for analysing human cytomegalovirus sequence data. Virus Evolution, 7(1), veaa099. (doi: 10.1093/ve/veaa099) (PMID:33505707) (PMCID:PMC7816668)

Al Qaffas, A., Nichols, J. , Davison, A. J. , Ourahmane, A., Hertel, L., McVoy, M. A. and Camiolo, S. (2021) LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data. Virus Evolution, 7(1), veab042. (doi: 10.1093/ve/veab042) (PMID:33996146) (PMCID:PMC8111061)

Hildebrandt, E., Penzes, J. J., Gifford, R. J. , Agbandje-Mckenna, M. and Kotin, R. M. (2020) Evolution of dependoparvoviruses across geological timescales – implications for design of AAV-based gene therapy vectors. Virus Evolution, 6(2), veaa043. (doi: 10.1093/ve/veaa043) (PMID:32913662) (PMCID:PMC7474932)

Masembe, C. , Phan, M. V.T., Robertson, D. L. and Cotten, M. (2020) Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains. Virus Evolution, 6(2), veaa044. (doi: 10.1093/ve/veaa044) (PMID:32913663) (PMCID:PMC7474929)

MacLean, O. A. , Orton, R. J. , Singer, J. B. and Robertson, D. L. (2020) No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolution, 6(1), veaa034. (doi: 10.1093/ve/veaa034) (PMID:32817804) (PMCID:PMC7197565)

Grant, H. E. et al. (2020) Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evolution, 6(1), veaa004. (doi: 10.1093/ve/veaa004) (PMID:32395255) (PMCID:PMC7204518)

Maabar, M., Davison, A. J. , Vučak, M., Thorburn, F., Murcia, P. , Gunson, R., Palmarini, M. and Hughes, J. (2019) DisCVR: rapid viral diagnosis from high-throughput sequencing data. Virus Evolution, 5(2), vez033. (doi: 10.1093/ve/vez033) (PMID:31528358) (PMCID:PMC6735924)

Jacquot, M. et al. (2019) Contrasting selective patterns across the segmented genome of bluetongue virus in a global reassortment hotspot. Virus Evolution, 5(2), vez027. (doi: 10.1093/ve/vez027) (PMID:31392031) (PMCID:PMC6680063)

Zhao, L. and Illingworth, C. J. R. (2019) Measurements of intrahost viral diversity require an unbiased diversity metric. Virus Evolution, 5(1), vey041. (doi: 10.1093/ve/vey041) (PMID:30723551) (PMCID:PMC6354029)

Zhao, L., Abbasi, A. B. and Illingworth, C. J. R. (2019) Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection. Virus Evolution, 5(1), vez008. (doi: 10.1093/ve/vez008) (PMID:31024738) (PMCID:PMC6476161)

Pénzes, J. J., Marsile-Medun, S., Agbandje-McKenna, M. and Gifford, R. J. (2018) Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. Virus Evolution, 4(2), vey026. (doi: 10.1093/ve/vey026) (PMID:30443409) (PMCID:PMC6232428)

Phan, M. V.T., Tri, T. N., Anh, P. H., Baker, S., VIZIONS Consortium, , Kellam, P. and Cotten, M. (2018) Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains. Virus Evolution, 4(2), vey035. (doi: 10.1093/ve/vey035) (PMID:30568804) (PMCID:PMC6295324)

Otieno, J.R. et al. (2018) Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains. Virus Evolution, 4(2), vey027. (doi: 10.1093/ve/vey027) (PMID:30271623) (PMCID:PMC6153471)

Olabode, A. S., Kandathil, S. M., Lovell, S. C. and Robertson, D. L. (2017) Adaptive HIV-1 evolutionary trajectories are constrained by protein stability. Virus Evolution, 3(2), vex019. (doi: 10.1093/ve/vex019) (PMID:28852572) (PMCID:PMC5570062)

Oude Munnink, B. B., Phan, M. V.T., The VIZIONS Consortium, , Simmonds, P., Koopmans, M. P.G., Kellam, P., van der Hoek, L. and Cotten, M. (2017) Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam. Virus Evolution, 3(2), vex002. (doi: 10.1093/ve/vex022) (PMID:28948041) (PMCID:PMC5597861)

Marston, D. A. et al. (2017) Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host. Virus Evolution, 3(2), vex038. (doi: 10.1093/ve/vex038) (PMID:29255631) (PMCID:PMC5729694)

Illingworth, C. J.R. , Roy, S., Beale, M. A., Tutill, H., Williams, R. and Breuer, J. (2017) On the effective depth of viral sequence data. Virus Evolution, 3(2), vex030. (doi: 10.1093/ve/vex030) (PMID:29250429) (PMCID:PMC5724399)

Agoti, C. N. et al. (2017) Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis. Virus Evolution, 3(1), vex006. (doi: 10.1093/ve/vex006) (PMID:28458916) (PMCID:PMC5399923)

Phan, M. V. T. et al. (2016) Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection. Virus Evolution, 2(2), vew027. (doi: 10.1093/ve/vew027) (PMID:28748110) (PMCID:PMC5522372)

Lassalle, F. et al. (2016) Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes. Virus Evolution, 2(1), vew017. (doi: 10.1093/ve/vew017)

Oude Munnink, B. B. et al. (2016) A novel astrovirus-like RNA virus detected in human stool. Virus Evolution, 2(1), vew005. (doi: 10.1093/ve/vew005) (PMID:27774298) (PMCID:PMC4989881)

Arias, A. et al. (2016) Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evolution, 2(1), vew016. (doi: 10.1093/ve/vew016) (PMID:28694998) (PMCID:PMC5499387)

Brunker, K. et al. (2015) Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing. Virus Evolution, 1(1), pp. 1-11. (doi: 10.1093/ve/vev011)