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Sugrue, E. et al. (2022) The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness. PLoS Pathogens, (doi: 10.1371/journal.ppat.1010973) (Early Online Publication)

Walker, P. J. et al. (2022) Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Archives of Virology, 167(11), pp. 2429-2440. (doi: 10.1007/s00705-022-05516-5) (PMID:35999326)

Cox, M. et al. (2022) SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nature Reviews Microbiology, (doi: 10.1038/s41579-022-00809-7) (PMID:36307535) (PMCID:PMC9616429) (Early Online Publication)

Tegally, H. et al. (2022) The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance. Science, 378(6615), eabq5358. (doi: 10.1126/science.abq5358) (PMID:36108049)

Chai, H., Gu, Q. , Robertson, D. L. and Hughes, J. (2022) Defining the characteristics of interferon-alpha-stimulated human genes: insight from expression data and machine-learning. GigaScience, (Accepted for Publication)

Willett, B. J. et al. (2022) SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7(8), pp. 1161-1179. (doi: 10.1038/s41564-022-01143-7) (PMID:35798890) (PMCID:PMC9352574)

Shah, R. et al. (2022) Characterisation of a hepatitis C virus subtype 2a cluster in Scottish PWID with a suboptimal response to glecaprevir/pibrentasvir treatment. Viruses, 14(8), 1678. (doi: 10.3390/v14081678)

Nickbakhsh, S. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)

Ho, A. et al. (2022) Adeno-associated virus 2 infection in children with non-A-E hepatitis. medRxiv, (doi: 10.1101/2022.07.19.22277425) (Submitted)

Xu, R., Rong, X., Aranday-Cortes, E., Vattipally, S. , Hughes, J. , McLauchlan, J. and Fu, Y. (2022) The transmission route and selection pressure in HCV subtype 3a and 3b Chinese infections: evolutionary kinetics and selective force analysis. Viruses, 14(7), 1514. (doi: 10.3390/v14071514) (PMID:35891494) (PMCID:PMC9324606)

Agoti, C. N. et al. (2022) Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: a retrospective genomic study. eLife, 11, e71703. (doi: 10.7554/elife.71703) (PMID:35699426) (PMCID:PMC9282859)

Dowell, A. C. et al. (2022) mRNA or ChAd0x1 COVID-19 vaccination of adolescents induces robust antibody and cellular responses with continued recognition of omicron following mRNA-1273. Frontiers in Immunology, 13, 882515. (doi: 10.3389/fimmu.2022.882515) (PMID:35720281) (PMCID:PMC9201026)

Modha, S. , Robertson, D. L. , Hughes, J. and Orton, R. J. (2022) Quantifying and cataloguing unknown sequences within human microbiomes. mSystems, 7(2), e01468-21. (doi: 10.1128/msystems.01468-21) (PMID:35258340) (PMCID:PMC9052204)

Worobey, M. et al. (2022) The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science, 377(6609), pp. 951-959. (doi: 10.1126/science.abp8715) (PMID:35881010) (PMCID:PMC9348750)

Zerbini, F. M. et al. (2022) Differentiating between viruses and virus species by writing their names correctly. Archives of Virology, 167(4), pp. 1231-1234. (doi: 10.1007/s00705-021-05323-4) (PMID:35043230) (PMCID:PMC9020231)

Griffiths, M. E., Broos, A. , Bergner, L. M. , Meza, D. K., Suarez, N. M., Da Silva Filipe, A. , Tello, C., Becker, D. J. and Streicker, D. G. (2022) Longitudinal deep sequencing informs vector selection and future deployment strategies for transmissible vaccines. PLoS Biology, 20(4), e3001580. (doi: 10.1371/journal.pbio.3001580) (PMID:35439242) (PMCID:PMC9017877)

Martin, D. P. et al. (2022) Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function. Molecular Biology and Evolution, 39(4), msac061. (doi: 10.1093/molbev/msac061) (PMID:35325204)

Maher, M. C. et al. (2022) Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Science Translational Medicine, 14(633), eabk3445. (doi: 10.1126/scitranslmed.abk3445) (PMID:35014856) (PMCID:PMC8939770)

Lytras, S., Hughes, J. , Martin, D., Swanepoel, P., de Klerk, A., Lourens, R., Kosakovsky Pond, S. L., Xia, W., Jiang, X. and Robertson, D. L. (2022) Exploring the natural origins of SARS-CoV-2 in the light of recombination. Genome Biology and Evolution, 14(2), evac018. (doi: 10.1093/gbe/evac018) (PMID:35137080) (PMCID:PMC8882382)

Chai, H., Gu, Q. , Hughes, J. and Robertson, D. L. (2022) In silico prediction of HIV-1-host molecular interactions and their directionality. PLoS Computational Biology, 18(2), e1009720. (doi: 10.1371/journal.pcbi.1009720) (PMID:35134057) (PMCID:PMC8856524)

Dowell, A. C. et al. (2022) Children develop robust and sustained cross-reactive spike-specific immune responses to SARS-CoV-2 infection. Nature Immunology, 23(1), pp. 40-49. (doi: 10.1038/s41590-021-01089-8) (PMID:34937928) (PMCID:PMC8709786)

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)

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)

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)

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)

Jackson, B. et al. (2021) Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell, 184(20), 5179-5188.e8. (doi: 10.1016/j.cell.2021.08.014) (PMID:34499854) (PMCID:PMC8367733)

Holmes, E. C. et al. (2021) The origins of SARS-CoV-2: a critical review. Cell, 184(19), pp. 4848-4856. (doi: 10.1016/j.cell.2021.08.017) (PMID:34480864) (PMCID:PMC8373617)

Baksmeier, C. et al. (2021) Modified recombinant human IgG1-Fc is superior to natural intravenous immunoglobulin at inhibiting immune-mediated demyelination. Immunology, 164(1), pp. 90-105. (doi: 10.1111/imm.13341) (PMID:33880776) (PMCID:PMC8358725)

Walker, P. J. et al. (2021) Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Archives of Virology, 166(9), pp. 2633-2648. (doi: 10.1007/s00705-021-05156-1) (PMID:34231026)

Lytras, S., Xia, W., Hughes, J. , Jiang, X. and Robertson, D. L. (2021) The animal origin of SARS-CoV-2. Science, 373(6558), pp. 968-970. (doi: 10.1126/science.abh0117) (PMID:34404734)

Hufsky, F. et al. (2021) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics, 22(2), pp. 642-663. (doi: 10.1093/bib/bbaa232) (PMID:33147627) (PMCID:PMC7665365)

Pénzes, J. J., Söderlund-Venermo, M., Canuti, M., Eis-Hübinger, A. M., Hughes, J. , Cotmore, S. F. and Harrach, B. (2020) Reorganizing the family Parvoviridae: a revised taxonomy independent of the canonical approach based on host association. Archives of Virology, 165(9), pp. 2133-2146. (doi: 10.1007/s00705-020-04632-4) (PMID:32533329)

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)

Alamil, M., Hughes, J. , Berthier, K., Desbiez, C., Thébaud, G. and Soubeyrand, S. (2019) Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1775), 20180258. (doi: 10.1098/rstb.2018.0258) (PMID:31056055) (PMCID:PMC6553606)

This list was generated on Sat Dec 3 23:29:27 2022 GMT.