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Ranum, J. N. et al. (2024) Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome. Nucleic Acids Research, (Accepted for Publication)

Lamb, K. D., Luka, M. M., Saathoff, M., Orton, R. J. , Phan, M. V.T., Cotten, M. , Yuan, K. and Robertson, D. L. (2024) Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Computational Biology, 20(1), e1011795. (doi: 10.1371/journal.pcbi.1011795) (PMID:38271457) (PMCID:PMC10868779)

Lytras, S. et al. (2023) Resurrection of 2′-5′-oligoadenylate synthetase 1 (OAS1) from the ancestor of modern horseshoe bats blocks SARS-CoV-2 replication. PLoS Biology, 21(11), e3002398. (doi: 10.1371/journal.pbio.3002398) (PMID:38015855)

Gonzalo Nadal, V. et al. (2023) Suspected tick-borne flavivirus meningoencephalomyelitis in dogs from the UK: six cases (2021). Journal of Small Animal Practice, (doi: 10.1111/jsap.13682) (PMID:37956993) (Early Online Publication)

Cao, G. et al. (2023) Single-cell dissection of cervical cancer reveals key subsets of the tumor immune microenvironment. EMBO Journal, 42(16), e110757. (doi: 10.15252/embj.2022110757) (PMID:37427448)

Pascall, D. J. et al. (2023) Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. Journal of Infection, 87(2), pp. 128-135. (doi: 10.1016/j.jinf.2023.05.019) (PMID:37270070) (PMCID:PMC10234362)

Hinsch, M., Silverman, E. and Robertson, D. L. (2023) Simulating the Evolutionary Response of a Viral Pandemic to Behaviour Change. In: ALIFE 2023: Ghost in the machine, Sapporo, Japan, 24-28 Jul 2023, isal_a_00691. (doi: 10.1162/isal_a_00691)

Pinto, R. M. et al. (2023) BTN3A3 evasion promotes the zoonotic potential of influenza A viruses. Nature, 619(7969), pp. 338-347. (doi: 10.1038/s41586-023-06261-8) (PMID:37380775)

Hinsch, M., Silverman, E. and Robertson, D. (2023) Whole-System Pandemic Modelling Including Pathogen Evolution. In: 18th Social Simulation Conference (SSC23), Glasgow, UK, 04-08 Sep 2023, (Accepted for Publication)

Dowell, A. C. et al. (2023) Immunological imprinting of humoral immunity to SARS-CoV-2 in children. Nature Communications, 14, 3845. (doi: 10.1038/s41467-023-39575-2) (PMID:37386081) (PMCID:PMC10310754)

Ho, A. et al. (2023) Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature, 617(7961), pp. 555-563. (doi: 10.1038/s41586-023-05948-2) (PMID:36996873)

Siddell, S. G. et al. (2023) Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV). Journal of General Virology, 104(5), 001840. (doi: 10.1099/jgv.0.001840) (PMID:37141106) (PMCID:PMC10227694)

Pascall, D. J. et al. (2023) The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis. PLoS ONE, 18(4), e0284187. (doi: 10.1371/journal.pone.0284187) (PMID:37053201) (PMCID:PMC10101505)

Griffiths, M. E. , Meza, D. K., Haydon, D. T. and Streicker, D. G. (2023) Inferring the disruption of rabies circulation in vampire bat populations using a betaherpesvirus-vectored transmissible vaccine. Proceedings of the National Academy of Sciences of the United States of America, 120(11), e2216667120. (doi: 10.1073/pnas.2216667120) (PMID:36877838) (PMCID:PMC10089182)

Carabelli, A. M., Peacock, T. P., Thorne, L. G., Harvey, W. T., Hughes, J. , Peacock, S. J., Barclay, W. S., de Silva, T. I., Towers, G. J. and Robertson, D. L. (2023) SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature Reviews Microbiology, 21(3), pp. 162-177. (doi: 10.1038/s41579-022-00841-7) (PMID:36653446) (PMCID:PMC9847462)

Alexander, A. J.T. et al. (2023) Characterisation of the antiviral RNA interference response to Toscana virus in sand fly cells. PLoS Pathogens, 19(3), e1011283. (doi: 10.1371/journal.ppat.1011283) (PMID:36996243) (PMCID:PMC10112792)

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)

Cox, M. et al. (2023) SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nature Reviews Microbiology, 21(2), pp. 112-124. (doi: 10.1038/s41579-022-00809-7) (PMID:36307535) (PMCID:PMC9616429)

Simmonds, P. et al. (2023) Four principles to establish a universal virus taxonomy. PLoS Biology, 21(2), e3001922. (doi: 10.1371/journal.pbio.3001922) (PMID:36780432) (PMCID:PMC9925010)

Atim, S. A. et al. (2023) Prevalence of Crimean-Congo haemorrhagic fever in livestock following a confirmed human case in Lyantonde district, Uganda. Parasites and Vectors, 16, 7. (doi: 10.1186/s13071-022-05588-x) (PMID:36611216) (PMCID:PMC9824997)

Cantoni, D. et al. (2023) Analysis of antibody neutralisation activity against SARS-CoV-2 variants and seasonal human coronaviruses NL63, HKU1, and 229E induced by three different COVID-19 vaccine platforms. Vaccines, 11(1), 58. (doi: 10.3390/vaccines11010058) (PMID:36679903) (PMCID:PMC9864028)

Liew, F. et al. (2023) SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination. EBioMedicine, 87, 104402. (doi: 10.1016/j.ebiom.2022.104402) (PMID:36543718) (PMCID:PMC9762734)

Iannucci, S., Harvey, W. T., Hughes, J. , Robertson, D. L. , Poyade, M. and Hutchinson, E. (2023) The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern. Journal of Visual Communication in Medicine, 46(3), pp. 122-132. (doi: 10.1080/17453054.2023.2237087) (PMID:37526402) (PMCID:PMC10726978)

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, 11, giac103. (doi: 10.1093/gigascience/giac103) (PMID:36399061) (PMCID:PMC9673497)

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)

Sugrue, E. et al. (2022) The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness. PLoS Pathogens, 18(11), e1010973. (doi: 10.1371/journal.ppat.1010973) (PMID:36399512) (PMCID:PMC9718408)

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) (PMCID:PMC9529057)

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) (PMID:36016300) (PMCID:PMC9416734)

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)

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) (PMCID:PMC9037384)

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) (PMID:35600095) (PMCID:PMC9115904)

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) (PMID:36533146) (PMCID:PMC9752770)

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)

Mollentze, N. and Streicker, D. G. (2020) Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts. Proceedings of the National Academy of Sciences of the United States of America, 117(17), pp. 9423-9430. (doi: 10.1073/pnas.1919176117) (PMID:32284401) (PMCID:PMC7196766)

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 Tue Feb 27 14:19:57 2024 GMT.