Dr Joseph Hughes

  • Bioinformatician (Virology)

email: Joseph.Hughes@glasgow.ac.uk

Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1qh

Import to contacts

ORCID iDhttps://orcid.org/0000-0003-2556-2563

Research interests

CVR logo

Viral genomics & bioinformatics programme

I am an evolutionary biologist with a particular interest in the evolution of host-parasite interactions. With evolution as a guiding theoretical principle, I am attempting to discover how evolutionary forces have shaped the solutions that parasites and viruses have found to adapt to their hosts and how these adaptations have resulted in the huge diversity of pathogens.

My current research focuses on various aspects of evolution in human and animal viruses using the wealth of sequence data generated by high-throughput sequencers. My research focuses on the following areas:

  • Intra-host virus diversity and evolution
  • Transmission network and disease outbreak analysis
  • Virus phylogenetics, recombination and reassortment
  • Immunoinformatics of T-cell receptors
  • Visualisation of large and complex datasets


Collaborators

I am collaborating with researchers within the Centre for Virus Research (Pablo Murcia, Emma Thomson), researchers within the Institute of Biodiversity, Animal Health and Comparative Medicine (Roman Biek, Richard Reeve, Richard Orton) and researchers at Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy (Isabella Monne, Alice Fusaro)


Selected Publications


Past research

For details on my research and publications before working at the CVR:

http://darwin.zoology.gla.ac.uk/%7Ejhughes/index.html

Publications

List by: Type | Date

Jump to: 2025 | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2007
Number of items: 107.

2025

Lytras, Spyros, Lamb, Kieran D., Ito, Jumpei, Grove, Joe ORCID logoORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID logoORCID: https://orcid.org/0000-0002-2318-1460, Sato, Kei, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99(2), e0160124. (doi: 10.1128/jvi.01601-24) (PMID:39878472) (PMCID:39878472)

Terhzaz, Selim ORCID logoORCID: https://orcid.org/0000-0002-6192-6558, Kerrigan, David, Almire, Floriane, Szemiel, Agnieszka M., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Parvy, Jean-Philippe, Palmarini, Massimo ORCID logoORCID: https://orcid.org/0000-0001-7007-4070, Kohl, Alain ORCID logoORCID: https://orcid.org/0000-0002-1523-9458, Shi, Xiaohong ORCID logoORCID: https://orcid.org/0000-0002-5289-7222 and Pondeville, Emilie (2025) NSm is a critical determinant for bunyavirus transmission between vertebrate and mosquito hosts. Nature Communications, 16, 1214. (doi: 10.1038/s41467-024-54809-7) (PMID:39890788) (PMCID:PMC11785797)

Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Orton, Richard J. ORCID logoORCID: https://orcid.org/0000-0002-3389-4325 and Lytras, Spyros (2025) Expanding the genomic diversity of human anelloviruses. Virus Evolution, 11(1), veaf002. (doi: 10.1093/ve/veaf002) (PMID:39839678) (PMCID:PMC11749082)

2024

Ruscica, V. et al. (2024) XRN1 supplies free nucleotides to feed alphavirus replication. bioRxiv, (doi: 10.1101/2024.12.09.625895)

McLachlan, I. et al. (2024) Evaluation of risk-based travel policy for the COVID-19 epidemic in Scotland: a population-based surveillance study. BMJ Open, 14(11), e085332. (doi: 10.1136/bmjopen-2024-085332) (PMID:39615890)

Li, Yao-Tsun, Ko, Hui-Ying, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Liu, Ming-Tsuan, Lin, Yi-Ling, Hampson, Katie ORCID logoORCID: https://orcid.org/0000-0001-5392-6884 and Brunker, Kirstyn ORCID logoORCID: https://orcid.org/0000-0001-9990-6299 (2024) From emergence to endemicity: highly pathogenic H5 avian influenza viruses in Taiwan. Nature Communications, 15(1), 9348. (doi: 10.1038/s41467-024-53816-y) (PMID:39472594) (PMCID:PMC11522503)

Lamb, Kieran D., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Lytras, Spyros, Young, Francesca, Koci, Orges, Herzig, James, Lovell, Simon C,, Grove, Joe ORCID logoORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID logoORCID: https://orcid.org/0000-0002-2318-1460 and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv, (doi: 10.1101/2024.07.05.602129)

Litvin, Ulad, Wang, Eddie C.Y., Stanton, Richard J., Fielding, Ceri A. and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (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)

Blanco-Melo, Daniel, Campbell, Matthew A., Zhu, Henan, Dennis, Tristan P., Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Lytras, Spyros, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID logoORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID logoORCID: https://orcid.org/0000-0003-4028-9884 (2024) A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biology, 25(1), 120. (doi: 10.1186/s13059-024-03258-y) (PMID:38741126) (PMCID:PMC11089739)

Gonzalo Nadal, V. et al. (2024) Suspected tick-borne flavivirus meningoencephalomyelitis in dogs from the UK: six cases (2021). Journal of Small Animal Practice, 65(2), pp. 132-143. (doi: 10.1111/jsap.13682) (PMID:37956993) (PMCID:PMC11497270)

2023

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)

Blanco-Melo, Daniel, Campbell, Matthew A., Zhu, Henan, Dennis, Tristan P.W., Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Lytras, Spyros, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID logoORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID logoORCID: https://orcid.org/0000-0003-4028-9884 (2023) A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus ‘fossil record’. bioRxiv, (doi: 10.1101/2023.10.17.562709)

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)

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)

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)

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)

Carabelli, Alessandro M., Peacock, Thomas P., Thorne, Lucy G., Harvey, William T., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Peacock, Sharon J., Barclay, Wendy S., de Silva, Thushan I., Towers, Greg J. and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (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)

Whitlock, A. O. B. et al. (2023) Identifying the genetic basis of viral spillover using Lassa virus as a test case. Royal Society Open Science, 10(3), 221503. (doi: 10.1098/rsos.221503) (PMID:36968239) (PMCID:PMC10031424)

Carrozza, Maria-Luisa, Niewiadomska, Anna-Maria, Mazzei, Maurizio, Abi-Said, Mounir R., Hue, Stephane, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID logoORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert James ORCID logoORCID: https://orcid.org/0000-0003-4028-9884 (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)

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)

Iannucci, Sarah, Harvey, William T., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221, Poyade, Matthieu and Hutchinson, Edward ORCID logoORCID: https://orcid.org/0000-0003-3673-9096 (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)

2022

Chai, Haiting, Gu, Quan ORCID logoORCID: https://orcid.org/0000-0002-1201-6734, Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (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)

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)

Willett, B. J. et al. (2022) Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7, 1709. (doi: 10.1038/s41564-022-01241-6) (PMID:36114232) (PMCID:PMC9483304)

Stirrup, O. et al. (2022) Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study. eLife, 11, e78427. (doi: 10.7554/elife.78427) (PMID:36098502) (PMCID:PMC9596156)

Iannucci, Sarah, Harvey, William, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221, Hutchinson, Edward ORCID logoORCID: https://orcid.org/0000-0003-3673-9096 and Poyade, Matthieu (2022) Using molecular visualisation techniques to explain the molecular biology of SARS-CoV-2 spike protein mutations to a general audience. In: Shapiro, Leonard and Rea, Paul M. (eds.) Biomedical Visualisation. Volume 12. Series: Advances in experimental medicine and biology (1388). Springer: Cham, pp. 129-152. ISBN 9783031108884 (doi: 10.1007/978-3-031-10889-1_6)

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)

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, Ru, Rong, Xia, Aranday-Cortes, Elihu, Vattipally, Sreenu ORCID logoORCID: https://orcid.org/0000-0001-6673-4697, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948 and Fu, Yongshui (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)

Vucak, M. et al. (2022) Genome sequences of five arenaviruses from pygmy mice (Mus minutoides) in Sierra Leone. Microbiology Resource Announcements, 11(5), e0009522. (doi: 10.1128/mra.00095-22) (PMID:35389260) (PMCID:PMC9119099)

Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Orton, Richard J. ORCID logoORCID: https://orcid.org/0000-0002-3389-4325 (2022) Quantifying and cataloguing unknown sequences within human microbiomes. mSystems, 7(2), e01468-21. (doi: 10.1128/msystems.01468-21) (PMID:35258340) (PMCID:PMC9052204)

Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z) (PMID:35197443) (PMCID:PMC8866425)

Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)

Chai, Haiting, Gu, Quan ORCID logoORCID: https://orcid.org/0000-0002-1201-6734, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (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)

Lytras, Spyros, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Martin, Darren, Swanepoel, Phillip, de Klerk, Arné, Lourens, Rentia, Kosakovsky Pond, Sergei L., Xia, Wei, Jiang, Xiaowei and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (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)

Twohig, K. A. et al. (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infectious Diseases, 22(1), pp. 35-42. (doi: 10.1016/S1473-3099(21)00475-8) (PMID:34461056) (PMCID:PMC8397301)

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)

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)

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)

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)

2021

Vöhringer, H. S. et al. (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), pp. 506-511. (doi: 10.1038/s41586-021-04069-y) (PMID:34649268) (PMCID:PMC8674138)

Boshier, F. A.T. et al. (2021) The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. Journal of Infection, 83(6), pp. 693-700. (doi: 10.1016/j.jinf.2021.09.022) (PMID:34610391) (PMCID:PMC8487101)

Wickenhagen, A. et al. (2021) A prenylated dsRNA sensor protects against severe COVID-19. Science, 374(6567), eabj3624. (doi: 10.1126/science.abj3624) (PMID:34581622) (PMCID:PMC7612834)

Lytras, Spyros, Xia, Wei, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Jiang, Xiaowei and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (2021) The animal origin of SARS-CoV-2. Science, 373(6558), pp. 968-970. (doi: 10.1126/science.abh0117) (PMID:34404734)

Li, K. K. et al. (2021) Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface. Journal of Infection, 83(1), pp. 96-103. (doi: 10.1016/j.jinf.2021.04.020) (PMID:33895226) (PMCID:PMC8061788)

Stirrup, O. et al. (2021) Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. eLife, 10, e65828. (doi: 10.7554/elife.65828) (PMID:34184637) (PMCID:PMC8285103)

Graham, M. S. et al. (2021) Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. Lancet Public Health, 6(5), e335-e345. (doi: 10.1016/S2468-2667(21)00055-4)

Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)

Thomson, E. C. et al. (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 184(5), 1171-1187.e20. (doi: 10.1016/j.cell.2021.01.037) (PMID:33621484) (PMCID:PMC7843029)

Rihn, S. J. et al. (2021) A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biology, 19(2), e3001091. (doi: 10.1371/journal.pbio.3001091) (PMID:33630831) (PMCID:PMC7906417)

Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)

Stirrup, O. et al. (2021) SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study. BMJ Open Respiratory Research, 8, e001029. (doi: 10.1136/bmjresp-2021-001029) (PMID:34544733) (PMCID:PMC8453594)

2020

Collados Rodríguez, Milagros ORCID logoORCID: https://orcid.org/0000-0002-2304-6402, Dybas, Joseph M., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Weitzman, Matthew D. and Boutell, Chris ORCID logoORCID: https://orcid.org/0000-0002-2970-7785 (2020) The HSV-1 ubiquitin ligase ICP0: modifying the cellular proteome to promote infection. Virus Research, 285, 198015. (doi: 10.1016/j.virusres.2020.198015) (PMID:32416261)

Pénzes, Judit J, Söderlund-Venermo, Maria, Canuti, Marta, Eis-Hübinger, Anna Maria, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Cotmore, Susan F and Harrach, Balázs (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)

Lytras, Spyros and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2020) Synonymous dinucleotide usage: a codon-aware metric for quantifying dinucleotide representation in viruses. Viruses, 12(4), 462. (doi: 10.3390/v12040462)

2019

Rihn, S. J. et al. (2019) TRIM69 inhibits vesicular stomatitis Indiana virus (VSIV). Journal of Virology, 93(20), e00951-19. (doi: 10.1128/JVI.00951-19) (PMID:31375575)

Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Bianco, Giovanni, Ferguson, Heather M. ORCID logoORCID: https://orcid.org/0000-0002-9625-5176, Helm, Barbara, Tong, Lily, Wilkie, Gavin S., Kohl, Alain ORCID logoORCID: https://orcid.org/0000-0002-1523-9458 and Schnettler, Esther (2019) Metaviromics reveals unknown viral diversity in the biting midge Culicoides impunctatus. Viruses, 11(9), 865. (doi: 10.3390/v11090865) (PMID:31533247) (PMCID:PMC6784199)

Suárez, N. M. et al. (2019) Human cytomegalovirus genomes sequenced directly from clinical material: variation, multiple-strain infection, recombination and gene loss. Journal of Infectious Diseases, 220(5), pp. 781-791. (doi: 10.1093/infdis/jiz208) (PMID:31050742) (PMCID:PMC6667795)

Maabar, Maha, Davison, Andrew J. ORCID logoORCID: https://orcid.org/0000-0002-4991-9128, Vučak, Matej, Thorburn, Fiona, Murcia, Pablo ORCID logoORCID: https://orcid.org/0000-0002-4352-394X, Gunson, Rory, Palmarini, Massimo ORCID logoORCID: https://orcid.org/0000-0001-7007-4070 and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2019) DisCVR: rapid viral diagnosis from high-throughput sequencing data. Virus Evolution, 5(2), vez033. (doi: 10.1093/ve/vez033) (PMID:31528358) (PMCID:PMC6735924)

Alamil, M., Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, 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)

Alamil, M., Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, 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. (PMID:31056055)

Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi: 10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)

Davis, C. et al. (2019) New highly diverse hepatitis C strains detected in sub‐Saharan Africa have unknown susceptibility to direct‐acting antiviral treatments. Hepatology, 69(4), pp. 1426-1441. (doi: 10.1002/hep.30342) (PMID:30387174) (PMCID:PMC6492010)

Cotmore, S. F. et al. (2019) ICTV virus taxonomy profile: Parvoviridae. Journal of General Virology, 100(3), pp. 367-368. (doi: 10.1099/jgv.0.001212) (PMID:30672729) (PMCID:PMC6537627)

Rezelj, Veronica V., Mottram, Timothy J., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Elliott, Richard M., Kohl, Alain ORCID logoORCID: https://orcid.org/0000-0002-1523-9458 and Brennan, Benjamin ORCID logoORCID: https://orcid.org/0000-0003-4707-726X (2019) M segment-based minigenomes and virus-like particle assays as an approach to assess the potential of tick-borne Phlebovirus genome reassortment. Journal of Virology, 93(6), e02068-18. (doi: 10.1128/JVI.02068-18) (PMID:30567991) (PMCID:PMC6401446)

Zhu, H. et al. (2019) Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds. PLoS Pathogens, 15(2), e1007531. (doi: 10.1371/journal.ppat.1007531) (PMID:30731004) (PMCID:PMC6366691)

2018

Singer, Joshua B., Thomson, Emma C. ORCID logoORCID: https://orcid.org/0000-0003-1482-0889, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Gifford, Robert J. ORCID logoORCID: https://orcid.org/0000-0003-4028-9884 (2018) GLUE: a flexible software system for virus sequence data. BMC Bioinformatics, 19, 532. (doi: 10.1186/s12859-018-2459-9) (PMID:30563445) (PMCID:PMC6299651)

Mercuri, Luca, Thomson, Emma C. ORCID logoORCID: https://orcid.org/0000-0003-1482-0889, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Karayiannis, Peter (2018) Quasispecies changes with distinctive point mutations in the Hepatitis C virus internal ribosome entry site (IRES) derived from PBMCs and plasma. Advances in Virology, 2018, 4835252. (doi: 10.1155/2018/4835252) (PMID:30581467) (PMCID:PMC6276526)

Dunlop, J. I. et al. (2018) Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas. PLoS Neglected Tropical Diseases, 12(10), e0006884. (doi: 10.1371/journal.pntd.0006884) (PMID:30372452) (PMCID:PMC6245839)

Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Thanki, Anil, Cotmore, Susan F., Davison, Andrew J. ORCID logoORCID: https://orcid.org/0000-0002-4991-9128 and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2018) ViCTree: an automated framework for taxonomic classification from protein sequences. Bioinformatics, 34(13), pp. 2195-2200. (doi: 10.1093/bioinformatics/bty099) (PMID:29474519) (PMCID:PMC6022645)

Saucedo, B. et al. (2018) Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (Pelophylax spp.). Emerging Microbes and Infections, 7(1), 56. (doi: 10.1038/s41426-018-0058-5) (PMID:29615625) (PMCID:PMC5882854)

da Silva Filipe, A. et al. (2018) Reply to: "Reply to: 'Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries'". Journal of Hepatology, 68(4), pp. 864-866. (doi: 10.1016/j.jhep.2017.11.044) (PMID:29339112)

2017

Shaw, A. E. et al. (2017) Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS Biology, 15(12), e2004086. (doi: 10.1371/journal.pbio.2004086) (PMID:29253856) (PMCID:PMC574750)

da Silva Filipe, A. et al. (2017) Response to DAA therapy in the NHS England early access programme for rare HCV subtypes from low and middle income countries. Journal of Hepatology, 67(6), pp. 1348-1350. (doi: 10.1016/j.jhep.2017.06.035) (PMID:28789880)

Saucedo, Bernardo, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, van Beurden, Steven J., Suárez, Nicolás M., Haenen, Olga L.M., Voorbergen-Laarman, Michal, Gröne, Andrea and Kik, Marja J.L. (2017) Complete genome sequence of Frog virus 3, isolated from a strawberry poison frog (Oophaga pumilio) imported from Nicaragua into the Netherlands. Genome Announcements, 5(35), e00863-17. (doi: 10.1128/genomeA.00863-17) (PMID:28860243) (PMCID:PMC5578841)

Milani, A. et al. (2017) Vaccine immune pressure influences viral population complexity of avian influenza virus during infection. Veterinary Microbiology, 203, pp. 88-94. (doi: 10.1016/j.vetmic.2017.02.016)

Rihn, Suzannah J. ORCID logoORCID: https://orcid.org/0000-0001-9495-4056, Foster, Toshana L., Busnadiego, Idoia, Aziz, Muhamad Afiq Bin, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Neil, Stuart J.D. and Wilson, Sam J. ORCID logoORCID: https://orcid.org/0000-0002-6065-0895 (2017) The envelope gene of transmitted HIV-1 resists a late interferon gamma-induced block. Journal of Virology, 91(7), e02254-16. (doi: 10.1128/JVI.02254-16) (PMID:28100611) (PMCID:PMC5355616)

2016

Donald, C. L. et al. (2016) Full genome sequence and sfRNA interferon antagonist activity of Zika virus from Recife, Brazil. PLoS Neglected Tropical Diseases, 10(10), e0005048. (doi: 10.1371/journal.pntd.0005048) (PMID:27706161) (PMCID:PMC5051680)

Franzo, Giovanni, Cortey, Martì, Segalés, Joaquim, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Drigo, Michele (2016) Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets. Data In Brief, 8, pp. 549-552. (doi: 10.1016/j.dib.2016.06.005) (PMID:27508215) (PMCID:PMC4962815)

Jacobs, M. et al. (2016) Late Ebola virus relapse causing meningoencephalitis: a case report. Lancet, 388(10043), pp. 498-503. (doi: 10.1016/S0140-6736(16)30386-5) (PMID:27209148) (PMCID:PMC4967715)

Franzo, Giovanni, Cortey, Marti, Segalés, Joaquim, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Drigo, Michele (2016) Phylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant forms. Molecular Phylogenetics and Evolution, 100, pp. 269-280. (doi: 10.1016/j.ympev.2016.04.028) (PMID:27114187)

Fusaro, A. et al. (2016) Unexpected interfarm transmission dynamics during a highly pathogenic avian influenza epidemic. Journal of Virology, 90(14), pp. 6401-6411. (doi: 10.1128/jvi.00538-16) (PMID:27147741) (PMCID:PMC4936132)

Robinson, Mark W., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Wilkie, Gavin S., Swann, Rachael ORCID logoORCID: https://orcid.org/0000-0002-3945-2253, Barclay, Stephen T., Mills, Peter R., Patel, Arvind H. ORCID logoORCID: https://orcid.org/0000-0003-4600-2047, Thomson, Emma C. ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 and McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948 (2016) Tracking TCRß sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region. Frontiers in Immunology, 7, 131. (doi: 10.3389/fimmu.2016.00131) (PMID:27092143) (PMCID:PMC4820669)

Orton, R.J. ORCID logoORCID: https://orcid.org/0000-0002-3389-4325, Gu, Q. ORCID logoORCID: https://orcid.org/0000-0002-1201-6734, Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Maabar, M., Modha, S. ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Vattipally, Sreenu ORCID logoORCID: https://orcid.org/0000-0001-6673-4697, Wilkie, G.S. and Davison, A. ORCID logoORCID: https://orcid.org/0000-0002-4991-9128 (2016) Bioinformatics tools for analysing viral genomic data. Revue scientifique et technique (International Office of Epizootics), 35(1), pp. 241-285. (doi: 10.20506/rst.35.1.2432) (PMID:27217183)

Rijks, J. M. et al. (2016) Investigation of amphibian mortality events in wildlife reveals an on-going ranavirus epidemic in the North of the Netherlands. PLoS ONE, 11(6), e0157473. (doi: 10.1371/journal.pone.0157473) (PMID:27315226) (PMCID:PMC4912076)

2015

Stewart, M. et al. (2015) Characterization of a second open reading frame in genome segment 10 of bluetongue virus. Journal of General Virology, 96(11), pp. 3280-3293. (doi: 10.1099/jgv.0.000267) (PMID:26290332) (PMCID:PMC4806581)

Fusaro, Alice, Tassoni, Luca, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Milani, Adelaide, Salviato, Annalisa, Schivo, Alessia, Murcia, Pablo R. ORCID logoORCID: https://orcid.org/0000-0002-4352-394X, Bonfanti, Lebana, Cattoli, Giovanni and Monne, Isabella (2015) Evolutionary trajectories of two distinct avian influenza epidemics: parallelisms and divergences. Infection, Genetics and Evolution, 34, pp. 457-466. (doi: 10.1016/j.meegid.2015.05.020) (PMID:26003682)

Nomikou, Kyriaki, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Wash, Rachael, Kellam, Paul, Breard, Emmanuel, Zientara, Stéphan, Palmarini, Massimo ORCID logoORCID: https://orcid.org/0000-0001-7007-4070, Biek, Roman ORCID logoORCID: https://orcid.org/0000-0003-3471-5357 and Mertens, Peter (2015) Widespread reassortment shapes the evolution and epidemiology of bluetongue virus following European invasion. PLoS Pathogens, 11(8), e1005056. (doi: 10.1371/journal.ppat.1005056) (PMID:26252219) (PMCID:PMC4529188)

Tilston-Lunel, Natasha L., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Olszanski Acrani, Gustavo, da Silva, Daisy E.A., Azevedo, Raimunda S.S., Rodrigues, Sueli G., Vasconcelos, Pedro F.C., Nunes, Marcio R.T. and Elliott, Richard M. (2015) Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence. Journal of General Virology, 96(7), pp. 1636-1650. (doi: 10.1099/vir.0.000108) (PMID:25735305) (PMCID:PMC4635451)

Zhu, Henan, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Murcia, Pablo R. ORCID logoORCID: https://orcid.org/0000-0002-4352-394X (2015) Origins and evolutionary dynamics of H3N2 canine influenza virus. Journal of Virology, 89(10), pp. 5406-5418. (doi: 10.1128/JVI.03395-14) (PMID:25740996) (PMCID:PMC4442499)

Abdelrahman, Tamer, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Main, Janice, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948, Thursz, Mark and Thomson, Emma ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 (2015) Reply. Hepatology, 61(4), p. 1438. (doi: 10.1002/hep.27393) (PMID:25147121) (PMCID:PMC4407921)

Ardelrahman, Tamer, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Main, Janice, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948, Thursz, Mark and Thomson, Emma ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 (2015) Waiting time and transplantation for hepatocellular cancer: a balance between tempus fugit and carpe diem. Hepatology, 61(4), pp. 1438-1439. (doi: 10.1002/hep.27434)

Beczkowski, Pawel M., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Biek, Roman ORCID logoORCID: https://orcid.org/0000-0003-3471-5357, Litster, Annette, Willett, Brian J. ORCID logoORCID: https://orcid.org/0000-0001-8912-3266 and Hosie, Margaret J. ORCID logoORCID: https://orcid.org/0000-0002-4313-5023 (2015) Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus (FIV). Journal of General Virology, 96(4), pp. 893-903. (doi: 10.1099/vir.0.000035) (PMID:25535323) (PMCID:PMC4361796)

Abdelrahman, Tamer, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Main, Janice, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948, Thursz, Mark and Thomson, Emma ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 (2015) Next generation sequencing sheds light on the natural history of hepatitis C infection in patients that fail treatment. Hepatology, 61(1), pp. 88-97. (doi: 10.1002/hep.27192) (PMID:24797101) (PMCID:PMC4303934)

Rihn, Suzannah J. ORCID logoORCID: https://orcid.org/0000-0001-9495-4056, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Wilson, Sam J. ORCID logoORCID: https://orcid.org/0000-0002-6065-0895 and Bieniasz, Paul D. (2015) Uneven genetic robustness of HIV-1 integrase. Journal of Virology, 89(1), pp. 552-567. (doi: 10.1128/JVI.02451-14)

2014

Bęczkowski, Paweł M, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Biek, Roman ORCID logoORCID: https://orcid.org/0000-0003-3471-5357, Litster, Annette, Willett, Brian J ORCID logoORCID: https://orcid.org/0000-0001-8912-3266 and Hosie, Margaret J ORCID logoORCID: https://orcid.org/0000-0002-4313-5023 (2014) Feline immunodeficiency virus (FIV) env recombinants are common in natural infections. Retrovirology, 11(80), (doi: 10.1186/s12977-014-0080-1) (PMID:25699660) (PMCID:PMC4180853)

Busnadiego, I. et al. (2014) Host and viral determinants of Mx2 antiretroviral activity. Journal of Virology, 88(14), pp. 7738-7752. (doi: 10.1128/JVI.00214-14) (PMID:24760893) (PMCID:PMC4097781)

Jombart, T. et al. (2014) OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, 7, pp. 28-34. (doi: 10.1016/j.epidem.2014.04.003)

Monne, I. et al. (2014) Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor. Journal of Virology, 88(8), pp. 4375-4388. (doi: 10.1128/JVI.03181-13)

2013

Varela, M. et al. (2013) Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in Rhesus Macaques. PLoS ONE, 8(8), e70814. (doi: 10.1371/journal.pone.0070814) (PMID:23967111) (PMCID:PMC3743870)

2012

Hughes, J. et al. (2012) Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS Pathogens, 8(12), e1003081. (doi: 10.1371/journal.ppat.1003081)

Murcia, P. R. et al. (2012) Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathogens, 8(5), e1002730. (doi: 10.1371/journal.ppat.1002730)

2011

Bass, C., Hebsgaard, M.B. and Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2011) Genomic resources for the brown planthopper, Nilaparvata lugens: transcriptome pyrosequencing and microarray design. Insect Science, 19(1), pp. 1-12. (doi: 10.1111/j.1744-7917.2011.01440.x)

Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2011) TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics, 12(1), p. 178. (doi: 10.1186/1471-2105-12-178)

2010

Hammer, S., Brown, R., Bugoni, L., Palma, R.L. and Hughes, J. (2010) On the origin of Halipeurus heraldicus on Round Island petrels: cophylogenetic relationships between petrels and their chewing lice. Molecular Phylogenetics and Evolution, 55(3), pp. 1111-1120. (doi: 10.1016/j.ympev.2010.01.013) (PMID:20079857)

2007

Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Page, R.D.M. (2007) Comparative tests of ectoparasite species richness in seabirds. BMC Evolutionary Biology, 7(227), pp. 1-21. (doi: 10.1186/1471-2148-7-227) (PMID:18005412) (PMCID:PMC2258205)

This list was generated on Sun Jun 15 15:35:21 2025 BST.
Jump to: Articles | Book Sections
Number of items: 107.

Articles

Lytras, Spyros, Lamb, Kieran D., Ito, Jumpei, Grove, Joe ORCID logoORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID logoORCID: https://orcid.org/0000-0002-2318-1460, Sato, Kei, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99(2), e0160124. (doi: 10.1128/jvi.01601-24) (PMID:39878472) (PMCID:39878472)

Terhzaz, Selim ORCID logoORCID: https://orcid.org/0000-0002-6192-6558, Kerrigan, David, Almire, Floriane, Szemiel, Agnieszka M., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Parvy, Jean-Philippe, Palmarini, Massimo ORCID logoORCID: https://orcid.org/0000-0001-7007-4070, Kohl, Alain ORCID logoORCID: https://orcid.org/0000-0002-1523-9458, Shi, Xiaohong ORCID logoORCID: https://orcid.org/0000-0002-5289-7222 and Pondeville, Emilie (2025) NSm is a critical determinant for bunyavirus transmission between vertebrate and mosquito hosts. Nature Communications, 16, 1214. (doi: 10.1038/s41467-024-54809-7) (PMID:39890788) (PMCID:PMC11785797)

Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Orton, Richard J. ORCID logoORCID: https://orcid.org/0000-0002-3389-4325 and Lytras, Spyros (2025) Expanding the genomic diversity of human anelloviruses. Virus Evolution, 11(1), veaf002. (doi: 10.1093/ve/veaf002) (PMID:39839678) (PMCID:PMC11749082)

Ruscica, V. et al. (2024) XRN1 supplies free nucleotides to feed alphavirus replication. bioRxiv, (doi: 10.1101/2024.12.09.625895)

McLachlan, I. et al. (2024) Evaluation of risk-based travel policy for the COVID-19 epidemic in Scotland: a population-based surveillance study. BMJ Open, 14(11), e085332. (doi: 10.1136/bmjopen-2024-085332) (PMID:39615890)

Li, Yao-Tsun, Ko, Hui-Ying, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Liu, Ming-Tsuan, Lin, Yi-Ling, Hampson, Katie ORCID logoORCID: https://orcid.org/0000-0001-5392-6884 and Brunker, Kirstyn ORCID logoORCID: https://orcid.org/0000-0001-9990-6299 (2024) From emergence to endemicity: highly pathogenic H5 avian influenza viruses in Taiwan. Nature Communications, 15(1), 9348. (doi: 10.1038/s41467-024-53816-y) (PMID:39472594) (PMCID:PMC11522503)

Lamb, Kieran D., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Lytras, Spyros, Young, Francesca, Koci, Orges, Herzig, James, Lovell, Simon C,, Grove, Joe ORCID logoORCID: https://orcid.org/0000-0001-5390-7579, Yuan, Ke ORCID logoORCID: https://orcid.org/0000-0002-2318-1460 and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv, (doi: 10.1101/2024.07.05.602129)

Litvin, Ulad, Wang, Eddie C.Y., Stanton, Richard J., Fielding, Ceri A. and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (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)

Blanco-Melo, Daniel, Campbell, Matthew A., Zhu, Henan, Dennis, Tristan P., Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Lytras, Spyros, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID logoORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID logoORCID: https://orcid.org/0000-0003-4028-9884 (2024) A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biology, 25(1), 120. (doi: 10.1186/s13059-024-03258-y) (PMID:38741126) (PMCID:PMC11089739)

Gonzalo Nadal, V. et al. (2024) Suspected tick-borne flavivirus meningoencephalomyelitis in dogs from the UK: six cases (2021). Journal of Small Animal Practice, 65(2), pp. 132-143. (doi: 10.1111/jsap.13682) (PMID:37956993) (PMCID:PMC11497270)

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)

Blanco-Melo, Daniel, Campbell, Matthew A., Zhu, Henan, Dennis, Tristan P.W., Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Lytras, Spyros, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID logoORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert J. ORCID logoORCID: https://orcid.org/0000-0003-4028-9884 (2023) A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus ‘fossil record’. bioRxiv, (doi: 10.1101/2023.10.17.562709)

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)

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)

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)

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)

Carabelli, Alessandro M., Peacock, Thomas P., Thorne, Lucy G., Harvey, William T., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Peacock, Sharon J., Barclay, Wendy S., de Silva, Thushan I., Towers, Greg J. and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (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)

Whitlock, A. O. B. et al. (2023) Identifying the genetic basis of viral spillover using Lassa virus as a test case. Royal Society Open Science, 10(3), 221503. (doi: 10.1098/rsos.221503) (PMID:36968239) (PMCID:PMC10031424)

Carrozza, Maria-Luisa, Niewiadomska, Anna-Maria, Mazzei, Maurizio, Abi-Said, Mounir R., Hue, Stephane, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Gatseva, Anna ORCID logoORCID: https://orcid.org/0000-0003-1601-5277 and Gifford, Robert James ORCID logoORCID: https://orcid.org/0000-0003-4028-9884 (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)

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)

Iannucci, Sarah, Harvey, William T., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221, Poyade, Matthieu and Hutchinson, Edward ORCID logoORCID: https://orcid.org/0000-0003-3673-9096 (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, Haiting, Gu, Quan ORCID logoORCID: https://orcid.org/0000-0002-1201-6734, Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (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)

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)

Willett, B. J. et al. (2022) Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7, 1709. (doi: 10.1038/s41564-022-01241-6) (PMID:36114232) (PMCID:PMC9483304)

Stirrup, O. et al. (2022) Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study. eLife, 11, e78427. (doi: 10.7554/elife.78427) (PMID:36098502) (PMCID:PMC9596156)

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)

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, Ru, Rong, Xia, Aranday-Cortes, Elihu, Vattipally, Sreenu ORCID logoORCID: https://orcid.org/0000-0001-6673-4697, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948 and Fu, Yongshui (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)

Vucak, M. et al. (2022) Genome sequences of five arenaviruses from pygmy mice (Mus minutoides) in Sierra Leone. Microbiology Resource Announcements, 11(5), e0009522. (doi: 10.1128/mra.00095-22) (PMID:35389260) (PMCID:PMC9119099)

Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Orton, Richard J. ORCID logoORCID: https://orcid.org/0000-0002-3389-4325 (2022) Quantifying and cataloguing unknown sequences within human microbiomes. mSystems, 7(2), e01468-21. (doi: 10.1128/msystems.01468-21) (PMID:35258340) (PMCID:PMC9052204)

Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z) (PMID:35197443) (PMCID:PMC8866425)

Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)

Chai, Haiting, Gu, Quan ORCID logoORCID: https://orcid.org/0000-0002-1201-6734, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (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)

Lytras, Spyros, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Martin, Darren, Swanepoel, Phillip, de Klerk, Arné, Lourens, Rentia, Kosakovsky Pond, Sergei L., Xia, Wei, Jiang, Xiaowei and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (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)

Twohig, K. A. et al. (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infectious Diseases, 22(1), pp. 35-42. (doi: 10.1016/S1473-3099(21)00475-8) (PMID:34461056) (PMCID:PMC8397301)

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)

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)

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)

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)

Vöhringer, H. S. et al. (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), pp. 506-511. (doi: 10.1038/s41586-021-04069-y) (PMID:34649268) (PMCID:PMC8674138)

Boshier, F. A.T. et al. (2021) The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. Journal of Infection, 83(6), pp. 693-700. (doi: 10.1016/j.jinf.2021.09.022) (PMID:34610391) (PMCID:PMC8487101)

Wickenhagen, A. et al. (2021) A prenylated dsRNA sensor protects against severe COVID-19. Science, 374(6567), eabj3624. (doi: 10.1126/science.abj3624) (PMID:34581622) (PMCID:PMC7612834)

Lytras, Spyros, Xia, Wei, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Jiang, Xiaowei and Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221 (2021) The animal origin of SARS-CoV-2. Science, 373(6558), pp. 968-970. (doi: 10.1126/science.abh0117) (PMID:34404734)

Li, K. K. et al. (2021) Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface. Journal of Infection, 83(1), pp. 96-103. (doi: 10.1016/j.jinf.2021.04.020) (PMID:33895226) (PMCID:PMC8061788)

Stirrup, O. et al. (2021) Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. eLife, 10, e65828. (doi: 10.7554/elife.65828) (PMID:34184637) (PMCID:PMC8285103)

Graham, M. S. et al. (2021) Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. Lancet Public Health, 6(5), e335-e345. (doi: 10.1016/S2468-2667(21)00055-4)

Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)

Thomson, E. C. et al. (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 184(5), 1171-1187.e20. (doi: 10.1016/j.cell.2021.01.037) (PMID:33621484) (PMCID:PMC7843029)

Rihn, S. J. et al. (2021) A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biology, 19(2), e3001091. (doi: 10.1371/journal.pbio.3001091) (PMID:33630831) (PMCID:PMC7906417)

Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)

Stirrup, O. et al. (2021) SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study. BMJ Open Respiratory Research, 8, e001029. (doi: 10.1136/bmjresp-2021-001029) (PMID:34544733) (PMCID:PMC8453594)

Collados Rodríguez, Milagros ORCID logoORCID: https://orcid.org/0000-0002-2304-6402, Dybas, Joseph M., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Weitzman, Matthew D. and Boutell, Chris ORCID logoORCID: https://orcid.org/0000-0002-2970-7785 (2020) The HSV-1 ubiquitin ligase ICP0: modifying the cellular proteome to promote infection. Virus Research, 285, 198015. (doi: 10.1016/j.virusres.2020.198015) (PMID:32416261)

Pénzes, Judit J, Söderlund-Venermo, Maria, Canuti, Marta, Eis-Hübinger, Anna Maria, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Cotmore, Susan F and Harrach, Balázs (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)

Lytras, Spyros and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2020) Synonymous dinucleotide usage: a codon-aware metric for quantifying dinucleotide representation in viruses. Viruses, 12(4), 462. (doi: 10.3390/v12040462)

Rihn, S. J. et al. (2019) TRIM69 inhibits vesicular stomatitis Indiana virus (VSIV). Journal of Virology, 93(20), e00951-19. (doi: 10.1128/JVI.00951-19) (PMID:31375575)

Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Bianco, Giovanni, Ferguson, Heather M. ORCID logoORCID: https://orcid.org/0000-0002-9625-5176, Helm, Barbara, Tong, Lily, Wilkie, Gavin S., Kohl, Alain ORCID logoORCID: https://orcid.org/0000-0002-1523-9458 and Schnettler, Esther (2019) Metaviromics reveals unknown viral diversity in the biting midge Culicoides impunctatus. Viruses, 11(9), 865. (doi: 10.3390/v11090865) (PMID:31533247) (PMCID:PMC6784199)

Suárez, N. M. et al. (2019) Human cytomegalovirus genomes sequenced directly from clinical material: variation, multiple-strain infection, recombination and gene loss. Journal of Infectious Diseases, 220(5), pp. 781-791. (doi: 10.1093/infdis/jiz208) (PMID:31050742) (PMCID:PMC6667795)

Maabar, Maha, Davison, Andrew J. ORCID logoORCID: https://orcid.org/0000-0002-4991-9128, Vučak, Matej, Thorburn, Fiona, Murcia, Pablo ORCID logoORCID: https://orcid.org/0000-0002-4352-394X, Gunson, Rory, Palmarini, Massimo ORCID logoORCID: https://orcid.org/0000-0001-7007-4070 and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2019) DisCVR: rapid viral diagnosis from high-throughput sequencing data. Virus Evolution, 5(2), vez033. (doi: 10.1093/ve/vez033) (PMID:31528358) (PMCID:PMC6735924)

Alamil, M., Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, 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)

Alamil, M., Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, 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. (PMID:31056055)

Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi: 10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)

Davis, C. et al. (2019) New highly diverse hepatitis C strains detected in sub‐Saharan Africa have unknown susceptibility to direct‐acting antiviral treatments. Hepatology, 69(4), pp. 1426-1441. (doi: 10.1002/hep.30342) (PMID:30387174) (PMCID:PMC6492010)

Cotmore, S. F. et al. (2019) ICTV virus taxonomy profile: Parvoviridae. Journal of General Virology, 100(3), pp. 367-368. (doi: 10.1099/jgv.0.001212) (PMID:30672729) (PMCID:PMC6537627)

Rezelj, Veronica V., Mottram, Timothy J., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Elliott, Richard M., Kohl, Alain ORCID logoORCID: https://orcid.org/0000-0002-1523-9458 and Brennan, Benjamin ORCID logoORCID: https://orcid.org/0000-0003-4707-726X (2019) M segment-based minigenomes and virus-like particle assays as an approach to assess the potential of tick-borne Phlebovirus genome reassortment. Journal of Virology, 93(6), e02068-18. (doi: 10.1128/JVI.02068-18) (PMID:30567991) (PMCID:PMC6401446)

Zhu, H. et al. (2019) Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds. PLoS Pathogens, 15(2), e1007531. (doi: 10.1371/journal.ppat.1007531) (PMID:30731004) (PMCID:PMC6366691)

Singer, Joshua B., Thomson, Emma C. ORCID logoORCID: https://orcid.org/0000-0003-1482-0889, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Gifford, Robert J. ORCID logoORCID: https://orcid.org/0000-0003-4028-9884 (2018) GLUE: a flexible software system for virus sequence data. BMC Bioinformatics, 19, 532. (doi: 10.1186/s12859-018-2459-9) (PMID:30563445) (PMCID:PMC6299651)

Mercuri, Luca, Thomson, Emma C. ORCID logoORCID: https://orcid.org/0000-0003-1482-0889, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Karayiannis, Peter (2018) Quasispecies changes with distinctive point mutations in the Hepatitis C virus internal ribosome entry site (IRES) derived from PBMCs and plasma. Advances in Virology, 2018, 4835252. (doi: 10.1155/2018/4835252) (PMID:30581467) (PMCID:PMC6276526)

Dunlop, J. I. et al. (2018) Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas. PLoS Neglected Tropical Diseases, 12(10), e0006884. (doi: 10.1371/journal.pntd.0006884) (PMID:30372452) (PMCID:PMC6245839)

Modha, Sejal ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Thanki, Anil, Cotmore, Susan F., Davison, Andrew J. ORCID logoORCID: https://orcid.org/0000-0002-4991-9128 and Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2018) ViCTree: an automated framework for taxonomic classification from protein sequences. Bioinformatics, 34(13), pp. 2195-2200. (doi: 10.1093/bioinformatics/bty099) (PMID:29474519) (PMCID:PMC6022645)

Saucedo, B. et al. (2018) Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (Pelophylax spp.). Emerging Microbes and Infections, 7(1), 56. (doi: 10.1038/s41426-018-0058-5) (PMID:29615625) (PMCID:PMC5882854)

da Silva Filipe, A. et al. (2018) Reply to: "Reply to: 'Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries'". Journal of Hepatology, 68(4), pp. 864-866. (doi: 10.1016/j.jhep.2017.11.044) (PMID:29339112)

Shaw, A. E. et al. (2017) Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS Biology, 15(12), e2004086. (doi: 10.1371/journal.pbio.2004086) (PMID:29253856) (PMCID:PMC574750)

da Silva Filipe, A. et al. (2017) Response to DAA therapy in the NHS England early access programme for rare HCV subtypes from low and middle income countries. Journal of Hepatology, 67(6), pp. 1348-1350. (doi: 10.1016/j.jhep.2017.06.035) (PMID:28789880)

Saucedo, Bernardo, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, van Beurden, Steven J., Suárez, Nicolás M., Haenen, Olga L.M., Voorbergen-Laarman, Michal, Gröne, Andrea and Kik, Marja J.L. (2017) Complete genome sequence of Frog virus 3, isolated from a strawberry poison frog (Oophaga pumilio) imported from Nicaragua into the Netherlands. Genome Announcements, 5(35), e00863-17. (doi: 10.1128/genomeA.00863-17) (PMID:28860243) (PMCID:PMC5578841)

Milani, A. et al. (2017) Vaccine immune pressure influences viral population complexity of avian influenza virus during infection. Veterinary Microbiology, 203, pp. 88-94. (doi: 10.1016/j.vetmic.2017.02.016)

Rihn, Suzannah J. ORCID logoORCID: https://orcid.org/0000-0001-9495-4056, Foster, Toshana L., Busnadiego, Idoia, Aziz, Muhamad Afiq Bin, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Neil, Stuart J.D. and Wilson, Sam J. ORCID logoORCID: https://orcid.org/0000-0002-6065-0895 (2017) The envelope gene of transmitted HIV-1 resists a late interferon gamma-induced block. Journal of Virology, 91(7), e02254-16. (doi: 10.1128/JVI.02254-16) (PMID:28100611) (PMCID:PMC5355616)

Donald, C. L. et al. (2016) Full genome sequence and sfRNA interferon antagonist activity of Zika virus from Recife, Brazil. PLoS Neglected Tropical Diseases, 10(10), e0005048. (doi: 10.1371/journal.pntd.0005048) (PMID:27706161) (PMCID:PMC5051680)

Franzo, Giovanni, Cortey, Martì, Segalés, Joaquim, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Drigo, Michele (2016) Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets. Data In Brief, 8, pp. 549-552. (doi: 10.1016/j.dib.2016.06.005) (PMID:27508215) (PMCID:PMC4962815)

Jacobs, M. et al. (2016) Late Ebola virus relapse causing meningoencephalitis: a case report. Lancet, 388(10043), pp. 498-503. (doi: 10.1016/S0140-6736(16)30386-5) (PMID:27209148) (PMCID:PMC4967715)

Franzo, Giovanni, Cortey, Marti, Segalés, Joaquim, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Drigo, Michele (2016) Phylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant forms. Molecular Phylogenetics and Evolution, 100, pp. 269-280. (doi: 10.1016/j.ympev.2016.04.028) (PMID:27114187)

Fusaro, A. et al. (2016) Unexpected interfarm transmission dynamics during a highly pathogenic avian influenza epidemic. Journal of Virology, 90(14), pp. 6401-6411. (doi: 10.1128/jvi.00538-16) (PMID:27147741) (PMCID:PMC4936132)

Robinson, Mark W., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Wilkie, Gavin S., Swann, Rachael ORCID logoORCID: https://orcid.org/0000-0002-3945-2253, Barclay, Stephen T., Mills, Peter R., Patel, Arvind H. ORCID logoORCID: https://orcid.org/0000-0003-4600-2047, Thomson, Emma C. ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 and McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948 (2016) Tracking TCRß sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region. Frontiers in Immunology, 7, 131. (doi: 10.3389/fimmu.2016.00131) (PMID:27092143) (PMCID:PMC4820669)

Orton, R.J. ORCID logoORCID: https://orcid.org/0000-0002-3389-4325, Gu, Q. ORCID logoORCID: https://orcid.org/0000-0002-1201-6734, Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Maabar, M., Modha, S. ORCID logoORCID: https://orcid.org/0000-0002-8440-885X, Vattipally, Sreenu ORCID logoORCID: https://orcid.org/0000-0001-6673-4697, Wilkie, G.S. and Davison, A. ORCID logoORCID: https://orcid.org/0000-0002-4991-9128 (2016) Bioinformatics tools for analysing viral genomic data. Revue scientifique et technique (International Office of Epizootics), 35(1), pp. 241-285. (doi: 10.20506/rst.35.1.2432) (PMID:27217183)

Rijks, J. M. et al. (2016) Investigation of amphibian mortality events in wildlife reveals an on-going ranavirus epidemic in the North of the Netherlands. PLoS ONE, 11(6), e0157473. (doi: 10.1371/journal.pone.0157473) (PMID:27315226) (PMCID:PMC4912076)

Stewart, M. et al. (2015) Characterization of a second open reading frame in genome segment 10 of bluetongue virus. Journal of General Virology, 96(11), pp. 3280-3293. (doi: 10.1099/jgv.0.000267) (PMID:26290332) (PMCID:PMC4806581)

Fusaro, Alice, Tassoni, Luca, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Milani, Adelaide, Salviato, Annalisa, Schivo, Alessia, Murcia, Pablo R. ORCID logoORCID: https://orcid.org/0000-0002-4352-394X, Bonfanti, Lebana, Cattoli, Giovanni and Monne, Isabella (2015) Evolutionary trajectories of two distinct avian influenza epidemics: parallelisms and divergences. Infection, Genetics and Evolution, 34, pp. 457-466. (doi: 10.1016/j.meegid.2015.05.020) (PMID:26003682)

Nomikou, Kyriaki, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Wash, Rachael, Kellam, Paul, Breard, Emmanuel, Zientara, Stéphan, Palmarini, Massimo ORCID logoORCID: https://orcid.org/0000-0001-7007-4070, Biek, Roman ORCID logoORCID: https://orcid.org/0000-0003-3471-5357 and Mertens, Peter (2015) Widespread reassortment shapes the evolution and epidemiology of bluetongue virus following European invasion. PLoS Pathogens, 11(8), e1005056. (doi: 10.1371/journal.ppat.1005056) (PMID:26252219) (PMCID:PMC4529188)

Tilston-Lunel, Natasha L., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Olszanski Acrani, Gustavo, da Silva, Daisy E.A., Azevedo, Raimunda S.S., Rodrigues, Sueli G., Vasconcelos, Pedro F.C., Nunes, Marcio R.T. and Elliott, Richard M. (2015) Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence. Journal of General Virology, 96(7), pp. 1636-1650. (doi: 10.1099/vir.0.000108) (PMID:25735305) (PMCID:PMC4635451)

Zhu, Henan, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Murcia, Pablo R. ORCID logoORCID: https://orcid.org/0000-0002-4352-394X (2015) Origins and evolutionary dynamics of H3N2 canine influenza virus. Journal of Virology, 89(10), pp. 5406-5418. (doi: 10.1128/JVI.03395-14) (PMID:25740996) (PMCID:PMC4442499)

Abdelrahman, Tamer, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Main, Janice, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948, Thursz, Mark and Thomson, Emma ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 (2015) Reply. Hepatology, 61(4), p. 1438. (doi: 10.1002/hep.27393) (PMID:25147121) (PMCID:PMC4407921)

Ardelrahman, Tamer, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Main, Janice, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948, Thursz, Mark and Thomson, Emma ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 (2015) Waiting time and transplantation for hepatocellular cancer: a balance between tempus fugit and carpe diem. Hepatology, 61(4), pp. 1438-1439. (doi: 10.1002/hep.27434)

Beczkowski, Pawel M., Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Biek, Roman ORCID logoORCID: https://orcid.org/0000-0003-3471-5357, Litster, Annette, Willett, Brian J. ORCID logoORCID: https://orcid.org/0000-0001-8912-3266 and Hosie, Margaret J. ORCID logoORCID: https://orcid.org/0000-0002-4313-5023 (2015) Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus (FIV). Journal of General Virology, 96(4), pp. 893-903. (doi: 10.1099/vir.0.000035) (PMID:25535323) (PMCID:PMC4361796)

Abdelrahman, Tamer, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Main, Janice, McLauchlan, John ORCID logoORCID: https://orcid.org/0000-0003-2217-9948, Thursz, Mark and Thomson, Emma ORCID logoORCID: https://orcid.org/0000-0003-1482-0889 (2015) Next generation sequencing sheds light on the natural history of hepatitis C infection in patients that fail treatment. Hepatology, 61(1), pp. 88-97. (doi: 10.1002/hep.27192) (PMID:24797101) (PMCID:PMC4303934)

Rihn, Suzannah J. ORCID logoORCID: https://orcid.org/0000-0001-9495-4056, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Wilson, Sam J. ORCID logoORCID: https://orcid.org/0000-0002-6065-0895 and Bieniasz, Paul D. (2015) Uneven genetic robustness of HIV-1 integrase. Journal of Virology, 89(1), pp. 552-567. (doi: 10.1128/JVI.02451-14)

Bęczkowski, Paweł M, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Biek, Roman ORCID logoORCID: https://orcid.org/0000-0003-3471-5357, Litster, Annette, Willett, Brian J ORCID logoORCID: https://orcid.org/0000-0001-8912-3266 and Hosie, Margaret J ORCID logoORCID: https://orcid.org/0000-0002-4313-5023 (2014) Feline immunodeficiency virus (FIV) env recombinants are common in natural infections. Retrovirology, 11(80), (doi: 10.1186/s12977-014-0080-1) (PMID:25699660) (PMCID:PMC4180853)

Busnadiego, I. et al. (2014) Host and viral determinants of Mx2 antiretroviral activity. Journal of Virology, 88(14), pp. 7738-7752. (doi: 10.1128/JVI.00214-14) (PMID:24760893) (PMCID:PMC4097781)

Jombart, T. et al. (2014) OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, 7, pp. 28-34. (doi: 10.1016/j.epidem.2014.04.003)

Monne, I. et al. (2014) Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor. Journal of Virology, 88(8), pp. 4375-4388. (doi: 10.1128/JVI.03181-13)

Varela, M. et al. (2013) Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in Rhesus Macaques. PLoS ONE, 8(8), e70814. (doi: 10.1371/journal.pone.0070814) (PMID:23967111) (PMCID:PMC3743870)

Hughes, J. et al. (2012) Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS Pathogens, 8(12), e1003081. (doi: 10.1371/journal.ppat.1003081)

Murcia, P. R. et al. (2012) Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathogens, 8(5), e1002730. (doi: 10.1371/journal.ppat.1002730)

Bass, C., Hebsgaard, M.B. and Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2011) Genomic resources for the brown planthopper, Nilaparvata lugens: transcriptome pyrosequencing and microarray design. Insect Science, 19(1), pp. 1-12. (doi: 10.1111/j.1744-7917.2011.01440.x)

Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 (2011) TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics, 12(1), p. 178. (doi: 10.1186/1471-2105-12-178)

Hammer, S., Brown, R., Bugoni, L., Palma, R.L. and Hughes, J. (2010) On the origin of Halipeurus heraldicus on Round Island petrels: cophylogenetic relationships between petrels and their chewing lice. Molecular Phylogenetics and Evolution, 55(3), pp. 1111-1120. (doi: 10.1016/j.ympev.2010.01.013) (PMID:20079857)

Hughes, J. ORCID logoORCID: https://orcid.org/0000-0003-2556-2563 and Page, R.D.M. (2007) Comparative tests of ectoparasite species richness in seabirds. BMC Evolutionary Biology, 7(227), pp. 1-21. (doi: 10.1186/1471-2148-7-227) (PMID:18005412) (PMCID:PMC2258205)

Book Sections

Iannucci, Sarah, Harvey, William, Hughes, Joseph ORCID logoORCID: https://orcid.org/0000-0003-2556-2563, Robertson, David L. ORCID logoORCID: https://orcid.org/0000-0001-6338-0221, Hutchinson, Edward ORCID logoORCID: https://orcid.org/0000-0003-3673-9096 and Poyade, Matthieu (2022) Using molecular visualisation techniques to explain the molecular biology of SARS-CoV-2 spike protein mutations to a general audience. In: Shapiro, Leonard and Rea, Paul M. (eds.) Biomedical Visualisation. Volume 12. Series: Advances in experimental medicine and biology (1388). Springer: Cham, pp. 129-152. ISBN 9783031108884 (doi: 10.1007/978-3-031-10889-1_6)

This list was generated on Sun Jun 15 15:35:21 2025 BST.

Grants

Grants and Awards listed are those received whilst working with the University of Glasgow.

  • Predictors of COVID-19 Outcomes
    Office of the Chief Scientific Adviser
    2022 - 2024
     
  • Genomic epidemiology of equine influenza virus in the United Kingdom
    Biotechnology and Biological Sciences Research Council
    2021 - 2024
     
  • HIV cluster detection pipeline for WoSSVC
    NHS Greater Glasgow and Clyde Endowment Funds
    2019 - 2020
     

Supervision

  • Kwok, Kirsty Tsoi Tung
    Genomic characterization of the virome in acute respiratory illness with no identifiable aetiology: supporting improved diagnostics in Malawi

Research datasets

Jump to: 2024 | 2022 | 2021 | 2019
Number of items: 5.

2024

Terhzaz, S. , Kerrigan, D., Almire, F., Szemiel, A. M., Hughes, J. , Parvy, J.-P., Palmarini, M. , Kohl, A. , Shi, X. and Pondeville, E. (2024) NSm is a critical determinant for bunyavirus transmission between vertebrate and mosquito hosts. [Data Collection]

2022

Alexander, A. , Salvemini, M., Sreenu, V. B., Hughes, J. , Telleria, E. L., Ratinier, M., Arnaud, F., Volf, P., Brennan, B. , Varjak, M. and Kohl, A. (2022) Characterisation of the antiviral RNA interference response to Toscana virus in sand fly cells. [Data Collection]

Sugrue, E. , Wickenhagen, A., Mollentze, N. , Aziz, M. A., Sreenu, V. B., Truxa, S., Tong, L., Da Silva Filipe, A. , Robertson, D. , Hughes, J. , Rihn, S. and Wilson, S. (2022) The Interferon Resistance of Transmitted HIV-1 is Possibly a Consequence of Enhanced Replicative Fitness. [Data Collection]

2021

Wickenhagen, A., Sugrue, E. , Lytras, S., Kuchi, S., Noerenberg, M. , Turnbull, M. , Loney, C. , Herder, V., Allan, J., Jarmson, I., Cameron Ruiz, N., Varjak, M. , Pinto, R. , Lee, J. Y., Iselin, L., Palmalux, N., Stewart, D., Swingler, S., Greenwood, E. J. D., Crozier, T. W. M., Gu, Q. , Davies, E., Clohisey, S., Wang, B., Trindade Maranhã Costa, F., Santana, M. F., Carlos de Lima Ferreira, L., Murphy, L., Fawkes, A., Meynert, A., Grimes, G., ISARICC investigators, , Da Silva Filho, J. , Marti, M. , Hughes, J. , Stanton, R. J., Wang, E. C. Y., Ho, A. , Davis, I., Jarrett, R. , Castello, A. , Robertson, D. , Semple, M. G., Openshaw, P. J. M., Palmarini, M. , Lehner, P. J., Baillie, K., Rihn, S. and Wilson, S. (2021) A Prenylated dsRNA Sensor Protects Against Severe COVID-19. [Data Collection]

2019

Rezelj, V. V., Mottram, T., Hughes, J., Elliott, R. M., Kohl, A. and Brennan, B. (2019) M segment-based minigenomes and virus-like particle assays as an approach to assess the potential of tick-borne Phlebovirus genome reassortment. [Data Collection]

This list was generated on Sun Jun 15 17:22:04 2025 BST.