2022

Campbell, K., Gifford, R. J. , Singer, J., Hill, V., O'Toole, A., Rambaut, A., Hampson, K. and Brunker, K. (2022) Making genomic surveillance deliver: a lineage classification and nomenclature system to inform rabies elimination. PLoS Pathogens, 18(5), e1010023. (doi: 10.1371/journal.ppat.1010023) (PMID:35500026) (PMCID:PMC9162366)

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)

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)

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

Smith, D. A. et al. (2021) Real world SOF/VEL/VOX retreatment outcomes and viral resistance analysis for HCV patients with prior failure to DAA therapy. Journal of Viral Hepatitis, 28(9), pp. 1256-1264. (doi: 10.1111/jvh.13549) (PMID:34003556)

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)

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)

MacLean, O. A. , Lytras, S., Weaver, S., Singer, J. B., Boni, M. F., Lemey, P., Kosakovsky Pond, S. L. and Robertson, D. L. (2021) Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. PLoS Biology, 19(3), e3001115. (doi: 10.1371/journal.pbio.3001115) (PMID:33711012) (PMCID:PMC7990310)

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)

2020

Mokaya, J. et al. (2020) Evidence of tenofovir resistance in chronic hepatitis B virus (HBV) infection: An observational case series of South African adults. Journal of Clinical Virology, 129, 104548. (doi: 10.1016/j.jcv.2020.104548) (PMID:32663786) (PMCID:PMC7408481)

Brunker, K. et al. (2020) Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Research, 5, 3. (doi: 10.12688/wellcomeopenres.15518.2) (PMID:32090172) (PMCID:PMC7001756)

Pascall, D. J. et al. (2020) "Frozen evolution" of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence. PLoS Biology, 18(4), e3000673. (doi: 10.1371/journal.pbio.3000673) (PMID:32343693) (PMCID:PMC7188197)

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

2019

Ankcorn, M. et al. (2019) Convalescent plasma therapy for persistent hepatitis E virus infection. Journal of Hepatology, 71(2), pp. 434-438. (doi: 10.1016/j.jhep.2019.04.008) (PMID:31075322)

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)

Dennis, T. P.W., Souza, W. M. d., Marsile-Medun, S., Singer, J. B., Wilson, S. J. and Gifford, R. J. (2019) The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. Virus Research, 262, pp. 15-23. (doi: 10.1016/j.virusres.2018.03.014) (PMID:29601845) (PMCID:PMC6372831)

2018

Singer, J. B., Thomson, E. C. , McLauchlan, J. , Hughes, J. and Gifford, R. J. (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)

Dennis, T. P.W., Flynn, P. J., Souza, W. M. d., Singer, J. B., Moreau, C. S., Wilson, S. J. and Gifford, R. J. (2018) Insights into circovirus host range from the genomic fossil record. Journal of Virology, 92(16), e00145-18. (doi: 10.1128/JVI.00145-18) (PMID:29875243) (PMCID:PMC6069186)

Cowton, V. M., Singer, J. B., Gifford, R. J. and Patel, A. H. (2018) Predicting the effectiveness of hepatitis C virus neutralizing antibodies by bioinformatic analysis of conserved epitope residues using public sequence data. Frontiers in Immunology, 9, 1470. (doi: 10.3389/fimmu.2018.01470) (PMID:30013555) (PMCID:PMC6036255)

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)

Niebel, M. , Singer, J. B., Nickbakhsh, S. , Gifford, R. J. and Thomson, E. C. (2017) Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination? Lancet Gastroenterology and Hepatology, 2(10), pp. 700-701. (doi: 10.1016/S2468-1253(17)30257-1) (PMID:28895545)