2025

Kugler, M. et al. (2025) Occupational Exposure of Healthcare Workers and Rural Communities to Viral Haemorrhagic Fever Viruses in Uganda. Project Report. University of Glasgow. (doi: 10.36399/gla.pubs.349489).

Ashraf, S. et al. (2025) Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing. Nature Communications, 16, 2844. (doi: 10.1038/s41467-025-57696-8) (PMID:40122843) (PMCID:PMC11930947)

2024

Shepherd, J. G. et al. (2024) Widespread human exposure to ledanteviruses in Uganda: A population study. PLoS Neglected Tropical Diseases, 18(7), e0012297. (doi: 10.1371/journal.pntd.0012297) (PMID:38976760) (PMCID:PMC11257405)

2023

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)

Shepherd, James G. ORCID: https://orcid.org/0000-0003-3915-048X, Davis, Chris ORCID: https://orcid.org/0000-0002-7317-3266, Streicker, Daniel G. ORCID: https://orcid.org/0000-0001-7475-2705 and Thomson, Emma C. ORCID: https://orcid.org/0000-0003-1482-0889 (2023) Emerging rhabdoviruses and human infection. Biology, 12(6), 878. (doi: 10.3390/biology12060878) (PMID:37372162) (PMCID:PMC10294888)

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)

2022

Atim, S. A. et al. (2022) Risk factors for Crimean-Congo Haemorrhagic Fever (CCHF) virus exposure in farming communities in Uganda. Journal of Infection, 85(6), pp. 693-701. (doi: 10.1016/j.jinf.2022.09.007) (PMID:36108783) (PMCID:PMC9731351)

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)

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)

Shepherd, J. G. et al. (2021) Seoul virus associated with pet pats, Scotland, UK, 2019. Emerging Infectious Diseases, 27(10), pp. 2677-2680. (doi: 10.3201/eid2710.211298) (PMID:34545785) (PMCID:PMC8462346)

Thomson, Emma ORCID: https://orcid.org/0000-0003-1482-0889, Shah, Rajiv, Ahovegbe, Lucrece, Niebel, Marc ORCID: https://orcid.org/0000-0003-2515-6151 and Shepherd, James ORCID: https://orcid.org/0000-0003-3915-048X (2021) Non-epidemic HCV genotypes in low- and middle-income countries and the risk of resistance to current direct-acting antiviral regimens. Journal of Hepatology, 75(2), pp. 462-473. (doi: 10.1016/j.jhep.2021.04.045) (PMID:33974951) (PMCID:PMC8310923)

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)

Lythgoe, K. A. et al. (2021) SARS-CoV-2 within-host diversity and transmission. Science, 372(6539), eabg0821. (doi: 10.1126/science.abg0821) (PMID:33688063) (PMCID:PMC8128293)

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)

Volz, E. et al. (2021) Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Cell, 184(1), 64-75.e11. (doi: 10.1016/j.cell.2020.11.020) (PMID:33275900) (PMCID:PMC7674007)

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)

Parker, M. D. et al. (2021) Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data. Genome Research, 31, pp. 645-658. (doi: 10.1101/gr.268110.120) (PMID:33722935) (PMCID:PMC8015849)

Articles

Ashraf, S. et al. (2025) Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing. Nature Communications, 16, 2844. (doi: 10.1038/s41467-025-57696-8) (PMID:40122843) (PMCID:PMC11930947)

Shepherd, J. G. et al. (2024) Widespread human exposure to ledanteviruses in Uganda: A population study. PLoS Neglected Tropical Diseases, 18(7), e0012297. (doi: 10.1371/journal.pntd.0012297) (PMID:38976760) (PMCID:PMC11257405)

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)

Shepherd, James G. ORCID: https://orcid.org/0000-0003-3915-048X, Davis, Chris ORCID: https://orcid.org/0000-0002-7317-3266, Streicker, Daniel G. ORCID: https://orcid.org/0000-0001-7475-2705 and Thomson, Emma C. ORCID: https://orcid.org/0000-0003-1482-0889 (2023) Emerging rhabdoviruses and human infection. Biology, 12(6), 878. (doi: 10.3390/biology12060878) (PMID:37372162) (PMCID:PMC10294888)

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)

Atim, S. A. et al. (2022) Risk factors for Crimean-Congo Haemorrhagic Fever (CCHF) virus exposure in farming communities in Uganda. Journal of Infection, 85(6), pp. 693-701. (doi: 10.1016/j.jinf.2022.09.007) (PMID:36108783) (PMCID:PMC9731351)

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)

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)

Shepherd, J. G. et al. (2021) Seoul virus associated with pet pats, Scotland, UK, 2019. Emerging Infectious Diseases, 27(10), pp. 2677-2680. (doi: 10.3201/eid2710.211298) (PMID:34545785) (PMCID:PMC8462346)

Thomson, Emma ORCID: https://orcid.org/0000-0003-1482-0889, Shah, Rajiv, Ahovegbe, Lucrece, Niebel, Marc ORCID: https://orcid.org/0000-0003-2515-6151 and Shepherd, James ORCID: https://orcid.org/0000-0003-3915-048X (2021) Non-epidemic HCV genotypes in low- and middle-income countries and the risk of resistance to current direct-acting antiviral regimens. Journal of Hepatology, 75(2), pp. 462-473. (doi: 10.1016/j.jhep.2021.04.045) (PMID:33974951) (PMCID:PMC8310923)

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)

Lythgoe, K. A. et al. (2021) SARS-CoV-2 within-host diversity and transmission. Science, 372(6539), eabg0821. (doi: 10.1126/science.abg0821) (PMID:33688063) (PMCID:PMC8128293)

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)

Volz, E. et al. (2021) Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Cell, 184(1), 64-75.e11. (doi: 10.1016/j.cell.2020.11.020) (PMID:33275900) (PMCID:PMC7674007)

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)

Parker, M. D. et al. (2021) Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data. Genome Research, 31, pp. 645-658. (doi: 10.1101/gr.268110.120) (PMID:33722935) (PMCID:PMC8015849)

Research Reports or Papers

Kugler, M. et al. (2025) Occupational Exposure of Healthcare Workers and Rural Communities to Viral Haemorrhagic Fever Viruses in Uganda. Project Report. University of Glasgow. (doi: 10.36399/gla.pubs.349489).