Research outputs
2026
Insecticide resistance is driven by distinct metabolic mechanisms across the lifespan of the major malaria vector Anopheles arabiensis
2025
Exogenous diatoms ameliorate thermal bleaching of symbiont bearing benthic foraminifera.
Titelboim, D., Dedman, C. J., Hodgson, R. P., Knowles, L. S., Liu, X., Lenzi, L., . . . Rickaby, R. E. M. (2025). Exogenous diatoms ameliorate thermal bleaching of symbiont bearing benthic foraminifera.. Proceedings. Biological sciences, 292(2049), 20250596. doi:10.1098/rspb.2025.0596
Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis
Hares, M. F., Griffiths, B. E., Barningham, L., Vamos, E. E., Gregory, R., Duncan, J. S., . . . Coombes, J. L. (2025). Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis. Animal Microbiome, 7(1). doi:10.1186/s42523-024-00352-1
2024
2023
The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis.
Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., . . . COVID-19 Genomics UK (COG-UK) Consortium. (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
Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.
Cotton, S., McHugh, M. P., Dewar, R., Haas, J. G., Templeton, K., & COVID-19 Genomics UK (COG-UK) Consortium. (2023). Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.. The Journal of hospital infection, 135, 28-36. doi:10.1016/j.jhin.2023.02.010
2022
COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study
Klaser, K., Molteni, E., Graham, M., Canas, L. S., Osterdahl, M. F., Antonelli, M., . . . Duncan, E. L. (2022). COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. SCIENTIFIC REPORTS, 12(1). doi:10.1038/s41598-022-14016-0
Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission
Aggarwal, D., Page, A. J., Schaefer, U., Savva, G. M., Myers, R., Volz, E., . . . Harrison, E. M. (2022). Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-28371-z
Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning
Nickbakhsh, S., Hughes, J., Christofidis, N., Griffiths, E., Shaaban, S., Enright, J., . . . Smith-Palmer, A. (2022). Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12(1). doi:10.1038/s41598-022-15661-1
SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2
Eales, O., Page, A. J., de Oliveira Martins, L., Wang, H., Bodinier, B., Haw, D., . . . Elliott, P. (2022). SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases, 22(1). doi:10.1186/s12879-022-07628-4
Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., . . . Gupta, R. K. (2022). Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.. Nature, 608(7922), E24. doi:10.1038/s41586-022-05103-3
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway
Willett, B. J., Grove, J., MacLean, O. A., Wilkie, C., De Lorenzo, G., Furnon, W., . . . Thomson, E. C. (2022). SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. NATURE MICROBIOLOGY, 7(8), 1161-+. doi:10.1038/s41564-022-01143-7
Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021
Smallman-Raynor, M. R., & Cliff, A. D. (2022). Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021. EPIDEMIOLOGY & INFECTION, 150. doi:10.1017/S0950268822001285
Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.
Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., . . . Gerstung, M. (2022). Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.. Nature, 606(7915), E18. doi:10.1038/s41586-022-04887-8
SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time.
Ashford, F., Best, A., Dunn, S. J., Ahmed, Z., Siddiqui, H., Melville, J., . . . McNally, A. (2022). SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time.. Journal of clinical microbiology, 60(4), e0240821. doi:10.1128/jcm.02408-21
Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.
Wright, D. W., Harvey, W. T., Hughes, J., Cox, M., Peacock, T. P., Colquhoun, R., . . . Carabelli, A. M. (2022). Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.. Virus evolution, 8(1), veac023. doi:10.1093/ve/veac023
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
Aggarwal, D., Warne, B., Jahun, A. S., Hamilton, W. L., Fieldman, T., du Plessis, L., . . . Consor, C. G. U. K. C. O. G. -U. K. (2022). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-021-27942-w
Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers
Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Donovan-Banfield, I., . . . Hiscox, J. A. (2022). Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers. GIGASCIENCE, 11. doi:10.1093/gigascience/giac045
2021
Genomic reconstruction of the SARS-CoV-2 epidemic in England
Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., . . . Gerstung, M. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), 506-511. doi:10.1038/s41586-021-04069-y
Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19
Salguero, F. J., White, A. D., Slack, G. S., Fotheringham, S. A., Bewley, K. R., Gooch, K. E., . . . Carroll, M. W. (2021). Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-21389-9
The impact of viral mutations on recognition by SARS-CoV-2 specific T cells
de, S. T. I., Liu, G., Lindsey, B. B., Dong, D., Moore, S. C., Hsu, N. S., . . . Dong, T. (2021). The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. ISCIENCE, 24(11). doi:10.1016/j.isci.2021.103353
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
Meng, B., Kemp, S. A., Papa, G., Datir, R., Ferreira, I. A. T. M., Marelli, S., . . . Gupta, R. K. (2021). Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. CELL REPORTS, 35(13). doi:10.1016/j.celrep.2021.109292
The impact of SARS-CoV-2 infection in children with rheumatic/autoinflammatory diseases on immunosuppressive treatment: a single centre experience
Maritsi, D. N., Krepis, P., Vartzelis, G., Syggelou, A., & Tsolia, M. N. (2023). The impact of SARS-CoV-2 infection in children with rheumatic/autoinflammatory diseases on immunosuppressive treatment: a single centre experience. CLINICAL AND EXPERIMENTAL RHEUMATOLOGY, 41(9), S4-S5. doi:10.1038/s41586-021-03470-x
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., . . . Gupta, R. K. (2021). Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. NATURE, 593(7857), 136-+. doi:10.1038/s41586-021-03412-7
Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study
Graham, M. S., Sudre, C. H., May, A., Antonelli, M., Murray, B., Varsaysky, T., . . . Ourselin, S. (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
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., . . . Gupta, R. K. (2021). SARS-CoV-2 evolution during treatment of chronic infection. NATURE, 592(7853), 277-+. doi:10.1038/s41586-021-03291-y
Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans
Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Salguero, J., . . . Hiscox, J. (2021). Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans. doi:10.1101/2021.03.03.433753
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O'Toole, A., . . . Connor, T. R. (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. CELL, 184(1), 64-+. doi:10.1016/j.cell.2020.11.020
2020
Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
Alm, E., Broberg, E. K., Connor, T., Hodcroft, E. B., Komissarov, A. B., Maurer-Stroh, S., . . . Pereyaslov, D. (2020). Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. EUROSURVEILLANCE, 25(32), 7-14. doi:10.2807/1560-7917.ES.2020.25.32.2001410
2018
Estimating intraspecific genetic diversity from community DNA metabarcoding data
Elbrecht, V., Vamos, E. E., Steinke, D., & Leese, F. (2018). Estimating intraspecific genetic diversity from community DNA metabarcoding data. PEERJ, 6. doi:10.7717/peerj.4644
Estimating intraspecific genetic diversity from community DNA metabarcoding data
Estimating intraspecific genetic diversity from community DNA metabarcoding data
Estimating intraspecific genetic diversity from community DNA metabarcoding data
Assessing intraspecific genetic diversity from community DNA metabarcoding data
Estimating intraspecific genetic diversity from community DNA metabarcoding data.
Elbrecht, V., Vamos, E. E., Steinke, D., & Leese, F. (2018). Estimating intraspecific genetic diversity from community DNA metabarcoding data.. PeerJ, 6, e4644. doi:10.7717/peerj.4644
2017
Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring
Elbrecht, V., Vamos, E. E., Meissner, K., Aroviita, J., & Leese, F. (2017). Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring. METHODS IN ECOLOGY AND EVOLUTION, 8(10), 1265-1275. doi:10.1111/2041-210X.12789
Short COI markers for freshwater macroinvertebrate metabarcoding
Vamos, E., Elbrecht, V., & Leese, F. (2017). Short COI markers for freshwater macroinvertebrate metabarcoding. Metabarcoding and Metagenomics, 1. doi:10.3897/mbmg.1.14625