Publications
2023
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
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
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
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
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
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
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 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
2021
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
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., . . . Ferguson, N. M. (2021). Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. NATURE, 593(7858), 266-+. 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
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
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, Á., . . . Connor, T. R. (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
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.
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. (n.d.). Short COI markers for freshwater macroinvertebrate metabarcoding. Metabarcoding and Metagenomics, 1, e14625. doi:10.3897/mbmg.1.14625