2022
Illingworth, CJR., Hamilton, WL., Jackson, C., Warne, B., Popay, A., Meredith, L., Hosmillo, M., Jahun, A., Fieldman, T., Routledge, M., Houldcroft, CJ., Caller, L., Caddy, S., Yakovleva, A., Hall, G., Khokhar, FA., Feltwell, T., Pinckert, ML., Georgana, I., Chaudhry, Y., Curran, M., Parmar, S., Sparkes, D., Rivett, L., Jones, NK., Sridhar, S., Forrest, S., Dymond, T., Grainger, K., Workman, C., Gkrania-Klotsas, E., Brown, NM., Weekes, MP., Baker, S., Peacock, SJ., Gouliouris, T., Goodfellow, I., Angelis, DD. and Török, ME., 2022. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events. Mol Biol Evol, v. 39
Doi: http://doi.org/10.1093/molbev/msac025
2021 (Accepted for publication)
Peacock, S., Illingworth, C., Torok, ME. and Goodfellow, I., 2021 (Accepted for publication). Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections eLife, v. 10
Doi: http://doi.org/10.7554/eLife.67308
Maes, M., Higginson, E., Pereira-Dias, J., Curran, MD., Parmar, S., Khokhar, F., Cuchet-Lourenço, D., Lux, J., Sharma-Hajela, S., Ravenhill, B., Hamed, I., Heales, L., Mahroof, R., Solderholm, A., Forrest, S., Sridhar, S., Brown, NM., Baker, S., Navapurkar, V., Dougan, G., Bartholdson Scott, J. and Conway Morris, A., 2021 (Accepted for publication). Ventilator-associated pneumonia in critically ill patients with COVID-19 Critical Care (UK),
Peacock, S., Hamilton, W., Torok, ME., COG-UK Consortium, , Goodfellow, I. and Dougan, G., 2021 (Accepted for publication). Genomic epidemiology of COVID-19 in 1 care homes in the
2 East of England eLife,
Doi: http://doi.org/10.7554/eLife.64618
Tonkin-Hill, G., Martincorena, I., Amato, R., Lawson, AR., Gerstung, M., Johnston, I., Jackson, DK., Park, N., Lensing, SV., Quail, MA., Gonçalves, S., Ariani, C., Spencer Chapman, M., Hamilton, WL., Meredith, LW., Hall, G., Jahun, AS., Chaudhry, Y., Hosmillo, M., Pinckert, ML., Georgana, I., Yakovleva, A., Caller, LG., Caddy, SL., Feltwell, T., Khokhar, FA., Houldcroft, CJ., Curran, MD., Parmar, S., COVID-19 Genomics UK (COG-UK) Consortium, , Alderton, A., Nelson, R., Harrison, EM., Sillitoe, J., Bentley, SD., Barrett, JC., Torok, ME., Goodfellow, IG., Langford, C., Kwiatkowski, D. and Wellcome Sanger Institute COVID-19 Surveillance Team, , 2021 (Accepted for publication). Patterns of within-host genetic diversity in SARS-CoV-2 eLife, v. 10
Doi: http://doi.org/10.7554/eLife.66857
Snell, LB., Fisher, CL., Taj, U., Stirrup, O., Merrick, B., Alcolea-Medina, A., Charalampous, T., Signell, AW., Wilson, HD., Betancor, G., Kia Ik, MT., Cunningham, E., Cliff, PR., Pickering, S., Galao, RP., Batra, R., Neil, SJD., Malim, MH., Doores, KJ., Douthwaite, ST., Nebbia, G., COVID-19 Genomics UK (COG-UK) consortium, , Edgeworth, JD. and Awan, AR., 2021 (Accepted for publication). Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission Clinical Microbiology and Infection,
Doi: http://doi.org/10.1016/j.cmi.2021.07.040
2021
Clark, JA., Kean, IRL., Curran, MD., Khokhar, F., White, D., Daubney, E., Conway Morris, A., Navapurkar, V., Bartholdson Scott, J., Maes, M., Bousfield, R., Gouliouris, T., Agrawal, S., Inwald, D., Zhang, Z., Török, ME., Baker, S. and Pathan, N., 2021. Rapid Assay for Sick Children with Acute Lung infection Study (RASCALS): diagnostic cohort study protocol. BMJ Open, v. 11
Doi: http://doi.org/10.1136/bmjopen-2021-056197
Volz, E., Hill, V., McCrone, JT., Price, A., Jorgensen, D., O'Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, FF., Rey, SM., Nicholls, SM., Colquhoun, RM., da Silva Filipe, A., Shepherd, J., Pascall, DJ., Shah, R., Jesudason, N., Li, K., Jarrett, R., Pacchiarini, N., Bull, M., Geidelberg, L., Siveroni, I., COG-UK Consortium, , Goodfellow, I., Loman, NJ., Pybus, OG., Robertson, DL., Thomson, EC., Rambaut, A. and Connor, TR., 2021. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity Cell, v. 184
Doi: http://doi.org/10.1016/j.cell.2020.11.020
Macleod, CK., Khokhar, FA., Warne, B., Wick, R., Butcher, R., Cassimon, B., Hayden, P., Holt, K. and Török, ME., 2021. Rapid Whole Genome Sequencing of Serotype K1 Hypervirulent Klebsiella pneumoniae from an Undocumented Chinese Migrant. Case Rep Infect Dis, v. 2021
Doi: http://doi.org/10.1155/2021/6638780
Srivastava, S., Khokhar, F., Madhav, A., Pembroke, B., Shetty, V. and Mutreja, A., 2021. COVID-19 lessons for climate change and sustainable health Energies, v. 14
Doi: http://doi.org/10.3390/en14185938
2020 (Accepted for publication)
Weekes, M., rivett, L., Sridhar, S., sparkes, D., routledge, M., jones, N., forrest, S., young, J., Pereira-Dias, J., hamilton, W., torok, E., Meredith, L., curran, M., fuller, S., Samworth, R., Bradley, J., Dougan, G., Smith, K., Lehner, P., Matheson, N., Goodfellow, I. and Baker, S., 2020 (Accepted for publication). Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission eLife,
Weekes, M., 2020 (Accepted for publication). Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 eLife,
Doi: http://doi.org/10.7554/eLife.59391
2020
Peacock, S., Meredith, L., Dougan, G., Torok, ME., Baker, S., Brwon, N. and Gouliouris, T., 2020. Rapid implementation of SARS-CoV-2 sequencing to
investigate cases of health-care associated COVID-19:
a prospective genomic surveillance study Lancet Infectious Diseases,
Doi: http://doi.org/10.1016/S1473-3099(20)30562-4
2018
Wilson, HJ., Khokhar, F., Enoch, DA., Brown, NM., Ahluwalia, J., Dougan, G. and Török, ME., 2018. Point-prevalence survey of carbapenemase-producing Enterobacteriaceae and vancomycin-resistant enterococci in adult inpatients in a university teaching hospital in the UK. J Hosp Infect, v. 100
Doi: http://doi.org/10.1016/j.jhin.2018.06.024