Applying prospective genomic surveillance to support investigation of hospital-onset COVID-19

Hamilton, W. L. et al. (2021) Applying prospective genomic surveillance to support investigation of hospital-onset COVID-19. Lancet Infectious Diseases, 21(7), pp. 916-917. (doi: 10.1016/S1473-3099(21)00251-6) (PMID:33984262) (PMCID:PMC8110208)

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Here, we provide an update on our previous Article,1 which described the use of rapid SARS-CoV-2 genome sequencing to investigate hospital-acquired infections (HAIs) at Cambridge University Hospitals NHS Foundation Trust (CUH), Cambridge, UK. CUH experienced a substantial second wave of COVID-19 (figure). Between Nov 2, 2020, and Feb 7, 2021, 162 (14%) of 1178 patients with COVID-19 at CUH had a suspected or definite HAI (as previously defined1), and 465 infected health-care workers (HCWs) were identified via the staff screening programme.2 Nanopore sequencing was attempted for 513 (44%) of 1178 patients, prioritising those with hospital-onset infections, and 324 (70%) of 465 HCWs; 252 (21%) of 1178 patients and 317 (68%) of 465 HCWs had SARS-CoV-2 genomes available after quality control filtering (as previously described1). Patient coverage was lower than in our previous study1 and for HCWs, reflecting different diagnostic testing methods and limitations on sequencing capacity. The frequency of the B.1.1.7 PANGO-lineage3 increased from 8% (nine of 109) in November, 2020, to 83% (257 of 311) in January, 2021.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Illingworth, Dr Chris
Authors: Hamilton, W. L., Fieldman, T., Jahun, A., Warne, B., Illingworth, C. J. R., Jackson, C., Blane, B., Moore, E., Weekes, M. P., Peacock, S. J., De Angelis, D., Goodfellow, I., Gouliouris, T., Török, M. E., Curran, M. D., Parmar, S., Hosmillo, M., Chaudhry, Y., Pinckert, M. L., Georgana, I., Izuagbe, R., Ferris, M., Workman, C., Jones, N. K., Rivett, L., Sparkes, D., Routledge, M., Enoch, D., Whitehorn, J., Moody, C., Brennan, L., Smith, R., Tsui, R., Bousfield, R., Pocock, J., Toleman, M., Payne, H., Coscione, S., Myers, C., Sharrocks, K., Ravji, P., Leong, C., and Ramsay, I.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
Journal Name:Lancet Infectious Diseases
ISSN (Online):1474-4457
Published Online:10 May 2021

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