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.


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Hamilton, W., Fieldman, T., Jahun, A., Warne, B., Illingworth, C., Jackson, C., Blane, B., Moore, E., Weekes, M., Peacock, S., De Angelis, D., Goodfellow, I., Gouliouris, T., Török, M., Curran, M., Parmar, S., Hosmillo, M., Chaudhry, Y., Pinckert, M., Georgana, I., Izuagbe, R., Ferris, M., Workman, C., Jones, N., 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. & Ramsay, I. 2021, 'Applying prospective genomic surveillance to support investigation of hospital-onset COVID-19', Lancet Infectious Diseases, 21(7), pp. 916-917. http://dx.doi.org/10.1016/S1473-3099(21)00251-6

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Last updated: 19 October 2023
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