Virus Hunters: Rapid sequencing for genomic surveillance of healthcare-associated COVID-19

Reviewed by James “Brad” Cutrell, MD FIDSA, UT Southwestern Medical School

Although rapid genomic sequencing has been used to supplement epidemiologic investigation of other infectious diseases such as C. difficile and MDR-GNRs, Meredith et al. are one of the first groups to report its use for SARS-CoV-2 to supplement traditional hospital infection control and contact tracing efforts. This prospective genomic surveillance study in the UK from one Cambridge hospital analyzed epidemiologic and genomic data from 299 patients and were able to identify 35 clusters of identical viruses in 159 patients. In addition to confirming transmission networks in cases with strong epidemiologic links, the analyses uncovered cryptic transmission including hospital-acquired ward outbreaks and transmission in health-care associated community settings not previously suspected. As rapid genomic sequencing for SARS-CoV-2 becomes more widely available, this tool can enhance infection control and public health surveillance tracking efforts.


Meredith LW, et al. Lancet Infect Dis. 2020; Published online July 14, 2020. doi: 

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