Utilization of Whole Genome Sequencing to Understand SARS-CoV-2 Transmission Dynamics in Long-Term Care Facilities, Correctional Facilities and Meat Processing Plants in Minnesota, March - June 2020

Lehnertz, N. B.; Wang, X.; Garfin, J.; Taylor, J.; Zipprich, J.; VonBank, B.; Martin, K.; Eikmeier, D.; Medus, C.; Wiedinmyer, B.; Bernu, C.; Plumb, M.; Pung, K.; Honein, M. A.; Carter, R.; MacCannell, D.; Smith, K. E.; Como-Sabetti, K.; Ehresmann, K.; Danila, R.; Lynfield, R.

Congregate settings and high-density workplaces have endured a disproportionate impact from COVID-19. In order to provide further understanding of the transmission patterns of SARS-CoV-2 in these settings, whole genome sequencing (WGS) was performed on samples obtained from 8 selected outbreaks in Minnesota from March -June, 2020. WGS and phylogenetic analysis was conducted on 319 samples, constituting 14.4% of the 2,222 total SARS-CoV-2-positive individuals associated with these outbreaks. Among the sequenced specimens, three LTCFs and both correctional facilities had spread associated with a single genetic sequence. A fourth LTCF had outbreak cases associated with two distinct sequences. In contrast, cases associated with outbreaks in the two meat processing plants represented multiple SARS-CoV-2 sequences. These results suggest that a single introduction of SARS-CoV-2 into a facility can result in a widespread outbreak, and early identification and cohorting of cases, along with continued vigilance with infection prevention and control measures is imperative.