Phylogenomics of Severe Acute Respiratory Syndrome Coronavirus 2 in Emergency Shelters for People Experiencing Homelessness

Using genomic data, we estimate that 28 cases of SARS-CoV-2 infection in 8 shelters in King County, Washington were the result of at least 12 introduction events and that at least 16 of these cases resulted from intrashelter viral transmission. Background Residents and staff of emergency shelters for people experiencing homelessness (PEH) are at high risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The importance of shelter-related transmission of SARS-CoV-2 in this population remains unclear. It is also unknown whether there is significant spread of shelter-related viruses into surrounding communities. Methods We analyzed genome sequence data for 28 SARS-CoV-2-positive specimens collected from 8 shelters in King County, Washington between March and October, 2020. Results We identified at least 12 separate SARS-CoV-2 introduction events into these 8 shelters and estimated that 57% (16 of 28) of the examined cases of SARS-CoV-2 infection were the result of intrashelter transmission. However, we identified just a few SARS-CoV-2 specimens from Washington that were possible descendants of shelter viruses. Conclusions Our data suggest that SARS-CoV-2 spread in shelters is common, but we did not observe evidence of widespread transmission of shelter-related viruses into the general population.