Serial Testing for SARS-CoV-2 and Virus Whole Genome Sequencing Inform Infection Risk at Two Skilled Nursing Facilities with COVID-19 Outbreaks - Minnesota, April-June 2020

Abstract

SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), can spread rapidly in high-risk congregate settings such as skilled nursing facilities (SNFs) (1). In Minnesota, SNF-associated cases accounted for 3,950 (8%) of 48,711 COVID-19 cases reported through July 21, 2020; 35% of SNF-associated cases involved health care personnel (HCP*), including six deaths. Facility-wide, serial testing in SNFs has been used to identify residents with asymptomatic and presymptomatic SARS-CoV-2 infection to inform mitigation efforts, including cohorting of residents with positive test results and exclusion of infected HCP from the workplace (2,3). During April-June 2020, the Minnesota Department of Health (MDH), with CDC assistance, conducted weekly serial testing at two SNFs experiencing COVID-19 outbreaks. Among 259 tested residents, and 341 tested HCP, 64% and 33%, respectively, had positive reverse transcription-polymerase chain reaction (RT-PCR) SARS-CoV-2 test results. Continued SARS-CoV-2 transmission was potentially facilitated by lapses in infection prevention and control (IPC) practices, up to 12-day delays in receiving HCP test results (53%) at one facility, and incomplete HCP participation (71%). Genetic sequencing demonstrated that SARS-CoV-2 viral genomes from HCP and resident specimens were clustered by facility, suggesting facility-based transmission. Residents and HCP working in SNFs are at risk for infection with SARS-CoV-2. As part of comprehensive COVID-19 preparation and response, including early identification of cases, SNFs should conduct serial testing of residents and HCP, maximize HCP testing participation, ensure availability of personal protective equipment (PPE), and enhance IPC practices^† (4-5).

FIGURE 1

Date of serial testing round and daily specimen test results^,†,§ for SARS-CoV-2 detection by reverse transcription–polymerase chain reaction (RT-PCR) testing — two skilled nursing facilities, Minnesota, April–June 2020 Abbreviation: HCP = health care personnel. * In facility A, two residents had indeterminate results for specimens collected on April 30; one resident had a positive test result on May 7 and one resident had another indeterminate test result on May 11 before a negative test result on May 14. ^† In facility A, one HCP had an indeterminate test result on May 21 and was not retested. ^§ In facility B, one resident had an indeterminate result on May 7 and had a positive test result on May 14, one resident had an indeterminate result on May 28 and had a negative test result on June 4, and one resident had an indeterminate result on June 4 and had a negative test result on June 8.

FIGURE 2

Phylogenetic trees showing genetic distance between available SARS-CoV-2 virus specimens collected from health care personnel (HCP) and residents at facility A^† and facility B^§— Minnesota, April–June 2020 * Genetic divergence based on nucleotide difference is indicated by length of branches. Available specimens included specimens tested and stored at Minnesota Public Health Laboratory and commercial labs where specimens could be retrieved and where RNA could be extracted. ^† Available specimens from facility A included HCP and residents diagnosed after April 29. At facility A, 17 resident and five HCP specimens had genetically similar virus strains, including one HCP with limited resident contact. Two HCP had virus sequences that were genetically different from the facility A cluster and were more similar to cases associated with community transmission in Minnesota. A third strain identified in a resident during the third testing round was genetically different from both HCP and resident strains. ^§ Available specimens from facility B included HCP diagnosed after May 6 and residents diagnosed after April 29, throughout the outbreak. At facility B, 75 resident specimens and five HCP specimens shared genetically related strains.