Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 in High-Density Settings

Minnesota, USA, March-June 2020

Nicholas B. Lehnertz; Xiong Wang; Jacob Garfin; Joanne Taylor; Jennifer Zipprich; Brittany VonBank; Karen Martin; Dana Eikmeier; Carlota Medus; Brooke Wiedinmyer; Carmen Bernu; Matthew Plumb; Kelly Pung; Margaret A. Honein; Rosalind Carter; Duncan MacCannell; Kirk E. Smith; Kathryn Como-Sabetti; Kris Ehresmann; Richard Danila; Ruth Lynfield

Disclosures

Emerging Infectious Diseases. 2021;27(8):2052-2063. 

In This Article

Abstract and Introduction

Abstract

Coronavirus disease has disproportionately affected persons in congregate settings and high-density workplaces. To determine more about the transmission patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in these settings, we performed whole-genome sequencing and phylogenetic analysis on 319 (14.4%) samples from 2,222 SARS-CoV-2–positive persons associated with 8 outbreaks in Minnesota, USA, during March–June 2020. Sequencing indicated that virus spread in 3 long-term care facilities and 2 correctional facilities was associated with a single genetic sequence and that in a fourth long-term care facility, outbreak cases were associated with 2 distinct sequences. In contrast, cases associated with outbreaks in 2 meat-processing plants were associated with 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. Early identification and cohorting (segregating) of virus-positive persons in these settings, along with continued vigilance with infection prevention and control measures, is imperative.

Introduction

In the United States, coronavirus disease (COVID-19) has disproportionately affected adults residing in long-term care facilities (LTCFs).[1–5] Outbreaks in LTCFs have caused high numbers of hospitalizations and deaths. Similar findings have been reported in correctional facilities, where severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection incidence among inmates and staff is ≈5 times greater and age-adjusted mortality rate 3 times greater than that of the general population.[6–8] Workers in high-density workplaces (e.g., meat-processing plants) have similarly been heavily affected; minority populations have been disproportionately affected.[9–11]

The first COVID-19 case in Minnesota was detected on March 6, 2020. Shortly thereafter, COVID-19 outbreaks occurred across the state, including in LTCFs (March 12, 2020) and meat-processing plants (March 15, 2020), followed shortly thereafter by correctional facilities (March 25, 2020). During March 6–June 30, 2020, the Minnesota Department of Health (MDH) identified and responded to 1,060 distinct outbreaks of COVID-19 in LTCFs, comprising 4,421 cases in residents and 3,002 in staff members. In addition, 4 discrete outbreaks in correctional facilities resulted in 382 cases, and 68 outbreaks in meat-processing plants resulted in ≈2,616 cases among employees (data only from persons interviewed and where workplace information was provided); outbreaks in these 3 settings accounted for 31.3% of all identified persons in Minnesota.

For outbreaks in congregate settings and high-density workplaces, confirming the temporal and relational aspects of SARS-CoV-2 transmission was difficult, and the role of intrafacility spread versus multiple introductions was difficult to disentangle on the basis of epidemiologic information alone. Whole-genome sequencing (WGS) of specimens from outbreak case-patients can be used to determine transmission dynamics and relatedness of viral pathogens in infectious disease outbreaks.[12–15] Unprecedented efforts to sequence SARS-CoV-2 genomes have occurred at the local, regional, national, and international levels to investigate potential reinfections,[16–19] nosocomial transmission,[20] patterns of community spread (G.K. Moreno et al., unpub. data, https://doi.org/10.1101/2020.07.09.20149104),[21,22] and sources of SARS-CoV-2 introduction without known epidemiologic links.[23]

In Minnesota, as part of the Centers for Disease Control and Prevention (CDC) SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) consortium, the Minnesota Molecular Surveillance of SARS-CoV-2 initiative solicited specimens from outbreak case-patients for sequencing and genetic variation analysis to determine virus transmission patterns in congregate settings and meat-processing plants. To supplement epidemiologic information, assess whether single or multiple introductions were likely to have occurred during a facility outbreak, and evaluate molecular relatedness, we performed WGS on a convenience sample of SARS-CoV-2–positive specimens associated with outbreaks.

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