Epidemiological and Genomic Analysis of a Large SARS-CoV-2 Outbreak in a Long-Term Care Facility in Catalonia, Spain

Abstract

Limiting outbreaks in long-term care facilities (LTCFs) is a cornerstone strategy to avoid an excess of COVID-19-related morbidity and mortality and to reduce its burden on the health system. We studied a large outbreak that occurred at an LTCF, combining methods of classical and genomic epidemiology analysis. The outbreak lasted for 31 days among residents, with an attack rate of 98% and 57% among residents and staff, respectively. The case fatality rate among residents was 16% (n = 15). Phylogenetic analysis of 59 SARS-CoV-2 isolates revealed the presence of two closely related viral variants in all cases (B.1.177 lineage), revealing a far more complex outbreak than initially thought and suggesting an initial spread driven by staff members. In turn, our results suggest that resident relocations to mitigate viral spread might have increased the risk of infection for staff members, creating secondary chains of transmission that were responsible for prolonging the outbreak. Our results highlight the importance of considering unnoticed chains of transmission early during an outbreak and making an adequate use and interpretation of diagnostic tests. Outbreak containment measures should be carefully tailored to each LTCF. IMPORTANCE The impact of COVID-19 on long-term care facilities (LTCFs) has been disproportionately large due to the high frailty of the residents. Here, we report epidemiological and genomic findings of a large outbreak that occurred at an LTCF, which ultimately affected almost all residents and nearly half of staff members. We found that the outbreak was initially driven by staff members; however, later resident relocation to limit the outbreak resulted in transmission from residents to staff members, evidencing the complexity and different phases of the outbreak. The phylogenetic analysis of SARS-CoV-2 isolates indicated that two closely related variants were responsible for the large outbreak. Our study highlights the importance of combining methods of classical and genomic epidemiology to take appropriate outbreak containment measures in LTCFs.

Keywords: COVID-19; SARS-CoV-2; occupational risk; residential facilities; transmission.

FIG 1

Outbreak development. (A) Ground floor layout of the long-term-care facility. Each sector and room numbers are indicated. The depicted situation corresponds to 15 December 2020. Colors indicate infection status at different time points during the initial phases of the outbreak and the corresponding SARS-CoV-2 cluster. (B) Chronology of outbreak events and cases. For each case detected among residents and workers, the date of sample collection and the SARS-CoV-2 cluster detected are indicated. The period with a yellow background corresponds to the time of resident relocations according to their infection status (phase III of the outbreak).

FIG 2

Kaplan-Meier survival estimates. Each phase of the outbreak is indicated. Survival estimate curves for staff (light gray) and residents (dark gray) had parallel trajectories, with a super spreading event (phase II) resulting in a great number of cases among residents, which in turn infected staff members during the relocation period (phase III).

FIG 3

Maximum-likelihood phylogenetic tree. Detail of the rooted phylogenetic tree, including the sequences from our study along with other sequences from Catalonia for the same time period. Shades in the tree branches and corresponding labels indicate each genomic cluster. Star shapes indicate staff members. The scale bar represents the number of substitutions per nucleotide position.