In a SNF with 90.4% of residents vaccinated, an outbreak of COVID-19 occurred after introduction from an unvaccinated, symptomatic HCP. WGS identified an R.1 lineage variant, characterized by E484K and other mutations within the spike protein. Attack rates were three to four times as high among unvaccinated residents and HCP as among those who were vaccinated; vaccinated persons were significantly less likely to experience symptoms or require hospitalization.
Although the R.1 variant is not currently identified as a CDC variant of concern or interest,*** it does have several mutations of importance. The D614G mutation demonstrates evidence of increasing virus transmissibility (4). The E484K mutation, found within the receptor-binding domain of the spike protein, is also seen in the variants of concern B.1.351 and P.1, which show evidence of reduced neutralization by convalescent and postvaccination sera (5,6). Mutation W152L might reduce the effectiveness of neutralizing antibodies (7). Although vaccination was associated with decreased likelihood of infection and symptomatic illness, 25.4% of vaccinated residents and 7.1% of vaccinated HCP were infected, supporting concerns about potential reduced protective immunity to R.1. In addition, four possible reinfections were identified, providing some evidence of limited or waning natural immunity to this variant.
Point estimates for VE against SARS-CoV-2 infections were lower than were those reported from Israel’s national vaccination program (8). Whereas this could reflect reduced protection against R.1, other factors to consider include the smaller sample size in this study and the higher exposure risk associated with an outbreak in a congregate setting. In addition, testing, regardless of symptoms, was performed with high frequency for both residents and HCP, which contrasts with VE studies that use a primary reliance on individual test-seeking behavior. Such differences could influence VE estimates for infection; therefore, caution is urged when comparing these studies. Regardless of VE differences in SARS-CoV-2 infection, the estimated VE for COVID-19 symptom prevention (86.5% for residents; 87.1% for HCP) demonstrates a strong protective effect of vaccination.
The risk for poor outcomes among unvaccinated SNF residents is highlighted by the hospitalization of four of the six unvaccinated, infected residents, and two subsequent deaths, including in one previously infected resident. This underscores the importance of the Advisory Committee on Immunization Practices’ recommendation that all persons, including those who have recovered from COVID-19, be vaccinated.†††
Low acceptance of vaccination among SNF HCP might increase the likelihood of SARS-CoV-2 introduction and transmission within a facility. Nationally, a median of 37.5% of HCP working in long-term care facilities had received at least 1 dose of vaccine by mid-January 2021 (9). Although the vaccination rate in this SNF surpassed this early national rate, approximately one half of HCP were vaccinated. To protect SNF residents, it is imperative that HCP, as well as SNF residents, be vaccinated. A continued emphasis on strategies for prevention of disease transmission, even among vaccinated populations, is also critical. Timely implementation of infection control strategies after outbreak identification likely contributed to the rapid decline in new cases during the second week of the outbreak.
The findings in this report are subject to at least three limitations. First, the health status of residents who declined vaccination might have differed from those who consented to vaccination. Thus, hospitalization and death outcomes might be biased when comparing the groups without controlling for underlying health conditions. Second, underlying health status and advance directives might affect decisions for resident hospitalization; therefore, association of vaccination with hospitalization in this SNF population might have limited generalizability. Finally, because of the reduced sensitivity of antigen testing in asymptomatic populations,§§§ it is possible that some asymptomatic cases were not identified. If this introduced differential bias for identification of cases in either the vaccinated or unvaccinated groups, actual VE for the prevention of SARS-CoV-2 infections could differ from measured effectiveness.
An R.1 lineage variant, not previously detected in Kentucky, was identified in a SNF outbreak where 46 residents and HCP were infected. Compared with unvaccinated persons, vaccinated persons had reduced risk for SARS-CoV-2 infection and symptomatic COVID-19. A continued emphasis on vaccination of SNF populations, including HCP, is essential to reduce the risk for SARS-CoV-2 introduction, transmission, and severe outcomes in SNFs. An ongoing focus on infection prevention and control practices is also critical.