In this study, we conducted genetic surveillance and identified R.1 lineage harboring E484K mutation in RBD by whole genome sequencing. The R.1 lineage was observed in three patients and transmitted among relatives in Japan. To investigate the global distribution of R.1 lineage, we next collected registration data from the EpiCoV of GISAID database . As of March 5, 2021, a total of 305 samples of R.1 lineage had been registered from all over the world, with the majority spread in the USA (44%, 135/305) and Japan (28%, 84/305) (Figure 1A and Table 1). R.1 lineage was first reported in Texas, USA at the end of October 2020, and was found in Japan at the end of November 2020. The number of detected lineages has changed in a similar trend between the USA, Japan and other countries (Figure 1A), implying that SARS-CoV-2 R.1 lineage may have emerged in several regions at approximately the same time.
The Kentucky Department for Public Health and a local health department investigated a COVID-19 outbreak in a skilled nursing facility that occurred after all residents and health care personnel had been offered vaccination. Among 83 residents and 116 health care personnel, 75 residents and 61 staff, respectively, received 2 vaccine doses. Twenty-six residents and 20 health care personnel received positive test results for SARS-CoV-2, the virus that causes COVID-19, including 18 residents and four health care personnel who had received their second vaccine dose >14 days before the outbreak began.
An R.1 lineage variant was detected with whole genome sequencing. Although the R.1 variant has multiple spike protein mutations, vaccinated residents and HCP were 87% less likely to have symptomatic COVID-19 compared with those who were unvaccinated. Vaccination of skilled nursing facility populations, including health care personnel, is critical to reduce the risk for SARS-CoV-2 introduction, transmission, and severe outcomes in skilled nursing facilities.