SARS-CoV-2 R.1 lineage variants prevailed in Tokyo in March 2021

Nagano, K.; Tani-Sassa, C.; Iwasaki, Y.; Takatsuki, Y.; Yuasa, S.; Takahashi, Y.; Nakajima, J.; Sonobe, K.; Ichimura, N.; Nukui, Y.; Takeuchi, H.; Tanimoto, K.; Tanaka, Y.; Kimura, A.; Tohda, S.

Background: The spread of SARS-CoV-2 variants, such as B.1.1.7 and B.1.351, has become a crucial issue worldwide. Therefore, we began testing all patients with COVID-19 for the N501Y and E484K mutations associated with SARS-CoV-2. Study design: Nasopharyngeal swab samples from 108 patients who visited our hospital between February and April 2021 were analyzed. The samples were analyzed using reverse transcription-polymerase chain reaction with melting curve analysis to detect the N501Y and E484K mutations. A part of the samples were also subjected to whole genome sequencing. Clinical parameters such as mortality and admission to the intensive care unit were analyzed to examine the association between increased disease severity and the E484K mutation. Results: The ratio of cases showing the 501N+484K mutation rapidly increased from 8% in February to 46% in March. Whole genome sequencing revealed that the viruses with 501N+484K mutation are R.1 lineage variants. Evidence of increased disease severity related to the R.1 variants were not found. Conclusions: We found that the R.1 lineage variants rapidly prevailed in Tokyo in March 2021.