SARS-CoV-2 R.1 lineage variants prevailed in Tokyo in March 2021
Abstract
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 by using polymerase chain reaction (PCR)-based methods.
Methods
Nasopharyngeal swab samples from 108 patients who visited our hospital between February and April 2021 were analyzed. The samples were analyzed using reverse transcription-PCR with melting curve analysis to detect the N501Y and E484K mutations. A part of the samples were also subjected to whole genome sequencing (WGS). 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. WGS 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, which suggests the increased transmissibility of R.1 variants while they showed no increased severity.
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