Last November, the researchers found that a patient in the Kanto region, which encompasses Tokyo, had a strain called "20C," which has mainly been spreading on the US West Coast.
The patient had not traveled abroad, which suggests the virus was community-acquired.
The current outbreak in Japan mainly consists of two types of the coronavirus that remained after the first wave last year. The 20C strain has not been detected since May last year, except at quarantine stations.
Genomic virus surveillance can lead to early identification of new variants and inform proper response during a pandemic. Using this approach, we have identified a new variant of the SARS-CoV-2 virus that emerged in the United States (U.S.) early in the coronavirus disease (COVID-19) pandemic and has become one of the most prevalent U.S variants. This new variant within the B.1.2 lineage referred to here as 20C-US, has not yet spread widely to other countries. The earliest 20C-US genomes can be traced to the southern U.S. in late May of 2020. A major early event was the rapid acquisition of five non-synonymous mutations. The changes carried by 20C-US now include mutations to genes involved in virus particle maturation and release, processing of viral proteins, and RNA genome integrity and translation genes, all important for efficient and accurate virus production. In addition, 20C-US has since acquired two new non-synonymous mutations that highlight its ongoing evolution, one of which is a Q677H mutation in the spike protein adjacent to the furin cleavage site. We predict that 20C-US may already be the most dominant variant of SARS-CoV-2 in the U.S. The ongoing evolution of 20C-US, as well as other dominant region-specific variants emerging around the world, should continue to be monitored with genomic, epidemiologic, and experimental studies to understand viral evolution and predict future outcomes of the pandemic.
