Molecular epidemiological insights into transmission trends in Nagoya area based on SARS-CoV-2 genome sequencing (Mar-Oct, 2020)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of coronavirus disease (COVID-19) which has spread rapidly worldwide to cause a global pandemic. The SARS-CoV-2 genome shows a lower mutation rate than other RNA viruses. However, because of the ongoing rapid worldwide transmission among humans, the genetic diversity of the SARS-CoV-2 genome has increased. In Japan, a previous study suggested that the distinct viral clades L, S, G and GR of SARS-CoV-2 had been imported from overseas and begun to circulate domestically by April 2020. However, little is known about molecular epidemiology of SARS-CoV-2 since then, because of the lack of sufficient information on the viral genome sequence information in Japan. Herein, to probe the molecular epidemiological trends in Japan, we determined the full genome sequences of SARS-CoV-2 (n=55) derived from patients admitted to our hospital and performed a comparative analysis with domestic and international sequence information available from GISAID and GenBank. The results showed that the dominant domestic genotypes, including our determined sequences, had shifted from clades S and L to clades G and GR, and dispersed widely during the first infection peak period (March to April). In contrast, all the SARS-CoV-2 genotypes after May 2020 are highly clustered as unique clade GR genotypes that are not detected outside Japan. This genetic clustering occurred during the period under which restrictions were placed on overseas travel in Japan. Similar trends of viral genotype clustering have also been observed worldwide, with regional disparities. Under these circumstances, we should adopt adequate preventive measures to prevent the viral genetic diversity from increasing, and also further extend the molecular epidemiological survey of SARS-CoV-2 genotypes in Japan. These efforts will aid in ensuring successful use of the novel vaccines and antiviral drugs in the near future.