Clinical Utility of SARS-CoV-2 Whole Genome Sequencing in Deciphering Source of Infection

Takenouchi, Toshiki; Iwasaki, Yuka W.; Harada, Sei; Ishizu, Hirotsugu; Uwamino, Yoshifumi; Uno, Shunsuke; Osada, Asami; Hasegawa, Naoki; Murata, Mitsuru; Takebayashi, Toru; Fukunaga, Koichi; Saya, Hideyuki; Kitagawa, Yuko; Amagai, Masayuki; Siomi, Haruhiko; Kosaki, Kenjiro

The novel coronavirus disease (COVID-19) pandemic caused by SARS-CoV-2 is a major threat to humans. Recently, we encountered two seemingly separate COVID-19 clusters in a tertiary care medical center. Whole viral genome sequencing detected the haplotype of the SARS-CoV-2 genome and the two clusters were successfully distinguished by the viral genome haplotype. Concurrently, there were nine COVID-19 patients clinically unlinked to clusters #1 or #2 that necessitated the determination of the source of infection. Such patients had similar haplotypes to that in cluster #2 but were devoid of two rare mutations characteristic to cluster #2. This suggested that these nine cases of "probable community infection" indeed had community infection and were not derived from cluster #2. Whole viral genome sequencing of SARS-CoV-2 is a powerful measure not only for monitoring the global trend of SARS-CoV-2 but also for identifying the source of infection of COVID-19 at a level of institution.