Molecular epidemiology of SARS-CoV-2 genome sentinel surveillance in commercial COVID-19 testing sites targeting asymptomatic individuals during Japan’s seventh epidemic wave

• Published in: Scientific reports Vol. 14; no. 1; pp. 20950 - 10
• Main Authors: Shiino, Teiichiro, Takeuchi, Junko S., Ohyanagi, Hajime, Kimura, Moto, Kazuyama, Yukumasa, Ikeda, Masato, Sugiura, Wataru
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09.09.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/326/1762; 631/326/596; Asymptomatic; Asymptomatic Infections - epidemiology; Coronaviruses; COVID-19; COVID-19 - diagnosis; COVID-19 - epidemiology; COVID-19 - transmission; COVID-19 - virology; COVID-19 diagnostic tests; Disease transmission; Epidemics; Epidemiology; Genome surveillance; Genome, Viral; Genomes; Humanities and Social Sciences; Humans; Infectious diseases; Japan - epidemiology; Molecular Epidemiology; multidisciplinary; Nucleotide sequence; Phylogeny; Public health; SARS-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Science; Science (multidisciplinary); Sentinel Surveillance; Severe acute respiratory syndrome coronavirus 2; Transmission network; Japan; SARS-CoV-2; Genome surveillance; Transmission network
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-71953-8

Eight peaks of coronavirus disease 2019 (COVID-19) outbreak occurred in Japan, each associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern. The National Epidemiological Surveillance of Infectious Diseases (NESID) analyzed viral genome sequences from symptomatic patients and submitted the results to GISAID. Meanwhile, commercial testing services occasionally sequence samples from asymptomatic individuals. We compared a total of 1248 SARS-CoV-2 full-genome sequences obtained from the SB Coronavirus Inspection Center Corp. (SBCVIC) during Japan’s seventh wave, which was dominated by Omicron variants, with 1764 sequences obtained in Japan from GISAID during the same period using chronological phylogenies and molecular transmission networks. The number of SBCVIC sequences was consistent with the number of cases reported by NESID. The SBCVIC detected a shift in the PANGO lineage from BA.2 to BA.5 earlier than that of GISAID. BA.2 lineages from the SBCVIC were distributed at different locations in the transmission network dominated by GISAID entries, whereas BA.5 lineages from SBCVIC and GISAID often formed distinct subclusters. Test-based sentinel surveillance of asymptomatic individuals may be a more manageable approach compared to notifiable disease surveillance; however, it may not necessarily capture all infection populations throughout Japan.