Infectious Deseases
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Pathogen Genomics Center, National Institute of Infectious Diseases.
Analysis of whole genome sequences provides information that is useful for tracing back infection using genome-wide SNVs among clusters. During the primary wave, local public health centers were able to identify likely COVID-19 patients and their close contacts within location-specific clusters by conducting active epidemiological surveillance using the keywords “Wuhan, Hubei, and China.” Just as the situation had begun to improve around mid-March, a large number of new COVID-19 patients were diagnosed, many of with unclear infection routes. Tracing the infection routes was difficult because some Japanese cases had no recent history of travel to China or any country outside Japan. The SARS-CoV-2 haplotype network analysis suggested that the second wave of COVID-19 cases could have been imported via the returnees from EU, North America, or other countries.