Comparison of COVID-19 infection status using PCR and NGS in three areas (Matsusaka City, Tokyo and Osaka)

<p>COVID-19 had continued to threaten the world as a category 2 infectious disease from the end of 2019 to May 8, 2023. Our hospital has introduced real-time PCR and NGS, actively conducting tests for SARS-CoV-2. In this report, we have compiled the results of SARS-CoV-2 testing over the past two years and summarized the infection situation in Matsusaka City. The results of 9,007 specimens that tested positive by real-time PCR at our hospital from January 2021 to April 2023 were analyzed. We compared the number of positive cases, the onset until the peak of each epidemic wave, and the emergence period of the main variants with Tokyo and Osaka prefectures. Additionally, we conducted a full genome analysis using NGS on 64 of those samples. Comparing the graphs of the respective positive counts, it was thought that the data from our hospital reflected the number of positive cases in Matsusaka City. While it showed a similar curve to Mie Prefecture, when compared to Tokyo and Osaka, it took longer to reach the peak of each infection wave. The occurrence of mutant strains was also detected earlier in Tokyo and Osaka. Furthermore, there were no variants that could have mutated uniquely in Matsusaka City. By understanding the infection situation in urban areas, it is believed that more time can be secured for implementing infection control measures. Our testing laboratory, equipped with both real-time PCR and NGS, is expected to contribute to Matsusaka City, infection control efforts in the future.</p>