Time-varying overdispersion of SARS-CoV-2 transmission during the periods when different variants of concern were circulating in Japan

Yura K Ko; Yuki Furuse; Kanako Otani; Masato Yamauchi; Kota Ninomiya; Mayuko Saito; Takeaki Imamura; Alex R Cook; Tadayuki Ahiko; Shunji Fujii; Yoshiharu Mori; Emiko Suzuki; Keiko Yamada; Yoshikazu Ashino; Hidetoshi Yamashita; Yuichi Kato; Katsumi Mizuta; Motoi Suzuki; Hitoshi Oshitani

doi:10.1038/s41598-023-38007-x

Time-varying overdispersion of SARS-CoV-2 transmission during the periods when different variants of concern were circulating in Japan

Sci Rep. 2023 Aug 14;13(1):13230. doi: 10.1038/s41598-023-38007-x.

Authors

Yura K Ko¹, Yuki Furuse², Kanako Otani³, Masato Yamauchi⁴, Kota Ninomiya⁵, Mayuko Saito¹, Takeaki Imamura¹, Alex R Cook⁶, Tadayuki Ahiko⁷, Shunji Fujii⁸, Yoshiharu Mori⁸, Emiko Suzuki⁹, Keiko Yamada¹⁰, Yoshikazu Ashino¹¹, Hidetoshi Yamashita¹², Yuichi Kato¹², Katsumi Mizuta¹³, Motoi Suzuki³, Hitoshi Oshitani¹⁴

Affiliations

¹ Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan.
² Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
³ Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan.
⁴ Japan International Cooperation Agency, Tokyo, Japan.
⁵ Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
⁶ Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore.
⁷ Division of Health and Welfare Planning, Yamagata Prefectural Government, Yamagata, Japan.
⁸ Murayama Public Health Center, Yamagata, Japan.
⁹ Mogami Public Health Center, Yamagata, Japan.
¹⁰ Okitama Public Health Center, Yamagata, Japan.
¹¹ Shonai Public Health Center, Yamagata, Japan.
¹² Yamagata City Institute of Public Health, Yamagata, Japan.
¹³ Yamagata Prefectural Institute of Public Health, Yamagata, Japan.
¹⁴ Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan. [email protected].

Abstract

Japan has implemented a cluster-based approach for coronavirus disease 2019 (COVID-19) from the pandemic's beginning based on the transmission heterogeneity (overdispersion) of severe acute respiratory coronavirus 2 (SARS-CoV-2). However, studies analyzing overdispersion of transmission among new variants of concerns (VOCs), especially for Omicron, were limited. Thus, we aimed to clarify how the transmission heterogeneity has changed with the emergence of VOCs (Alpha, Delta, and Omicron) using detailed contact tracing data in Yamagata Prefecture, Japan. We estimated the time-varying dispersion parameter ([Formula: see text]) by fitting a negative binomial distribution for each transmission generation. Our results showed that even after the emergence of VOCs, there was transmission heterogeneity of SARS-CoV-2, with changes in [Formula: see text] during each wave. Continuous monitoring of transmission dynamics is vital for implementing appropriate measures. However, a feasible and sustainable epidemiological analysis system should be established to make this possible.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / epidemiology
Contact Tracing
Humans
Japan / epidemiology
Respiratory Rate
SARS-CoV-2* / genetics