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Genetic diversity and declining norovirus prevalence in infants and children during Japan's COVID-19 pandemic: a three-year molecular surveillance

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Abstract

Noroviruses (NoVs) are a global concern, causing widespread outbreaks and sporadic acute gastroenteritis (AGE) cases across all age groups. Recent research has shed light on the emergence of novel recombinant strains of NoV in various countries. To delve deeper into this phenomenon, we extensively analyzed 1,175 stool samples collected from Japanese infants and children with AGE from six different prefectures in Japan over three years, from July 2018 to June 2021. Our investigation aimed to determine the prevalence and genetic characteristics of NoV associated with sporadic AGE while exploring the possibility of detecting NoV recombination events. Among the analyzed samples, we identified 355 cases positive for NoV, 11 cases attributed to GI genotypes, and 344 associated with GII genotypes. Notably, we discovered four distinct GI genotypes (GI.2, GI.3, GI.4, and GI.6) and seven diverse GII genotypes (GII.2, GII.3, GII.4, GII.6, GII.7, GII.14, and GII.17). The predominant genotypes were GII.4 (56.4%; 194 out of 344), followed by GII.2 and GII.3. Through dual genotyping based on sequencing of the ORF1/ORF2 junction region, we identified a total of 14 different RdRp/capsid genotypes. Of particular interest were the prevalent recombinant genotypes GII.4[P31] and GII.2[P16]. Notably, our study revealed a decrease in the number of children infected with NoV during and after the COVID-19 pandemic. These findings underscore the importance of continuous NoV surveillance efforts.

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Data Availability

A data availability statement has been already included in the Materials and Methods section (Nucleotide sequence accession numbers).

Abbreviations

AGE:

Acute gastroenteritis

COVID-19:

Coronavirus disease 2019

ORFs:

Open reading frames

RdRp:

RNA-dependent RNA polymerase

VP:

Viral protein

RT-PCR:

Reverse transcription polymerase chain reaction

bp:

Base pair

BLAST:

Basic Local Alignment Search Tool

RDP4:

Recombination Detection Program v.4.71

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Acknowledgements

We are grateful to Dr. Shuichi Nishimura, Dr. Hideaki Kikuta, Dr. Atsuko　Yamamoto, Dr. Kumiko Sugita, Dr. Masaaki Kobayashi, and Dr. Tsuneyoshi Baba for collecting specimens, and we are also grateful to all parents and children who willingly participated in this study.

Funding

This study was supported by Grants-in-Aid for Japan Agency for Medical Research and Development (AMED) [grant number JP22fk0108122 and JP22wm0225006 to S.S., T.K., and H.U]; and the Nihon University Research Grant for 2022.

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Authors and Affiliations

  1. Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Ohyaguchi Kamicho, Itabashi-ku, Tokyo, 173-8610, Japan

    Ngan Thi Kim Pham, Yuko Shimizu-Onda, Quang Duy Trinh, Shihoko Komine-Aizawa, Shoko Okitsu, Satoshi Hayakawa & Hiroshi Ushijima

  2. Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Chiba, Japan

    Ngan Thi Kim Pham & Kazuaki Yoshimune

  3. Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand

    Pattara Khamrin & Niwat Maneekarn

  4. Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh

    Sheikh Ariful Hoque

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  1. Ngan Thi Kim Pham
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Correspondence to Hiroshi Ushijima.

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Pham, N.T.K., Khamrin, P., Shimizu-Onda, Y. et al. Genetic diversity and declining norovirus prevalence in infants and children during Japan's COVID-19 pandemic: a three-year molecular surveillance. Arch Virol 168, 231 (2023). https://doi.org/10.1007/s00705-023-05856-w

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