Molecular epidemiology and genetic diversity of norovirus infection in children hospitalized with acute gastroenteritis in East Java, Indonesia in 2015-2019

Takako Utsumi; Maria Inge Lusida; Zayyin Dinana; Rury Mega Wahyuni; Soegeng Soegijanto; Soetjipto; Alpha Fardah Athiyyah; Subijanto Marto Sudarmo; Reza Gunadi Ranuh; Andy Darma; Juniastuti; Laura Navika Yamani; Yen Hai Doan; Hiroyuki Shimizu; Koji Ishii; Chieko Matsui; Lin Deng; Takayuki Abe; Kazuhiko Katayama; Ikuo Shoji

doi:10.1016/j.meegid.2020.104703

Molecular epidemiology and genetic diversity of norovirus infection in children hospitalized with acute gastroenteritis in East Java, Indonesia in 2015-2019

Infect Genet Evol. 2021 Mar:88:104703. doi: 10.1016/j.meegid.2020.104703. Epub 2021 Jan 2.

Authors

Takako Utsumi¹, Maria Inge Lusida², Zayyin Dinana², Rury Mega Wahyuni², Soegeng Soegijanto², Soetjipto², Alpha Fardah Athiyyah³, Subijanto Marto Sudarmo³, Reza Gunadi Ranuh³, Andy Darma³, Juniastuti², Laura Navika Yamani², Yen Hai Doan⁴, Hiroyuki Shimizu⁵, Koji Ishii⁶, Chieko Matsui⁷, Lin Deng⁷, Takayuki Abe⁷, Kazuhiko Katayama⁸, Ikuo Shoji⁹

Affiliations

¹ Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia; Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan.
² Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia.
³ Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia; Department of Child Health, Soetomo Hospital, Airlangga University, Surabaya, Indonesia.
⁴ Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan; Department of Environmental Parasitology, Tokyo Medical and Dental University, Japan.
⁵ Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
⁶ Department of Quality Assurance and Radiological Protection, National Institute of Infectious Diseases, Tokyo, Japan.
⁷ Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan.
⁸ Laboratory of Viral Infection 1, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan.
⁹ Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan. Electronic address: ishoji@med.kobe-u.ac.jp.

PMID: 33401005
DOI: 10.1016/j.meegid.2020.104703

Abstract

Noroviruses are recognized as a leading cause of outbreaks and sporadic cases of acute gastroenteritis (AGE) among individuals of all ages worldwide, especially in children <5 years old. We investigated the epidemiology of noroviruses among hospitalized children at two hospitals in East Java, Indonesia. Stool samples were collected from 966 children with AGE during September 2015-July 2019. All samples were analyzed by reverse transcription-polymerase chain reaction (RT-PCR) for the amplification of both the RNA-dependent RNA polymerase (RdRp) and the capsid genes of noroviruses. The genotypes were determined by phylogenetic analyses. In 2015-2019, noroviruses were detected in 12.3% (119/966) of the samples. Children <2 years old showed a significantly higher prevalence than those ≥2 years old (P = 0.01). NoV infections were observed throughout the year, with the highest prevalence in December. Based on our genetic analyses of RdRp, GII.[P31] (43.7%, 31/71) was the most prevalent RdRp genotype, followed by GII.[P16] (36.6%, 26/71). GII.[P31] was a dominant genotype in 2016 and 2018, whereas GII.[P16] was a dominant genotype in 2015 and 2017. Among the capsid genotypes, the most predominant norovirus genotype from 2015 to 2018 was GII.4 Sydney_2012 (33.6%, 40/119). The most prevalent genotype in each year was GII.13 in 2015, GII.4 Sydney_2012 in 2016 and 2018, and GII.3 in 2017. Based on the genetic analyses of RdRp and capsid sequences, the strains were clustered into 13 RdRp/capsid genotypes; 12 of them were discordant, e.g., GII.4 Sydney[P31], GII.3[P16], and GII.13[P16]. The predominant genotype in each year was GII.13[P16] in 2015, GII.4 Sydney[P31] in 2016, GII.3[P16] in 2017, and GII.4 Sydney[P31] in 2018. Our results demonstrate high detection rates and genetic diversity of norovirus GII genotypes in pediatric AGE samples from Indonesia. These findings strengthen the importance of the continuous molecular surveillance of emerging norovirus strains.

Keywords: Children; Epidemiology; Indonesia; Norovirus; RdRp/capsid genotype.

Publication types

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

MeSH terms

Adolescent
Biodiversity
Caliciviridae Infections / epidemiology*
Caliciviridae Infections / virology*
Capsid Proteins / genetics
Child
Child, Preschool
Feces / virology
Female
Gastroenteritis / epidemiology*
Gastroenteritis / virology*
Genetic Variation
Genotype
Hospitalization
Humans
Indonesia / epidemiology
Infant
Male
Molecular Epidemiology
Norovirus / classification*
Norovirus / genetics*
Norovirus / isolation & purification
Phylogeny
Prevalence
RNA, Viral
RNA-Dependent RNA Polymerase / genetics
Real-Time Polymerase Chain Reaction

Substances

Capsid Proteins
RNA, Viral
RNA-Dependent RNA Polymerase