Surveillance of norovirus among children with diarrhea in four major hospitals in Bhutan: Replacement of GII.21 by GII.3 as a dominant genotype

Wangchuk, Sonam; Matsumoto, Takashi; Iha, Hidekatsu; Ahmed, Kamruddin

doi:10.1371/journal.pone.0184826

Cited by 16 publications

(16 citation statements)

References 35 publications

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“…The amplicon size of the partial RdRp gene is 470 bp. The RT-PCR results were confirmed by nucleotide sequencing of the amplicons 5 . The nucleotide sequence of the amplicons was determined by the BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA) according to the manufacturer's instructions and the product was run on a ABI Prism 3100 Genetic Analyzer (Applied Biosystems).…”

Section: Methodsmentioning

confidence: 74%

An outbreak of gastroenteritis by emerging norovirus GII.2[P16] in a kindergarten in Kota Kinabalu, Malaysian Borneo

Ahmed

Dony²,

Mori

et al. 2020

Sci Rep

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outbreaks of diarrhea in kindergartens are underreported and frequently go unnoticed in developing countries. to better understand the etiology this study was performed during an outbreak of diarrhea in a kindergarten in Sabah, Malaysia. outbreak investigation was performed according to the standard procedures. In this outbreak a total of 34 (36.5%) children and 4 (30.8%) teachers suffered from gastroenteritis. Stool samples from seven children and 13 teachers were tested for rotavirus and norovirus. During the investigation stool samples were collected and sent in cold chain to the laboratory. the samples were subjected to rotavirus enzyme linked immunosorbent assay, and reverse transcription pcR for norovirus. All samples were negative for rotavirus but positive for norovirus. to determine the genogroup and genotype of norovirus, nucleotide sequencing of the amplicons was performed. All norovirus from the outbreak was of genotype GII.2[16]. To determine the relatedness of the strains phylogenetic analysis was done using neighbor-joining method. phylogenetically these strains were highly related to GII.2[P16] noroviruses from China and Japan. This study provided evidence that a diarrheal outbreak in a kindergarten was caused by GII.2[P16] norovirus which is an emerging strain in east Asia and europe.Norovirus is highly infectious and is transmitted primarily from person-to-person through the fecal-oral route within closed settings such as schools, cruise ships, hospitals, childcare facilities and aged-care institutions 1,2 . Currently this virus is divided into ten genogroups GI-GX based on the genetic differences of the capsid protein 3 . GI and GII are primarily responsible for human infection 4 . GII.4 causes most infections worldwide, followed by GII.3 or GII.6 and then other genotypes in varying proportions 5-10 . Although norovirus infection is an important cause of diarrhea in developing countries, outbreaks are under reported and frequently go unnoticed. In Kota Kinabalu, the capital of Sabah state in Malaysia, only two diarrheal outbreaks, including this one, have been reported in kindergartens between 2014 and June 2018. However, kindergartens are vulnerable to norovirus outbreaks: in Pudong district, Shanghai, China, 29 of 60 reported norovirus outbreaks occurred in kindergartens over a period of one year 11 . Therefore, understanding the epidemic situation, relationship with other strains, evolution, genetic variants and the genotype distribution of norovirus during outbreaks is important to determine the best strains to include in future norovirus vaccines. Global surveillance data indicates that several norovirus genotypes are responsible for outbreak but majority are caused by GII.4 12,13 . Since 2002, new GII.4 variants have emerged every two to three years, resulting in epidemics and global pandemics 13 . To emerge and persist in human population norovirus generate diverse strains by point mutations and recombination 14 . However, recent outbreaks of norovirus particularly in Asia and Europe wer...

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Section: Methodsmentioning

confidence: 74%

An outbreak of gastroenteritis by emerging norovirus GII.2[P16] in a kindergarten in Kota Kinabalu, Malaysian Borneo

Ahmed

Dony²,

Mori

et al. 2020

Sci Rep

Self Cite

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“…The oldest GII.3 NV strain identified to date is from a 1983 sample isolated in the Goulburn Valley of Australia [13], and GII.3 has been reported to be the major cause of sporadic pediatric NV infection [15,17,35,36]. In China, early reports on NV showed GII.3 was prevalent in 1999 [37,38], and until now, GII.3 was reported as the dominant genotype next to GII.4 in sporadic NV infection [39,40].…”

Section: Discussionmentioning

confidence: 99%

“…Despite the large number of NV genotypes cocirculating in children over the past decade, genotypes GII.4 and GII.3 have predominated worldwide [13][14][15][16][17]. Up to nowadays, six outbreaks of acute gastroenteritis are associated with at least seven distinct GII.4 NV variants [14].…”

Section: Introductionmentioning

confidence: 99%

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Prevalence of noroviruses in children hospitalized for acute gastroenteritis in Hohhot, China, 2012-2017

Yugeng

Lei

et al. 2019

BMC Infect Dis

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Background Noroviruses (NVs) are an important cause of acute gastroenteritis (AGE) worldwide. There are limited data on the prevalence and molecular characterization of NVs in children in Hohhot, China. Methods Between January 2012 and December 2017, 1863 stool samples were collected at Maternal and Child Health Hospital in Hohhot. All samples were screened for NVs by real-time reverse transcription polymerase chain reaction (real-time RT-PCR). Results NVs were detected in 24.15% of these inpatient cases, ranging from 12.78 to 32.92% in different years. NV was detected throughout the year, with a peak in winter. Based on sequence analysis of the partial VP1 gene, the 306 identified NV strains were divided into six genotypes: GII.3 (71.24%), GII.4 (23.53%), and GII.2, GII.5, GII.6, and GII.13 (total 5.23%). Based on further sequence analysis of the RNA-dependent RNA polymerase (RdRp), GII.P12/GII.3, GII.Pe/GII.4, and GII.P4/GII.4 were identified as predominant genotypes, accounting for 92.6% of genotyped strains. The median age of the children with NV infection was 8.0 (range 0–59) months. However, children infected with GII.3 were younger (median 7.0 months) than GII.4-positive patients (median 10.0 months). Conclusion NV contributed greatly to AGE among hospitalized children in Hohhot in China. Continuous surveillance is important for understanding the local prevalence and characterization of NV.

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“…GI and GII viruses are frequently detected in humans, and are further classified into 9 and 27 genotypes, respectively, based on the capsid region sequences (Chhabra et al, 2019). Previous molecular epidemiological studies have shown that some NoV GII genotypes, including GII.2,GII.3,GII.4,GII.6,and GII.17 are prevalent in different countries (Matsushima et al, 2015;Bruggink et al, , 2018Cannon et al, 2017;Wangchuk et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Molecular Evolution of the Protease Region in Norovirus Genogroup II

et al. 2020

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Noroviruses are a major cause of viral epidemic gastroenteritis in humans worldwide. The protease (Pro) encoded in open reading frame 1 (ORF1) is an essential enzyme for proteolysis of the viral polyprotein. Although there are some reports regarding the evolutionary analysis of norovirus GII-encoding genes, there are few reports focused on the Pro region. We analyzed the molecular evolution of the Pro region of norovirus GII using bioinformatics approaches. A time-scaled phylogenetic tree of the Pro region constructed using a Bayesian Markov chain Monte Carlo method indicated that the common ancestor of GII diverged from GIV around 1680 CE [95% highest posterior density (HPD), 1607-1749]. The GII Pro region emerged around 1752 CE (95%HPD, 1707-1794), forming three further lineages. The evolutionary rate of GII Pro region was estimated at more than 10 −3 substitutions/site/year. The distribution of the phylogenetic distances of each genotype differed, and showed genetic diversity. Mapping of the negative selection and substitution sites of the Pro structure showed that the substitution sites in the Pro protein were mostly produced under neutral selection in positions structurally adjacent to the active sites for proteolysis, whereas negative selection was observed in residues distant from the active sites. The phylodynamics of GII.P4, GII.P7, GII.P16, GII.P21, and GII.P31 indicated that their effective population sizes increased during the period from 2005 to 2016 and the increase in population size was almost consistent with the collection year of these genotypes. These results suggest that the Pro region of the norovirus GII evolved rapidly, but under no positive selection, with a high genetic divergence, similar to that of the RNA-dependent RNA polymerase (RdRp) region and the VP1 region of noroviruses.

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Surveillance of norovirus among children with diarrhea in four major hospitals in Bhutan: Replacement of GII.21 by GII.3 as a dominant genotype

Cited by 16 publications

References 35 publications

An outbreak of gastroenteritis by emerging norovirus GII.2[P16] in a kindergarten in Kota Kinabalu, Malaysian Borneo

An outbreak of gastroenteritis by emerging norovirus GII.2[P16] in a kindergarten in Kota Kinabalu, Malaysian Borneo

Prevalence of noroviruses in children hospitalized for acute gastroenteritis in Hohhot, China, 2012-2017

Molecular Evolution of the Protease Region in Norovirus Genogroup II

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