Full genome characterization of novel DS-1-like G9P[8] rotavirus strains that have emerged in Thailand

Fukuda, Seisuke; Tacharoenmuang, Ratana; Guntapong, Ratigorn; Upachai, Sompong; Singchai, Phakapun; Ide, Tomihiko; Hatazawa, Riona; Sutthiwarakom, Karun; Kongjorn, Santip; Onvimala, Napa; Ruchusatsawast, Kriangsak; Rungnopakun, Pimpa; Mekmallika, Jutarat; Kawamura, Yoshiki; Motomura, Kazushi; Tatsumi, Masashi; Takeda, Naokazu; Murata, Takayuki; Yoshikawa, Tetsushi; Uppapong, Ballang; Taniguchi, Koki; Komoto, Satoshi

doi:10.1371/journal.pone.0231099

Cited by 15 publications

(9 citation statements)

References 47 publications

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“…G3P [8], G8P [8], or G9P [8]: G1/3/8/9-P [8]-I2-R2-C2-M2-A2-N2-T2-E2-H2, which had never been previously observed, have been reported in the last decade (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)…”

Section: Accepted Manuscriptmentioning

confidence: 88%

Rapid Spread in Japan of Unusual G9P[8] Human Rotavirus Strains Possessing NSP4 Genes of E2 Genotype

et al. 2022

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The emergence of unusual G9P[8]-E2 human rotaviruses in the Tokyo metropolis, Japan in 2018 has been reported. During rotavirus strain surveillance in different regions of Japan (Mie, Okayama, and Chiba prefectures), G9P[8]-E2 strains were detected in diarrheic children in all three prefectures. Here, we characterized the whole genomes of seven representative G9P[8]-E2 strains. On full-genome-based analysis, the seven study strains exhibited a unique genotype configuration having the NSP4 gene of genogroup 2 in a genogroup 1 genomic backbone: G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1. This genotype constellation is shared by Tokyo G9P[8]-E2 strains. Phylogenetic analysis showed that all the 11 genes, except the NSP4 one, of the seven study strains appeared to have originated from co-circulating Wa-like G9P[8]-E1 strains. On the other hand, the NSP4 gene appeared to have originated from co-circulating DS-1-like G2P[4]-E2 strains. Thus, these study G9P[8]-E2 strains appeared to be derived through reassortment between G9P[8]-E1 and G2P[4]-E2 strains in Japan. Notably, the seven study G9P[8]-E2 strains and Tokyo G9P[8]-E2 strains were revealed to have 11-segment genomes almost indistinguishable from one another in their sequences (99.3-100%), indicating all these G9P[8]-E2 strains had a common origin. To our knowledge, this is the first description of the rapid spread of G9P[8]-E2 strains across a country.

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Section: Accepted Manuscriptmentioning

confidence: 88%

Rapid Spread in Japan of Unusual G9P[8] Human Rotavirus Strains Possessing NSP4 Genes of E2 Genotype

et al. 2022

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“…Unusual human G/P combinations (i.e., G5P[6], G9P[23]) tend to possess more diverse genetic backbones [ 9 , 10 ]. Recently, an emergence of novel human intergenogroup ressortant strains, DS-1-like G1/G3/G9/G8P[8], were reported globally, including in Brazil [ 11 , 12 , 13 , 14 , 15 ]. Moreover, some of these atypical emergent strains resulted from human/animal reassortment events, such as the equine-like G3P[8] DS-1-like and the bovine-like G8P[8] strains with the DS-1-like backbone [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic Constellation of Human Rotavirus G8 Strains in Brazil over a 13-Year Period: Detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like Backbone

Medeiros

França

Viana

et al. 2023

Viruses

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Rotavirus (RVA) G8 is frequently detected in animals, but only occasionally in humans. G8 strains, however, are frequently documented in nations in Africa. Recently, an increase in G8 detection was observed outside Africa. The aims of the study were to monitor G8 infections in the Brazilian human population between 2007 and 2020, undertake the full-genotype characterization of the four G8P[4], six G8P[6] and two G8P[8] RVA strains and conduct phylogenetic analysis in order to understand their genetic diversity and evolution. A total of 12,978 specimens were screened for RVA using ELISA, PAGE, RT-PCR and Sanger sequencing. G8 genotype represented 0.6% (15/2434) of the entirely RVA-positive samples. G8P[4] comprised 33.3% (5/15), G8P[6] 46.7% (7/15) and G8P[8] 20% (3/15). All G8 strains showed a short RNA pattern. All twelve selected G8 strains displayed a DS-1-like genetic backbone. The whole-genotype analysis on a DS-1-like backbone identified four different genotype-linage constellations. According to VP7 analysis, the Brazilian G8P[8] strains with the DS-1-like backbone strains were derived from cattle and clustered with newly DS-1-like G1/G3/G9/G8P[8] strains and G2P[4] strains. Brazilian IAL-R193/2017/G8P[8] belonged to a VP1/R2.XI lineage and were grouped with bovine-like G8P[8] strains with the DS-1-like backbone strains detected in Asia. Otherwise, the Brazilian IAL-R558/2017/G8P[8] possess a “Distinct” VP1/R2 lineage never previously described and grouped apart from any of the DS-1-like reference strains. Collectively, our findings suggest that the Brazilian bovine-like G8P[8] strains with the DS-1-like backbone strains are continuously evolving and likely reassorting with local RVA strains rather than directly relating to imports from Asia. The Brazilian G8P[6]-DS-1-like strains have been reassorted with nearby co-circulating American strains of the same DS-1 genotype constellation. However, phylogenetic analyses revealed that these strains have some genetic origin from Africa. Finally, rather than being African-born, Brazilian G8P[4]-DS-1-like strains were likely imported from Europe. None of the Brazilian G8 strains examined here exhibited signs of recent zoonotic reassortment. G8 strains continued to be found in Brazil according to their intermittent and localized pattern, thus, does not suggest that a potential emergence is taking place in the country. Our research demonstrates the diversity of G8 RVA strains in Brazil and adds to the understanding of G8P[4]/P[6]/P[8] RVA genetic diversity and evolution on a global scale.

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“…G1P[8] strains have been reported in many regions of the world ( Komoto et al, 2018 ), including in Indonesia. G9P[8] strains were found in Thailand in 2015–2018 ( Fukuda et al, 2020 ). However, our data are too limited to completely rule out the circulation of equine-like G3P[8] strains in West Nusa Tenggara.…”

Section: Discussionmentioning

confidence: 99%

Prevalence and Distribution of Rotavirus Genotypes Among Children With Acute Gastroenteritis in Areas Other Than Java Island, Indonesia, 2016–2018

et al. 2021

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Group A rotaviruses (RVAs) are the leading cause of acute gastroenteritis, which is often associated with severe symptoms in children under 5 years old. Genetic reassortments and interspecies transmission commonly occur, resulting in a great diversity of RVA circulating in the world. The aim of this study is to determine the prevalence and distribution of RVA genotypes among children in Indonesia over the years 2016–2018 across representative areas of the country. Stool samples were collected from 202 pediatric patients with acute gastroenteritis in three regions of Indonesia (West Nusa Tenggara, South Sumatra, and West Papua) in 2016–2018. Rotavirus G and P genotypes were determined by reverse transcription PCR (RT-PCR) and direct sequencing analysis. The prevalences of RVA in South Sumatra (55.4%) and West Papua (54.0%) were significantly higher than that in East Java (31.7%) as determined in our previous study. The prevalence in West Nusa Tenggara (42.6%) was the lowest among three regions, but higher than that in East Java. Interestingly, equine-like G3 rotavirus strains were found as predominant strains in South Sumatra in 2016 and in West Papua in 2017–2018. Moreover, the equine-like G3 strains in South Sumatra detected in 2016 were completely replaced by human G1 and G2 in 2018. In conclusion, RVA infection in South Sumatra and West Papua was highly endemic. Equine-like G3 strains were also spread to South Sumatra (West Indonesia) and West Papua (East Indonesia), as well as Java Island. Dynamic change in rotavirus genotypes from equine-like G3 to human genotypes was also observed. Continuous monitoring may be warranted in isolated areas in Indonesia.

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Full genome characterization of novel DS-1-like G9P[8] rotavirus strains that have emerged in Thailand

Cited by 15 publications

References 47 publications

Rapid Spread in Japan of Unusual G9P[8] Human Rotavirus Strains Possessing NSP4 Genes of E2 Genotype

Rapid Spread in Japan of Unusual G9P[8] Human Rotavirus Strains Possessing NSP4 Genes of E2 Genotype

Genomic Constellation of Human Rotavirus G8 Strains in Brazil over a 13-Year Period: Detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like Backbone

Prevalence and Distribution of Rotavirus Genotypes Among Children With Acute Gastroenteritis in Areas Other Than Java Island, Indonesia, 2016–2018

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