Human-porcine reassortant rotavirus generated by multiple reassortment events in a Sri Lankan child with diarrhea

Yahiro, Takaaki; Takaki, Minako; Chandrasena, T.G.A.N.; Rajindrajith, Shaman; Iha, Hidekatsu; Ahmed, Kamruddin

doi:10.1016/j.meegid.2018.07.014

Cited by 13 publications

(25 citation statements)

References 29 publications

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“…Because only the VP7 and VP4 genes of G4P[6] strains have been analyzed previously, this is the first study to analyze whole-genome sequences of all 11 genes of G4P[6] strains detected in Korea, particularly in Korean neonates. The genotype constellation, G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, found in this study was also detected in Sri Lanka in 2009, in Hungary in 2002, and in Italy in 2017 (Table 2) [16, 17]. However, neither case involved neonates.…”

Section: Discussionsupporting

confidence: 56%

Whole-genome analysis of rotavirus G4P[6] strains isolated from Korean neonates: association of Korean neonates and rotavirus P[6] genotypes

et al. 2019

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Background Group A rotaviruses are the major causative agents of pediatric gastroenteritis worldwide. Several studies have reported the predominance of G4P[6] rotavirus genotypes in Korean neonates, which is uncommon in other countries. Therefore, the purposes of this study were to determine the genotype constellations of complete genomes of G4P[6] rotavirus strains isolated from Korean neonates using next-generation sequencing, to compare these sequences with other G4P[6] strains in other countries, and to determine the reason for the predominance of G4P[6] genotypes in Korean neonates. Results Twenty rotavirus G4P[6] strains, isolated from January 2013 to January 2016, were selected for whole-genome sequencing. Eleven rotavirus genes were amplified using specific primer sets, and sequencing was carried out using an Ion S5 XL next-generation sequencing platform. Genotypes of each gene were determined, and phylogenetic analyses were performed to investigate genetic distances between genes of rotaviruses in this study and those of other rotavirus G4P[6] strains whose whole-genome sequences were previously published. All 20 rotavirus strains in this study had the same genotype: G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, representing the Wa-like genotype constellation. BLAST searches of 20 G4P[6] rotavirus strains revealed that all G4 sequences in this study showed the highest nucleotide identity to G4 sequences of G4P[6] rotavirus strains isolated in Korea in 2008 (GenBank accession number: FJ603447). Additionally, P[6] gene sequences in this study showed the highest nucleotide identity to P[6] sequences of G4P[6] strains detected in Korea in 2002 (AY158093). Phylogenetic and nucleotide sequence analyses showed that G4P[6] strains in this study and previously reported G4P[6] strains in Korea were mostly detected in neonates and had similar G4 and P[6] sequences compared with other G4P[6] strains detected in other countries. Conclusions This study showed that the whole-genome constellation of rotavirus G4P[6] strains from Korean neonates resembled a Wa-like genotype constellation. Additionally, rotavirus genotypes detected in Korean neonates had unique P[6] sequences, which may be the cause of Korean neonatal rotavirus infection. Electronic supplementary material The online version of this article (10.1186/s13099-019-0318-5) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 56%

Whole-genome analysis of rotavirus G4P[6] strains isolated from Korean neonates: association of Korean neonates and rotavirus P[6] genotypes

et al. 2019

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“…NSP3 was discovered to belong to the T1 genotype, forming three distinct phylogenetic clusters ( Figure 2 C). One cluster includes Iringa and Morogoro strains (IP044, RP072 and RP074) that are close related and clustered with human origin isolates from Sri Lanka (LC389882) ( Yahiro et al., 2018 ), China (KF041437) ( Dong et al., 2013 ), and Nepal (LC433782) ( Takatsuki et al., 2019 ) with nucleotide identities ranging from 95.32% to 96.56%, suggesting our strains are porcine-human reassortant. Another cluster contained two Iringa (IP058) and Morogoro (RP019) strains that were closely related to pig (MK379193) and human (KC149929) strains.…”

Section: Resultsmentioning

confidence: 99%

Prevalence and genomic characterization of rotavirus group A genotypes in piglets from southern highlands and eastern Tanzania

Malakalinga

Misinzo

Msalya

et al. 2022

Heliyon

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“…Rotavirus genotypes G1-G4, G9 and G12 in combination with P [8], P [6] and P [4] are responsible for more than 90% of rotavirus diarrhea cases worldwide [18]. Sporadic incidence of infection with rare genotypes like G5, G6, G8, G10, G11, P [1], P [3], P [9], P [10], P [19], P [14] and P [25] have been detected [11,18,27,[32][33][34][35][36]. In general, the G and P distribution patterns of rotavirus fluctuates place to place and year to year [37].…”

Section: Discussionmentioning

confidence: 99%

“…The P [6] genotype is mainly distributed in pigs [60][61][62]. Studies have shown that uncommon rotaviruses with P [6] genotypes emerged in human populations as a result of genetic reassortment between human and porcine rotaviruses [36]. The phylogenetic analysis also showed that the Sabahan P [6] was similar to human P [6] strains rather than porcine P [6] strains, although human P [6] was originally derived from porcine P [6] strains.…”

Section: Plos Onementioning

confidence: 99%

Emergence of equine-like G3 strains as the dominant rotavirus among children under five with diarrhea in Sabah, Malaysia during 2018–2019

et al. 2021

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Rotavirus infection is a dilemma for developing countries, including Malaysia. Although commercial rotavirus vaccines are available, these are not included in Malaysia’s national immunization program. A scarcity of data about rotavirus genotype distribution could be partially to blame for this policy decision, because there are no data for rotavirus genotype distribution in Malaysia over the past 20 years. From January 2018 to March 2019, we conducted a study to elucidate the rotavirus burden and genotype distribution in the Kota Kinabalu and Kunak districts of the state of Sabah. Stool specimens were collected from children under 5 years of age, and rotavirus antigen in these samples was detected using commercially available kit. Electropherotypes were determined by polyacrylamide gel electrophoresis of genomic RNA. G and P genotypes were determined by RT-PCR using type specific primers. The nucleotide sequence of the amplicons was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method. Rotavirus was identified in 43 (15.1%) children with watery diarrhea. The male:female ratio (1.9:1) of the rotavirus-infected children clearly showed that it affected predominantly boys, and children 12–23 months of age. The genotypes identified were G3P[8] (74% n = 31), followed by G1P[8] (14% n = 6), G12P[6](7% n = 3), G8P[8](3% n = 1), and GxP[8] (3% n = 1). The predominant rotavirus circulating among the children was the equine-like G3P[8] (59.5% n = 25) with a short electropherotype. Eleven electropherotypes were identified among 34 strains, indicating substantial diversity among the circulating strains. The circulating genotypes were also phylogenetically diverse and related to strains from several different countries. The antigenic epitopes present on VP7 and VP4 of Sabahan G3 and equine-like G3 differed considerably from that of the RotaTeq vaccine strain. Our results also indicate that considerable genetic exchange is occurring in Sabahan strains. Sabah is home to a number of different ethnic groups, some of which culturally are in close contact with animals, which might contribute to the evolution of diverse rotavirus strains. Sabah is also a popular tourist destination, and a large number of tourists from different countries possibly contributes to the diversity of circulating rotavirus genotypes. Considering all these factors which are contributing rotavirus genotype diversity, continuous surveillance of rotavirus strains is of utmost importance to monitor the pre- and post-vaccination efficacy of rotavirus vaccines in Sabah.

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Human-porcine reassortant rotavirus generated by multiple reassortment events in a Sri Lankan child with diarrhea

Cited by 13 publications

References 29 publications

Whole-genome analysis of rotavirus G4P[6] strains isolated from Korean neonates: association of Korean neonates and rotavirus P[6] genotypes

Whole-genome analysis of rotavirus G4P[6] strains isolated from Korean neonates: association of Korean neonates and rotavirus P[6] genotypes

Prevalence and genomic characterization of rotavirus group A genotypes in piglets from southern highlands and eastern Tanzania

Emergence of equine-like G3 strains as the dominant rotavirus among children under five with diarrhea in Sabah, Malaysia during 2018–2019

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