Genetic characterization of group-A rotaviruses among children in eastern India during 2014–2016: Phylodynamics of co-circulating genotypes

Nayak, Malabika; Banerjee, Anindita; Sarkar, Rakesh; Mitra, Suvrotoa; Dutta, Kunal; Ganguly, Nupur; Ghosh, Chandradipa; Kumar, C. P. Girish; Niyogi, Prabal; Panda, Samiran; Chawla‐Sarkar, Mamta

doi:10.1016/j.vaccine.2019.06.062

Cited by 7 publications

(10 citation statements)

References 46 publications

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“…The phylogenetic relationship of the RVA G1 VP7 gene was also evaluated through the construction of an ML tree, and we revealed two lineages which are consistent with Novikova's and Fujii's results [27,28]. At present, there is no clear criterion to define a lineage of the RVA G1 VP7 gene and many studies have identified a different number of genetic lineages [14,29,30]. Previous research by Phan et al recognized more than 10 lineages [31].…”

Section: Discussionsupporting

confidence: 80%

“…of 38 and 82 negative sites were identified by the SLAC and FEL methods, respectively. Five sites (at positions: 14,19,23,323,326) under positive selection were observed by the MEME method. For lineage II, a total of 82 and 122 negative sites were identified by the SLAC and FEL methods, respectively.…”

Section: Root-to-tip Divergence Analysismentioning

confidence: 99%

“…Nevertheless, at present, little is known about the molecular evolution of specific RVA genotypes. The two licensed vaccines both include the G1 genotype, and G1 still remains a largely dominant G genotype worldwide [ 12 , 13 , 14 ]. It was also reported that G1 was the predominant shedding vaccine-related viral particle in vaccines [ 15 , 16 ], which may have an effect on the evolution of wild-type G1 circulating in populations.…”

Section: Introductionmentioning

confidence: 99%

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Genetic Characterizations and Molecular Evolution of VP7 Gene in Human Group A Rotavirus G1

Zhou

Wang

2020

Viruses

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Rotavirus group A (RVA) G1 is one leading genotype circulating in humans worldwide, and related molecular information from a global perspective is still limited. Here, we present a comprehensive description of the genetic characterizations and molecular evolution of the RVA G1 VP7 gene. Our results show that RVA G1 can be divided into two lineages and multiple sub-lineages with a relatively high genetic diversity. Vaccine strains are phylogenetic, closer to lineage I. The evolutionary rate of the RVA G1 VP7 gene is 8.869 × 10−4 substitutions/site/year, and its most recent common ancestor was in 1933. The RVA G1 VP7 gene shows a linear evolution at the nucleotide level and a linear accumulation of difference at the amino acid level. Sub-lineage replacement of G1 VP7 gene is also observed and the effective population size of the G1 VP7 gene has had great change in the past decades and has remained stable in recent years. Altogether, the RVA G1 VP7 gene constantly evolves and there is no clear evidence that the evolution of the RVA G1 VP7 gene was influenced by vaccines. Continuous surveillance is still indispensable to evaluate the molecular epidemiology of RVA, especially in the post-vaccination era.

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Section: Discussionsupporting

confidence: 80%

Section: Root-to-tip Divergence Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genetic Characterizations and Molecular Evolution of VP7 Gene in Human Group A Rotavirus G1

Zhou

Wang

2020

Viruses

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“…This vaccine is listed as a prequalified vaccine by the WHO [16]. In 2018, India included Rotasil, a multivalent (G1, G2, G3, G4, G9 and P [8]) rotavirus vaccine, in its national immunization program [18].…”

Section: Introductionmentioning

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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“…G12 rotaviruses have been reported at significant prevalence rates from different geographical regions of India since its first detection in 2001; and observed in combination with various P‐types mainly with P[6] and P[8] and rarely with P[4] and P[11] 10–12,19,23–26 . Literature reviewed from 2001 to 2016 showed the proportion of rotavirus infections attributed to G12 strains ranged from 0.5% to 33% in the Northern region, 2.4%–18.2% in the Western region, 0.8%–5.6% in the Southern region, and 0.4%–25% in the Eastern region of India 19,26–32 . Earlier, we documented the rotavirus disease burden in children aged <5 years, taking into account rotavirus positivity and strain diversity in HP (North India), where G12 was detected as the most predominant genotype mainly associated with P[6].…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic analysis of VP7 and VP4 genes of the most predominant human group A rotavirus G12 identified in children with acute gastroenteritis in Himachal Pradesh, India during 2013–2016

Gupta

Gauhar

Bubber

et al. 2021

Journal of Medical Virology

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G12 strains are now considered to be the sixth most prevalent human rotaviruses globally. India has introduced rotavirus vaccine Rotavac® into the national immunization program in 2016 and Himachal Pradesh (HP) is the first state to launch it. During epidemiological rotavirus surveillance in HP, predominance of G12 rotaviruses was observed. This study investigated the genetic variability and evolution of HP G12 strains (n = 15) associated with P-genotypes P[6], P[4], and P[8] identified between 2013 and 2016. Phylogenetic analysis of VP7 gene revealed that all characterized G12 strains clustered in lineage-III and diversified into three subclusters indicating that these strains may have originated from three different ancestral G12 strains. The comparative sequence analysis of HP strains with Rotavac® and Rotarix® vaccine strains revealed various amino acid substitutions in epitope regions of VP7 and VP4 proteins especially at the antibody neutralization sites. Only 12/29 VP7 epitope residues and 2/25 VP4 epitope residues were found to be conserved between HP rotavirus strains and vaccine strains. Both long and short electropherotypes were observed in G12P[4] strains, while a single long electropherotype was observed in G12P[6] strains. Children of ≤11 months were significantly infected with G12 rotaviruses. The frequency of vomiting episodes (≥5/ day) was significantly higher in children infected with G12 rotavirus strains as compared to non-G12 rotaviruses (p = 0.0405). Our study provides the comprehensive data on clinical characteristics and evolutionary pattern of the G12 rotavirus, the most prevalent strain in HP and emphasizes the need to monitor these strains for inclusion in future vaccine.

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Genetic characterization of group-A rotaviruses among children in eastern India during 2014–2016: Phylodynamics of co-circulating genotypes

Cited by 7 publications

References 46 publications

Genetic Characterizations and Molecular Evolution of VP7 Gene in Human Group A Rotavirus G1

Genetic Characterizations and Molecular Evolution of VP7 Gene in Human Group A Rotavirus G1

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

Phylogenetic analysis of VP7 and VP4 genes of the most predominant human group A rotavirus G12 identified in children with acute gastroenteritis in Himachal Pradesh, India during 2013–2016

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