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Gene & Protein in Disease Rotavirus diversity in Uttar Pradesh

1. Introduction epidemiology and antigenic diversity of circulating RVA,
particularly in animals, is crucial for the development and
According to the Foodborne Disease Burden potential modification of effective indigenous vaccines to
Epidemiology Reference Group, diarrheal diseases result address RV episodes. Our previous experiment identified
in 420,000 fatalities globally, with rotaviruses identified the circulating piglet strain G9P[13] in the Bareilly region.
as the predominant cause of diarrhea among young While characterizing this strain for multiple sequence
children in India, accounting for an estimated 21,357 alignment and phylogenetic analysis of each gene (VP6,
deaths in 2010. There are nine Rotavirus (RV) species VP4, VP7, NSP, and NSP4), it was observed that the VP7,
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referred to as A, B, C, D, F, G, H, I, and J, and among NSP3, and NSP4 genes are closely related to human strains,
these, RVA is the predominant viral agent responsible whereas the VP4 gene was closely related to porcine
for diarrhea, resulting in around 100,000 fatalities and 9
400,000 – 800,000 hospitalizations among children in strain. However, reports on the circulation of the same
G9P[13] strain in humans/children from the same area are
India. It has significant genetic diversity attributed to not available. Further, some of the pig farms located in this
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frequent genetic reassortment and/or mutations. All
3,4
11 segments of the RV genome, which include VP1, VP2, region also need to be investigated for the presence/absence
VP3, VP4, VP6, VP7, NSP1, NSP2, NSP3, NSP4, and NSP5 of this RVA strain. Therefore, in this study, we determined
genes showing nucleotide variations, result in genotypes the incidence of RVA in piglets from different farms and
children from five different hospitals and characterized
R28, C20, L24, P[58], I32, G42, A32, N28, T28, E32,
and H28, respectively (https://rega.kuleuven.be/cev/ the VP4, VP6, VP7, and NSP4 genes of RVA to identify the
viralmetagenomics/virus-classification/rcwg, accessed circulating genotypes in humans and piglets from in and
on 06.11.2024). The majority of human rotaviruses around Bareilly, Uttar Pradesh, India.
exhibit Wa-like (Gx-P[x]-I1-R1- C1-M1-A1-N1-T1- 2. Materials and methods
E1-H1) or DS-1-like (Gx-P[x]-I2-R2-C2-M2-A2-N2-
T2-E2-H2) constellations, which originate from pigs or 2.1. Specimen collection
cattle. In addition, a few strains derived from felines Institute Biosafety Committee (IBSC) approval was
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belong to the AU-1-like (Gx-P[x]-I3-R3-C3-M3-A3- obtained from ICAR-Indian Veterinary Research Institute,
N3-T3-E3-H3) constellation. This genetic variation in Bareilly, Uttar Pradesh, India, for the research project
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RV constellations observed globally in both animals and on “Genotypic diversity of human, bovine and porcine
humans is a result of distinct evolutionary processes. group A rotaviruses,” under which the present study was
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Moreover, the Indian RVA strains from both animals and carried out (proceedings of the IBSC meeting held on July
humans exhibit diverse genotypic traits. In general, the 06, 2018). Children under 3 years old who exhibited acute
common genotypes observed among Indian RV strains gastroenteritis with at least five episodes of watery stools
are G1, G2, G3, G4, G9, and G12, often associated with per day (with or without vomiting and fever) were included
P[6], P[8], and P[4]. While 89% of strains (92% from in a study conducted between 2017 and 2019. Informed
Wa-like and 86% from DS-1-like) showed classical consent was obtained from each child’s guardian and from
constellations, reassortant constellations were identified the administrators of five childcare hospitals in the Bareilly
in 11% of the strains (8% from Wa-like and 14% from district of Uttar Pradesh. Two to ten mL/g stool samples
DS-1-like). 7 were collected from each child experiencing diarrhea
In India, the introduction of the RV vaccine to the in sterile containers. In addition, a total of 136 diarrheal
Union Government’s Universal Immunization Programme and 64 non-diarrheal fecal samples were obtained (after
in March 2016 has led to a significant reduction in the proper consent from the owners) from three pig farms in
prevalence of cases among children under five. Reports the Bareilly district: Izatnagar (n = 14), Rupapur (n = 171),
indicate a decrease of approximately 33.7% in cases, 38.3% and Ismilepur (n = 15). During previous analyses of some
in deaths, and about 21.8% in overall antibiotic misuse samples from the Rupapur farms, it was noted that many
related to RV infections. However, despite the vaccine’s piglets were affected during that period. Thus, an outbreak
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availability and its impressive preventive results, there of diarrhea in piglets was reported at the Rupapur farm,
are still frequent reports of diarrheal episodes caused by leading to extensive sampling in this farm. In the end, a
RVA in both children and animals, particularly during total of 300 stool samples were collected: 100 samples
the winter months across the country. This ongoing issue from children and 200 samples from piglets, and they
may be attributed to several contributing factors, with were subsequently screened for RV, followed by genotypic
genotypic diversity and reassortment of the virus being analysis of positive samples to characterize the VP4, VP6,
significant. Therefore, conducting studies on the molecular VP7, and NSP4 genes.

Volume 4 Issue 1 (2025) 2 doi: 10.36922/gpd.6237