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Journal of virology2022; 96(20); e0140822; doi: 10.1128/jvi.01408-22

Complete Genome Sequencing Reveals Unusual Equine Rotavirus A of Bat Origin from India.

Abstract: Rotaviruses are the most common viral agents associated with foal diarrhea. Between 2014 and 2017, the annual prevalence of rotavirus in diarrheic foals ranged between 18 and 28% in Haryana (India). Whole-genome sequencing of two equine rotavirus A (ERVA) isolates (RVA/Horse-wt/IND/ERV4/2017 and RVA/Horse-wt/IND/ERV6/2017) was carried out to determine the genotypic constellations (GCs) of ERVAs. The GCs of both the isolates were G3-P[3]-I8-R3-C3-M3-A9-N3-T3-E3-H6, a unique combination reported for ERVAs so far. Both the isolates carried VP6 of genotype I8, previously unreported from equines. Upon comparison with RVAs of other species, the GC of both isolates was identical to that of a bat rotavirus strain, MSLH14, isolated from China in 2012. The nucleotide sequences of the genes encoding VP3, NSP2, and NSP3 shared >95.81% identity with bat RVA strains isolated from Africa (Gabon). The genes encoding VP1, VP2, VP7, NSP1, and NSP4 shared 94.82% to 97.12% nucleotide identities with the human strains which have zoonotic links to bats (RCH272 and MS2015-1-0001). The VP6 genes of both strains were distinct and had the highest similarity of only 87.08% with that of CMH222, a human strain of bat origin. The phylogenetic analysis and lineage studies revealed that VP7 of both isolates clustered in a new lineage (lineage X) of the G3 genotype with bat, human, and alpaca strains. Similarly, VP4 clustered in a distinct P[3] lineage. These unusual findings highlight the terra incognita of the genomic diversity of equine rotaviruses and support the need for the surveillance of RVAs in animals and humans with a "one health" approach. Rotaviruses are globally prevalent diarrheal pathogens in young animals including foals, piglets, calves, goats, sheep, cats, and dogs along with humans. The genome of rotaviruses consists of 11 segments, which enables them to undergo reshuffling by reassortment of segments from multiple species during mixed infections. In this study, the prevalence of equine rotaviruses was 32.11% in organized equine farms of North India. The complete genome analysis of two ERVA isolates revealed an unusual genomic constellation, which was previously reported only in a bat RVA strain. A segment-wise phylogenetic analysis revealed that most segments of both isolates were highly similar either to bat or to bat-like human rotaviruses. The occurrence of unusual bat-like rotaviruses in equines emphasizes the need of extensive surveillance of complete genomes of both animal and human rotaviruses with a "one health" approach.
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Publication Date: 2022-10-10 PubMed ID: 36214578PubMed Central: PMC9599578DOI: 10.1128/jvi.01408-22Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research study conducted complete genetic sequencing on two isolates of equine rotavirus A (ERVA), a common cause of diarrhea in foals, in North India. The discovered genetic composition was unusually similar to a bat strain, marking the first time such similarity is reported in ERVA strains, highlighting the need for comprehensive examination considering the “one health” approach.

Background and Objectives

  • The study arose from the need to examine the genetic structure or genotypic constellations (GCs) of ERVA, the leading cause of diarrhea in young horses, prevalent in North India.
  • Rotaviruses have a complex genomic structure, facilitating genetic reshuffling, leading to the possibility of hybrid strains. Therefore, understanding ERVA strains’ genetic composition is crucial.

Methods

  • Researchers performed a whole-genome sequencing of two ERVA isolates (RVA/Horse-wt/IND/ERV4/2017 and RVA/Horse-wt/IND/ERV6/2017).
  • They then compared the genotypic constellations (GCs) of these isolates with other known rotavirus strains from various species.

Findings

  • Both isolates exhibited a unique combination of GCs (G3-P[3]-I8-R3-C3-M3-A9-N3-T3-E3-H6) not previously reported in ERVAs.
  • The nucleotide sequences for several encoding genes in the isolates showed high (>95.81%) identity with bat rotavirus stains.
  • Certain gene sequences demonstrated a similarity of 94.82% to 97.12% with bat-derived human strains characterized by their zoonotic links (transmissible from animals to humans).
  • The part of the genome responsible for the assembly of the viral shell (VP6) found in both strains was unique and only had a similarity of 87.08% with human strains originating from bats.

Implications

  • The study unveils the unusual genetic diversity among equine rotaviruses, necessitating a more comprehensive approach to their surveillance.
  • This discovery underlines the potential for viral transmission or reshuffling between species, particularly from bats to horses.
  • The study emphasizes the importance of integrative surveillance of rotaviruses in animals and humans under the “one health” approach, considering the interconnectedness of human, animal, and environmental health.

Cite This Article

APA
Pathak A, Gulati BR, Maan S, Mor S, Kumar D, Soman R, Punia S, Chaudhary D, Khurana SK. (2022). Complete Genome Sequencing Reveals Unusual Equine Rotavirus A of Bat Origin from India. J Virol, 96(20), e0140822. https://doi.org/10.1128/jvi.01408-22

Publication

Journal of virology
ISSN: 1098-5514
NlmUniqueID: 0113724
Country: United States
Language: English
Volume: 96
Issue: 20
Pages: e0140822
PII: e01408-22

Researcher Affiliations

Pathak, A
  • Indian Council of Agricultural Research-National Research Centre on Equines, Hisar, Haryana, India.
Gulati, B R
  • Indian Council of Agricultural Research-National Research Centre on Equines, Hisar, Haryana, India.
Maan, S
  • Department of Animal Biotechnology, College of Veterinary Sciences, LLR University of Veterinary and Animal Sciences, Hisar, Haryana, India.
Mor, S
  • Department of Veterinary Population Medicine, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA.
  • Veterinary Diagnostic Laboratory, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA.
Kumar, D
  • Equine Breeding Stud, Hisar, Haryana, India.
Soman, R
  • Indian Council of Agricultural Research-National Research Centre on Equines, Hisar, Haryana, India.
Punia, S
  • Indian Council of Agricultural Research-National Research Centre on Equines, Hisar, Haryana, India.
Chaudhary, D
  • Department of Animal Biotechnology, College of Veterinary Sciences, LLR University of Veterinary and Animal Sciences, Hisar, Haryana, India.
Khurana, S K
  • Indian Council of Agricultural Research-National Research Centre on Equines, Hisar, Haryana, India.

MeSH Terms

  • Animals
  • Horses / genetics
  • Humans
  • Sheep
  • Swine
  • Dogs
  • Rotavirus
  • Chiroptera / genetics
  • Rotavirus Infections / epidemiology
  • Rotavirus Infections / veterinary
  • Rotavirus Infections / genetics
  • Phylogeny
  • Genome, Viral
  • Diarrhea / veterinary
  • Genotype
  • Whole Genome Sequencing
  • Camelids, New World / genetics
  • Goats / genetics
  • Nucleotides
  • Gabon

Conflict of Interest Statement

The authors declare no conflict of interest.

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Citations

This article has been cited 2 times.
  1. Díaz Alarcón RG, Salvatierra K, Gómez Quintero E, Liotta DJ, Parreño V, Miño SO. Complete Genome Classification System of Rotavirus alphagastroenteritidis: An Updated Analysis. Viruses 2025 Jan 31;17(2).
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  2. Uprety T, Soni S, Sreenivasan C, Hause BM, Naveed A, Ni S, Graves AJ, Morrow JK, Meade N, Mellits KH, Adam E, Kennedy MA, Wang D, Li F. Genetic and antigenic characterization of two diarrhoeicdominant rotavirus A genotypes G3P[12] and G14P[12] circulating in the global equine population. J Gen Virol 2024 Aug;105(8).
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