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First report on co-isolation and whole-genomic characterisation of mammalian orthorubulavirus 5 and mammalian orthoreovirus type 3 from domestic pigs in India

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Abstract

During a surveillance study to monitor porcine epidemic diarrohoea virus and transmissible gastroenteritis virus in India, a total of 1043 swine samples including faeces (n = 264) and clotted blood (n = 779) were collected and tested. Five samples (four faecal and one serum) showed cytopathic effects in Vero cells. Transmission electron microscopy of infectious cell supernatant revealed the presence of two types of virions. Next-generation sequencing (de novo) allowed the complete genome sequence of mammalian orthorubulavirus 5 (MRuV5; 15246 bp) and that of all 10 gene segments of mammalian orthoreovirus to be determined. Genetic analysis of MRuV5 revealed grouping of the Indian MRuV5 with isolates from various mammalian species in South Korea and China, sharing more than 99% nucleotide sequence identity. The deduced amino acid sequences of the HN, NP, and F genes of MRuV5 isolates showed three (92L, 111R, 447H), two (86S, 121S), and two (139T, 246T) amino acid substitutions, respectively, compared to previously reported virus strains. Phylogenic analysis based on S1 gene sequences showed the Indian MRV isolates to be clustered in lineage IV of MRV type 3, with the highest nucleotide sequence identity (97.73%) to MRV3 strain ZJ2013, isolated from pigs in China. The protein encoded by the MRV3 S1 gene was found to contain the amino acid residues 198-204NLAIRLP, 249I, 340D, and 419E, which are known to be involved in sialic acid binding and neurotropism. This is the first report of co-isolation and whole-genomic characterisation of MRuV5 and MRV3 in domestic pigs in India. The present study lays a foundation for further surveillance studies and continuous monitoring of the emergence and spread of evolving viruses that might have pathogenic potential in animal and human hosts.

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Acknowledgements

The authors are thankful to the Indian Council of Agricultural Research, New Delhi, for funding to carry out this study. We also thank the staff of the Department of Animal Husbandry and Veterinary of the Government of Mizoram, Assam and Chhattisgarh, who helped in collection of blood and faecal samples from pigs.

Funding

The present research work was carried out under the institutional project entitled “Diagnostic preparedness for porcine epidemic diarrhoea and transmissible gastroenteritis in pigs” (Project code IXX 13779) funded by the Indian Council of Agricultural Research, New Delhi, through institutional research contingency.

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  1. ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, 462022, India

    Fateh Singh, Katherukamem Rajukumar, Dhanapal Senthilkumar, Govindarajulu Venkatesh, Deepali Srivastava, Subbiah Kombiah, Sandeep Kumar Jhade & Vijendra Pal Singh

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Contributions

All authors contributed to the study conception and design. Samples were collected by FS, KR, DS, and GV. Material preparation, laboratory tests and analyses were performed by FS, KR, DS, DS, SK, and SKJ. The first draft of the manuscript was written by FS and KR, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Fateh Singh.

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This study did not involve any human participants or animals.

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Singh, F., Rajukumar, K., Senthilkumar, D. et al. First report on co-isolation and whole-genomic characterisation of mammalian orthorubulavirus 5 and mammalian orthoreovirus type 3 from domestic pigs in India. Arch Virol 167, 1529–1545 (2022). https://doi.org/10.1007/s00705-022-05459-x

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