Molecular characterisation of porcine reproductive and respiratory syndrome virus from pigs in Kerala

Abstract

Porcine reproductive and respiratory syndrome (PRRS) caused by an arterivirus is characterised by reproductive disorders in sows, and post-weaning pneumonia and growth reduction in piglets. Though the virus has been detected in Kerala, no systematic study has been carried out to ascertain its genotype and molecular epidemiology. In the present study, 7 PRRS virus (PRRSV) positive samples collected from incidences of PRRS in Kerala during 2017–2019 were subjected to ORF5, ORF7 and Nsp2 gene based reverse transcription polymerase chain reaction and the specific amplicons generated were sequenced. On BLAST analysis it was revealed that all the sequences were of genotype 2 (North American genotype). Phylogenetic analysis of ORF5 sequences, grouped them under subgenotype 4 with close clustering with other isolates from Kerala, Mizoram and Assam. Nsp2 gene sequence based phylogenetic analysis grouped the isolates under subgenotype 3 with similarities to isolates from Mizoram. Phylogenetic analysis based on ORF7, clustered the isolates under study with PRRSV isolates from Mizoram and Meghalaya. In Nsp2 sequences, a 30 amino acid discontinuous deletion was observed. On analysis of amino acid sequences of ORF5 of Kerala isolates and those from India, it was seen that the Kerala isolates showed closer similarity to PRRSV isolates from Assam than to the other Indian isolates. The study reveals that PRRSV strains prevalent in Kerala share close relationship with other PRRSV isolates in India. This may be due to spread of the virus from these regions to Kerala due to animal movement. Concerted efforts should be undertaken to check unauthorized animal movement to control spread of this economically important disease.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

References

  1. 1.

    An TQ, Zhou YJ, Liu GQ, Tian ZJ, Li J, Qiu H, Tong GZ. Genetic diversity and phylogenetic analysis of glycoprotein 5 of PRRSV isolates in mainland China from 1996 to 2006: coexistence of two NA-subgenotypes with great diversity. Vet Microbiol. 2007;123:43–52.

    CAS  Article  Google Scholar 

  2. 2.

    Deng Y, Pan Y, Wang D, Zhou Q, Bi Y, Chen F, Song Y. Complete genome sequence of porcine reproductive and respiratory syndrome virus strain QY2010 reveals a novel subgroup emerging in China. J Virol. 2012;86:7719–20.

    CAS  Article  Google Scholar 

  3. 3.

    Do HQ, Trinh DT, Nguyen TL, Vu TT, Than DD, Lo TV, Yeom M, Song D, Choe S, An DJ, Le VP. Molecular evolution of type 2 porcine reproductive and respiratory syndrome viruses circulating in Vietnam from 2007 to 2015. BMC Vet Res. 2016;12:256. https://doi.org/10.1186/s12917-016-0885-3.

    Article  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Dortmans JCFM, Buter GJ, Dijkman R, Houben M, Duinhof TF. Molecular characterization of type 1 porcine reproductive and respiratory syndrome viruses (PRRSV) isolated in the Netherlands from 2014 to 2016. PLoS ONE. 2019;14:1–13.

    Article  Google Scholar 

  5. 5.

    Guo Z, Chen XX, Li R, Qiao S, Zhang G. The prevalent status and genetic diversity of porcine reproductive and respiratory syndrome virus in China: a molecular epidemiological perspective. J Virol. 2018;15:2.

    Article  Google Scholar 

  6. 6.

    Hu H, Li X, Zhang Z, Shuai J, Chen N, Liu G, Fang W. Porcine reproductive and respiratory syndrome viruses predominant in southeastern China from 2004 to 2007 were from a common source and underwent further divergence. Arch Virol. 2009;154:391–8.

    CAS  Article  Google Scholar 

  7. 7.

    International Committee on Taxonomy of Viruses. Virus Taxonomy: 2019 Release. https://talk.ictvonline.org/taxonomy/ Accessed on 21.4.2020.

  8. 8.

    Kang H, Yu JE, Shin JE, Kang A, Kim WI, Lee C, Lee J, Cho IS, Choe SE, Cha SH. Geographic distribution and molecular analysis of porcine reproductive and respiratory syndrome viruses circulating in swine farms in the Republic of Korea between 2013 and 2016. BMC Vet Res. 2018;14:160.

    Article  Google Scholar 

  9. 9.

    Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9.

    CAS  Article  Google Scholar 

  10. 10.

    Li Y, Wang X, Bo K, Wang X, Tang B, Yang B, Jiang W, Jiang P. Emergence of a highly pathogenic porcine reproductive and respiratory syndrome virus in the Mid-Eastern region of China. Vet J. 2007;174:577–84.

    CAS  Article  Google Scholar 

  11. 11.

    Martínez-Bautista NR, Sciutto-Conde E, Cervantes-Torres J, Segura-Velázquez R, Mercado García MC, Ramírez-Mendoza H, Trujillo Ortega ME, Delgadillo Alvarez J, Castillo-Juárez H, Sanchez-Betancourt JI. Phylogenetic analysis of ORF 5 and ORF 7 of porcine reproductive and respiratory syndrome (PRRS) virus and the frequency of wild-type PRRS virus in México. Transbound Emerg Dis. 2018;65:993–1008.

    Article  Google Scholar 

  12. 12.

    Neira V, Brito B, Mena J, Culhane M, Apel MI, Max V, Perez P, Moreno V, Mathieu C, Johow M, Badia C. Epidemiological investigations of the introduction of porcine reproductive and respiratory syndrome virus in Chile, 2013–2015. PLoS ONE. 2017;12:1–15.

    Article  Google Scholar 

  13. 13.

    Paploski IAD, Corzo C, Rovira A, Murtaugh MP, Sanhueza JM, Vilalta Sans C, Schroeder DC, VanderWaal K. Temporal dynamics of co-circulating lineages of porcine reproductive and respiratory syndrome virus. Front Microbiol. 2019;10:2486.

    Article  Google Scholar 

  14. 14.

    Rajkhowa TK, Gogoi A, Hauhnar L, Isaac I. Molecular detection, epidemiology and clinico-pathological studies on first outbreak of porcine reproductive and respiratory syndrome (PRRS) in pig population of Mizoram, India. Indian J Anim Sci. 2015;85:13.

    Google Scholar 

  15. 15.

    Rajkhowa TK, Mohanarao GJ, Gogo A, Hauhnar L. Indian porcine reproductive and respiratory syndrome virus bears discontinuous deletion of 30 amino acids in nonstructural protein 2. Virus Dis. 2016;27:287–93.

    CAS  Article  Google Scholar 

  16. 16.

    Ravishankar C, John K, Ravindran R, Sebastian SR, Rajasekhar R, Anoopraj R, Hamza P. Molecular detection of classical swine fever virus and porcine reproductive and respiratory syndrome virus in pigs in Kerala. In: Proceedings of the 30th Kerala science congress. Thalassery: Government Brennan College; 28–30 January, 2018.

  17. 17.

    Wang PP, Dong JG, Zhang LY, Liang PS, Liu YL, Wang L, Fan FH, Song CX. Sequence and phylogenetic analyses of the Nsp2 and ORF5 genes of porcine reproductive and respiratory syndrome virus in boars from South China in 2015. Transbound Emerg Dis. 2017;64:1953–64.

    CAS  Article  Google Scholar 

  18. 18.

    Wu Q, Li Z, Zhang G, Niu J, Zeng X, Sun B, Ma J. Genetic diversity and phylogenetic analysis of porcine reproductive and respiratory syndrome virus in southern China from 2007 to 2014. J of Vet Sci. 2017;18:317–26.

    Article  Google Scholar 

  19. 19.

    Zhou L, Zhang J, Zeng J, Yin S, Li Y, Zheng L, Guo X, Ge X, Yang H. The 30-amino-acid deletion in the Nsp2 of highly pathogenic porcine reproductive and respiratory syndrome virus emerging in China is not related to its virulence. J Virol. 2009;83:5156–67.

    CAS  Article  Google Scholar 

  20. 20.

    Zhou Z, Ni J, Cao Z, Han X, Xia Y, Zi Z, Ning K, Liu Q, Cai L, Qiu P, Deng X. The epidemic status and genetic diversity of 14 highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) isolates from China in 2009. Vet Microbiol. 2011;150:257–69.

    CAS  Article  Google Scholar 

Download references

Acknowledgements

The study has been carried out under the Science Research Scheme (SRS) funded by Kerala State Council for Science Technology and Environment (KSCSTE), Pattom, Thiruvananthapuram, Kerala, India. The authors thank the Dean, College of Veterinary and Animal Sciences, Pookode for providing facilities for conduct of the study.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Chintu Ravishankar.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 19 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Chaithra, G., Ravishankar, C., Sebastian, S.R. et al. Molecular characterisation of porcine reproductive and respiratory syndrome virus from pigs in Kerala. VirusDis. 31, 560–565 (2020). https://doi.org/10.1007/s13337-020-00634-7

Download citation

Keywords

  • PRRSV
  • ORF5
  • ORF7
  • Nsp2
  • RT-PCR
  • Phylogeny