Authors: Alka Galav, Sunil Maherchndani, Vikas Galav and SK Kashyap

Source: Ruminant Science (2018)-7(2):289-296.

Cite this reference as: Galav Alka, Maherchndani Sunil, Galav Vikas and Kashyap SK (2018). Identification, genetic characterization and phylodynamics of PPR virus from goat herds of Bandikui, India. Ruminant Science 7(2):289-296.


An outbreak of PPRV (peste des petits ruminants virus) was attended in a remote area of Bandikui in state of Rajasthan. The N and M genes of virus were analyzed using phylogenetic and dynamic evolution tools to get insights of phylodynamics of PPRV in Rajasthan. The estimated nucleotide substitution rate of PPRV was estimated to be 6.727×10-4¬†substitutions/site/year at with 95% highest posterior density (HPD). The temporal dynamics revealed that TMRCA for the outbreak virus of estimated approximately 1995 with 95% HPD. The Bayesian skyline plot (BSP) suggested about demographic history of genetic diversity in virus population. The M gene based phylogenetic analysis grouped the outbreak virus in same cluster as N gene based analysis. Also, M gene showed 4 unique amino acid mutations. To summarize, the virus evolution is constant process and therefore our surveillance and control strategies also must evolve together with phylodynamic analysis to combat the disease.


Andino R and Domingo E (2015). Viral quasispecies. 60:46-51, 479-480.

Bailey D, Banyard A, Dash P, Ozkul A and Barrett T (2005). Full genome sequence of peste des petits ruminants virus, a member of the Morbillivirus genus. Virus Research 110(1):119-124.

Balamurugan V, Hemadri D, Gajendragad MR, Singh RK and Rahman H (2014). Diagnosis and control of peste des petits ruminants: A comprehensive review. Virus Disease 25(1):39-56.

Couacy-Hymann E, Roger F, Hurard C, Guillou J, Libeau G and Diallo A (2002). Rapid and sensitive detection of peste des petits ruminants virus by a polymerase chain reaction assay. Journal of Virological Methods 100(1):17-25.

Diallo A (1990). Morbillivirus group: Genome organisation and proteins. Advances in Veterinary Virology 23(1):155-163.

Domingo E (2010). Mechanisms of viral emergence. Veterinary Research 41(6):38.

Drake JW and Holland JJ (1999). Mutation rates among RNA viruses. Proceedings of the National Academy of Sciences 96(24):13910.

Drummond AJ, Suchard MA, Xie D and Rambaut A (2012). Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29(8):1969-1973.

Jupille HJ, Medina-Rivera M, Hawman DW, Oko L and Morrison TE (2013). A tyrosine-to-histidine switch at position 18 of the Ross river virus e2 glycoprotein is a determinant of virus fitness in disparate hosts. Journal of Virology 87(10):5970-5984.

Karam Amarjit, Chakraborty Amit, Puro Kekungu-u, Kakoti Kaushik, Das Samir, Ghatak Sandeep, Shakuntala Ingudam and Sen Arnab (2017). Peste des petits ruminants-A threat to the growing small ruminant for livelihood sustenance in Meghalaya in north eastern India. Ruminant Science 6(1):125-128.  

Kimura M (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16(2):111-120.

Kumar N, Chaubey KK, Chaudhary K, Singh SV, Sharma DK, Gupta VK and Sharma S (2013). Isolation, identification and characterization of a peste des petits ruminants virus from an outbreak in Nanakpur, India. Journal of Virological Methods 189(2):388-392.

Kumar N, Barua S, Thachamvally R and Tripathi BN (2016a). Systems perspective of morbillivirus replication. Journal of Molecular Microbiology and Biotechnology 26(6):389-400.

Kumar S, Stecher G and Tamura K (2016b). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7):1870-1874.

Kumar SK, Babu A, Sundarapandian G, Roy P, Thangavelu A, Siva Kumar K and Parida S (2014). Molecular characterisation of lineage IV peste des petits ruminants virus using multi gene sequence data. Veterinary Microbiology 174(1):39-49.

Kwiatek O, Ali YH, Saeed IK, Khalafalla AI, Mohamed OI, Obeida AA and Libeau G (2011). Asian lineage of peste des petits ruminants virus, Africa. Emerging Infectious Disease Journal 17(7):1223.

Lam TY, Hon CC and Tang JW (2010). Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections. Critical Reviews in Clinical Laboratory Sciences 47(1):5-49.

Lee JS, Mackie RS, Harrison T, Shariat B, Kind T, Kehl T and VandeWoude S (2017). Targeted enrichment for pathogen detection and characterization in three felid species. Journal of Clinical Microbiology 55(6):1658-1670.

Mair CM, Meyer T, Schneider K, Huang Q, Veit M and Herrmann A (2014). A histidine residue of the influenza virus hemagglutinin controls the pH dependence of the conformational change mediating membrane fusion. Journal of Virology 88(22):13189-13200.

Milind Mahender, Joseph Bincy, Sharma DK, Gaurav Abhishek, Sharma MC, Prakash Chandan, Rathore K and Patel P (2017). Seroprevalence of peste des petits ruminants in goats of southern Rajasthan, India. Ruminant Science 6(1):133-136.

Muniraju M, Munir M, Parthiban AR, Banyard AC, Bao J, Wang Z and Parida S (2014). Molecular evolution of peste des petits ruminants virus. Emerging Infectious Diseases 20(12):2023-2033.

Muthuchelvan D, Sanyal A, Sreenivasa BP, Saravanan P, Dhar P, Singh RP and Bandyopadhyay SK (2006). Analysis of the matrix protein gene sequence of the Asian lineage of peste-des-petits ruminants vaccine virus. Veterinary Microbiology 113(1):83-87.

Sahu AR, Wani SA, Saminathan M, Rajak KK, Sahoo AP, Pandey A and Gandham RK (2017). Genome sequencing of an Indian peste des petits ruminants virus isolate, Izatnagar/94, and its implications for virus diversity, divergence and phylogeography. Archives of Virology 162(6):1677-1693.

Singh RP and Bandyopadhyay SK (2015). Peste des petits ruminants vaccine and vaccination in India: Sharing experience with disease endemic countries. Virus Disease 26(4):215-224. 

Tang P, Croxen MA, Hasan MR, Hsiao WWL and Hoang LM (2017). Infection control in the new age of genomic epidemiology. American Journal of Infection Control 45(2):170-179.

Volz EM, Koelle K and Bedford T (2013). Viral Phylodynamics. PLOS Computational Biology 9(3):e1002947.