Phylogenetic Analysis of Peste des Petits Ruminants Virus Isolates on the Basis of Nucleocapsid Gene Sequence

Abstract

A Peste des petits ruminant (PPR) is an acute and highly contagious viral disease of small ruminants. The disease is endemic in Pakistan and causes considerable economic losses due to its high morbidity and mortality. The study was undertaken to detect and characterize the PPR virus (PPRV) circulating in Pakistan. For a better understanding of the molecular epidemiology of PPRV full N gene was targeted to the phylogenetic links of PPRV circulating in neighbouring countries.Twenty local isolates of Pakistani PPRV were successfully detected from nasal and ocular swabs and post mortem samples (lymph node, spleen) of goats and sheep during the year 2015-2016. The full N gene of 10 outbreak isolates was amplified by RT-PCR, and was sequenced. On genetic analyses, it appeared that the N gene of PPRV is more conserved as compared to the F gene. The phylogenetic analysis revealed that PPRVs circulating in Pakistan belonged to Lineage IV and they formed a separate sub-cluster along with recent isolates from India and China. The isolates investigated in the current study revealed an identity of 85-90% with neighbouring countries isolates. A proper understanding of PPRVgenome will help to devise control strategies in PPR epidemic countries such as Pakistan.