Phosphoprotein gene of peste des petits ruminants virus: unsuitable for lineage determination

The nucleotide sequence of phosphorprotein (P) gene of a recent isolate of Peste des petits ruminants virus (PPRV/INDIA/TN/Apampattu/2014) was determined by RT-PCR amplification and sequencing. The sequence analysis showed that phosphoprotein gene sequence of this isolate has 87-98 percent identity with other Indian PPRV. At amino acid level, the identity was 84-98 percent with recent Indian PPRV isolates and 95 percent with Sungri/96 isolate. Surprisingly, when phylogenetic analysis was conducted with all the available 'P' gene sequences in genbank along with our sequence, it depicted more than four lineages in the phylogenetic tree. This is not in compliance with the PPRV 'F' and 'N' gene based and whole genome sequence based phylogenetic analysis. This concluded that PPRV 'P' gene based analysis is not suitable for lineage detection. Meanwhile, the PPRV/INDIA/TN/Apampattu/2014 isolate was found to group with Indian isolates coming under lineage IV. Therefore, 'P' gene based analysis could be of help to cluster new isolates into close related groups.