Molecular and genetic characterization of peste des petits ruminants virus Kurdistan 2011 strain based on the haemagglutinin and fusion protein genes sequences

Severe outbreaks of peste des petits ruminants virus (PPRV) occurred during 2011 in wild goats in the Kurdistan region in Iraq. Based on a partial sequence of the nucleoprotein (N) gene the causative virus, named PPRV Kurdistan 2011, was classified as PPRV lineage IV genotype. For further characterization, the open reading frames (ORFs) coding for the haemagglutinin (H) and fusion (F) protein of PPRV Kurdistan 2011 were amplified from infected-cell RNA by RT-PCR. Sequencing of the ORFs revealed sizes of 1830 nucleotides (nt) for the H-ORF and 1641 nt for the F-ORF. This study represents the first report describing the full length ORFs of H and F for a PPRV strain from Kurdistan, Iraq. Comparative sequence analysis performed for the entire H- and F- ORFs of Kurdistan 2011 with respective sequences of PPRV isolates showed the highest homology with PPRV lineage IV isolates which is also reflected by comparative amino acid analysis. Phylogenetic analysis performed based on the partial and complete nucleotide sequences of both H- and F-ORFs clustered Kurdistan 2011 within PPRV lineage IV genotype. H-gene based phylogenetic trees aligned Kurdistan 2011 strain along with Turkey/TR/AFYON/2011-35H and Turkey/2000 strains whereas F-gene based phylogenetic trees aligned Kurdistan 2011 strain along with Qatar/37/10-02, Kurdistan/2012 and Egypt/2009 strains.