Phylogenetic and sequencing analysis of Chikungunya virus strains from local Pakistani population.

Abstract

To outline the genotype of Chikungunya virus strains and to form their phylogenetic tree. The cross-sectional study was conducted at the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from August 2016 to September 2017, and comprised suspected Chikungunya samples. The viral ribonucleic acid was extracted and amplified. The purified product was sequenced using Sanger dideoxy method. Phylogenetic tree was constructed. Sequences generated were checked for alignment with sequences reported globally. Structural prediction and analysis was performed using Phyre2 and the models were visualised in PyMol2.2. In the 11 suspected samples, 7(63.6%) were found to be positive for Chikungunya. Of them, 5(71.4%) sequences generated were found to be aligned with other full structural polyprotein sequences, having 99% similarity with amino acid sequences. The Chikungunya strains in the study belonged to the East/Central/South African genotype.