Open AccessChikungunya virus: Molecular epidemiology of nonstructural proteins in Pakistan
Author(s) -
Nazish Badar,
Aamer Ikram,
Muhammad Salman,
Muhammad Masroor Alam,
Massab Umair,
Yasir Arshad,
Naveed Mushtaq,
Hamza Ahmad Mirza,
Abdul Ahad,
Umer Farooq,
Muhammad Talha Yasin,
Javaria Qazi
Publication year - 2021
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0260424
Subject(s) - chikungunya , outbreak , virology , biology , phylogenetic tree , genotype , virus , molecular epidemiology , virulence , transmission (telecommunications) , lineage (genetic) , phylogenetics , clade , genetic diversity , genetics , gene , medicine , environmental health , population , electrical engineering , engineering
Chikungunya virus (CHIKV) is considered a public health problem due to its rapid spread and high morbidity. In 2016–2017 an outbreak of CHIKV was occurred in Pakistan but the data regarding the genomic diversity of CHIKV was not reported. Hence, the current study aimed to determine the genetic diversity of CHIKVs in Pakistan. A cross sectional study was carried out using sera of infected CHIKV patients (n = 1549) during the outbreak in Pakistan (2016–2018). Nucleotide sequencing of non-structural genes of CHIKV from eight isolates were performed followed by phylogenetic analysis using Bayesian method. Phylogenetic analysis suggested that the Pakistani CHIKV strains belonged to Indian Ocean Lineage (IOL) of genotype ECSA and C1.3a clade. Furthermore, the Pakistani isolates showed several key mutations (nsP2-H130Y, nsP2-E145D, nsP4-S55N and nsP4- R85G) corresponding to mutations reported in 2016 Indian strains of CHIKV. The molecular analysis revealed high evolutionary potential of CHIKV strains as well as better understanding of enhanced virulence and pathogenesis of this outbreak. The study highlights the need to continue surveillance in order to understand viral diversity over time and to devise preventive measures to limit disease s transmission in the region.