Abstract
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 diseases transmission in the region.
Highlights
Increased virulence of emerging and re-emerging pathogens, like Chikungunya (CHIKV), Dengue (DENV) and Zika (ZIKV) viruses is of serious public health concern [1,2,3]
A total of 1549 blood samples from suspected cases were processed by Real-Time PCR at virology department, National Institute of health Pakistan during 20th December, 2016 to July, 2018
Karachi is a provincial capital of Sindh, Pakistan, largest coastal city that observed Chikungunya virus (CHIKV) outbreak in 2016 and 2017
Summary
Increased virulence of emerging and re-emerging pathogens, like Chikungunya (CHIKV), Dengue (DENV) and Zika (ZIKV) viruses is of serious public health concern [1,2,3]. Chikungunya (CHIK) is zoonotic viral infection transmitted by the bite of female mosquito of Aedes family (Ae. aegypti and Ae. albopictus species). The debilitating nature of this disease leads to outbreaks of considerable economic burden and can breakdown health systems [4,5,6]. The clinical presentation of CHIK resembles with other viral diseases, like Dengue and Zika as they share same vectors for transmission. It is not possible to differentiate between CHIK, DENV and ZIKV infections without laboratory diagnosis [7, 8]
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