Epidemiology of Chikungunya virus isolates 2016‐2018 in Pakistan

The chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus, which has infected millions of people in Africa, Asia, Americas, and Europe since it remerged in India and Indian Ocean regions in 2005-2006. The purpose of this study was to evaluate the genetic diversity and evolutionary changes in Chikungunya virus from 2016-2018 in Pakistan. Blood specimens were collected and processed following the Centres for Disease Control and Prevention Trioplex Protocol. Sequencing and phylogenetic analysis of complete coding sequence of representative isolates from the CHIKV outbreak was carried out during December 2016 to July 2018, a total of 1549 samples were received, out of which 50% (n=774) were found positive for CHIKV RNA. Mean age of chikungunya positive patients was 31.8±15.7 years and most affected were between 21-40 years of age. The Pakistan CHIKV strains clustered with the Indian Ocean sub-lineage of ECSA (East/Central/South African) with Co circulation of some variants In the structural proteins region, two noteworthy changes (A226V and D284E) were observed in the membrane fusion glycoprotein E1. Key substitutions in the neutralizing epitopes site and a few changes indicative of adaptive to other insect cells were also detected in Pakistani strains. This study provides the emerging trend of Chikungunya virus in the country for early identification of potential variants of high virulence and preventive measures for vector borne disease especially in the endemic areas. This article is protected by copyright. All rights reserved.