Abstract

In recent decades, chikungunya virus (CHIKV) has become geographically widespread. In 2004, the CHIKV East/Central/South African (ECSA) genotype moved from Africa to Indian ocean islands and India followed by a large epidemic in Southeast Asia. In 2013, the CHIKV Asian genotype drove an outbreak in the Americas. Since 2016, CHIKV has re-emerged in the Indian subcontinent and Southeast Asia. In the present study, CHIKVs were obtained from Bangladesh in 2017 and Thailand in 2019, and their nearly full genomes were sequenced. Phylogenetic analysis revealed that the recent CHIKVs were of Indian Ocean Lineage (IOL) of genotype ECSA, similar to the previous outbreak. However, these CHIKVs were all clustered into a new distinct sub-lineage apart from the past IOL CHIKVs, and they lacked an alanine-to-valine substitution at position 226 of the E1 envelope glycoprotein, which enhances CHIKV replication in Aedes albopictus. Instead, all the re-emerged CHIKVs possessed mutations of lysine-to-glutamic acid at position 211 of E1 and valine-to-alanine at position 264 of E2. Molecular clock analysis suggested that the new sub-lineage CHIKV was introduced to Bangladesh around late 2015 and Thailand in early 2017. These results suggest that re-emerged CHIKVs have acquired different adaptations than the previous CHIKVs.

Highlights

  • Chikungunya virus (CHIKV) is a mosquito-borne virus transmitted via Aedes mosquitoes that causes a febrile illness accompanied by rash and arthralgia

  • High viral load (Ct value less than 20) sera were directly used for RT-PCR amplification of the chikungunya virus (CHIKV) genome, while the other sera were subjected to virus isolation in the C6/36 mosquito cell line cultivated in L-15 medium (Hyclone, UT, USA) supplemented with 2%

  • Except for the CP10 strain that was collected during the previous outbreak in 2010, all of our Bangladesh and Thailand sequences formed a distinct monophyletic cluster apart from the previous Indian Ocean Lineage (IOL) clusters with bootstrap support of 100, and the most closely related virus was the Indian strain reported in 2016 (MK473624)

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Summary

Introduction

Chikungunya virus (CHIKV) is a mosquito-borne virus transmitted via Aedes mosquitoes that causes a febrile illness accompanied by rash and arthralgia. CHIKV belongs to genus Alphavirus, family Togaviridae, and it contains a single-stranded RNA genome of approximately 11–12 kb with two open reading frames (ORFs) flanked by untranslated regions (UTRs) at the 50 and 30 ends. CHIKV is phylogenetically classified into three genotypes reflecting the geographical locations where the respective strains were first isolated, East/Central/South African (ECSA), West African (WA), and Asian. CHIKV is transmitted by Aedes mosquitoes that are found in tropical and temperate regions. Ae. aegypti is predominant in tropical areas in East Africa, South Asia, and Southeast Asia where a re-emergence of CHIKV has occurred [3]

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