Spread of a Novel Indian Ocean Lineage Carrying E1-K211E/E2-V264A of Chikungunya Virus East/Central/South African Genotype across the Indian Subcontinent, Southeast Asia, and Eastern Africa.

Juthamas Phadungsombat,Emi E Nakayama,Wasin Matsee,Pornsawan Leaungwutiwong,Tatsuo Shioda,Pongrama Ramasoota,Wang Nguitragool,Hisham A Imad,Watcharapong Piyaphanee

doi:10.3390/microorganisms10020354

Juthamas Phadungsombat, Emi E Nakayama + Show 7 more

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https://doi.org/10.3390/microorganisms10020354

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Abstract

The Indian Ocean Lineage (IOL) of the chikungunya virus (CHIKV) East/Central/South African (ECSA) genotype, which originated in Kenya, spread to the Indian ocean and the Indian subcontinent, and then expanded through Southeast Asia in the previous decade. It carried an adaptive mutation E1-A226V, which enhances CHIKV replication in Aedes albopictus. However, the IOL CHIKV of the most recent outbreaks during 2016–2020 in India, Pakistan, Bangladesh, the Maldives, Myanmar, Thailand, and Kenya lacked E1-A226V but carried E1-K211E and E2-V264A. Recent CHIKV genome sequences of the Maldives and Thailand were determined, and their phylogenetic relationships were further investigated together with IOL sequences reported in 2004–2020 in the database. The results showed that the ancestral IOLs diverged to a sub-lineage E1-K211E/E2-V264A, probably in India around 2008, and caused sporadic outbreaks in India during 2010–2015 and in Kenya in 2016. The massive expansion of this new sub-lineage occurred after the acquisition of E1-I317V in other neighboring and remote regions in 2014–2020. Additionally, the phylogenetic tree indicated that independent clades formed according to the geographical regions and introduction timing. The present results using all available partial or full sequences of the recent CHIKVs emphasized the dynamics of the IOL sub-lineages in the Indian subcontinent, Southeast Asia, and Eastern Africa.

Highlights

Chikungunya virus (CHIKV) is a member of the genus Alphavirus, family Togaviridae, and causes fever, arthralgia, and rash in humans
A total of 26 CHIKV sequences of nearly the whole genome, including 16 Maldives strains from the 2019 outbreak and 10 Thailand strains from the 2020 outbreak, were generated (Table 1)
CHIKV genomes shared a high degree of similarity since the nucleotide and amino acid identities among Maldives strains were 99.93–99.99% and 99.84–100%, respectively, while those among Thailand strains were 99.68–99.97% and 99.72–100%, respectively (Supplementary Table S2)

Summary

Introduction

Chikungunya virus (CHIKV) is a member of the genus Alphavirus, family Togaviridae, and causes fever, arthralgia, and rash in humans. The first CHIKV was isolated during an outbreak in Tanzania in 1953. CHIKV is phylogenetically classified into three major genotypes: East/Central/South/African (ECSA), West African (WA), and Asian, named after the location where these genotypes were first recognized [1]. Asian CHIKV that had diverged from ECSA once emerged in South Asia in the 1960s and subsequently spread to Asia [1]. In 2005, CHIKV re-emerged in these regions as the ECSA genotype that was later referred to as the Indian Ocean Lineage (IOL). The IOL CHIKV caused epidemics and consequent outbreaks during the last decade.

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