A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand

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.

Chikungunya Manifestations and Viremia in Patients Who Presented to the Fever Clinic at Bangkok Hospital for Tropical Diseases During the 2019 Outbreak in Thailand

“…The structural protein regions in the amplified fragment were directly sequenced. The phylogenetic tree showed that the virus clustered into the previous 14 strains and other Thailand strains in the same clade of C2.3c (45), which is related to recent CHIKVs detected in Myanmar, China, and Taiwan in 2018-2019 ( Figure 2). The E1-K211E and E2-V264A mutations were present in this clade (Supplementary Table S3).…”

“…Since then, the number of cases rapidly increased across the country and surged in Bangkok (21). Based on phylogenetic analysis, the recent CHIKVs circulating 2016-present, particularly in India, Pakistan, Bangladesh, and Thailand, were classified as belonging to the new IOL sub-lineage of genotype ECSA with specific amino acid mutations of E1-K211E and E2-V264A (45). The present study showed that the 23 CHIKVs collected in October 2019 were closely related to CHIKVs from southern Thailand collected earlier in late 2018 and recent circulating strains in 2019 from Myanmar, China, and Taiwan.…”

“…The obtained sequences were aligned to S27 (NC_004162.2) in AliView V1.26 (89), and the consensus sequence of the entire structural polyprotein region (3747 bp) was manually extracted and deposited in GenBank (Accession number LC598202-LC598210). The newly obtained sequences were combined with the previously published sequences (45) and other public ECSA genotype in GenBank. The maximum likelihood tree of the dataset was constructed using IQTREE (90).…”

“…Fourteen nearly whole CHIKV genomes from infected patients were sequenced and the genotypes determined in a previous study (45). All of them were the new IOL sub-lineage of ECSA CHIKV, closely related to the Bangladesh CHIKV strains of 2017 harboring E1-K211E and E2-V264A in the background of E1-226A.…”

Chikungunya Manifestations and Viremia in Patients Who Presented to the Fever Clinic at Bangkok Hospital for Tropical Diseases during the 2019 Outbreak in Thailand

“…Fourteen nearly whole CHIKV genomes from infected patients were sequenced and the genotypes determined in a previous study [ 52 ]. We were able to amplify the CHIKV structural protein gene regions from the sera of an additional 9 patients, though we failed to do so in the remaining 3 patients, probably due to low amounts of the virus within the sera ( Supplementary Table S3 ).…”