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.

Keywords: Bangladesh; East/Central/South African genotype; Indian Ocean lineage; Thailand; chikungunya virus; molecular clock analysis; mosquito; outbreaks.

Figure 1

Locations of chikungunya virus (CHIKVs) collection in the present study. Bangladesh and Thailand, where CHIKV sera were collected, are indicated in the dark grey shade area.

Figure 2

Genotype classification of CHIKV. The maximum-likelihood tree of open reading frames (ORFs) were constructed using GTR+F+I with 1000 ultrafast bootstrap replications. The Bangladesh and Thailand sequences obtained in the present study are labeled with blue and red, respectively. The CHIKV genotypes are indicated to the right. The recent lineages are shaded in the gray box and indicated to the right. Bootstrap support values exceeding 80% are shown as black nodes and the actual values are indicated only in key important nodes.

Figure 3

Molecular clock analysis of ECSA-genotype CHIKV. (A) Temporal signal analysis of regression of root-to-tip divergence against date. The color marker represents the location indicated in the left panel. (B) Maximum clade credibility (MCC) tree of East/Central/South African (ECSA)-genotype CHIKV ORFs. The timescale in years is shown in the x-axis at the bottom. Black nodes are shown only for those with the posterior probability (PP) more than 0.8. Yellow triangles indicate the key nodes, and PP values are shown adjacent to the corresponding key nodes. CP10 is shown by a red arrow. The round tip color of each sequence corresponds to the location indicated in panel C. (C) Magnification of a gray-shaded area in B including recent India, Bangladesh, and Thailand clades. The Bangladesh and Thailand sequences obtained in the present study are labeled with blue and red, respectively. Sequences are designated in the format of country/accession number/year of collection. The amino acid mutations specific to the Indian Ocean Lineage (IOL) correspond to their sequences shown next to the sequence tip of the MCC tree in panel B and indicated in the right panel.