Genetic Diversity of Dengue Virus in Clinical Specimens from Bangkok, Thailand, during 2018-2020: Co-Circulation of All Four Serotypes with Multiple Genotypes and/or Clades

Abstract

Dengue is an arboviral disease highly endemic in Bangkok, Thailand. To characterize the current genetic diversity of dengue virus (DENV), we recruited patients with suspected DENV infection at the Hospital for Tropical Diseases, Bangkok, during 2018-2020. We determined complete nucleotide sequences of the DENV envelope region for 111 of 276 participant serum samples. All four DENV serotypes were detected, with the highest proportion being DENV-1. Although all DENV-1 sequences were genotype I, our DENV-1 sequences were divided into four distinct clades with different distributions in Asian countries. Two genotypes of DENV-2 were identified, Asian I and Cosmopolitan, which were further divided into two and three distinct clades, respectively. In DENV-3, in addition to the previously dominant genotype III, a cluster of 6 genotype I viruses only rarely reported in Thailand was also observed. All of the DENV-4 viruses belonged to genotype I, but they were separated into three distinct clades. These results indicated that all four serotypes of DENV with multiple genotypes and/or clades co-circulate in Bangkok. Continuous investigation of DENV is warranted to further determine the relationship between DENV within Thailand and neighboring countries in Southeast Asia and Asia.

Keywords: Bangkok; DENVs; clades; co-circulation; genetic diversity; genotypes.

Figure 1

Phylogenetic analysis of Thailand DENV-1 in 2015–2020. The maximum-likelihood (ML) tree was constructed based on the complete envelope (E) region sequences (1485 nucleotides) under TIM2 + F + I + G4 with 1000 ultrafast bootstrap replicates. The ML tree included 46 newly determined sequences of DENV-1 from clinical specimens from Bangkok in 2018–2020, their related strains, Thailand strains during 2015–2020, and the reference genotypes. The sequences collected in 2018, 2019, and 2020 are labeled in pink, green, and blue, respectively, and indicated in the upper left corner. The sequences newly determined in the present study are marked with asterisks (*). Viral genotypes and clades are indicated by black and dotted brackets, respectively, on the right. Sequences are shown by serotype, accession number, country, and reported year. Numbers on branches are bootstrap support values exceeding 80%. Details of the collapsed portion of the tree in the red square in the upper right including clades b and c are shown in the middle.

Figure 2

Phylogenetic analysis of Thailand DENV-2 in 2015–2020. The maximum-likelihood (ML) tree was constructed based on the complete envelope (E) region sequences (1485 nucleotides) under TIM2 + F + I + G4 with 1000 ultrafast bootstrap replicates. The ML tree included 44 newly determined sequences of DENV-2 from clinical specimens from Bangkok in 2018–2020, their related strains, Thailand strains during 2015–2020, and the reference genotypes. The sequences collected in 2018, 2019, and 2020 are labeled in pink, green, and blue, respectively, and indicated in the upper left corner. The sequences newly determined in the present study are marked with asterisks (*). Viral genotypes and clades are indicated by black and dotted brackets, respectively, on the right. Sequences are shown by serotype, accession number, country, and reported year. Numbers on branches are bootstrap support values exceeding 80%, except for clades Cb (73%) and Cc (74%).

Figure 3

Phylogenetic analysis of Thailand DENV-3 in 2015–2020. The maximum-likelihood (ML) tree was constructed based on the complete envelope (E) region sequences (1479 nucleotides) under TN + F + I + G4 with 1000 ultrafast bootstrap replicates. The ML tree included eight newly determined sequences of DENV-3 from clinical specimens in Bangkok in 2018–2020, their related strains, Thailand strains during 2015–2020, and the reference genotypes. The sequences collected in 2018 and 2020 are labeled in pink and blue, respectively, and indicated in the upper left corner. Viral genotypes are indicated by black brackets on the right. The sequences newly determined in the present study are marked with asterisks (*). Sequences are shown by serotype, accession number, country, and reported year. Numbers on branches are bootstrap support values exceeding 80%.

Figure 4

Phylogenetic analysis of Thailand DENV-4 in 2015–2020. The maximum-likelihood (ML) tree was constructed based on the complete envelope (E) gene sequences (1485 nucleotides) under TIM2 + F + G4 with 1000 ultrafast bootstrap replicates. The ML tree included 13 newly determined sequences of DENV-4 from clinical specimens from Bangkok in 2018–2020, their related strains, Thailand strains during 2015–2020, and the reference genotypes. The sequences collected in 2018, 2019, and 2020 are labeled in pink, green, and blue, respectively, and indicated in the upper left corner. The sequences newly determined in the present study are marked with asterisks (*). Viral genotypes and clades are indicated by black and dotted brackets, respectively, on the right. Sequences are shown by serotype, accession number, country, and reported year. Numbers on branches are bootstrap support values exceeding 80%.