Molecular Characterization of Dengue Type 2 Outbreak in Pacific Islands Countries and Territories, 2017-2020

Abstract

Dengue virus (DENV) serotype-2 was detected in the South Pacific region in 2014 for the first time in 15 years. In 2016-2020, DENV-2 re-emerged in French Polynesia, Vanuatu, Wallis and Futuna, and New Caledonia, co-circulating with and later replacing DENV-1. In this context, epidemiological and molecular evolution data are paramount to decipher the diffusion route of this DENV-2 in the South Pacific region. In the current work, the E gene from 23 DENV-2 serum samples collected in Vanuatu, Fiji, Wallis and Futuna, and New Caledonia was sequenced. Both maximum likelihood and Bayesian phylogenetic analyses were performed. While all DENV-2 strains sequenced belong to the Cosmopolitan genotype, phylogenetic analysis suggests at least three different DENV-2 introductions in the South Pacific between 2017 and 2020. Strains retrieved in these Pacific Islands Countries and Territories (PICTs) in 2017-2020 are phylogenetically related, with strong phylogenetic links between strains retrieved from French PICTs. These phylogenetic data substantiate epidemiological data of the DENV-2 diffusion pattern between these countries.

Keywords: Pacific; dengue; molecular evolution; phylogeny.

Figure 1

Dengue virus type 2 (DENV-2) emergence and circulation in the Pacific region, 2014–2020. (A) Map of the Pacific region showing the temporality of DENV-2 emergence and circulation between 2014 and 2019. DENV-2 emerged in Fiji and Tuvalu in 2014 (blue) and Solomon Islands and Vanuatu in 2016 (green). DENV-2 was then imported from Vanuatu in New Caledonia and French Polynesia in 2017 (purple), and from New Caledonia in French Polynesia in 2019 (red). Arrows indicate putative routes of introductions. (B) Temporality of DENV circulation in Fiji, Vanuatu, New Caledonia, French Polynesia, and Wallis and Futuna between 2014 and 2020 (according to the Pacific Public Health Surveillance Network [10]).

Figure 2

Maximum likelihood evolutionary (MLE) relationships of DENV-2 E gene sequences. Maximum likelihood tree derived from 89 DENV-2 E gene sequences (23 from Fiji, Vanuatu, Wallis and Futuna, and New Caledonia in red, and 66 from the 5 genotypes retrieved from GenBank, including isolates collected in 2010–2019 in the Pacific and in South East Asia). The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown for values over 80. The country and year of collection are indicated along with the GenBank accession number; imp = imported from.

Figure 3

Maximum clade credibility (MCC) evolutionary relationships of DENV-2 E gene sequences from the Pacific and South East Asia. Maximum clade credibility tree of 48 complete E gene nucleotide sequences of isolates collected in Pacific and South East Asia, among which 20 were generated in the current study. The two shorter sequences retrieved in Fiji, as well as the sequence “New Caledonia-2020-MT799882”, which does not cluster with the other strains retrieved in the South Pacific region in 2017–2020, were excluded from the analysis. This MCC tree was obtained for a constant population size and a relaxed clock with a lognormal relaxed distribution. This model yielded the lowest MLE. For clarity, the tree displays all South Pacific virus branches in purple. The 20 virus sequences obtained in this study are indicated in red. Posterior probabilities higher than 0.80 are specified for each node; TMRCA = Time to the Most Recent Common Ancestor.