Genomic Sequencing of Dengue Virus Strains Associated with Papua New Guinean Outbreaks in 2016 Reveals Endemic Circulation of DENV-1 and DENV-2

Abstract

Over the past decade, the Pacific region has experienced many arboviral outbreaks, including dengue, chikungunya, and Zika viruses. Papua New Guinea (PNG) has a high burden of arboviral diseases, but there is a paucity of knowledge about the epidemiology and circulation of these viruses in the country. In this study, we report investigations into suspected arboviral outbreaks of febrile disease in PNG from December 2015 to June 2017. DENV-1 and DENV-2 were the mostly commonly detected viruses, and low circulation of DENV-3 and ZIKV was also detected. DENV-4 and CHIKV were not detected during this period. Full genome sequencing of selected positive samples revealed that circulation was dominated by endemic indigenous strains belonging to DENV-1 (genotype IV) and DENV-2 (genotype C) that have been present in the country for up to a decade. A DENV-2 sublineage was also identified that has been associated with outbreaks of severe dengue in both PNG and the Solomon Islands.

Figure 1.

Maximum likelihood phylogenetic tree of whole DENV-1 genomes. The TIM2 model with empirical base frequencies and gamma rate heterogeneity was chosen as the best fit by IQ-TREE v.2.0.6. The percentage results from 1,000 bootstrap replicates are given on the nodes (if > 50%) and the scale represents the number of nucleotide substitutions per site. Sequences generated in this study are colored red.

Figure 2.

Maximum likelihood phylogenetic tree of whole DENV-2 genomes. The TN model with empirical base frequencies and gamma rate heterogeneity was chosen as the best fit by IQ-TREE v.2.0.6. The percentage results from 1,000 bootstrap replicates are given on the nodes (if > 50%) and the scale represents the number of nucleotide substitutions per site. Sequences generated in this study are colored red.