PHYLOGENETIC ANALYSIS OF DENGUE VIRUS TYPE 2 IN RECURRING OUTBREAKS IN MALAYSIA

Abstract

Intro: In Malaysia, dengue is hyperendemic with recurrent outbreaks occurring since 1980s. Dengue virus type-2 (DENV-2) is one of the predominant serotypes causing the recurring outbreaks with an increase in the number of cases. This study aimed to investigate the evolutionary dynamics driving the DENV-2 recurring outbreaks over the past three decades. Methods: Two hundred and three Malaysian DENV-2 isolates from 1987-2018 were isolated from dengue patient sera retrieved from the WHOCC for Arbovirus Reference & Research depository at TIDREC, University Malaya. The DENV-2 RNA was extracted and amplified for the envelope (E) gene by RT-PCR assay. The complete E gene was sequenced, and the sequences obtained were subjected to phylogenetic and mutational analyses. Findings: Our Bayesian maximum clade credibility tree revealed two circulating DENV-2 genotypes in Malaysia: Cosmopolitan and Asian I. The DENV-2 Cosmopolitan (86%) is the most prevalent genotype and responsible for the recurring outbreaks from 1989-2018, while the Asian I (14%) genotype was scarcely detected in the region from 1987 to 1998. Phylogenetic analysis showed that there were two lineages of DENV-2 Cosmopolitan clustered into two clades, CI and CII. In comparison to the CI lineage, the CII lineage was more efficiently evolved and expanded with many recurrent outbreak-causing strains in 1995- 1997, 2005-2007, and 2017-2018, clustered in ladder-like topology. In contrast, only a few virus strains from 1995-1997 and 2005-2007 outbreaks were clustered into CI lineage. The virus strains of CI showed slower estimated evolutionary rates (9.553 × 10-4 rates/site/year) than the CII viruses (1.407 × 10-3 rates/site/year). One non-conservative amino acid substitution, H52Q (Domain I/II hinge), was observed to distinguish the CI from CII. Conclusion: We conclude that the recurring DENV-2 outbreaks in Malaysia were caused by the viruses that evolved from the pre-existing Cosmopolitan gene pool and might be associated with naïve human population present in the endemic region.