Genotypic persistence of dengue virus in the Philippines.

The Philippines is known to have one of the world's highest prevalences of dengue infection. The disease has been endemic in the country since 1956 and the severe form was first reported during an outbreak in Manila in 1954. Among all of the countries in the world, the Philippines had the highest case fatality rate from 2008 to 2012. With the increasing rate of international travel, the country is also considered one of the primary sources of imported dengue cases in non-endemic areas in Asia, Australia, and Europe. Despite this high prevalence, there is a dearth of literature describing the circulating strains in the Philippines at the genotype level. Using data from sequence databases, this study aimed to characterize all available Philippine sequences, at the molecular level. Capsid/pre-membrane (C/prM) junction gene and envelope (E) gene sequences of dengue serotypes 1, 2, 3 and 4 from 1956 to 2016 were used for phylogenetic analysis and genotypic identification. All four serotypes co-circulate in the country over the last 50 years with conspicuous genotypic characteristics. DENV-1 exhibited an apparent persistence of a single genotype since 1974. DENV-2 showed strong evidence of genotypic shift in 1999-2002 accompanied by a genotypic persistence thereafter. DENV-3 and DENV-4 displayed a temporal domination of a single genotype, with evidence of a minor co-circulating genotypic population. The persistence and pre-domination of specific DENV genotypes warrant continuous molecular surveillance for signs of genotypic shifts that can cause local outbreak events or an increased risk for severity.