Molecular epidemiology of dengue virus type I - the phylogenetic analysis and population dynamic
Date Issued
2006
Date
2006
Author(s)
Chien, Li-Jung
DOI
en-US
Abstract
Background: Dengue is among the most important mosquito-borne viral diseases in tropical and subtropical regions. All four serotypes of dengue viruses (DENV-1 through DENV-4) can cause severe disease and can be further divided into several genotypes. Dengue, being present in over 100 countries, is estimated to affect ~2.5 billion residing in dengue endemic areas with up to 50 million infections annually. The disease burden in Southeast Asia may be as high as 900 disability adjusted life years/million residents/year. In Taiwan, we had indigenous dengue outbreaks almost every year since 1987, with most of them occurred in southern Taiwan.
Methods: Genetic database for the 5’UTR and structural genes of 88 DENV-1 strains collected in Taiwan during 1987 to 2004 were established by RT-PCR and direct sequencing. These data were analyzed along with the E gene sequence of 40 representative global strains from the US-CDC, the sequence data of 95 DENV-1 strains available from GeneBack, and 6 E gene sequences (by J. Askove). All duplicated identical sequences were removed before analysis. Phylogenetic analyses using Maximum likelihood (ML) and Bayesian methods were constructed by PHYLIP and MrBayes 3.1, respectively. Application of Bayesian skyline plot by BEAST allows to infer the population dynamics as well as to co-estimate the substitution rates. PAML is used to test for positive selection pressure at amino acid sites and CodonW is used to exam for codon usage bias.
Results: Based on phylogenetic analysis, three major genotypes of DENV-1 are currently circulating in the world; each genotype exhibits unique geographical distributions, and linage extinction occurred through time. In Taiwan, DENV-1 isolated from different season (or cluster) of indigenous transmission fell into two genotypes (I and II); and indigenous strains from sequential years usually showed >1% p-distances, both findings were not supporting endemic transmission. The phylogenetic characteristics of an unusual indigenous dengue case in relation to the genetic database have assisted to trace the possible origin of dengue infection to laboratory-acquired in nature. The mean substitution rate estimated from 185 E gene sequences dataset was 0.743x10-3 substitution/site/year (95% highest probability densities (HPD), 0.663-0.824 x10-3). DENV-1 strains, was estimated to evolve ~96.8 years before 2004 (88.1-106.7 years). All three genotypes experienced significant population expansions in recent 40 years with the most recent event occurred around the year 2000. Selection analysis identified no positive selection on any site or specific lineage of DENV-1. The amino acid substitutions that characterize strains from different clades or subclades in genotype I and II are all conservative changes. Analysis of the codon usage on E gene indicated that genotype I had the lowest G+C3s (0.404±0.006), followed by genotype II (0.432±0.007) and then genotype III (0.448±0.009), while the Nc was significant higher in genotype II (52.57±0.65) than in genotype I (49.02±0.63); and genotype III was intermediate (50.22±0.53). Correspondence analysis showed exclusiveness in the usage of codon CGU (Arg), CGG (Arg), and CCG (Pro) is different among genotype.
Conclusions: Based on these results, we concluded that DENV-1 is reintroduced to Taiwan and resulted in subsequent indigenous transmission yearly without establishing endemicity in the most part. Establishment of comprehensive genetic database together with phylogenetic analysis is proven useful in tracking the source of transmission and in investigation of evolutionary parameters. The timeline of virus population expansion derived from Bayesian skyline plot was supported by the available epidemiological evidences, demonstrating the value in reconstructing the transition history of population growth of DENV-1. Whether the codon usage bias and composition difference observed among genotypes is a result of random drift or selection under some novel mechanism, needs to be further elucidated.
Subjects
登革病毒
親緣性分析
溯祖理論
dengue virus
phylogenetic analysis
coalescent theory
SDGs
Type
thesis
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