The evolutionary dynamics of DENV 4 genotype I over a 60-year period

PLoS Negl Trop Dis. 2019 Jul 29;13(7):e0007592. doi: 10.1371/journal.pntd.0007592. eCollection 2019 Jul.

Abstract

Dengue virus serotype 4 (DENV 4) has had a relatively low prevalence worldwide for decades; however, likely due to data paucity, no study has investigated the epidemiology and evolutionary dynamics of DENV 4 genotype I (DENV 4-I). This study aims to understand the diversity, epidemiology and dynamics of DENV 4-I. We collected 404 full length DENV4-1 envelope (E) gene sequences from 14 countries using two sources: Yunnan Province in China (15 strains during 2013-2016) and GenBank (489 strains up to 2018-01-11). Conducting phylogenetic and phylogeographical analyses, we estimated the virus spread, population dynamics, and selection pressures using different statistical analysis methods (substitution saturation, likelihood mapping, Bayesian coalescent inference, and maximum likelihood estimation). Our results show that during the last 60 years (1956-2016), DENV 4-I was present in mainland and maritime Southeast Asia, the Indian subcontinent, the southern provinces of China, parts of Brazil and Australia. The recent spread of DENV 4-I likely originated in the Philippines and later spread to Thailand. From Thailand, it spread to adjacent countries and eventually the Indian subcontinent. Apparently diverging around years 1957, 1963, 1976 and 1990, the different Clades (Clade I-V) were defined. The mean overall evolution rate of DENV 4-I was 9.74 (95% HPD: 8.68-10.82) × 10-4 nucleotide substitutions/site/year. The most recent common ancestor for DENV 4-I traces back to 1956. While the demographic history of DENV 4-I fluctuated, peaks appeared around 1982 and 2006. While purifying selection dominated the majority of E-gene evolution of DENV 4-I, positive selection characterized Clade III (Vietnam). DENV 4-I evolved in situ in Southeast Asia and the Indian subcontinent. Thailand and Indian acted as the main and secondary virus distribution hubs globally and regionally. Our phylogenetic analysis highlights the need for strengthened regional cooperation on surveillance and sharing of sample sequences to improve global dengue control and cross-border transmission prevention efforts.

Publication types

  • Historical Article
  • Research Support, Non-U.S. Gov't

MeSH terms

  • China
  • Dengue / epidemiology
  • Dengue / history*
  • Dengue / transmission
  • Dengue / virology*
  • Dengue Virus / genetics*
  • Evolution, Molecular*
  • Genetic Variation
  • Genome, Viral
  • Genotype
  • Global Health
  • History, 20th Century
  • History, 21st Century
  • Humans
  • Phylogeography

Grants and funding

SS was supported by the National Natural Science Foundation of China (NSFC) (Grant No.81602898) and China Postdoctoral Science Foundation (2018M630790). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.