Research Article: Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission

Date Published: September 1, 2015

Publisher: Public Library of Science

Author(s): Shuzhen Sim, Pauline P. K. Aw, Andreas Wilm, Garrett Teoh, Kien Duong Thi Hue, Nguyet Minh Nguyen, Niranjan Nagarajan, Cameron P. Simmons, Martin L. Hibberd, Paulo Filemon Pimenta.

Abstract: Dengue virus (DENV) infection of an individual human or mosquito host produces a dynamic population of closely-related sequences. This intra-host genetic diversity is thought to offer an advantage for arboviruses to adapt as they cycle between two very different host species, but it remains poorly characterized. To track changes in viral intra-host genetic diversity during horizontal transmission, we infected Aedes aegypti mosquitoes by allowing them to feed on DENV2-infected patients. We then performed whole-genome deep-sequencing of human- and matched mosquito-derived DENV samples on the Illumina platform and used a sensitive variant-caller to detect single nucleotide variants (SNVs) within each sample. >90% of SNVs were lost upon transition from human to mosquito, as well as from mosquito abdomen to salivary glands. Levels of viral diversity were maintained, however, by the regeneration of new SNVs at each stage of transmission. We further show that SNVs maintained across transmission stages were transmitted as a unit of two at maximum, suggesting the presence of numerous variant genomes carrying only one or two SNVs each. We also present evidence for differences in selection pressures between human and mosquito hosts, particularly on the structural and NS1 genes. This analysis provides insights into how population drops during transmission shape RNA virus genetic diversity, has direct implications for virus evolution, and illustrates the value of high-coverage, whole-genome next-generation sequencing for understanding viral intra-host genetic diversity.

Partial Text: With 3.6 billion people at risk and nearly 400 million infections annually [1,2], dengue has become the most important mosquito-borne viral disease affecting humans today. Dengue virus (DENV) is a positive-sense, single-stranded RNA virus of the family Flaviviridae, genus Flavivirus. The ~10.7 kb DENV genome encodes three structural proteins (capsid [C], premembrane [prM], and envelope [E]) and seven non-structural (NS) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5).

Here we report the use of next-generation, whole-genome DENV sequencing to follow within- and between-host differences in viral populations in naturally-infected humans and their infected Ae. aegypti mosquito counterparts.



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