Limits...
Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission.

Sim S, Aw PP, Wilm A, Teoh G, Hue KD, Nguyen NM, Nagarajan N, Simmons CP, Hibberd ML - PLoS Negl Trop Dis (2015)

Bottom Line: 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.We also present evidence for differences in selection pressures between human and mosquito hosts, particularly on the structural and NS1 genes.

View Article: PubMed Central - PubMed

Affiliation: Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore.

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.

No MeSH data available.


Related in: MedlinePlus

Mutational hot- and coldspots in the DENV2 genome.Circos plot [26] of mutational hot- and coldspots detected in human- and mosquito-derived DENV2 populations. Red, hotspots in human-derived populations; orange, hotspots in mosquito-derived populations; each hotspot was found in a single population. Purple, coldspots indicating a depletion of SNVs across all 46 mosquito-derived populations. No coldspots were detected in human-derived populations.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4556672&req=5

pntd.0004052.g006: Mutational hot- and coldspots in the DENV2 genome.Circos plot [26] of mutational hot- and coldspots detected in human- and mosquito-derived DENV2 populations. Red, hotspots in human-derived populations; orange, hotspots in mosquito-derived populations; each hotspot was found in a single population. Purple, coldspots indicating a depletion of SNVs across all 46 mosquito-derived populations. No coldspots were detected in human-derived populations.

Mentions: We also used a scanning window approach to identify mutational hot- and coldspots in the DENV genome; i.e. regions containing a statistically significant excess or lack of SNVs compared with the genome-wide average (Fig 6). We identified a hotspot in E, the gene encoding the DENV envelope protein, in a single human-derived sample from Vietnam, but not in any of the mosquito-derived samples (Fig 6). An E hotspot was also found in a DENV3 human-derived sample from the EDEN study (S4B Fig). These hotspots were located in E domains (ED) II and I respectively, which are known targets of the antibody response [24]. Taken together with our finding that the E #NS/#S ratio is significantly higher in humans compared to mosquitoes (Fig 5A), we speculate that immune pressure on the E protein may play a bigger role in generating diversity in the DENV population in humans than in mosquitoes.


Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission.

Sim S, Aw PP, Wilm A, Teoh G, Hue KD, Nguyen NM, Nagarajan N, Simmons CP, Hibberd ML - PLoS Negl Trop Dis (2015)

Mutational hot- and coldspots in the DENV2 genome.Circos plot [26] of mutational hot- and coldspots detected in human- and mosquito-derived DENV2 populations. Red, hotspots in human-derived populations; orange, hotspots in mosquito-derived populations; each hotspot was found in a single population. Purple, coldspots indicating a depletion of SNVs across all 46 mosquito-derived populations. No coldspots were detected in human-derived populations.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556672&req=5

pntd.0004052.g006: Mutational hot- and coldspots in the DENV2 genome.Circos plot [26] of mutational hot- and coldspots detected in human- and mosquito-derived DENV2 populations. Red, hotspots in human-derived populations; orange, hotspots in mosquito-derived populations; each hotspot was found in a single population. Purple, coldspots indicating a depletion of SNVs across all 46 mosquito-derived populations. No coldspots were detected in human-derived populations.
Mentions: We also used a scanning window approach to identify mutational hot- and coldspots in the DENV genome; i.e. regions containing a statistically significant excess or lack of SNVs compared with the genome-wide average (Fig 6). We identified a hotspot in E, the gene encoding the DENV envelope protein, in a single human-derived sample from Vietnam, but not in any of the mosquito-derived samples (Fig 6). An E hotspot was also found in a DENV3 human-derived sample from the EDEN study (S4B Fig). These hotspots were located in E domains (ED) II and I respectively, which are known targets of the antibody response [24]. Taken together with our finding that the E #NS/#S ratio is significantly higher in humans compared to mosquitoes (Fig 5A), we speculate that immune pressure on the E protein may play a bigger role in generating diversity in the DENV population in humans than in mosquitoes.

Bottom Line: 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.We also present evidence for differences in selection pressures between human and mosquito hosts, particularly on the structural and NS1 genes.

View Article: PubMed Central - PubMed

Affiliation: Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore.

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.

No MeSH data available.


Related in: MedlinePlus