Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission.
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.
Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore.
Shuzhen
S
Sim
Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore.
Pauline P K
PP
Aw
Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore.
Andreas
A
Wilm
Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore.
Garrett
G
Teoh
Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.
Kien Duong Thi
KD
Hue
Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.
Nguyet Minh
NM
Nguyen
Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore.
Niranjan
N
Nagarajan
Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; Department of Microbiology and Immunology, University of Melbourne, Carlton, Victoria, Australia.
Cameron P
CP
Simmons
Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore.
Martin L
ML
Hibberd
D000328:Adult; D000330:Aedes / Q000821:virology*; D000818:Animals; D003715:Dengue / Q000821:virology*; D003716:Dengue Virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D041981:Gastrointestinal Tract / Q000821:virology; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide; D012367:RNA, Viral / Q000235:genetics; D012469:Salivary Glands / Q000821:virology; D012641:Selection, Genetic; D017361:Viral Nonstructural Proteins / Q000235:genetics; D055815:Young Adult
C079340:NS1 protein, Dengue virus type 2; D012367:RNA, Viral; D017361:Viral Nonstructural Proteins