Data from: Intra-host evolution of cell-fusing agent virus following acute infection in Aedes aegypti mosquito
Data files
Jun 17, 2026 version files 42.46 KB
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CFAV_genome_coverage_info.csv
618 B
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heterozygosity_value_per_SNV.csv
10.24 KB
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Nonsynonymous_SNV.csv
2.25 KB
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Primer_info.csv
2.69 KB
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README.md
2.28 KB
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Sn_value_per_SNV.csv
10.24 KB
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SNV_frequency.csv
11.41 KB
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Synonymous_SNV.csv
2.73 KB
Abstract
While intra-host evolution of arboviruses in mosquitoes has been documented, studies of insect-specific viruses (ISVs) remain limited. This study examines the evolutionary patterns of the cell fusing agent virus (CFAV), an ISV that infects adult Aedes aegypti, over a period of 21 days post-infection (dpi), with a focus on the relationship between viral population dynamics and genetic diversity. High-throughput sequencing of amplification products covering the entire viral genome revealed a significant positive correlation between the genetic diversity of CFAV and viral population size. Notably, synonymous single nucleotide variant (SNV) sites displayed a stronger correlation with population size compared to nonsynonymous SNV sites, suggesting that genetic drift—a form of neutral evolution—may drive this relationship. Additionally, we confirmed that smaller viral population sizes lead to greater temporal changes in genetic structure, particularly evident between day 1 dpi and day 3 dpi when genetic drift was most pronounced. We found that non-structural genes accumulated a higher frequency of synonymous SNV sites than structural genes, likely due to reduced selection pressure acting on non-structural genes. In contrast, structural genes, particularly the E gene, exhibited strong selective pressure, as indicated by a significant frequency of nonsynonymous SNV sites. Overall, this study elucidated the evolutionary patterns of CFAV, highlighting the roles of both neutral evolution—characterized by reduced genetic drift associated with increasing population size—and adaptive evolution within structural genes, such as the E gene.
https://doi.org/10.5061/dryad.fn2z34v5x
Description of the data and file structure
Data were extracted from the frequency value of single nucleotide variant (SNV) sites of the cell fusing agent virus (CFAV) from the amplicon-based whole genome high-throughput sequencing. The detailed procedure for high-throughput sequencing library preparation and SNV calling has been described elsewhere in the manuscript.
Using the SNV frequency value, genetic diversity indices such as Shannon entropy (Sn) and heterozygosity values were computed.
Files and variables
All the data are available in the Dryad data file as follows.
CFAV_genome_coverage_info.csv
This file contains the CFAV genome coverage and breadth of the coverage information which were computed based on the NGS reads.
heterozygosity_value_per_SNV.csv
Heterzygosity value was computed using the SNV frequency value. The formula has been provided in the manuscript.
Nonsynonymous_SNV.csv
This file contain the binary data generated based on the absence and presence of nonsynonymous SNV sites.
Primer_info.csv
This file contain the overlapping primer info covering the entire genome of CFAV. The primers were used for whole genome amplicon generation and NGS sequencing.
Sn_value_per_SNV.csv
Sn value was computed using the SNV frequency value. The formula has been provided in the manuscript.
SNV_frequency.csv
This file contains the SNV frequency values. SNV frequency values were generated using NGS read and the application of bioinformatic tool iVAR for variant calling.
Synonymous_SNV.csv
This file contains the binary data generated based on the absence and presence of synonymous SNV sites.
Description: Using the SNV frequency value, genetic diversity indices such as Shannon entropy and heterozygosity were computed. As frequency is a count-based measure, the variables do not have associated units.
Variables
- Shannon entropy (Sn) value
- Heterozygosity value
Access information
Other publicly accessible locations of the data:
- NCBI BioProject ID: PRJNA1224956