Wolbachia, a common vertically transmitted symbiont, can protect insects against viral infection and prevent mosquitoes from transmitting viral pathogens. For this reason, Wolbachia-infected mosquitoes are being released to prevent the transmission of dengue and other arboviruses. An important question for the long-term success of these programs is whether viruses can evolve to escape the antiviral effects of Wolbachia. We have found that Wolbachia altered the outcome of competition between strains of the DCV virus in Drosophila. However, Wolbachia still effectively blocked the virus genotypes that were favoured in the presence of the symbiont. We conclude that Wolbachia did cause an evolutionary response in viruses but this has little or no impact on the effectiveness of virus-blocking.
Clustal alignment of Drosophila C Virus isolates genome sequences
alignment_DCV_isolates.fas
Allele frequency analysis of evovled DCV populations
Output file generated using PoPoolation2
DCV_snps_rc.txt
R script for reformatting and filtering DCV sequencing data
Sequencing data reformatting and filtering.R
R script for Principal Component and Discriminant Analysis
PCA and DAPC.R
R script for running Mantel test on pairwise genetic distances
Mantel test.R
Virus titer data for isolates DCV-C -EB and -M
Virus titer data - DCV isolates.txt
R function to compute nls mcmc confidence intervals
nls mcmc confidence intervals.R
R script for DCV titer time-course analysis
DCV titer time-course analysis_DCV isolates.R
DCV-C and non-DCV-C base calls per sequencing read
Base calls matching DCV-C specific alleles were identified using custom script snps_by_read.R and the 150 bp paired-end sequencing data generated from the 24 DCV populations evolved with and without Wolbachia. Each row stands for a given sequencing read. Each column indicates for each DCV-C specific allele whether the base call matches the DCV-C
enome (D) or not (ND). x and y respectively stand for forward and reverse sequencing read belonging to the same pair.
readsummary_overlap_allsamples.csv
R script for generating DCV-C and non DCV-C base calls by sequencing read
snps_by_read.R
R script for estimating sequencing error rate and recombination
recombination2.R
DCV-C and non-DCV-C base calls per sequencing read
Base calls matching DCV-C specific alleles were identified using custom script snps_by_read.R and the 250 bp paired-end sequencing data generated from the 24 DCV populations evolved with and without Wolbachia. Each row stands for a given sequencing read. Each column indicates for each DCV-C specific allele whether the base call matches the DCV-C genome (D) or not (ND). x and y respectively stand for forward and reverse sequencing read belonging to the same read pair.
readsummary_overlap_allsamples_allinvariantreads.csv
R script for generating DCV-C and non DCV-C base calls by sequencing read
snps_by_read.R
R script for estimating sequencing error and recombination rates
recombination2.R
