Literature analysis of the host range (Host) and geographic range (Country) of known generalist viruses found in this study.

The "Weighted_Avg_contigs_p_id" columns provide the average value of the identity percentages associated with the contigs. The column "Blastn" indicates other virus names given to a virus species in the NCBI database (e.g., different virus strains or naming errors during submission). (XLSX)</p

Distribution and relative abundance of viral taxonomic units (VTUs) in the libraries of <i>Culex poicilipes</i> and <i>Culex tritaeniorhynchus</i>.

Library names are indicated on top of the heatmap (see Table 1 for explanation of acronyms), along with a hierarchical clustering, and library colour indicates mosquito species (red: Culex poicilipes, blue: Culex tritaeniorhynchus). Tile colour stands for read abundance; the more abundant a cluster, the warmer the colour. The VTUs are ranked following total read abundance. (TIF)</p

Distribution and relative abundance of viral clusters in the libraries of <i>Culex poicilipes</i> and <i>Culex tritaeniorhynchus</i>.

Library names are indicated on top of the heatmap (see Table 1 for explanation of acronyms), along with a hierarchical clustering, and library colour indicates mosquito species (red: Culex poicilipes, blue: Culex tritaeniorhynchus). Tile colour stands for read abundance; the more abundant a cluster, the warmer the colour. The clusters are ranked following total read abundance.</p

S2 Fig -

Distribution of viral taxonomic units (VTUs) among orders (external donut chart) and phyla (inner pie chart) found in (A) Culex poicilipes and Culex tritaeniorhynchus, and (B) Aedes vexans. Percentages between brackets represent the proportion of all VTUs in each order or phyla. The term “Incertae sedis” stands for taxa whose classification is still undefined at the phylum level. (TIF)</p

Location of the three sampling sites in northern Senegal.

KMS: Keur Momar Sarr. Upper right corner: Map of Africa with Senegal coloured in yellow. Main figure: The solid circles correspond to the sampling points: Diama (River), Keur Momar Sarr (Lake) and Younoufere (Ponds).</p

Sequenced isolates.

(XLSX)</p

Distribution of the highly-conserved viral taxonomic units (VTUs) over sites, mosquito species and years.

The VTUs are named after their best hit on the y axis. Each combination of mosquito species and site is presented on the x axis. Labels for the mosquito/site combinations are coded with the first letter standing for mosquito species (A for Aedes vexans, P for Culex poicilipes and T for Culex tritaeniorhynchus), and the second letter for site (F for the Ferlo Region (Ponds), D for the Diama village (River) and K for the Keur Momar Sarr village (Lake)). Tile color stands for number of years with detection in a mosquito/site combination (red: Two years, yellow: One year, gray: No detection). The year of detection is provided within the tile whenever the virus was detected only one year. (TIF)</p

S3 Fig -

Average percent identities at the amino acid level from all the contigs of each viral taxonomic units (VTUs) with their best hit in the viromes of (A) Culex mosquitoes and (B) Aedes vexans. The bars in blue indicate an average percent identity higher than 90% and thus VTUs likely including sequences of the virus species found as their best hit. The red bars represent VTUs with less than 90% identity to their best hit and thus probably involving sequences of new virus species. (TIF)</p

Output of the homology and taxonomy search for the Culex dataset.

The "Best-hit" column provides the accession with the lowest e-value found by Diamond. The “VTU” column contains the VTU names. The “cluster” to “genus” columns provide the VTU taxonomy as stated by the ICTV. All columns from "sum_reads" to "max coverage" provide information on the contigs of each VTU (column fields described below). sum_reads = total number of reads for each VTU, Avg_match_length = length of the alignment on the reference, n_Contigs = number of contigs associated with each VTU, Avg_contigs_length = average length of the contigs of each VTU, Sum_contigs_length = sum of all the contig lengths for each VTU, Avg_Coverage_contigs = average coverage of the alignment on the contigs, Avg_Coverage_subject = average coverage on the reference (alignment length / accession length), Pond_Avg_contigs_p_id = average percent identity at the amino-acid level of the contigs of a VTU, weighted by the length of the alignments, min_contigs_p_id = minimum percent identity at the amino-acid level of the contigs of a VTU with their best-hits, max_contig_p_id = maximum percent identity at the amino-acid level of the contigs of a VTU with their best-hits, avg_contigs p_id = average percent identity at the amino-acid level of the contigs with their best-hits, min_coverage = minimum read coverage, max_coverage = maximum read coverage, Avg_read_depth = average read depth for each VTU. (XLSX)</p

Rarefaction curve analysis of each library (see Table 1 for explanation of acronyms).

The x-axis shows the number of virus-like reads, and the y-axis the number of viral taxonomic units (VTUs) per library. (A) Libraries of Culex poicilipes (red) and Culex tritaeniorhynchus (blue). (B) Libraries of Aedes vexans. (TIF)</p