Local-scale virome depiction in Medellín, Colombia, supports significant differences between Aedes aegypti and Aedes albopictus

Abstract

Aedes spp. comprise the primary group of mosquitoes that transmit arboviruses such as dengue, Zika, and chikungunya viruses to humans, and thus these insects pose a significant burden on public health worldwide. Advancements in next-generation sequencing and metagenomics have expanded our knowledge on the richness of RNA viruses harbored by arthropods such as Ae. aegypti and Ae. albopictus. Increasing evidence suggests that vector competence can be modified by the microbiome (comprising both bacteriome and virome) of mosquitoes present in endemic zones. Using an RNA-seq-based metataxonomic approach, this study determined the virome structure, Wolbachia presence and mitochondrial diversity of field-caught Ae. aegypti and Ae. albopictus mosquitoes in Medellín, Colombia, a municipality with a high incidence of mosquito-transmitted arboviruses. The two species are sympatric, but their core viromes differed considerably in richness, diversity, and abundance; although the community of viral species identified was large and complex, the viromes were dominated by few virus species. BLAST searches of assembled contigs suggested that at least 17 virus species (16 of which are insect-specific viruses [ISVs]) infect the Ae. aegypti population. Dengue virus 3 was detected in one sample and it was the only pathogenic virus detected. In Ae. albopictus, up to 11 ISVs and one plant virus were detected. Therefore, the virome composition appears to be species-specific. The bacterial endosymbiont Wolbachia was identified in all Ae. albopictus samples and in some Ae. aegypti samples collected after 2017. The presence of Wolbachia sp. in Ae. aegypti was not related to significant changes in the richness, diversity, or abundance of this mosquito's virome, although it was related to an increase in the abundance of Aedes aegypti To virus 2 (Metaviridae). The mitochondrial diversity of these mosquitoes suggested that the Ae. aegypti population underwent a change that started in the second half of 2017, which coincides with the release of Wolbachia-infected mosquitoes in Medellín, indicating that the population of wMel-infected mosquitoes released has introduced new alleles into the wild Ae. aegypti population of Medellín. However, additional studies are required on the dispersal speed and intergenerational stability of wMel in Medellín and nearby areas as well as on the introgression of genetic variants in the native mosquito population.

Fig 1. Boxplot of contigs length of each virus species identified.

Fig 2

A. Rarefaction curves representing the viruses in Ae. aegypti and Ae. albopictus. B. Proportion of viral sequences relative to the number of mosquito host sequences. Mann–Whitney Test: p < 0.05 (*) and p < 0.01 (**).

Fig 3. Heatmap showing the normalized abundance of reads on a log2 scale.

The viral species names are from the taxonomic annotation based on DIAMOND and KronaTools. The average BLASTx identity of each virus species to a reference sequence is shown in the blue-green boxes on the left.

Fig 4. Diversity analysis of the Ae. aegypti and Ae. albopictus viromes.

A. Alpha diversity of viruses in Ae. aegypti and Ae. albopictus at the species level. Mann–Whitney Test: p < 0.05 (*), p < 0.01 (**), and p < 0.001 (***). B. Nonmetric multidimensional scaling (NMDS) of viruses associated with the two mosquito species. STRESS = 0.023, PERMANOVA test on mosquito species: p = 0.004 and R2 = 0.59. C. Comparison of normalized and relative abundance levels of Aedes aegypti To virus 2 in the samples of Ae. aegypti with and without Wolbachia sp.

Fig 5. Phylogenetic reconstruction of the Wolbachia consensus sequences associated with Ae. albopictus (blue) and Ae. aegypti (red).

Fig 6. Mitochondrial SNP density per site in Ae. aegypti and Ae. albopictus samples collected between 2015 and 2019 in Medellín, Colombia.

Fig 7. Distance-based tree based on mitochondrial sequences in Ae. aegypti and Ae. albopictus collected between 2015 and 2019 in Medellín, Colombia.