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Abstract MultipleWolbachiastrains can block pathogen infection, replication and/or transmission inAedes aegyptimosquitoes under both laboratory and field conditions. However,Wolbachiaeffects on pathogens can be highly variable across systems and the factors governing this variability are not well understood. It is increasingly clear that the mosquito host is not a passive player in whichWolbachiagoverns pathogen transmission phenotypes; rather, the genetics of the host can significantly modulateWolbachia‐mediated pathogen blocking. Specifically, previous work linked variation inWolbachiapathogen blocking to polymorphisms in the mosquito alpha‐mannosidase‐2 (αMan2) gene. Here we use CRISPR‐Cas9 mutagenesis to functionally test this association. We developed αMan2 knockouts and examined effects on bothWolbachiaand virus levels, using dengue virus (DENV;Flaviviridae) and Mayaro virus (MAYV;Togaviridae).Wolbachiatitres were significantly elevated in αMan2 knockout (KO) mosquitoes, but there were complex interactions with virus infection and replication. InWolbachia‐uninfected mosquitoes, the αMan2 KO mutation was associated with decreased DENV titres, but in aWolbachia‐infected background, the αMan2 KO mutation significantly increased virus titres. In contrast, the αMan2 KO mutation significantly increased MAYV replication inWolbachia‐uninfected mosquitoes and did not affectWolbachia‐mediated virus blocking. These results demonstrate that αMan2 modulates arbovirus infection inA. aegyptimosquitoes in a pathogen‐ andWolbachia‐specific manner, and thatWolbachia‐mediated pathogen blocking is a complex phenotype dependent on the mosquito host genotype and the pathogen. These results have a significant impact for the design and use ofWolbachia‐based strategies to control vector‐borne pathogens.