Winning the Tug-of-War Between Effector Gene Design and Pathogen Evolution in Vector Population Replacement Strategies

Abstract

While efforts to control malaria with available tools have stagnated, and arbovirus outbreaks persist around the globe, the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-based gene editing has provided exciting new opportunities for genetics-based strategies to control these diseases. In one such strategy, called “population replacement”, mosquitoes, and other disease vectors are engineered with effector genes that render them unable to transmit pathogens. These effector genes can be linked to “gene drive” systems that can bias inheritance in their favor, providing novel opportunities to replace disease-susceptible vector populations with disease-refractory ones over the course of several generations. While promising for the control of vector-borne diseases on a wide scale, this sets up an evolutionary tug-of-war between the introduced effector genes and the pathogen. Here, we review the disease-refractory genes designed to date to target Plasmodium falciparum malaria transmitted by Anopheles gambiae, and arboviruses transmitted by Aedes aegypti, including dengue serotypes 2 and 3, chikungunya, and Zika viruses. We discuss resistance concerns for these effector genes, and genetic approaches to prevent parasite and viral escape variants. One general approach is to increase the evolutionary hurdle required for the pathogen to evolve resistance by attacking it at multiple sites in its genome and/or multiple stages of development. Another is to reduce the size of the pathogen population by other means, such as with vector control and antimalarial drugs. We discuss lessons learned from the evolution of resistance to antimalarial and antiviral drugs and implications for the management of resistance after its emergence. Finally, we discuss the target product profile for population replacement strategies for vector-borne disease control. This differs between early phase field trials and wide-scale disease control. In the latter case, the demands on effector gene efficacy are great; however, with new possibilities ushered in by CRISPR-based gene editing, and when combined with surveillance, monitoring, and rapid management of pathogen resistance, the odds are increasingly favoring effector genes in the upcoming evolutionary tug-of-war.

Improved reference genome of the arboviral vectorAedes albopictus

“…These are biological features important to estimate the epidemiological relevance of Ae. albopictus populations and to account for in the design of novel genetic-based strategies of vector control (36,52). As for the analyses of the landscape of viral integrations, we used whole-genome sequencing (WGS) data of mosquitoes from Tapachula and Tampon (53) to show the usefulness of AalbF2 in understanding the genomic diversity of Ae.…”

A population genomic unveiling of a new cryptic mosquito taxon within the malaria-transmittingAnopheles gambiaecomplex

“…Regardless of any direct vectorial capacity, cryptic Anopheles taxa have the potential to stymie malaria control efforts in at least three ways. First, reproductive barriers can thwart efforts to eliminate or modify the A. gambiae complex via gene drive (Marshall et al, 2019). A gene drive targeting A. coluzzii will not necessarily spread to sympatric AT, which might even expand its population size in response to a population crash of A. coluzzii .…”

“…However, evolutionary processes such as selection for resistance to insecticides have repeatedly allowed mosquitoes to evade control efforts (Ranson & Lissenden, 2016). Similarly, adaptive resistance is likely to frustrate new control technologies such as gene drives, which involve manipulating mosquito evolution directly (Marshall et al, 2019). Control strategies will need to anticipate and foil these adaptive responses and thus can only succeed if Anopheles population genetics is thoroughly understood.…”

Progress towards engineering gene drives for population control

“…Essentially, females with a Medea drive deposit a toxin into all their eggs that must be counteracted by an antidote that is expressed early in development, or the offspring dies. In successive generations, this system results in a disadvantage for wild-type alleles and, therefore, if the Medea system is linked to an effector to make the population disease resistant, for example in mosquitoes (Buchman et al, 2019a(Buchman et al, preprint, 2019bMarshall et al, 2019), or an effector targeting a conditional essential gene, or another conditional lethal effector such as one that confers temperature or small-molecule sensitivity to kill the population, it is predicted to favorably bias inheritance of the effector and therefore modify the population. The drive could also behave as a non-localized drive when released over a certain threshold, which is dependent on the fitness cost of the gene drive and its associated genetic elements as well as the rate of toxin resistance or natural genetic resistance in the population.…”

“…Larger scale, longer-term studies will be required to determine the resistance allele generation rate and their long-term impact on population suppression strategies. For homingbased population replacement, higher resistance allele generation rates can be tolerated (Noble et al, 2017); but an additional concern is the stability of the drive system and effector gene cargo over time (Marshall et al, 2019). If some time elapses between the system reaching fixation in one population and an individual migrating from that population to another, then will the gene drive system and effector still be functional and seed a new wave of spread?…”