Integral gene drives for population replacement

Abstract

A first generation of CRISPR-based gene drives has now been tested in the laboratory in a number of organisms, including malaria vector mosquitoes. Challenges for their use in the area-wide genetic control of vector-borne disease have been identified, including the development of target site resistance, their long-term efficacy in the field, their molecular complexity, and practical and legal limitations for field testing of both gene drive and coupled anti-pathogen traits. We have evaluated theoretically the concept of integral gene drive (IGD) as an alternative paradigm for population replacement. IGDs incorporate a minimal set of molecular components, including drive and anti-pathogen effector elements directly embedded within endogenous genes – an arrangement that in theory allows targeting functionally conserved coding sequences without disrupting their function. Autonomous and non-autonomous IGD strains could be generated, optimized, regulated and imported independently. We performed quantitative modeling comparing IGDs with classical replacement drives and show that selection for the function of the hijacked host gene can significantly reduce the establishment of resistant alleles in the population, while drive occurring at multiple genomic loci prolongs the duration of transmission blockage in the face of pre-existing target site variation. IGD thus has potential as a more durable and flexible population replacement strategy.

Converting endogenous genes of the malaria mosquito into simple non-autonomous gene drives for population replacement

“…However, not only could such approaches increase molecular complexity of the constructs (and likely also their regulatory approval) but it could also complicate the deployment of multiple waves or combinations of drive and effector within a population. We have recently modelled an alternative approach to achieve population replacement, that was specifically designed to address these questions (30). The approach we have termed integral gene drive (IGD) imitates the way naturally occurring homing endonuclease genes propagate i.e.…”

“…They do not disrupt their target genes due to their association with introns or inteins (31,32). We analysed the theoretical behaviour of IGDs featuring the complete molecular separation of drive and effector functions into minimal modifications of endogenous host genes at two or more different genomic loci (30). This approach takes advantage of the promoter and also of its surrounding regulatory regions of the modified endogenous locus.…”

Vector genetics, insecticide resistance and gene drives: an agent-based modeling approach to evaluate malaria transmission and elimination

“…35 Gene drive methods for the purposes of vector control broadly fall under two categories: 36 first, modifying a population to make it refractory to malaria, a practice referred to as 37 population replacement [17], and second, restricting the population of a specific 38 subspecies, which is referred to as population suppression [18]. James et al [19], and 39 Hammond and Galizi [20] provide an overview of different gene drive strategies being 40 currently considered or developed. 41 There are a number of challenges to be addressed before gene drives become an 42 accepted tool for vector control.…”

“…Various gene drive strategies can also be simulated using this model such as classic 98 endonuclease drives where driver and effector genes are driven as one construct [38], 99 integral drives with independent autonomous driver and non-autonomous effector 100 genes [39], as well as daisy-chain drives with serially dependent but unlinked drive 101 elements [40]. Cleaving at the target site and copying of the desired allele occurs during 102 gametogenesis (Fig.…”

“…The model is limited to 8 alleles and 10 loci to make the model computationally 360 efficient by limiting the amount of memory allotted to each genome to 64 bits, which is 361 a common width for registers in a CPU. Additionally, a 10 loci genome is sufficient to 362 model a number of complicated scenarios ranging from single gene mutations in kdr 363 resistant mosquitoes [48] to complicated multi driver effector gene drives that could be 364 developed using emerging constructs [39]. There are, of course, limitations to this model 365 such as the absence of a framework to account for genetic linkage of resistant alleles 366 with alleles coding for other phenotypic characteristics, which could impact how 367 genomes are selected for under insecticide pressure.…”