PT  - JOURNAL ARTICLE
AU  - Bhavin S. Khatri
AU  - Austin Burt
TI  - Weakly deleterious natural genetic variation greatly amplifies probability of resistance in multiplexed gene drive systems
AID  - 10.1101/2021.12.23.473701
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2021.12.23.473701
4099  - http://biorxiv.org/content/early/2022/01/11/2021.12.23.473701.short
4100  - http://biorxiv.org/content/early/2022/01/11/2021.12.23.473701.full
AB  - Evolution of resistance is a major barrier to successful deployment of gene drive systems to suppress natural populations, which could greatly reduce the burden of many vector borne diseases. Multiplexed guide RNAs that require resistance mutations in all target cut sites is a promising anti-resistance strategy, since in principle resistance would only arise in unrealistically large populations. Using novel stochastic simulations that accurately model evolution at very large population sizes, we explore the probability of resistance due to three important mechanisms: 1) non-homologous end-joining mutations, 2) single nucleotide mutants arising de novo or, 3) single nucleotide polymorphisms pre-existing as standing variation. Our results explore the relative importance of these mechanisms and highlight a complexity of the mutation-selection-drift balance between haplotypes with complete resistance and those with an incomplete number of resistant alleles. We find this leads to a qualitatively new phenomenon where weakly deleterious naturally occurring variants greatly amplify the probability of multi-site resistance. This challenges the intuition that many target sites would guarantee prevention of resistance, where in the face of standing genetic variation, it can be probable even in not very large populations. This result has broad application to resistance arising in many multi-site evolutionary scenarios including multi-drug resistance to antibiotics, antivirals and cancer treatments, as well as the evolution of vaccine escape mutations in large populations.Competing Interest StatementThe authors have declared no competing interest.