# Development of a multiplex SNaPshot assay for simultaneous detection of multiple insecticide-resistance mutations in Anopheles sinensis

## TL;DR

A new test was developed to quickly detect insecticide resistance in a key malaria-carrying mosquito species.

## Contribution

A multiplex SNaPshot assay for simultaneous detection of six insecticide-resistance mutations in Anopheles sinensis.

## Key findings

- The HN-PY population showed high resistance to multiple insecticides with low mortality rates.
- The SNaPshot assay detected high frequencies of resistance mutations at multiple loci in field-collected mosquitoes.
- The assay showed strong agreement with PCR–Sanger sequencing (Kappa > 0.90 at all loci).

## Abstract

Anopheles sinensis, the primary malaria vector in China, is a potential threat to the prevention of re-establishment of malaria transmission following imported cases. The extensive use of insecticides has led to widespread resistance. Conventional bioassays and molecular detection are limited in sensitivity, throughput, and efficiency, underscoring the need for a rapid and cost-effective genotyping tool for large-scale multiple insecticide-resistance markers surveillance.

A multiplex SNaPshot assay was developed to simultaneously detect six SNPs (kdr1014-F, kdr1014-R, Ace-1, RDL296, RDL327, and RDL345) in An. sinensis. Positive plasmids carrying known resistance-associated genotypes and laboratory-reared An. sinensis samples were used to optimize and validate the reactions. Wild An. sinensis collected from Henan Puyang (HN-PY) and Anhui Shucheng (AH-SC) were used for bioassays with 0.05% deltamethrin, 0.15% beta-cyfluthrin, 5% malathion, 0.1% propoxur, and 0.06% flufenoxuron. Then samples randomly selected on the basis of 24 h survival status were genotyped via PCR–Sanger sequencing and the SNaPshot assay. Consistency was assessed using the Kappa testing, and genotype–phenotype correlations were evaluated by chi-squared tests.

Bioassays showed that the HN-PY An. sinensis population was resistant to deltamethrin, beta-cyfluthrin, malathion, propoxur, and flufenoxuron, with adjusted mortality rates of 5.2%, 24.4%, 9.1%, 24.3%, and 5.8%, respectively. In contrast, the AH-SC population remained susceptible to malathion (100% mortality) but exhibited resistance to deltamethrin, beta-cyfluthrin, propoxur, and flufenoxuron, with adjusted mortality rates of 71.6%, 78.6%, 44.9%, and 33.4%, respectively. Multiplex SNaPshot genotyping of 272 field-collected mosquitoes revealed high frequencies of resistance-associated mutations at the kdr1014-F, kdr1014-R, Ace-1, RDL296, RDL327, and RDL345 loci, with frequencies of 4.7%, 99.3%, 53.3%, 89.7%, 96.0%, and 53.3% in the HN-PY population and 25.5%, 78.0%, 55.3%, 89.8%, 89.8%, and 46.3% in the AH-SC population, respectively. Additionally, the SNaPshot assay showed strong agreement with PCR–Sanger sequencing (Kappa > 0.90 at all loci).

The multiplex SNaPshot assay provides a reliable, rapid, and economical tool for detecting multiple resistance mutations in An. sinensis. Its application in routine entomological surveillance will provide an alternative tool for early warning of insecticide resistance.

The online version contains supplementary material available at 10.1186/s13071-026-07250-2.