{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,2]],"date-time":"2026-11-02T23:12:21Z","timestamp":1793661141498,"version":"4.5.1"},"reference-count":108,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:00:00Z","timestamp":1781740800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>Mosquito-borne virus surveillance increasingly requires rapid, distributed detection of co-circulating pathogens, serotypes, and lineages across clinical and vector-sampling sites. CRISPR-Cas platforms offer a programmable toolkit for this purpose, but their readiness differs substantially across surveillance functions. Here, we review CRISPR-Cas methods for mosquito-borne virus surveillance across detection, tracing, and discovery-supporting targeted screening. Detection is the most advanced application: selected Cas12- and Cas13-based assays for dengue, Zika, chikungunya, West Nile, Japanese encephalitis, and related mosquito-associated viruses report sub-hour workflows, portable readouts, and targeted serotype- or lineage-marker discrimination. However, performance remains assay-, target-, and sample-matrix-dependent, and validation in pooled mosquito samples and field settings is still limited. Tracing currently relies mainly on validated portable amplicon-sequencing workflows, whereas CRISPR-aided sample-preparation methods such as DASH, FLASH, RAPID-DASH, and Cas9-targeted enrichment remain transferable opportunities for host depletion or target enrichment rather than established mosquito-borne virus genomic-surveillance workflows. For discovery-oriented surveillance, multiplex CRISPR-Cas systems such as CARMEN can support targeted screening of known or near-neighbor viruses represented by predesigned crRNAs, while metagenomic next-generation sequencing remains necessary for divergent or previously unknown viruses. Across these functions, CRISPR-Cas programmability may accelerate parts of assay redesign, but practical retargeting still requires compatible amplification primers, effector-specific target constraints, cross-reactivity assessment, and analytical revalidation. Routine surveillance use will require integrated demonstrations with clinical and pooled-vector samples, comparison against established molecular and sequencing methods, cost validation, and regulatory evidence.<\/jats:p>","DOI":"10.3389\/fcimb.2026.1873187","type":"journal-article","created":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T05:30:49Z","timestamp":1781760649000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["The CRISPR-Cas toolkit for mosquito-borne virus surveillance: detection, tracing, and discovery"],"prefix":"10.3389","volume":"16","author":[{"given":"Yang","family":"Wu","sequence":"first","affiliation":[{"name":"Guangzhou Customs Technology Center","place":["Guangzhou, China"]},{"name":"State Key Laboratory of Respiratory Disease","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiling","family":"Cai","sequence":"additional","affiliation":[{"name":"Guangzhou Customs Technology Center","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qipeng","family":"Wu","sequence":"additional","affiliation":[{"name":"Guangzhou Customs Technology Center","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Wu","sequence":"additional","affiliation":[{"name":"Guangzhou Customs Technology Center","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Hu","sequence":"additional","affiliation":[{"name":"Guangzhou Customs Technology Center","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enjiong","family":"Huang","sequence":"additional","affiliation":[{"name":"Fuzhou International Travel Healthcare Center","place":["Fuzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongqi","family":"Li","sequence":"additional","affiliation":[{"name":"Jilin International Travel Healthcare Center","place":["Tonghua, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaojun","family":"Liang","sequence":"additional","affiliation":[{"name":"Guangzhou International Travel Healthcare Center","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuefeng","family":"Hu","sequence":"additional","affiliation":[{"name":"Jiangsu International Travel Healthcare Center","place":["Nanjing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Dai","sequence":"additional","affiliation":[{"name":"Guangzhou Customs Technology Center","place":["Guangzhou, China"]},{"name":"State Key Laboratory of Respiratory Disease","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruyan","family":"Liao","sequence":"additional","affiliation":[{"name":"Guangzhou Customs Technology Center","place":["Guangzhou, China"]},{"name":"State Key Laboratory of Respiratory Disease","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf5573","article-title":"C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector","volume":"353","author":"Abudayyeh","year":"2016","journal-title":"Sci. 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