In-silico DNA barcoding surpasses whole genome sequencing for species identification from vector surveillance pools

In-silico DNA barcoding surpasses whole genome sequencing for species identification from vector surveillance pools | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article In-silico DNA barcoding surpasses whole genome sequencing for species identification from vector surveillance pools C. L. Nascimento, D. P. Tonge, F. Tripet This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7651154/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 23 Feb, 2026 Read the published version in Scientific Reports → Version 1 posted 14 You are reading this latest preprint version Abstract Mosquito borne diseases are responsible for over 600,000 deaths annually, mainly in sub-Saharan countries. Mosquito surveillance is a crucial element of vector control programmes to assure they remain effective. This study focused on optimizing the use of the MinION sequencer for interrogating mosquito pools from surveillance programmes, with simplified bioinformatic workflows for use in African laboratories nearer to the field. Mosquito pools were created using different human disease vector species, mimicking possible field trap’ content. Some pools were spiked with DNA from the malaria parasite Plasmodium falciparum and filarial worm Brugia malayi. In the first instance, three pipelines were used to map reads to full reference genomes and their accuracy was compared. Subsequently, mapping reads to full assembled genomes was compared to mapping to a concatenate of diagnostic barcoding sequences for evaluation of relative abundances of mosquito vector species and pathogens. The results show that a combination of Minimap2 with samtools is the most accurate pipeline and a targeted approach preferable to whole genome in estimating species abundance. The MinION device was shown to be effective for interrogating mosquito pools, with moderate training requirements in terms of analyses, thereby offering a solution to vector surveillance challenges in sub-Saharan Africa. Biological sciences/Computational biology and bioinformatics Health sciences/Diseases Biological sciences/Genetics Biological sciences/Microbiology Full Text Additional Declarations No competing interests reported. Supplementary Files InsilicoDNAbarcodingsurpasseswholegenomesequencingforspeciesidentificationfromvectorsurveillancepoolsSupplementaryMaterials.pdf Cite Share Download PDF Status: Published Journal Publication published 23 Feb, 2026 Read the published version in Scientific Reports → Version 1 posted Editorial decision: Revision requested 24 Nov, 2025 Reviews received at journal 20 Nov, 2025 Reviews received at journal 12 Nov, 2025 Reviews received at journal 09 Nov, 2025 Reviewers agreed at journal 30 Oct, 2025 Reviewers agreed at journal 29 Oct, 2025 Reviewers agreed at journal 29 Oct, 2025 Reviewers agreed at journal 27 Oct, 2025 Reviewers agreed at journal 27 Oct, 2025 Reviewers invited by journal 27 Oct, 2025 Editor invited by journal 17 Oct, 2025 Editor assigned by journal 22 Sep, 2025 Submission checks completed at journal 19 Sep, 2025 First submitted to journal 18 Sep, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7651154","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":539177408,"identity":"0dfccc6a-8f65-4b6d-962c-837557662b8b","order_by":0,"name":"C. L. 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