{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T11:04:39Z","timestamp":1791284679839,"version":"4.1.0"},"reference-count":17,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T00:00:00Z","timestamp":1760054400000},"content-version":"vor","delay-in-days":9,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2025,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Accurate genotyping of Human papillomavirus (HPV) is essential for cervical cancer screening, prognostic risk assessment, and epidemiological surveillance. Conventional methods, such as Sanger sequencing and hybridization\u2010based assays, often fail to detect mixed infections, particularly in cases involving DNA from formalin\u2010fixed paraffin\u2010embedded (FFPE) tissues. In this protocol, we present an optimized next\u2010generation sequencing (NGS) based pipeline for comprehensive HPV genotyping. Our workflow includes a curated HPV reference database of 229 HPV genotypes and a proportional read\u2010mapping algorithm. We validated our method using 30 samples from the Quality Control for Molecular Diagnostics (QCMD) proficiency testing panel and were able to fully replicate the expected outcomes\u2014including detecting the defined co\u2010infection with HPV16\/18. We then applied our approach to 50 clinical FFPE samples, identifying 44 HPV\u2010positive samples, including a co\u2010infection scenario that traditional diagnostic assays might have missed. This low\u2010cost, open\u2010source NGS\u2010based pipeline improves the sensitivity and accuracy of HPV detection from archival FFPE tissue specimens, cervical screening specimens, and other fresh tissue, and successfully closes the gap between research applications and clinical usage. \u00a9 2025 Wiley Periodicals LLC.<\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 1<\/jats:bold>\n                    : DNA isolation\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 2<\/jats:bold>\n                    : PCR amplification\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 3<\/jats:bold>\n                    : NGS\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol 4<\/jats:bold>\n                    : Data analysis\n                  <\/jats:p>","DOI":"10.1002\/cpz1.70231","type":"journal-article","created":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:36:26Z","timestamp":1760106986000},"source":"Crossref","is-referenced-by-count":2,"title":["A Novel NGS\u2010Based Algorithm for Precise HPV Genotyping and Co\u2010infection Detection in QCMD Samples and FFPE Tissues"],"prefix":"10.1002","volume":"5","author":[{"given":"Natalia","family":"Kuriata","sequence":"first","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"},{"name":"These authors contributed equally to this work."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katarzyna Zofia","family":"Mazur","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"},{"name":"These authors contributed equally to this work."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magn\u00fas M\u00e1ni","family":"S\u00e6mundarson","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"},{"name":"These authors contributed equally to this work."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zarko","family":"Urosevic","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"},{"name":"These authors contributed equally to this work."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Freyja","family":"Valsd\u00f3ttir","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia Yanzhong","family":"Xiao","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brynja","family":"\u00c1rmannsd\u00f3ttir","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gu\u00f0r\u00fan Erna","family":"Baldvinsd\u00f3ttir","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arthur","family":"L\u00f6ve","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c1sgeir Erlendur","family":"\u00c1sgeirsson","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk Iceland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4911-0729","authenticated-orcid":false,"given":"Huiping","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital of Iceland  Reykjav\u00edk 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