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The rapid and accurate diagnosis of pathogens causing ARIs is crucial for treating diseases and controlling pathogen transmission. Quantitative real-time polymerase chain reaction (qRT-PCR) serves as the primary detection method, yet current workflows are time-consuming and have limited multiplexing capacity; thus, they fail to meet on-site diagnostic requirements. Our aim is to develop a novel method that enhances heating and cooling rates, thereby significantly shortening PCR cycling time and enabling the on-site rapid detection of ARI pathogens.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A high-efficiency temperature cycling technology controlled by a time-based algorithm was developed. Its core mechanism involves the precise cyclic movement of reaction tubes among three independent temperature modules, utilizing the large temperature differences between the modules to significantly enhance heating and cooling rates. Employing this innovation, a portable fluorescence quantitative PCR (qPCR) instrument FQ-8B was developed that completed amplification in as little as 15\u00a0min. While substantially reducing amplification time, the FQ-8B maintains performance comparable to conventional instruments, demonstrating 95\u2013105% amplification efficiency across six-channel fluorescence. The instrument exhibits exceptional specificity and reproducibility, achieving detection sensitivities of 75\u2013100 copies\/mL across diverse viruses. Clinical validation of 208 suspected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and 216 suspected influenza A virus (IAV) specimens showed overall concordance rates of 99.04% (kappa\u2009=\u20090.852,\n                      <jats:italic>P<\/jats:italic>\n                      \u2009&lt;\u20090.001) and 95.37% (kappa\u2009=\u20090.881,\n                      <jats:italic>P<\/jats:italic>\n                      \u2009&lt;\u20090.001), respectively, compared to standard instrument detection. The on-site rapid detection capacity of FQ-8B was validated using 1227 respiratory specimens from a primary hospital, demonstrating 15-pathogen screening capability per specimen within 30\u00a0min. Testing results revealed a local epidemic of four pathogens: SARS-CoV-2, influenza B virus,\n                      <jats:italic>Mycoplasma pneumoniae<\/jats:italic>\n                      , and IAV, from August 2023 to January 2024.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The FQ-8B, developed based on three independent temperature modules and a time-based algorithm, demonstrates rapid, sensitive, specific, cost-effective, and portable characteristics. It provides timely on-site screening of multiple respiratory pathogens, rendering it a potent tool for infectious disease diagnosis and monitoring.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Graphical Abstract<\/jats:title>\n                  <\/jats:sec>","DOI":"10.1186\/s12985-025-03003-2","type":"journal-article","created":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T14:05:44Z","timestamp":1763733944000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Development and clinical application of a rapid qPCR instrument featuring three independent temperature modules and a time-based algorithm for respiratory pathogen diagnosis"],"prefix":"10.1186","volume":"22","author":[{"given":"Yu","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meizhi","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingzhen","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianyuan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siyuan","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaohong","family":"Liao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenkuan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiwei","family":"Zhuang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhichao","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rong","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,11,21]]},"reference":[{"issue":"8","key":"3003_CR1","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1586\/eri.11.75","volume":"9","author":"S Olofsson","year":"2011","unstructured":"Olofsson S, Brittain-Long R, Andersson LM, Westin J, Lindh M. 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