[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-0-en-105":3,"doc-seo-431003-105":59,"doc-detail-431003-en":131},{"code":4,"msg":5,"data":6},0,"success",[7,13,18,23,28,33,38,43,48,51,55],{"id":8,"doc_module":4,"doc_module_name":9,"category_name":10,"show_sort_weight":11,"slug":12},1,"Document","Story & Novel",90,"story-novel",{"id":14,"doc_module":4,"doc_module_name":9,"category_name":15,"show_sort_weight":16,"slug":17},2,"Literature",80,"literature",{"id":19,"doc_module":4,"doc_module_name":9,"category_name":20,"show_sort_weight":21,"slug":22},4,"Exam",70,"exam",{"id":24,"doc_module":4,"doc_module_name":9,"category_name":25,"show_sort_weight":26,"slug":27},5,"Comic",60,"comic",{"id":29,"doc_module":4,"doc_module_name":9,"category_name":30,"show_sort_weight":31,"slug":32},6,"Technology",50,"technology",{"id":34,"doc_module":4,"doc_module_name":9,"category_name":35,"show_sort_weight":36,"slug":37},7,"Healthcare",40,"healthcare",{"id":39,"doc_module":4,"doc_module_name":9,"category_name":40,"show_sort_weight":41,"slug":42},8,"Research & Report",30,"research-report",{"id":44,"doc_module":4,"doc_module_name":9,"category_name":45,"show_sort_weight":46,"slug":47},9,"Religion & Spirituality",20,"religion-spirituality",{"id":46,"doc_module":4,"doc_module_name":9,"category_name":49,"show_sort_weight":46,"slug":50},"World Cup","world-cup",{"id":52,"doc_module":4,"doc_module_name":9,"category_name":53,"show_sort_weight":52,"slug":54},10,"Lifestyle","lifestyle",{"id":56,"doc_module":4,"doc_module_name":9,"category_name":57,"show_sort_weight":24,"slug":58},19,"General","general",{"code":4,"msg":60,"data":61},"ok",{"site_id":62,"language":63,"slug":64,"title":65,"keywords":66,"description":67,"schema_data":68,"social_meta":124,"head_meta":126,"extra_data":128,"updated_unix":130},105,"en","multiplexed-detection-of-febrile-infections-using-carmen","Multiplexed detection of febrile infections using CARMEN","","Development and diagnosis of bloodborne pathogen and sexually transmitted infection cases relies on accurate detection of early, nonspecific febrile symptoms, yet existing PCR workflows face constraints in throughput, cost, and complexity. CARMEN technology, previously advanced for multiplexed nucleic acid detection, is extended here through three panels covering viral hemorrhagic fevers, mosquito-borne viruses, and STIs for 23 pathogens. Deep learning guides assay design and validation on synthetic targets, spiked serum, and patient samples for gonorrhea, Lassa, and mpox, demonstrating sensitivity and matched specificity comparable to or exceeding individual RT-qPCR.",{"@graph":69,"@context":123},[70,84,106],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":35,"@type":76,"position":81},"https://docshare.wps.com/document/healthcare/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/multiplexed-detection-of-febrile-infections-using-carmen/431003/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/multiplexed-detection-of-febrile-infections-using-carmen/431003.png","ImageObject",300,407,{"name":92,"@type":93},"Riley West","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-31","2026-09-29",true,{"@type":102,"interactionType":103,"userInteractionCount":105},"InteractionCounter",{"@type":104},"ViewAction",13,{"@type":107,"mainEntity":108},"FAQPage",[109,115,119],{"name":110,"@type":111,"acceptedAnswer":112},"What clinical problem does the study address?","Question",{"text":113,"@type":114},"Early symptoms of bloodborne pathogens and sexually transmitted infections are often nonspecific, making diagnosis difficult and increasing outbreak risk.","Answer",{"name":116,"@type":111,"acceptedAnswer":117},"What does the CARMEN approach add in this work?",{"text":118,"@type":114},"Three CARMEN panels are developed to collectively detect 23 pathogens spanning viral hemorrhagic fevers, mosquito-borne viruses, and STIs.",{"name":120,"@type":111,"acceptedAnswer":121},"How were the CARMEN assays evaluated and compared?",{"text":122,"@type":114},"Assays were tested on synthetic targets, spiked healthy serum, and patient samples for specific pathogens, and multiplexed CARMEN performance matched or outperformed individual assay RT-qPCR on sensitivity with matched specificity.","https://schema.org",{"og:url":83,"og:type":125,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":127,"canonical":83},"index,follow",{"doc_id":129,"site_id":62},431003,1790763187,{"code":4,"msg":5,"data":132},{"doc_id":129,"user_id":133,"nickname":92,"user_avatar":134,"doc_module":4,"category_id":34,"category_name":35,"doc_title":65,"doc_description":67,"doc_content":135,"file_id":136,"file_url":137,"file_type":138,"file_size":139,"view_count":105,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":140,"language":141,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":142,"faqs":143,"seo_title":144,"seo_description":67,"update_tm":145,"read_time":146,"preview_page_count":4},1099523885074,"https://ap-avatar.wpscdn.com/davatar_9964176cb1d06d4a9deccf72a44ae3dc","Article [https://doi.org/10.1038/s41467-025-66243-4](https://doi.org/10.1038/s41467-025-66243-4)  \nMultiplexed detection of febrile infections using CARMEN  \nReceived: 6 July 2025  \n\n| Accepted: 3 November 2025 |\n| --- |\n| |\n| Check for updates |\n\nM. Kamariza1,2 , K. McMahon1, L. Kim 1, N. L. Welch1,3, L. Stenson1,  \nL. T. Allan-Blitz1,4,5, G. Sanders4, P. Eromon6, A. Muhammad 6, A. E. Sijuwola 6, O. O. Ope-ewe6, A. O. Ayinla6, C. l’Anson1, I. Baudi1, M. F. Paye1, C. Wilkason1,  \nJ. Lemieux1,4, A. Ozonoff 1,3, E. Stachler1, C. T. Happi 6,7 & P. C. Sabeti 1,8   \nDetection and diagnosis of bloodborne pathogens are critical for patients and for preventing outbreaks, yet challenging due to these diseases’ nonspecific initial symptoms. We previously advanced CRISPR-based Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN) technology for simultaneous detection of pathogens on numerous samples. Here, we develop three CARMEN panels that target viral hemorrhagic fevers, mosquito-borne viruses, and sexually transmitted infections, collectively identifying 23 pathogens. We use deep learning to design CARMEN assays with enhanced sensitivity and specificity, validating them and evaluating their performance on synthetic targets, spiked healthy normal serum samples, and patient samples for Neisseria gonorrhoeae in the United States and for Lassa and mpox virus in Nigeria. Our results show multiplexed CARMEN assays match or outperform individual assay RT-qPCR in sensitivity, with matched specificity. These findings underscore CARMEN’s potential as a highly effective tool for accurate pathogen detection for clinical diagnosis and public health surveillance.  \nBloodborne pathogens (BBPs) cause major disruptions to human life and public health. While the prevalence of bloodborne viruses varies widely across the world1, BBPs harbor some of the deadliest diseases driven by hemorrhagic fevers (e.g., Ebola, Lassa). These diseases are often difficult to diagnose because early symptoms, including fever, vomiting, and aches, are indistinguishable from each other2–7. Similarly, sexually-transmitted infections (STIs) (e.g., HIV, mpox, Hepatitis B) are endemic throughout the world, and present a particularly significant burden on morbidity and mortality in low- or middle-income countries (LMICs)8–10. Furthermore, such settings often lack the required tools to support pathogen diagnosis, and instead rely onsyndromic management of symptomatic cases. Thus, accurate diagnostic testing is needed to control the disease spread.  \nThe gold standard for diagnosing BBPs and STIs are polymerase chain reaction (PCR)-based methods, such as reverse transcription quantitative polymerase chain reaction (RT-qPCR), due to their high sensitivity and specificity11. However, these methods present several limitations, such as low throughput, high cost, and complexity12–15. In particular, the time-consuming nature of RT-qPCRs for each test has led to a growing interest in developing alternative diagnostic tools that are equally robust yet more cost-effective, and with increased throughput and multiplexing capabilities16,17.  \nMoreover, an ideal diagnostic and surveillance technology should be capable of processing hundreds of patient samples simultaneously and detecting multiple pathogens concurrently. Indeed, circulating and emerging diseases require widespread deployability of molecular  \n1Broad Institute of MIT and Harvard, Cambridge, MA, USA. 2Harvard Society of Fellows, Harvard University, Boston, MA, USA. 3Department of Pediatrics, Harvard Medical School, Boston, MA, USA. 4Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. 5Division of Global Health Equity: Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA. 6Institute of Genomics and Global Health (IGH), Redeemer’s University, Ede, Osun State, Nigeria. 7Department of Biological Sciences, College of Natural Sciences, Redeem","cbCailvxVEhdtGvH","https://ap.wps.com/l/cbCailvxVEhdtGvH","pdf",3440077,11,"English","# Background and clinical need\n## Challenges of diagnosing febrile and infectious diseases\n# CARMEN development and panel design\n## Targeting viral hemorrhagic fevers, mosquito-borne viruses, and STIs\n## Deep learning for sensitivity and specificity\n# Validation and performance evaluation\n## Synthetic and spiked samples\n## Patient sample testing for specific pathogens\n# Clinical and public health implications\n## Comparison with individual RT-qPCR","[{\"question\":\"What clinical problem does the study address?\",\"answer\":\"Early symptoms of bloodborne pathogens and sexually transmitted infections are often nonspecific, making diagnosis difficult and increasing outbreak risk.\"},{\"question\":\"What does the CARMEN approach add in this work?\",\"answer\":\"Three CARMEN panels are developed to collectively detect 23 pathogens spanning viral hemorrhagic fevers, mosquito-borne viruses, and STIs.\"},{\"question\":\"How were the CARMEN assays evaluated and compared?\",\"answer\":\"Assays were tested on synthetic targets, spiked healthy serum, and patient samples for specific pathogens, and multiplexed CARMEN performance matched or outperformed individual assay RT-qPCR on sensitivity with matched specificity.\"}]","Multiplexed detection of febrile infections using CARMEN | PDF",1790654264,28]