{"id":"https://openalex.org/W7214769805","doi":"https://doi.org/10.64898/2026.09.26.26364094","title":"Integrated CRISPR-based detection of HIV, tuberculosis, malaria, and resistance-associated variants","display_name":"Integrated CRISPR-based detection of HIV, tuberculosis, malaria, and resistance-associated variants","publication_year":2026,"publication_date":"2026-09-29","ids":{"openalex":"https://openalex.org/W7214769805","doi":"https://doi.org/10.64898/2026.09.26.26364094"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.26.26364094","doi":"https://doi.org/10.64898/2026.09.26.26364094","is_oa":false,"landing_page_url":"https://doi.org/10.64898/2026.09.26.26364094","pdf_url":null,"source":{"id":"https://openalex.org/S3005729997","display_name":"medRxiv","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"medRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001920718","display_name":"Ashvi Sanjay Jain","orcid":"https://orcid.org/0000-0002-9858-4280","observed_orcids":["https://orcid.org/0000-0002-9858-4280"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ashvi S. Jain","raw_affiliation_strings":["Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024"],"raw_orcid":"https://orcid.org/0000-0002-9858-4280","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138500297","display_name":"Austin Si","orcid":"https://orcid.org/0009-0005-9453-3653","observed_orcids":["https://orcid.org/0009-0005-9453-3653"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Austin Si","raw_affiliation_strings":["Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024"],"raw_orcid":"https://orcid.org/0009-0005-9453-3653","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5153528173","display_name":"Joshua Yap","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua Yap","raw_affiliation_strings":["Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108500228","display_name":"L. Schwartz","orcid":"https://orcid.org/0009-0002-3439-790X","observed_orcids":["https://orcid.org/0009-0002-3439-790X"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lilith A Schwartz","raw_affiliation_strings":["UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, USA"],"raw_orcid":"https://orcid.org/0009-0002-3439-790X","affiliations":[{"raw_affiliation_string":"UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5118603250","display_name":"Cara T Susilo","orcid":"https://orcid.org/0009-0000-5059-4001","observed_orcids":["https://orcid.org/0009-0000-5059-4001"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cara Susilo","raw_affiliation_strings":["Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024"],"raw_orcid":"https://orcid.org/0009-0000-5059-4001","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045989873","display_name":"Arumugam Balamurugan","orcid":"https://orcid.org/0000-0002-4561-7368","observed_orcids":["https://orcid.org/0000-0002-4561-7368"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arumugam Balamurugan","raw_affiliation_strings":["Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040060443","display_name":"Arrmund Neal","orcid":"https://orcid.org/0000-0002-1735-4919","observed_orcids":["https://orcid.org/0000-0002-1735-4919"]},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arrmund Neal","raw_affiliation_strings":["Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-1735-4919","affiliations":[{"raw_affiliation_string":"Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032942104","display_name":"Karine G. Le Roch","orcid":"https://orcid.org/0000-0002-4862-9292","observed_orcids":["https://orcid.org/0000-0002-4862-9292","https://orcid.org/0000-0003-3608-2418"]},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karine G. Le Roch","raw_affiliation_strings":["Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-4862-9292","affiliations":[{"raw_affiliation_string":"Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062526829","display_name":"Otto O. Yang","orcid":"https://orcid.org/0000-0003-1970-8992","observed_orcids":["https://orcid.org/0000-0003-1970-8992"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Otto Yang","raw_affiliation_strings":["Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA","Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA","UCLA AIDS Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA"],"raw_orcid":"https://orcid.org/0000-0003-1970-8992","affiliations":[{"raw_affiliation_string":"Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"UCLA AIDS Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087846986","display_name":"Omai B. Garner","orcid":"https://orcid.org/0000-0002-7366-2692","observed_orcids":["https://orcid.org/0000-0002-7366-2692"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Omai Garner","raw_affiliation_strings":["Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA"],"raw_orcid":"https://orcid.org/0000-0002-7366-2692","affiliations":[{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071000467","display_name":"Mireille Kamariza","orcid":"https://orcid.org/0000-0003-1255-0803","observed_orcids":["https://orcid.org/0000-0003-1255-0803"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mireille Kamariza","raw_affiliation_strings":["Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024","UCLA Molecular Biology Institute, Los Angeles, CA, USA"],"raw_orcid":"https://orcid.org/0000-0003-1255-0803","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California Los Angeles, LA, CA, USA 90024","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"UCLA Molecular Biology Institute, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11393","display_name":"Biosensors and Analytical Detection","score":0.6557999849319458,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11393","display_name":"Biosensors and Analytical Detection","score":0.6557999849319458,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.23569999635219574,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11754","display_name":"SARS-CoV-2 detection and testing","score":0.017500000074505806,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/crispr-cas13a","display_name":"CRISPR-Cas13a","score":0.949999988079071},{"id":"https://openalex.org/keywords/hiv-1-detection","display_name":"HIV-1 detection","score":0.9110000133514404},{"id":"https://openalex.org/keywords/tuberculosis","display_name":"tuberculosis","score":0.550000011920929},{"id":"https://openalex.org/keywords/malaria","display_name":"malaria","score":0.6209999918937683},{"id":"https://openalex.org/keywords/mycobacterium-tuberculosis","display_name":"Mycobacterium tuberculosis","score":0.9229999780654907},{"id":"https://openalex.org/keywords/isoniazid-resistance","display_name":"isoniazid resistance","score":0.9589999914169312},{"id":"https://openalex.org/keywords/katg","display_name":"katG","score":0.6290000081062317},{"id":"https://openalex.org/keywords/inha","display_name":"InhA","score":0.9929999709129333},{"id":"https://openalex.org/keywords/hiv-tb-co-infection","display_name":"HIV/TB coinfection","score":0.8090000152587891},{"id":"https://openalex.org/keywords/malaria-hiv-coinfection","display_name":"malaria-HIV coinfection","score":0.7950000166893005},{"id":"https://openalex.org/keywords/dried-blood-spots","display_name":"dried blood spots","score":0.8980000019073486},{"id":"https://openalex.org/keywords/sputum","display_name":"sputum","score":0.6039999723434448}],"concepts":[{"id":"https://openalex.org/C2777813720","wikidata":"https://www.wikidata.org/wiki/Q1243018","display_name":"Coinfection","level":3,"score":0.7214999794960022},{"id":"https://openalex.org/C2777975735","wikidata":"https://www.wikidata.org/wiki/Q130971","display_name":"Mycobacterium tuberculosis","level":3,"score":0.6654000282287598},{"id":"https://openalex.org/C2781069245","wikidata":"https://www.wikidata.org/wiki/Q12204","display_name":"Tuberculosis","level":2,"score":0.6424999833106995},{"id":"https://openalex.org/C2776301714","wikidata":"https://www.wikidata.org/wiki/Q259346","display_name":"Sputum","level":3,"score":0.5590999722480774},{"id":"https://openalex.org/C2778048844","wikidata":"https://www.wikidata.org/wiki/Q12156","display_name":"Malaria","level":2,"score":0.5185999870300293},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5059000253677368},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.41850000619888306},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4169999957084656},{"id":"https://openalex.org/C2779790121","wikidata":"https://www.wikidata.org/wiki/Q5779917","display_name":"Mycobacterium tuberculosis complex","level":4,"score":0.41499999165534973},{"id":"https://openalex.org/C2780687663","wikidata":"https://www.wikidata.org/wiki/Q18027924","display_name":"INHA","level":4,"score":0.3849000036716461},{"id":"https://openalex.org/C2778371730","wikidata":"https://www.wikidata.org/wiki/Q311383","display_name":"Plasmodium falciparum","level":3,"score":0.3174000084400177},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2906999886035919},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.2784000039100647},{"id":"https://openalex.org/C2776460866","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogen","level":2,"score":0.2678000032901764}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.26.26364094","doi":"https://doi.org/10.64898/2026.09.26.26364094","is_oa":false,"landing_page_url":"https://doi.org/10.64898/2026.09.26.26364094","pdf_url":null,"source":{"id":"https://openalex.org/S3005729997","display_name":"medRxiv","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"medRxiv","raw_type":"posted-content"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.9763000011444092,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1978340412","https://openalex.org/W1994333367","https://openalex.org/W2028522909","https://openalex.org/W2038001025","https://openalex.org/W2123861280","https://openalex.org/W2124243126","https://openalex.org/W2137617609","https://openalex.org/W2397891977","https://openalex.org/W2538382920","https://openalex.org/W2606498452","https://openalex.org/W2606915822","https://openalex.org/W2763042654","https://openalex.org/W2785904295","https://openalex.org/W2794044688","https://openalex.org/W2892675630","https://openalex.org/W2973445868","https://openalex.org/W3020077371","https://openalex.org/W3021896513","https://openalex.org/W3203018491","https://openalex.org/W4210752017","https://openalex.org/W4214837065","https://openalex.org/W4226372101","https://openalex.org/W4388692989","https://openalex.org/W4394870664","https://openalex.org/W4400940190","https://openalex.org/W4403338427","https://openalex.org/W4408251788","https://openalex.org/W4408359654","https://openalex.org/W4417152270"],"related_works":["https://openalex.org/W2027579225","https://openalex.org/W3020077371","https://openalex.org/W4386158162","https://openalex.org/W7203440939","https://openalex.org/W4413010834","https://openalex.org/W7204076526","https://openalex.org/W7221359714","https://openalex.org/W4281757796","https://openalex.org/W4409134096","https://openalex.org/W4400905493"],"abstract_inverted_index":{"Abstract":[0],"HIV,":[1],"tuberculosis":[2,54],"(TB)":[3],"and":[4,27,52,61,72,79,89,111,132,166,185,211],"malaria":[5,160],"are":[6],"major":[7],"infectious":[8],"diseases":[9],"that":[10,43,66],"frequently":[11,112],"co-circulate":[12],"in":[13,76,179,190,226],"high-burden":[14],"settings,":[15],"yet":[16],"their":[17],"diagnostic":[18],"pathways":[19],"remain":[20],"largely":[21],"disease-specific,":[22],"complicating":[23],"detection":[24,45,57,104,213],"of":[25,29,46,58,105,116,143,157,202],"coinfection":[26,195,212],"integration":[28],"antimicrobial-resistance":[30],"testing.":[31],"Here":[32],"we":[33],"developed":[34],"HTM":[35,67,101,151],"CARMEN,":[36],"a":[37,141,215,220],"highly":[38],"multiplexed":[39],"CRISPR-Cas13a":[40],"molecular-testing":[41,217],"framework":[42,221],"integrates":[44],"HIV-1,":[47],"HIV-2,":[48],"four":[49],"Plasmodium":[50],"species":[51,206],"Mycobacterium":[53],"(Mtb)":[55],"with":[56,171],"isoniazid-resistance-associated":[59],"inhA":[60],"katG":[62],"variants.":[63],"We":[64],"find":[65],"CARMEN":[68,152],"retained":[69],"target":[70,145,178],"selectivity":[71],"single-nucleotide":[73],"discrimination":[74],"across":[75,108,140],"vitro":[77],"experiments":[78],"clinically":[80],"relevant":[81],"sample":[82],"matrices,":[83],"including":[84],"whole":[85],"blood,":[86],"serum,":[87],"sputum":[88],"dried":[90],"blood":[91],"spots.":[92],"Across":[93],"20":[94],"contrived":[95,128],"samples":[96,118],"for":[97,159,163,168,176,222],"each":[98,177],"condition,":[99],"the":[100,124,180,200],"panel":[102],"supported":[103],"low-abundance":[106],"targets":[107],"multiple":[109],"matrices":[110],"detected":[113,139,189],"greater":[114],"number":[115],"low-input":[117],"as":[119],"positive":[120,154],"than":[121],"qPCR":[122],"under":[123],"conditions":[125],"tested.":[126],"In":[127],"P.":[129],"falciparum":[130],"/HIV-1":[131],"Mtb/HIV-1":[133],"coinfections,":[134],"both":[135],"pathogens":[136],"were":[137,187],"simultaneously":[138],"range":[142],"relative":[144],"concentrations.":[146],"Using":[147],"confirmed-positive":[148,193],"clinical":[149],"samples,":[150],"achieved":[153],"percent":[155,174],"agreement":[156,175],"95%":[158,162],"(19/20),":[161],"HIV-1":[164,184],"(19/20)":[165],"100%":[167,172],"Mtb":[169,186],"(30/30),":[170],"negative":[173],"confirmed-negative":[181],"samples.":[182],"Both":[183],"additionally":[188],"all":[191],"nine":[192],"HIV-TB":[194],"specimens.":[196],"These":[197],"findings":[198],"establish":[199],"feasibility":[201],"integrating":[203],"pathogen":[204],"detection,":[205],"differentiation,":[207],"resistance-associated":[208],"variant":[209],"interrogation":[210],"within":[214],"programmable":[216],"platform,":[218],"providing":[219],"high-throughput":[223],"integrated":[224],"testing":[225],"co-endemic":[227],"settings.":[228]},"counts_by_year":[],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2026-09-30T00:00:00"}