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We amplified full-length HIV envelope and pol gene sequences within microdroplets, and this compartmental amplification with long-read high-throughput sequencing enabled us to recover multiple unique sequences.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We achieved greater precision in determining the stage of infection than current incidence assays, with a 1.2% false recency rate (proportion of misclassified chronic infections) and a 262-day mean duration of recent infection (average time span of recent infection classification) from 83 recently infected and 81 chronically infected individuals. Microdrop HIV sequencing demonstrated an increased capacity to detect minority variants and linked DRMs. By screening all 93 World Health Organization surveillance DRMs, we detected 6 pretreatment drug resistance mutations with 2.6%\u201313.2% prevalence and cross-linked mutations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>HIDA with microdrop HIV sequencing may promote global HIV real-time surveillance by serving as a precise and high-throughput cross-sectional survey tool that can be generalized for surveillance of other pathogens.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/infdis\/jiab060","type":"journal-article","created":{"date-parts":[[2021,1,26]],"date-time":"2021-01-26T20:10:43Z","timestamp":1611691843000},"page":"1048-1059","source":"Crossref","is-referenced-by-count":7,"title":["Microdrop Human Immunodeficiency Virus Sequencing for Incidence and Drug Resistance Surveillance"],"prefix":"10.1093","volume":"224","author":[{"given":"Sung Yong","family":"Park","sequence":"first","affiliation":[{"name":"Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gina","family":"Faraci","sequence":"additional","affiliation":[{"name":"Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary","family":"Murphy","sequence":"additional","affiliation":[{"name":"Public Health England, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Pilcher","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California, San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael P","family":"Busch","sequence":"additional","affiliation":[{"name":"Research and Scientific Programs, Vitalant Research Institute, San Francisco, California, USA"},{"name":"Deparment of Laboratory Medicine, University of California, California, San Francisco, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ha Youn","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,1,31]]},"reference":[{"key":"2021091718335383600_CIT0001","article-title":"UNAIDS; Global HIV & AIDS statistics \u2014 2020 fact sheet."},{"key":"2021091718335383600_CIT0002","volume-title":"World Health Organization working group on HIV incidence measurement and data use. 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