{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:36:26Z","timestamp":1772138186766,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T00:00:00Z","timestamp":1646870400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"Stephany W. Holloway University of Florida Chair"},{"name":"University of Florida Office of Research and Health Science Center"},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000155","name":"Division of Environmental Biology","doi-asserted-by":"publisher","award":["2028221"],"award-info":[{"award-number":["2028221"]}],"id":[{"id":"10.13039\/100000155","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100002554","name":"AIDS HealthCare Foundation","doi-asserted-by":"publisher","award":["OS00000633"],"award-info":[{"award-number":["OS00000633"]}],"id":[{"id":"10.13039\/100002554","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000877","name":"Rockefeller Foundation","doi-asserted-by":"publisher","award":["2021 HTH 012"],"award-info":[{"award-number":["2021 HTH 012"]}],"id":[{"id":"10.13039\/100000877","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant has caused a dramatic resurgence in infections in the United Sates, raising questions regarding potential transmissibility among vaccinated individuals.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Between October 2020 and July 2021, we sequenced 4439 SARS-CoV-2 full genomes, 23% of all known infections in Alachua County, Florida, including 109 vaccine breakthrough cases. Univariate and multivariate regression analyses were conducted to evaluate associations between viral RNA burden and patient characteristics. Contact tracing and phylogenetic analysis were used to investigate direct transmissions involving vaccinated individuals.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The majority of breakthrough sequences with lineage assignment were classified as Delta variants (74.6%) and occurred, on average, about 3 months (104\u2005\u00b1\u200557.5 days) after full vaccination, at the same time (June-July 2021) of Delta variant exponential spread within the county. Six Delta variant transmission pairs between fully vaccinated individuals were identified through contact tracing, 3 of which were confirmed by phylogenetic analysis. Delta breakthroughs exhibited broad viral RNA copy number values during acute infection (interquartile range, 1.2-8.64 Log copies\/mL), on average 38% lower than matched unvaccinated patients (3.29-10.81 Log copies\/mL, P\u2005&amp;lt;\u2005.00001). Nevertheless, 49% to 50% of all breakthroughs, and 56% to 60% of Delta-infected breakthroughs exhibited viral RNA levels above the transmissibility threshold (4 Log copies\/mL) irrespective of time after vaccination.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Delta infection transmissibility and general viral RNA quantification patterns in vaccinated individuals suggest limited levels of sterilizing immunity that need to be considered by public health policies. In particular, ongoing evaluation of vaccine boosters should specifically address whether extra vaccine doses curb breakthrough contribution to epidemic spread.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/cid\/ciac197","type":"journal-article","created":{"date-parts":[[2022,3,8]],"date-time":"2022-03-08T15:12:10Z","timestamp":1646752330000},"page":"1618-1627","source":"Crossref","is-referenced-by-count":6,"title":["Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida"],"prefix":"10.1093","volume":"75","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6088-4651","authenticated-orcid":false,"given":"Brittany","family":"Rife Magalis","sequence":"first","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, Florida , USA"},{"name":"Department of Pathology, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shannan","family":"Rich","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, University of Florida , Gainesville, Florida , USA"},{"name":"Florida Department of Health , Alachua County, Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Massimiliano S","family":"Tagliamonte","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, Florida , USA"},{"name":"Department of Pathology, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carla","family":"Mavian","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, Florida , USA"},{"name":"Department of Pathology, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melanie N","family":"Cash","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, Florida , USA"},{"name":"Department of Pathology, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alberto","family":"Riva","sequence":"additional","affiliation":[{"name":"Interdisciplinary Center for Biotechnology Research, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simone","family":"Marini","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Florida , Gainesville, Florida , USA"},{"name":"Department of Epidemiology, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David Moraga","family":"Amador","sequence":"additional","affiliation":[{"name":"Interdisciplinary Center for Biotechnology Research, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanping","family":"Zhang","sequence":"additional","affiliation":[{"name":"Interdisciplinary Center for Biotechnology Research, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jerne","family":"Shapiro","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, University of Florida , Gainesville, Florida , USA"},{"name":"Florida Department of Health , Alachua County, Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amelia","family":"Horine","sequence":"additional","affiliation":[{"name":"Florida Department of Health , Alachua County, Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petr","family":"Starostik","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maura","family":"Pieretti","sequence":"additional","affiliation":[{"name":"BayCare Laboratories LLC , Tampa, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samantha","family":"Vega","sequence":"additional","affiliation":[{"name":"BayCare Laboratories LLC , Tampa, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana","family":"Paula Lacombe","sequence":"additional","affiliation":[{"name":"University of Miami Miller School of Medicine , Miami, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica","family":"Salinas","sequence":"additional","affiliation":[{"name":"University of Miami Miller School of Medicine , Miami, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mario","family":"Stevenson","sequence":"additional","affiliation":[{"name":"University of Miami Miller School of Medicine , Miami, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Myers","sequence":"additional","affiliation":[{"name":"Florida Department of Health , Alachua County, Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"Jr.","given":"J","family":"Glenn Morris","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, Florida , USA"},{"name":"Department of Medicine, College of Medicine, University of Florida , Gainesville, Florida"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Lauzardo","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, Florida , USA"},{"name":"Florida Department of Health , Alachua County, Gainesville, Florida , USA"},{"name":"Department of Medicine, College of Medicine, University of Florida , Gainesville, Florida"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mattia","family":"Prosperi","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Salemi","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida , Gainesville, Florida , USA"},{"name":"Department of Pathology, University of Florida , Gainesville, Florida , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,3,10]]},"reference":[{"key":"2022102916082810200_CIT0001","author":"CDC."},{"key":"2022102916082810200_CIT0002","author":"Rambaut"},{"key":"2022102916082810200_CIT0003","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2102214","article-title":"Efficacy of the ChAdOx1 nCoV-19 Covid-19 vaccine against the B.1.351 variant.","author":"Madhi","year":"2021","journal-title":"N Engl J Med"},{"key":"2022102916082810200_CIT0004","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1126\/science.abe9728","article-title":"Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic.","volume":"371","author":"Buss","year":"2021","journal-title":"Science"},{"key":"2022102916082810200_CIT0005","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1080\/23744235.2020.1837944","article-title":"Long-term intermittent detection of SARS CoV 2 in the upper respiratory tract: what is the meaning of it?","volume":"53","author":"Sabino","year":"2021","journal-title":"Infect Dis (Lond)"},{"key":"2022102916082810200_CIT0006","doi-asserted-by":"crossref","first-page":"2603","DOI":"10.1056\/NEJMoa2034577","article-title":"Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine.","volume":"383","author":"Polack","year":"2020","journal-title":"N Engl J Med"},{"key":"2022102916082810200_CIT0007","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1056\/NEJMoa2108891","article-title":"Effectiveness of Covid-19 vaccines against the B.1.617.2 (Delta) variant.","volume":"385","author":"Lopez Bernal","year":"2021","journal-title":"N Engl J Med"},{"key":"2022102916082810200_CIT0008","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/d41586-021-01390-4","article-title":"What scientists know about new, fast-spreading coronavirus variants.","volume":"594","author":"Adam","year":"2021","journal-title":"Nature"},{"key":"2022102916082810200_CIT0009","doi-asserted-by":"crossref","first-page":"1324","DOI":"10.1001\/jama.2021.1612","article-title":"Emergence of a novel SARS-CoV-2 variant in Southern California.","volume":"325","author":"Zhang","year":"2021","journal-title":"JAMA"},{"key":"2022102916082810200_CIT0010","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1016\/j.chom.2021.06.006","article-title":"SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity.","volume":"29","author":"Motozono","year":"2021","journal-title":"Cell Host Microbe"},{"key":"2022102916082810200_CIT0011","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2021.100255","article-title":"Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016.","volume":"2","author":"Starr","year":"2021","journal-title":"Cell Rep Med"},{"key":"2022102916082810200_CIT0012","author":"CDC."},{"key":"2022102916082810200_CIT0013","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.15585\/mmwr.mm7031e2","article-title":"Outbreak of SARS-CoV-2 infections, including COVID-19 vaccine breakthrough infections, associated with large public gatherings - Barnstable County, Massachusetts, July 2021.","volume":"70","author":"Brown","year":"2021","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"2022102916082810200_CIT0014","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.15585\/mmwr.mm7028e2","article-title":"SARS-CoV-2 B.1.617.2 (Delta) variant COVID-19 outbreak associated with a gymnastics facility - Oklahoma, April-May 2021.","volume":"70","author":"Dougherty","year":"2021","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"2022102916082810200_CIT0015","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1186\/s12916-021-02103-4","article-title":"Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections.","volume":"19","author":"Farinholt","year":"2021","journal-title":"BMC Med"},{"key":"2022102916082810200_CIT0016","doi-asserted-by":"publisher","DOI":"10.1038\/d41586-021-02259-2","article-title":"Delta\u2019s rise is fuelled by rampant spread from people who feel fine.","author":"Mallapaty","year":"2021","journal-title":"Nature"},{"key":"2022102916082810200_CIT0017","article-title":"Transmission dynamics and epidemiological characteristics of Delta variant infections in China. [Preprint].","author":"Kang","year":"2021","journal-title":"medRxiv"},{"key":"2022102916082810200_CIT0018","doi-asserted-by":"crossref","first-page":"584","DOI":"10.46234\/ccdcw2021.148","article-title":"Transmission dynamics of an outbreak of the COVID-19 Delta variant B.1.617.2 - Guangdong Province, China, May-June 2021.","volume":"3","author":"Zhang","year":"2021","journal-title":"China CDC Wkly"},{"key":"2022102916082810200_CIT0019","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1056\/NEJMoa2035389","article-title":"Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine.","volume":"384","author":"Baden","year":"2021","journal-title":"N Engl J Med"},{"key":"2022102916082810200_CIT0020","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2110345","article-title":"Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine through 6 months.","author":"Thomas","year":"2021","journal-title":"N Engl J Med"},{"key":"2022102916082810200_CIT0021","first-page":"792","article-title":"COVID-19 vaccine breakthrough infections reported to CDC - United States, January 1-April 30, 2021.","author":"CC-VBCI T.","year":"2021; 70","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"2022102916082810200_CIT0022","article-title":"Shedding of infectious SARS-CoV-2 despite vaccination when the Delta variant is prevalent - Wisconsin, July 2021.","author":"Riemersma","year":"2021","journal-title":"medRxiv"},{"key":"2022102916082810200_CIT0023","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2020.25.32.2001483","article-title":"Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020.","volume":"25","author":"Singanayagam","year":"2020","journal-title":"Euro Surveill"},{"key":"2022102916082810200_CIT0024","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.63537","article-title":"Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events.","volume":"10","author":"Goyal","year":"2021","journal-title":"Elife"},{"key":"2022102916082810200_CIT0025","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/S1473-3099(20)30985-3","article-title":"Transmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study.","volume":"21","author":"Marks","year":"2021","journal-title":"Lancet Infect Dis"},{"key":"2022102916082810200_CIT0026","doi-asserted-by":"publisher","DOI":"10.1101\/2021.08.06.21261707","article-title":"Comparison of two highly-effective mRNA vaccines for COVID-19 during periods of Alpha and Delta variant prevalence.","author":"Puranik","year":"2021","journal-title":"medRxiv"},{"key":"2022102916082810200_CIT0027","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/s42003-021-02025-0","article-title":"SARS-CoV-2 shifting transmission \u00addynamics and hidden reservoirs potentially limit efficacy of public health \u00adinterventions in Italy.","volume":"4","author":"Giovanetti","year":"2021","journal-title":"Commun Biol"},{"key":"2022102916082810200_CIT0028","doi-asserted-by":"crossref","first-page":"22640","DOI":"10.1038\/s41598-021-02097-2","article-title":"Saliva is superior over nasopharyngeal swab for detecting SARS-CoV2 in COVID-19 patients.","volume":"11","author":"Beyene","year":"2021","journal-title":"Sci Rep"},{"key":"2022102916082810200_CIT0029","doi-asserted-by":"crossref","first-page":"3134","DOI":"10.1038\/s41598-021-82787-z","article-title":"Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection.","volume":"11","author":"Teo","year":"2021","journal-title":"Sci Rep"},{"key":"2022102916082810200_CIT0030","volume-title":"COVID-19 Case Surveillance Public Use Data with Geography","author":"CDC."},{"key":"2022102916082810200_CIT0031","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1098\/rstb.1989.0106","article-title":"The phylogenetic regression.","volume":"326","author":"Grafen","year":"1989","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"2022102916082810200_CIT0032","doi-asserted-by":"crossref","first-page":"2675","DOI":"10.1111\/evo.12463","article-title":"A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data.","volume":"68","author":"Adams","year":"2014","journal-title":"Evolution"},{"key":"2022102916082810200_CIT0033","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/s41591-021-01316-7","article-title":"Initial report of decreased SARS-CoV-2 viral load after inoculation with the BNT162b2 vaccine.","volume":"27","author":"Levine-Tiefenbrun","year":"2021","journal-title":"Nat Med"},{"key":"2022102916082810200_CIT0034","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1056\/NEJMoa2114255","article-title":"Protection of BNT162b2 vaccine booster against Covid-19 in Israel.","volume":"385","author":"Bar-On","year":"2021","journal-title":"N Engl J Med"},{"key":"2022102916082810200_CIT0035","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2022102916082810200_CIT0036","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/s41564-020-0770-5","article-title":"A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.","volume":"5","author":"Rambaut","year":"2020","journal-title":"Nat Microbiol"},{"key":"2022102916082810200_CIT0037","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/s41564-021-00872-5","article-title":"Addendum: a dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.","volume":"6","author":"Rambaut","year":"2021","journal-title":"Nat Microbiol"},{"key":"2022102916082810200_CIT0038","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.cegh.2020.08.007","article-title":"Estimates of serial interval for COVID-19: a systematic review and meta-analysis.","volume":"9","author":"Rai","year":"2021","journal-title":"Clin Epidemiol Glob Health"},{"key":"2022102916082810200_CIT0039","volume-title":"CDC real-time reverse transcriptase PCR (rRT-PCR) diagnostic test for COVID-19","author":"CDC."}],"container-title":["Clinical Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/cid\/advance-article-pdf\/doi\/10.1093\/cid\/ciac197\/43691851\/ciac197.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/cid\/article-pdf\/75\/9\/1618\/46684659\/ciac197.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/cid\/article-pdf\/75\/9\/1618\/46684659\/ciac197.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,29]],"date-time":"2022-10-29T12:10:04Z","timestamp":1667045404000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/cid\/article\/75\/9\/1618\/6546683"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,3,10]]},"references-count":39,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2022,3,10]]},"published-print":{"date-parts":[[2022,10,29]]}},"URL":"https:\/\/doi.org\/10.1093\/cid\/ciac197","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.11.10.21266134","asserted-by":"object"}]},"ISSN":["1058-4838","1537-6591"],"issn-type":[{"value":"1058-4838","type":"print"},{"value":"1537-6591","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,11,1]]},"published":{"date-parts":[[2022,3,10]]}}}