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dc.contributor.authorHay, James
dc.contributor.authorKissler, Stephen
dc.contributor.authorFauver, Joseph R.
dc.contributor.authorMack, Christina
dc.contributor.authorTai, Caroline G.
dc.contributor.authorSamant, Radhika M.
dc.contributor.authorConnelly, Sarah
dc.contributor.authorAnderson, Deverick J.
dc.contributor.authorKhullar, Gaurav
dc.contributor.authorMacKay, Matthew
dc.contributor.authorPatel, Miral
dc.contributor.authorKelly, Shannan
dc.contributor.authorManhertz, April
dc.contributor.authorEiter, Isaac
dc.contributor.authorSalgado, Daisy
dc.contributor.authorBaker, Tim
dc.contributor.authorDudley, Joel T.
dc.contributor.authorMason, Christopher E.
dc.contributor.authorHo, David D.
dc.contributor.authorGrubaugh, Nathan D.
dc.contributor.authorGrad, Yonatan
dc.date.accessioned2022-01-13T16:26:15Z
dc.date.issued2022
dc.identifier.citationHay, James, Stephen Kissler, Joseph R. Fauver, Christina Mack, Caroline G. Tai, et al. 2022. "Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant." Pre-print.en_US
dc.identifier.urihttps://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37370587*
dc.description.abstractBackground: The Omicron SARS-CoV-2 variant is responsible for a major wave of COVID-19, with record case counts reflecting high transmissibility and escape from prior immunity. Defining the time course of Omicron viral proliferation and clearance is crucial to inform isolation protocols aiming to minimize disease spread. Methods: We obtained longitudinal, quantitative RT-qPCR test results using combined anterior nares and oropharyngeal samples (n = 10,324) collected between July 5th, 2021 and January 10th, 2022 from the National Basketball Association’s (NBA) occu-pational health program. We quantified the fraction of tests with PCR cycle threshold (Ct) values <30, chosen as a proxy for potential infectivity and antigen test positivity, on each day after first detection of suspected and confirmed Omicron infections, stratified by individuals detected under frequent testing protocols and those detected due to symptom onset or concern for contact with an infected individual. We quantified the du-ration of viral proliferation, clearance rate, and peak viral concentration for individuals with acute Omicron and Delta variant SARS-CoV-2 infections. Results: A total of 97 infections were confirmed or suspected to be from the Omicron variant and 107 from the Delta variant. Of 27 Omicron-infected individuals testing posi-tive ≤1 day after a previous negative or inconclusive test, 52.0% (13/25) were PCR positive with Ct values <30 at day 5, 25.0% (6/24) at day 6, and 13.0% (3/23) on day 7 post detection. Of 70 Omicron-infected individuals detected ≥2 days after a previous negative or inconclusive test, 39.1% (25/64) were PCR positive with Ct values <30 at day 5, 33.3% (21/63) at day 6, and 22.2% (14/63) on day 7 post detection. Overall, Omicron infections featured a mean duration of 9.87 days (95% CI 8.83-10.9) relative to 10.9 days (95% CI 9.41-12.4) for Delta infections. The peak viral RNA based on Ct values was lower for Omicron infections than for Delta infections (Ct 23.3, 95% CI 22.4-24.3 for Omicron; Ct 20.5, 95% CI 19.2-21.8 for Delta) and the clearance phase was shorter for Omicron infections (5.35 days, 95% CI 4.78-6.00 for Omicron; 6.23 days, 95% CI 5.43-7.17 for Delta), though the rate of clearance was similar (3.13 Ct/day, 95% CI 2.75-3.54 for Omicron; 3.15 Ct/day, 95% CI 2.69-3.64 for Delta). Conclusions: While Omicron infections feature lower peak viral RNA and a shorter clearance phase than Delta infections on average, it is unclear to what extent these differences are attributable to more immunity in this largely vaccinated population or intrinsic characteristics of the Omicron variant. Further, these results suggest that Omi-cron’s infectiousness may not be explained by higher viral load measured in the nose and mouth by RT-PCR. The substantial fraction of individuals with Ct values <30 at days 5 of infection, particularly in those detected due to symptom onset or concern for contact with an infected individual, underscores the heterogeneity of the infectious pe-riod, with implications for isolation policies.en_US
dc.language.isoen_USen_US
dash.licenseLAA
dc.titleViral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron varianten_US
dc.typeJournal Articleen_US
dc.description.versionAuthor's Originalen_US
dash.depositing.authorGrad, Yonatan
dc.date.available2022-01-13T16:26:15Z
dash.contributor.affiliatedHay, James
dash.contributor.affiliatedKissler, Stephen
dash.contributor.affiliatedGrad, Yonatan


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