Duration of Shedding of Culturable Virus in SARS-CoV-2 Omicron (BA.1) Infection

Boucau, Julie; Marino, Caitlin; Regan, James; Uddin, Rockib; Choudhary, Manish; Flynn, James P.; Chen, Geoffrey; Stuckwisch, Ashley; Mathews, Josh; Liew, May Y.; Singh, Arshdeep; Lipiner, Taryn; Kittilson, Autumn; Melberg, Meghan; Li, Yijia; Gilbert, Rebecca F; Reynolds, Zahra; Iyer, Surabhi; Chamberlin, Grace; Vyas, Tammy D.; Goldberg, Marcia B.; Vyas, Jatin M.; Li, Jonathan Z.; Lemieux, Jacob E.; Siedner, Mark J.; Barczak, Amy K.

doi:10.1056/nejmc2202092

Cited by 153 publications

(161 citation statements)

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“…Lastly, some people test multiple times with providers after their initial positive test 40 , and subsequently, many can expect positive PCR and antigen test results for 10 or more days. 44,45 This could have caused some people who were diagnosed prior to the study period to have positive tests during the study period which could have inflated our prevalence estimates relative to official case counts. But from an epidemiologic standpoint, these individuals should be reflected in prevalence estimates as they are actively infected.…”

Section: Discussionmentioning

confidence: 99%

The prevalence of SARS-CoV-2 infection and other public health outcomes during the BA.2/BA.2.12.1 surge, New York City, April-May 2022

Qasmieh

Robertson

Teasdale

et al. 2022

Preprint

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ImportanceRoutine case surveillance data for SARS-CoV-2 are incomplete, biased, missing key variables of interest, and may be unreliable for both timely surge detection and understanding the burden of infection.ObjectiveTo determine the prevalence of SARS-CoV-2 infection during the Omicron BA.2/BA.2.12.1 surge in relation to official case counts, and to assess the epidemiology of infection and uptake of SARS-CoV-2 antivirals.DesignCross-sectional survey of a representative sample of New York City (NYC) adult residents, conducted May 7-8, 2022.SettingNYC, April 23-May 8, 2022, during which the official SARS-CoV-2 case count was 49,253 and BA.2.12.2 comprised 20% of reported cases.ParticipantsA representative sample of 1,030 NYC adult residents >18 years.Exposure(s)Vulnerability to severe COVID-19, including vaccination/booster status, prior COVID, age, and presence of comorbidities.Main Outcome(s) and Measure(s)Prevalence of SARS-CoV-2 infection during a 14-day period, weighted to represent the NYC adult population. Respondents self-reported on SARS-CoV-2 testing (including at-home rapid antigen tests), testing outcomes, COVID-like symptoms, and contact with confirmed/probable cases. Individuals with SARS-CoV-2 were asked about awareness/use of antiviral medications.ResultsAn estimated 22.1% (95%CI 17.9%-26.2%) of respondents had SARS-CoV-2 infection during the study period, corresponding to ∼1.5 million adults (95%CI 1.3-1.8 million). Prevalence was estimated at 34.9% (95%CI 26.9%-42.8%) among individuals with co-morbidities, 14.9% (95% CI 11.0%-18.8%) among those 65+ years, and 18.9% (95%CI 10.2%-27.5%) among unvaccinated persons. Hybrid protection against severe disease (i.e., from both vaccination and prior infection) was 66.2% (95%CI 55.7%-76.7%) among those with COVID and 46.3% (95%CI 40.2-52.2) among those without. Among individuals with COVID, 55.9% (95%CI 44.9%-67.0%) were not aware of the antiviral nirmatrelvir/ritonavir (Paxlovid™), and 15.1% (95%CI 7.1%-23.1%) reported receiving it.Conclusions and RelevanceThe true magnitude of NYC’s BA.2/BA.2.12.1 surge was vastly underestimated by routine SARS-CoV-2 surveillance. Until there is more certainty that the impact of future pandemic surges on severe population health outcomes will be diminished, representative surveys are needed for timely surge detection, and to estimate the true burden of infection, hybrid protection, and uptake of time-sensitive treatments.

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Section: Discussionmentioning

confidence: 99%

The prevalence of SARS-CoV-2 infection and other public health outcomes during the BA.2/BA.2.12.1 surge, New York City, April-May 2022

Qasmieh

Robertson

Teasdale

et al. 2022

Preprint

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“…Studies that have assessed the period of infectiousness by viral culture of only one specimen type may have underestimated the total infectious period. 12,26,40,41 Evidence for recommended isolation periods should consider multiple specimen types, 40 particularly if negative Ag-RDT results are used to release individuals from isolation. Moreover, studies evaluating low-analytical-sensitivity testing relative to infectiousness in only one specimen type will likely overestimate the performance of that test to detect the full infectious period.…”

Section: Discussionmentioning

confidence: 99%

Why Daily SARS-CoV-2 Nasal Rapid Antigen Testing Poorly Detects Infected and Infectious Individuals

Winnett

Akana

Shelby

et al. 2022

Preprint

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Background. To limit viral transmission, COVID-19 testing strategies must evolve as new SARS-CoV-2 variants (and new respiratory viruses) emerge to ensure that the specimen types and test analytical sensitivities being used will reliably detect individuals during the pre-infectious and infectious periods. Our accompanying work demonstrated that there are extreme differences in viral loads among paired saliva (SA), anterior-nares swab (ANS) and oropharyngeal swab (OPS) specimens collected from the same person and timepoint. We hypothesized that these extreme differences may prevent low-analytical-sensitivity assays (such as antigen rapid diagnostic tests, Ag-RDTs) performed on a single specimen type from reliably detecting pre-infectious and infectious individuals. Methods. We conducted a longitudinal COVID-19 household-transmission study in which 228 participants collected SA, ANS, and OPS specimens for viral-load quantification by RT-qPCR, and performed an ANS Ag-RDT (Quidel QuickVue At-Home OTC COVID-19 Test) daily. We evaluated the performance of the Ag-RDT (n=2215 tests) to detect infected individuals (positive results in any specimen type by RT-qPCR) and individuals with presumed infectious viral loads (at or above thresholds of 10^4, 10^5, 10^6, or 10^7 copies/mL). Results. Overall, the daily Ag-RDT detected 44% (358/811) timepoints from infected individuals. From 17 participants who enrolled early in the course of infection, we found that daily Ag-RDT performance was higher at timepoints when symptoms were reported, but symptoms only weakly correlated with SARS-CoV-2 viral loads, so ANS Ag-RDT clinical sensitivity remained below 50%. The three specimen types exhibited asynchronous presumably-infectious periods (regardless of the infectious viral-load threshold chosen) and the rise in ANS viral loads was delayed relative to SA or OPS for nearly all individuals, which resulted in the daily ANS Ag-RDT detecting only 3% in the pre-infectious period and 63% in the infectious period. We evaluated a computationally-contrived combined AN-OP swab based on viral loads from ANS and OPS specimens collected at the same timepoint; when tested with similar analytical sensitivity as the Ag-RDT, this combined swab was predicted to have significantly better performance, detecting up to 82% of infectious individuals. Conclusion. Daily ANS rapid antigen testing missed virtually all pre-infectious individuals, and more than one third of presumed infectious individuals due to low-analytical-sensitivity of the assay, a delayed rise in ANS viral loads, and asynchronous infectious viral loads in SA or OPS. When high-analytical-sensitivity assays are not available and low-analytical-sensitivity tests such as Ag-RDTs must be used for SARS-CoV-2 detection, an AN-OP combination swab is predicted to be most effective for detection of pre-infectious and infectious individuals. More generally, low-analytical-sensitivity tests are likely to perform more robustly using oral-nasal combination specimen types to detect new SASR-CoV-2 variants and emergent upper respiratory viruses.

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“…It is also possible that participants inadvertently recalled and reported positive tests that were beyond the 14-day study period (recall bias). In addition, some people test multiple times over a period of days or weeks with providers after their initial positive test 25 , and subsequently, many can expect positive PCR and antigen test results for 10 or more days 26,27 . This could have caused some people who were diagnosed prior to the study period to have positive tests during the study period which could have inflated our prevalence estimates relative to official case counts.…”

Section: Discussionmentioning

confidence: 99%

The prevalence of SARS-CoV-2 infection and long COVID in US adults during the BA.5 surge, June-July 2022

Qasmieh

Robertson

Teasdale

et al. 2022

Preprint

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Due to changes in SARS-CoV-2 testing practices, passive case-based surveillance may be an increasingly unreliable indicator for monitoring the burden of SARS-CoV-2, especially during surges. We conducted a cross-sectional survey of a population-representative sample of 3,042 U.S. adults between June 30 and July 2, 2022, during the Omicron BA.5 surge. Respondents were asked about SARS-CoV-2 testing and outcomes, COVID-like symptoms, contact with cases, and experience with prolonged COVID-19 symptoms following prior infection. We estimated the weighted age and sex-standardized SARS-CoV-2 prevalence, during the 14-day period preceding the interview. We estimated age and gender adjusted prevalence ratios (aPR) for current SARS-CoV-2 infection using a log-binomial regression model. An estimated 17.3% (95% CI 14.9, 19.8) of respondents had SARS-CoV-2 infection during the two-week study period, equating to 44 million cases as compared to 1.8 million per the CDC during the same time period. SARS-CoV-2 prevalence was higher among those 18-24 years old (aPR 2.2, 95% CI 1.8, 2.7) and among non-Hispanic Black (aPR 1.7, 95% CI 1.4 ,2.2) and Hispanic (aPR 2.4, 95% CI 2.0 , 2.9). SARS-CoV-2 prevalence was also higher among those with lower income (aPR 1.9, 95% CI 1.5, 2.3), lower education (aPR 3.7 95% CI 3.0,4.7), and those with comorbidities (aPR 1.6, 95% CI 1.4, 2.0). An estimated 21.5% (95% CI 18.2, 24.7) of respondents with a SARS-CoV-2 infection more than 4 weeks prior reported long COVID symptoms. The inequitable distribution of SARS-CoV-2 prevalence during the BA.5 surge will likely drive inequities in the future burden of long COVID.

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Duration of Shedding of Culturable Virus in SARS-CoV-2 Omicron (BA.1) Infection

Cited by 153 publications

References 4 publications

The prevalence of SARS-CoV-2 infection and other public health outcomes during the BA.2/BA.2.12.1 surge, New York City, April-May 2022

The prevalence of SARS-CoV-2 infection and other public health outcomes during the BA.2/BA.2.12.1 surge, New York City, April-May 2022

Why Daily SARS-CoV-2 Nasal Rapid Antigen Testing Poorly Detects Infected and Infectious Individuals

The prevalence of SARS-CoV-2 infection and long COVID in US adults during the BA.5 surge, June-July 2022

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