Viral culture and immunofluorescence for the detection of SARS-CoV-2 infectivity in RT-PCR positive respiratory samples

Berengua, Carla; Lopez, M Padilla; Esteban, Montserrat; Marín, Pilar; Ramos, P.; Cuerpo, Margarita Del; Gich, Ignasi; Navarro, Ferrán; Miró, Elisenda; Rabella, N

doi:10.1016/j.jcv.2022.105167

Cited by 12 publications

(17 citation statements)

References 31 publications

(39 reference statements)

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“…Future studies for new SARS-CoV-2 variants and new respiratory viruses should ideally involve multi-institution partnerships to enroll a diverse cohort from a broad geographic range. Second, we presumed infectiousness based on viral-load thresholds in three specimen types; we did not perform viral culture on these specimens (we also acknowledge that specimen types not collected here could have contained infectious viral loads 25,78,79 ). Third, Omicron remains a relevant variant, but additional variants will continue to develop and may exhibit different patterns in their viral-load timecourses by specimen type, so community-based studies like this one will need to be done regularly to identify optimal testing methods for new variants (and emerging respiratory viruses).…”

Section: Discussionmentioning

confidence: 99%

Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods

Winnett

Akana

Shelby

et al. 2022

Preprint

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Background. Screening testing, often via self-collected specimens, remains a key strategy to detect infections early and prevent SARS-CoV-2 transmission, and to enable earlier initiation of treatment. However, which specimen type best detects the earliest days of infection remains controversial. Further, the analytical sensitivity of diagnostic tests must also be considered, as viral loads below a test's limit of detection (LOD) are likely to yield false-negative results. Comparisons of quantitative, longitudinal SARS-CoV-2 viral-load timecourses in multiple specimen types can determine the best specimen type and test analytical sensitivity for earliest detection of infection. Methods. We conducted a COVID-19 household transmission study between November 2021 and February 2022 that enrolled 228 participants and analyzed 6,825 samples using RT-qPCR to quantify viral-load timecourses in three specimen types (saliva [SA], anterior-nares swab [ANS], and oropharyngeal swab [OPS]). From this study population, 14 participants enrolled before or at the incidence of infection with the Omicron variant. We compared the viral loads in specimens collected from each person at the same timepoint, and the longitudinal viral load timecourses from each participant. Using these viral loads, we inferred the clinical sensitivity of each specimen type to detect infected, pre-infectious and infectious individuals (based on presumably infectious viral load levels) using assays with a range of analytical sensitivities. We also inferred the clinical sensitivity of computationally contrived specimen types representing combinations of single specimen types. Results. We found extreme differences (up to 109 copies/mL) in viral loads between paired specimen types in the same person at the same timepoint, and that longitudinal viral load timecourses across specimen types did not correlate. Because of this lack of correlation, infectious viral loads were often observed in different specimen types asynchronously throughout the course of the infection. In the first 4 days of infection, no single specimen type was inferred to achieve >95% detection of infected or infectious individuals, even with the highest analytical sensitivity assays. In nearly all participants (11/14), a rise in ANS viral loads was delayed (as many as 7 days) relative to SA and OPS. We also observed that ANS and OPS had the most complementary viral load timecourses, resulting in optimal inferred performance with a computationally contrived combined anterior nares-oropharyngeal (AN-OP) swab specimen type. The combination AN-OP swab had superior inferred clinical sensitivity the first 8 days of infection with both high- and low-analytical-sensitivity assays. This AN-OP swab was also inferred to significantly improve detection of pre-infectious and infectious individuals over any single specimen type. Conclusion. Our work demonstrates that the viral load in one specimen type cannot reliably predict the viral load in another specimen type. Combination specimen types may offer a more robust approach for earliest detection of new variants and respiratory viruses when viral kinetics are still unknown.

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Section: Discussionmentioning

confidence: 99%

Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods

Winnett

Akana

Shelby

et al. 2022

Preprint

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“…Only screening points with a paired RT-PCR and Ag-test result were included. Different studies report different cycling threshold values (Ct-values) of the SARS-CoV-2 RT-PCR as cut-off for infectiousness [13] , [14] , [15] , [16] . We included both Ct-values ≤30 and ≤25 as cut-offs to show the performance of Ag-tests at both levels.…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 antigen tests for screening of healthcare workers; experience with over 48,000 combined antigen tests and RT-PCR tests

Piek

Knoester

Gard

et al. 2023

Journal of Clinical Virology

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“…1,2 Based on viral-culture of PCR-positive samples, Berengua et al contributes clinically important knowledge that in immunocompetent individuals SARS-CoV-2 infectivity lasts < 15 days from symptom onset, and that Ct value > 27 indicates low probability (3.1%) for infectivity. 3 We salute the authors on this important investigation, and would like to highlight several points.…”

Section: Editorialmentioning

confidence: 97%

MD Cycle Threshold and SARS-CoV-2 Infectivity

Raveh

Nicolau‐Raducu

2022

MRAJ

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The ability of the cycle threshold to inform the infectivity of SARS-CoV-2 polymerase chain reaction (PCR)-positive individuals remains controversial. Berengua et al. have recently reported that in immunocompetent individuals SARS-CoV-2 infectivity lasts < 15 days and that Ct value > 27 indicates low probability for infectivity. This important study, however, comes with several caveats. The authors performed a single cell culture for each sample. Additionally, cycle threshold values and corresponding viral loads differ between variants. During the study period at least four strains were prevalent in Europe, yet the authors do not provide information regarding the isolated strains. Lastly, this hospital-based study seems to involve sampling bias. The findings of Berengua et al. may be leveraged to guide clinical decision in SARS-CoV-2 PCR-positive convalescing candidates for organ donation or transplantation.

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Viral culture and immunofluorescence for the detection of SARS-CoV-2 infectivity in RT-PCR positive respiratory samples

Cited by 12 publications

References 31 publications

Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods

Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods

SARS-CoV-2 antigen tests for screening of healthcare workers; experience with over 48,000 combined antigen tests and RT-PCR tests

MD Cycle Threshold and SARS-CoV-2 Infectivity

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