Infectious viral shedding of SARS-CoV-2 Delta following vaccination: A longitudinal cohort study
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Abstract
The impact of vaccination on SARS-CoV-2 infectiousness is not well understood. We compared longitudinal viral shedding dynamics in unvaccinated and fully vaccinated adults. SARS-CoV-2-infected adults were enrolled within 5 days of symptom onset and nasal specimens were self-collected daily for two weeks and intermittently for an additional two weeks. SARS-CoV-2 RNA load and infectious virus were analyzed relative to symptom onset stratified by vaccination status. We tested 1080 nasal specimens from 52 unvaccinated adults enrolled in the pre-Delta period and 32 fully vaccinated adults with predominantly Delta infections. While we observed no differences by vaccination status in maximum RNA levels, maximum infectious titers and the median duration of viral RNA shedding, the rate of decay from the maximum RNA load was faster among vaccinated; maximum infectious titers and maximum RNA levels were highly correlated. Furthermore, amongst participants with infectious virus, median duration of infectious virus detection was reduced from 7.5 days (IQR: 6.0–9.0) in unvaccinated participants to 6 days (IQR: 5.0–8.0) in those vaccinated (P = 0.02). Accordingly, the odds of shedding infectious virus from days 6 to 12 post-onset were lower among vaccinated participants than unvaccinated participants (OR 0.42 95% CI 0.19–0.89). These results indicate that vaccination had reduced the probability of shedding infectious virus after 5 days from symptom onset.
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SciScore for 10.1101/2022.05.15.22275051: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was reviewed by the UCSF Institutional Review Board and given a designation of public health surveillance according to federal regulations as summarized in 45 CFR 46.102(d)(1)(2).
Consent: Written informed consent was obtained from all participants.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Vero-hACE2-TMPRSS2 cells form characteristic syncytia upon infection with SARS-CoV-2, enabling rapid and specific visual evaluation for CPE. Vero-hACE2-TMPRSS2suggested: NoneSoftware and Algorithms Sentences Resources All… SciScore for 10.1101/2022.05.15.22275051: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was reviewed by the UCSF Institutional Review Board and given a designation of public health surveillance according to federal regulations as summarized in 45 CFR 46.102(d)(1)(2).
Consent: Written informed consent was obtained from all participants.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Vero-hACE2-TMPRSS2 cells form characteristic syncytia upon infection with SARS-CoV-2, enabling rapid and specific visual evaluation for CPE. Vero-hACE2-TMPRSS2suggested: NoneSoftware and Algorithms Sentences Resources All assays were done in the BSL3 facility at Genentech Hall, UCSF, following the study protocol that had received Biosafety Use Authorization. Genentechsuggested: (Genentech, RRID:SCR_003997)Consensus sequences were generated using the nCoV-2019 novel coronavirus bioinformatics protocol using the MinIon Pipeline.43 Lineage determination was done using the online Pangolin COVID-19 Lineage Assigner. MinIonsuggested: (MinION, RRID:SCR_017985)All analyses were performed using STATA/IC 16.1 (STATA Corporation, College Station, Texas, USA) and R version 3.3.2 (R Project for Statistical Computing, Vienna, Austria) R Project for Statisticalsuggested: (R Project for Statistical Computing, RRID:SCR_001905)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study has some limitations. Unvaccinated individuals in our analysis were mostly enrolled prior to the emergence and global spread of the Delta lineage, whereas fully vaccinated individuals were almost exclusively enrolled once Delta was the dominant circulating lineage. Thus, we were unable to control for this as a potential confounder. However, previous studies have indicated that infections with Delta lineage viruses have higher peak viral loads30,39 and longer duration of shedding than pre-Delta lineages40,41. This suggests that we may have underestimated differences between vaccination groups, bringing our results from early infection in line with those from Puhach et al. In addition, index cases were from the list of SARS-CoV-2 positive cases at UCSF-affiliated medical centers in San Francisco and may not be representative of all SARS-CoV-2 infections occurring in the same jurisdiction. Furthermore, we were underpowered to analyze shedding dynamics during the pre-symptomatic and early symptomatic period and thus we may have missed the peak viral RNA load in some individuals and thus underestimated maximum values (Supp. Figure 1). Lastly, our study was likely underpowered to detect differences in overall infectious virus shedding duration between groups, though our comparison when restricted to participants with infectious virus (Table 2) is in line with the regression analysis in Figure 3. In summary, in addition to the protective effect of COVID-19 vaccines against...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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