Variant‐specific SARS‐CoV‐2 within‐host kinetics
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Abstract
Since early 2021, SARS‐CoV‐2 variants of concern (VOCs) have been causing epidemic rebounds in many countries. Their properties are well characterized at the epidemiological level but the potential underlying within‐host determinants remain poorly understood. We analyze a longitudinal cohort of 6944 individuals with 14 304 cycle threshold ( Ct ) values of reverse‐transcription quantitative polymerase chain reaction (RT‐qPCR) VOC screening tests performed in the general population and hospitals in France between February 6 and August 21, 2021. To convert Ct values into numbers of virus copies, we performed an additional analysis using droplet digital PCR (ddPCR). We find that the number of viral genome copies reaches a higher peak value and has a slower decay rate in infections caused by Alpha variant compared to that caused by historical lineages. Following the evidence that viral genome copies in upper respiratory tract swabs are informative on contagiousness, we show that the kinetics of the Alpha variant translate into significantly higher transmission potentials, especially in older populations. Finally, comparing infections caused by the Alpha and Delta variants, we find no significant difference in the peak viral copy number. These results highlight that some of the differences between variants may be detected in virus load variations.
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SciScore for 10.1101/2021.05.26.21257835: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
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:A limitation of this analysis is that we do not have any indication regarding the date of the infection or of the symptom onset. This uncertainty prevents us from analyzing more mechanistic models with nonlinear mixed-effect models [10]. However, since we the nature of the virus causing the infection is unlikely to affect the number of …
SciScore for 10.1101/2021.05.26.21257835: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
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:A limitation of this analysis is that we do not have any indication regarding the date of the infection or of the symptom onset. This uncertainty prevents us from analyzing more mechanistic models with nonlinear mixed-effect models [10]. However, since we the nature of the virus causing the infection is unlikely to affect the number of days between infection and screening, we do not expect our assumption that the lowest Ct value corresponds to the peak viral load to introduce biases. Furthermore, the variant assessment for V2/V3 should be treated with caution because it only relies on the N501Y mutation. However, the assessment of the V1 variant is robust. Combining longitudinal Ct data and sequencing data [19] could be a way to improve the resolution of the analyses. Another future extension of this approach will be to combine Ct data with serological data analyse the immune evasion properties of V2 and V3 variants [5, 6].
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04653844 Recruiting RT-PCR Database Analysis for COVID-19 Infections and Re-infe… 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.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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