A tale of two variants: Spread of SARS-CoV-2 variants Alpha in Geneva, Switzerland, and Beta in South Africa
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Abstract
Several SARS-CoV-2 variants of concern (VOC) are spreading rapidly in different regions of the world. The underlying mechanisms behind their transmission advantage remain unclear. We measured viral load in 950 individuals and found that infections with variant Alpha exhibit a higher viral load and longer viral shedding compared to non-VOC. We then used a transmission model to analyze the spread of variant Alpha in Geneva, Switzerland, and variant Beta in South Africa. We estimated that Alpha is either associated with a 37% (95% compatibility interval, CI: 25–63%) increase in transmissibility or a 51% (95% CI: 32–80%) increase of the infectious duration, or a combination of the two mechanisms. Assuming 50% immune evasion for Beta, we estimated a 23% (95% CI: 10–37%) increase in transmissibility or a 38% (95% CI: 15–78%) increase of the infectious duration for this variant. Beta is expected to outgrow Alpha in regions where the level of naturally acquired immunity from previously circulating variants exceeds 20% to 40%. Close monitoring of Alpha and Beta in regions with different levels of immunity will help to anticipate the global spread of these and future variants.
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SciScore for 10.1101/2021.06.10.21258468: (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: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study has a number of limitations. First, we inferred specimens from Geneva, Switzerland, as being Alpha by using mutation specific RT-PCR only. However, NGS surveillance of circulating variants in Switzerland confirmed that presence of 501Y was closely correlated with Alpha. Second, we only included samples with a Ct value ≤ 32 to account for testing selection for mutation specific RT-PCR, so absolute viral loads could be biased …
SciScore for 10.1101/2021.06.10.21258468: (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: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study has a number of limitations. First, we inferred specimens from Geneva, Switzerland, as being Alpha by using mutation specific RT-PCR only. However, NGS surveillance of circulating variants in Switzerland confirmed that presence of 501Y was closely correlated with Alpha. Second, we only included samples with a Ct value ≤ 32 to account for testing selection for mutation specific RT-PCR, so absolute viral loads could be biased towards higher values. Third, the threshold for infectious virus (106 SARS-CoV-2 RNA copies/ml) was assessed for non-VOC at the beginning of the pandemic (Wölfel et al., 2020; L’Huillier et al., 2020). As no experimental data on this threshold have been published for Alpha, we assumed that Alpha shows a similar pattern for the presence of culturable virus compared to non-VOC. Fourth, the transmission model did not allow us to quantify the individual contribution of the different mechanisms to the transmission advantage. Fifth, we assumed an exponentially distributed generation time for estimating the increase in transmissibility. A delta distributed generation time would result in slightly higher estimates (Davies et al., 2021a; Volz et al., 2021; Chen et al., 2021). Sixth, estimates of the effective reproduction number based on confirmed cases come with considerable uncertainty. We took this uncertainty into account by sampling from daily estimates over a period of 2 to 3 months. Finally, we used seroprevalence estimates from single studies (Sou...
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.
- 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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