Increased risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variant compared to Alpha variant in vaccinated individuals

SciScore for 10.1101/2021.11.24.21266735: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Ethics	not detected.
Sex as a biological variable	not detected.
Randomization	SARS-CoV-2 molecular surveillance program sequences whole virus genomes of randomly selected SARS-CoV-2 positive specimens from both community testing (via PHS) and hospitals, using a proper nationwide geographical distribution.
Blinding	not detected.
Power Analysis	not detected.

Table 2: Resources

Software and Algorithms
Sentences	Resources
GridION data was analyzed to get consensus genomes, with the SARS2seq pipeline and additional manual curation24.	SARS2seq suggested: None

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Results from OddPub: Thank you for sharing your code and data.

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Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

Some limitations of our study need to be addressed. Asymptomatic or mild cases with low viral load are less likely to be identified and only detectable infections can be sequenced and included. In addition, sequencing is more successful in samples with low to medium Ct values (high to medium viral load). If infection with Beta, Gamma or Delta leads to lower Ct values than Alpha and Ct values are higher for infections after vaccination30–32, this could have led to an overestimation of the studied association. Another limitation is that prior infections could go undetected, especially if occurred during the first wave when there was no mass scale testing capacity. This could lead to an underestimation of cases with a previous infection, as we do not directly measure pre-existing infection-induced immunity. In conclusion, our results confirm a lower vaccine effectiveness against infection for the Delta variant, and similarly the Beta and Gamma variant, compared to Alpha. This effect was largest early after complete vaccination. These findings are informative for considerations on vaccine updates, future vaccination and pandemic control strategies.

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Results from TrialIdentifier: No clinical trial numbers were referenced.

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Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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Results from JetFighter: We did not find any issues relating to colormaps.

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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.

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Results from scite Reference Check: We found no unreliable references.

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