Reconstruction of a large-scale outbreak of SARS-CoV-2 infection in Iceland informs vaccination strategies

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1. Version published to 10.1016/j.cmi.2022.02.012

   Jun 1, 2022
2. 

   ScreenIT

   Jun 18, 2021

   SciScore for 10.1101/2021.06.11.21258741: (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

   Software and Algorithms
   Sentences	Resources
   Illumina sequencing was performed using MiSeq sequencers (MiSeq v2 reagent kits) with 2 x 150 cycle paired-end reads, with up to 48 multiplexed samples per run.	MiSeq suggested: (A5-miseq, RRID:SCR_012148)
   Samples for ONT were multiplexed using native barcodes and sequenced using either GridION or PromethION flowcells, version R.9.4.1.	PromethION suggested: (PromethION, RRID:SCR_017987)
   For Illumina sequences we used the latest Burrows– Wheeler Aligner (BWA-MEM) and variants were called with sequencing utilities bcftools21 as previously described2.	BWA-MEM suggested: (Sniffles, RRID:SCR_017619)

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   R…

   SciScore for 10.1101/2021.06.11.21258741: (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

   Software and Algorithms
   Sentences	Resources
   Illumina sequencing was performed using MiSeq sequencers (MiSeq v2 reagent kits) with 2 x 150 cycle paired-end reads, with up to 48 multiplexed samples per run.	MiSeq suggested: (A5-miseq, RRID:SCR_012148)
   Samples for ONT were multiplexed using native barcodes and sequenced using either GridION or PromethION flowcells, version R.9.4.1.	PromethION suggested: (PromethION, RRID:SCR_017987)
   For Illumina sequences we used the latest Burrows– Wheeler Aligner (BWA-MEM) and variants were called with sequencing utilities bcftools21 as previously described2.	BWA-MEM suggested: (Sniffles, RRID:SCR_017619)

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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:

   By reconstructing the third wave from real-world data we have circumvented these limitations by removing the behavioral modeling assumptions and simulating the vaccinations directly on the transmission tree. We found that vaccinating persons in ascending order of age or uniformly at random would have prevented more transmissions per vaccination than vaccinating in descending order of age, in the third wave of SARS-CoV-2 infections in Iceland. Vaccine efficacy is different for different vaccines. Our estimates of the final size of the third wave are sensitive to the assumed vaccine efficacy. However, the relative difference between the modeled vaccination strategies is independent of the efficacy. Furthermore, recent studies suggest that vaccinated persons who become infected have a lower viral load19 and may therefore be less likely to infect others. This is not taken into account in the model presented here. It is important to note that vaccination of a population serves two distinct purposes: firstly, to prevent death and severe illness in groups at high risk, and secondly to curb the spread of the virus in the population. Our results could inform the strategy for vaccinating the remaining adult population once the high-risk groups have been vaccinated. However, while our results for the third wave indicate that vaccinating in ascending order of age would have curtailed the outbreak sooner, this reflects the age composition of this particular outbreak. Vaccinating the remai...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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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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3. 

   Version published to 10.1101/2021.06.11.21258741v1 on medRxiv

   Jun 16, 2021