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Review 2: "Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 Variant Transition in the Swedish Population Reveals Higher Viral Quantity in BA.2 Cases"

In general, reviewers believe this preprint sets useful groundwork for future research, though somewhat lacking in explanation of the methods used to choose the analyzed sample and other details.

Published onMay 26, 2022
Review 2: "Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 Variant Transition in the Swedish Population Reveals Higher Viral Quantity in BA.2 Cases"

RR:C19 Evidence Scale rating by reviewer:

  • Reliable. The main study claims are generally justified by its methods and data. The results and conclusions are likely to be similar to the hypothetical ideal study. There are some minor caveats or limitations, but they would/do not change the major claims of the study. The study provides sufficient strength of evidence on its own that its main claims should be considered actionable, with some room for future revision.

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Review:

The authors present a research article entitled “Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 variant transition in the Swedish population reveals higher viral quantity in BA.2 cases”. In this study, authors introduced a modified version of the CDC SARS-CoV-2 RT-PCR assay capable of genotyping Omicron BA.1 cases and reported the remarkable drastic shift from Omicron BA.1 to BA.2 sub-variant among the Swedish population between January-March 2022. Overall, the observations showed that the custom variant-typing RT-PCR assay are satisfactory which will further inform tackling of the transmission of novel emerging variant of concerns in future.

Comments for the Authors

1. Authors should include a specific section to the manuscript that reflects on the limitation of this study and elaborate the “SARS-CoV-2 samples” in the method section by addressing details about the study design, study participants, patient sample collection and any other specific components.

2. Authors selected 698 samples from the SARS-CoV-2 positive specimens for whole genome sequencing and variant typing PCR. It is very important to mention the criteria of sample section (for example: Ct value and proper distribution of sample number covering each month and such details).

3. Author claimed here demonstrating how the omicron BA.1 wave was replaced by BA.2 and partial explanation of why Omicron BA.2 is more contagious than BA.1. But the explanation was not clearly understood from the result and discussion sections. These need to be improved to justify the major focus point of this study.

Overall the variant typing PCR introduced in this study is promising and could be used widely for rapid isolation of future outbreaks to minimize the global spread of SARS-CoV-2.

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