Understanding the immunological landscape of England during SARS-CoV2 Omicron variant wave
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Abstract
Understanding the scale of the threat posed by SARS-CoV2 B.1.1.529, or Omicron , variant formed a key problem in public health in the early part of 2022. Early evidence indicated that the variant was more transmissible and less severe than previous variants. As the virus was expected to spread quickly through the population of England, it was important that some understanding of the immunological landscape of the country was developed. This paper attempts to estimate the number of people with good immunity to the Omicron variant, defined as either recent infection with two doses of vaccine, or two doses of vaccine with a recent booster dose. To achieve this, we use a process of iterative proportional fitting to estimate the cell values of a contingency table, using national immunisation records and real-time model infection estimates as marginal values. Our results indicate that, despite the increased risk of immune evasion with the Omicron variant, a high proportion of England’s population had good immunity to the virus, particularly in older age groups. However, low rates of immunity in younger populations may allow endemic infection to persist for some time.
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SciScore for 10.1101/2022.02.21.22271270: (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:However, there are some limitations to the analysis which should be considered. The IPF analysis is a purely statistical method, with no mechanistic aspect. As such, the analysis does not account for the protection against disease afforded by vaccination. This means that prior infections are likely under-estimated in unvaccinated groups. …
SciScore for 10.1101/2022.02.21.22271270: (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:However, there are some limitations to the analysis which should be considered. The IPF analysis is a purely statistical method, with no mechanistic aspect. As such, the analysis does not account for the protection against disease afforded by vaccination. This means that prior infections are likely under-estimated in unvaccinated groups. This effect is mitigated somewhat by the analysis focussing mainly on broad groups of ‘good’ and ‘poor’ immunity, as unvaccinated individuals are considered as having poor immunity, regardless of prior infection status. The analysis does not consider time since vaccination as a factor influencing immunity. Once again this is mitigated by the broad characterisation of ‘good’ and ‘poor’ immunity, and the assumption that all third doses are immunologically recent. While a recent second dose of vaccine likely confers more immunity than a non-recent one, we consider both to provide ‘poor’ immunity to Omicron variant. Similarly, we assume that two doses of mRNA vaccine (Moderna or Pfizer) plus a booster dose offers a similar level of protection as two doses of Astra-Zeneca vaccine plus a booster dose of mRNA vaccine. The interpretation of this analysis is based on a number of assumptions on the level of immunity offered by vaccination status and prior infection. Further work is necessary to properly quantify this immunity, and more accurately estimate the level of protection present in the population. Similarly, it would be useful to consider immun...
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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