Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England
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Abstract
Rapid transmission of the SARS-CoV-2 Omicron variant has led to record-breaking case incidence rates around the world. Since May 2020, the REal-time Assessment of Community Transmission-1 (REACT-1) study tracked the spread of SARS-CoV-2 infection in England through RT-PCR of self-administered throat and nose swabs from randomly-selected participants aged 5 years and over. In January 2022, we found an overall weighted prevalence of 4.41% (n = 102,174), three-fold higher than in November to December 2021; we sequenced 2,374 (99.2%) Omicron infections (19 BA.2), and only 19 (0.79%) Delta, with a growth rate advantage for BA.2 compared to BA.1 or BA.1.1. Prevalence was decreasing overall (reproduction number R = 0.95, 95% credible interval [CrI], 0.93, 0.97), but increasing in children aged 5 to 17 years (R = 1.13, 95% CrI, 1.09, 1.18). In England during January 2022, we observed unprecedented levels of SARS-CoV-2 infection, especially among children, driven by almost complete replacement of Delta by Omicron.
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SciScore for 10.1101/2022.02.03.22270365: (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 limitations. In round 17, 12.2% of the invited participants returned swabs producing valid RT-PCR test results, which is similar to what was observed in round 16 (response rate 12.1%). We use weights, calculated for each participant in each round, to adjust for differential response rates in calculating prevalence estimates, but these corrections may not fully eliminate all biases. Our results on reported previous …
SciScore for 10.1101/2022.02.03.22270365: (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 limitations. In round 17, 12.2% of the invited participants returned swabs producing valid RT-PCR test results, which is similar to what was observed in round 16 (response rate 12.1%). We use weights, calculated for each participant in each round, to adjust for differential response rates in calculating prevalence estimates, but these corrections may not fully eliminate all biases. Our results on reported previous COVID-19 are based on self-reported data. While it is uncertain what proportion of these are reinfections or recent infections picked up due to the sensitivity of PCR testing, among the swab-positive participants reporting previous COVID-19, 64.4% reported a date of most recent positive test within 30 days prior to swabbing, most likely due to residual infection. On the other hand, it is likely that some previous infections were under-reported, especially those occurring in the first wave when routine PCR testing was not readily available. Changes in the way the swab samples were transported and tested may have introduced small changes in results across rounds, although these should not have affected within-round trends. In conclusion, we have documented a substantial and rapid rise in infections from early December 2021 through January 2022 as the Omicron variant took hold and almost completely replaced Delta in England. Although we have subsequently seen falls in prevalence in adults, prevalence remains very high. Among school-aged children there has...
Results from TrialIdentifier: No clinical trial numbers were referenced.
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).
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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