REACT-1 round 8 interim report: SARS-CoV-2 prevalence during the initial stages of the third national lockdown in England
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Abstract
Background
High prevalence of SARS-CoV-2 virus in many northern hemisphere populations is causing extreme pressure on healthcare services and leading to high numbers of fatalities. Even though safe and effective vaccines are being deployed in many populations, the majority of those most at-risk of severe COVID-19 will not be protected until late spring, even in countries already at a more advanced stage of vaccine deployment.
Methods
The REal-time Assessment of Community Transmission study-1 (REACT-1) obtains throat and nose swabs from between 120,000 and 180,000 people in the community in England at approximately monthly intervals. Round 8a of REACT-1 mainly covers a period from 6th January 2021 to 15th January 2021. Swabs are tested for SARS-CoV-2 virus and patterns of swab-positivity are described over time, space and with respect to individual characteristics. We compare swab-positivity prevalence from REACT-1 with mobility data based on the GPS locations of individuals using the Facebook mobile phone app. We also compare results from round 8a with those from round 7 in which swabs were collected from 13th November to 24th November (round 7a) and 25th November to 3rd December 2020 (round 7b).
Results
In round 8a, we found 1,962 positives from 142,909 swabs giving a weighted prevalence of 1.58% (95% CI, 1.49%, 1.68%). Using a constant growth model, we found no strong evidence for either growth or decay averaged across the period; rather, based on data from a limited number of days, prevalence may have started to rise at the end of round 8a. Facebook mobility data showed a marked decrease in activity at the end of December 2020, followed by a rise at the start of the working year in January 2021. Between round 7b and round 8a, prevalence increased in all adult age groups, more than doubling to 0.94% (0.83%, 1.07%) in those aged 65 and over. Large household size, living in a deprived neighbourhood, and Black and Asian ethnicity were all associated with increased prevalence. Both healthcare and care home workers, and other key workers, had increased odds of swab-positivity compared to other workers.
Conclusion
During the initial 10 days of the third COVID-19 lockdown in England in January 2021, prevalence of SARS-CoV-2 was very high with no evidence of decline. Until prevalence in the community is reduced substantially, health services will remain under extreme pressure and the cumulative number of lives lost during this pandemic will continue to increase rapidly.
Article activity feed
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SciScore for 10.1101/2021.01.20.21250158: (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:A key limitation in our analysis is that the trends showing a plateau or upturn in prevalence are based on data for a small number of days. However, regional prevalence trends also support there being a plateau and possible upturn (Figure 3): seven of the nine regions exhibited this pattern, while in one region (South West) there was a sharp decline. Also, the trend we report could be biased by short-term changes in testing behaviour …
SciScore for 10.1101/2021.01.20.21250158: (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:A key limitation in our analysis is that the trends showing a plateau or upturn in prevalence are based on data for a small number of days. However, regional prevalence trends also support there being a plateau and possible upturn (Figure 3): seven of the nine regions exhibited this pattern, while in one region (South West) there was a sharp decline. Also, the trend we report could be biased by short-term changes in testing behaviour among symptomatic individuals as they return to work. However, we obtain similar results for the constant growth model when fitting only to swab-positivity among non-symptomatic individuals (Table 2). In the period prior to the widespread acquisition of vaccine-acquired immunity, high constant or increasing prevalence -- with high rates in at-risk age groups -- has clear downstream implications for healthcare utilization and deaths. A daily average of 950 deaths were reported in England for the seven days prior to 8th January 2021 in people who had tested positive for SARS-CoV-2 in the previous 28 days [8]. Also on 8th of January, there were 29,346 COVID-19 inpatients in English hospitals, 55% more than the maximum during the first wave [8]. If the prevalence of infections in the community does not drop substantially in the immediate future, these levels of hospitalization will lead to very high numbers of additional deaths and potentially long-term negative impact on healthcare delivery in England.
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.
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