Baseline incidence of cough or fever in England. The first ten days of follow-up after each participant was recruited into the study were excluded to remove prevalent infection syndromes. For participants reporting cough or fever symptoms within these first ten days, follow-up was started on the first day after this period with no symptoms. Incident cough or fever were defined as i) when a participant reported cough or fever for the first time (one day of symptoms was recorded as a case); or ii) when either symptom was reported after a period of at least 10 days without symptoms. Non-specific symptoms could extend the duration of a cough or fever infection period. Public Health England reported that there were “low to moderate levels of influenza activity” in the 2018–2019 influenza season, which was comparable to the 2017–2018 season and higher than all other seasons since 2010–2011 10.

Monthly adjusted incidence rates per 100,000-person-week for cough or fever and confidence intervals were calculated for England, weighting to the mid-2019 population structure of England for age, sex and region 11 by post-stratification using a quasi-Poisson regression model (with the R ‘survey’ package version 4.0 12). Monthly age-specific incidence rates per 100,000-person-week for cough or fever in England were calculated, weighting by sex and region, and are included in Extended data, S2 9.

UK testing demand due to baseline cough and fever cases. Monthly all-age adjusted incidence rates of baseline (non-COVID-19) cough or fever were estimated for the UK, weighting to the mid-2019 population structure of the UK for age and sex 11. These rates were used to estimate the average number of individuals in the UK with an incident case of non-COVID-19 cough or fever each day for each month in the period July 2020 – June 2021.

Predictions for the daily testing demand expected in the UK between July 2020 and June 2021 due to baseline cough or fever cases were made based on our incidence estimates. We assumed that individuals only request a test on the first day that they experience symptoms. We explored a range of scenarios for the proportion of cough or fever cases that request a test (PROPTEST). Four values were explored: 40%, 60%, 80% and 100%. The predicted impact of baseline cough or fever cases on UK testing capacity was calculated as the difference between UK Pillar 1 and 2 laboratory testing capacity estimates from August 2020 and predicted testing demand between July 2020 and June 2021 based on these scenarios. Capacity estimates used in this analysis were reported by the UK government for the period 6–12th August 2020 as 1,459,418 tests per week for Pillars 1 and 2, and 880,000 tests per week for only Pillar 2 13.

Total UK testing demand including symptomatic COVID-19 cases. Four scenarios (C1–C4) for additional demand due to a second COVID-19 wave in the UK during winter 2020–2021 were explored. A range of average daily incidences for COVID-19 cases for each month between July 2020 and June 2021 were considered to reflect uncertainty about future COVID-19 transmission levels, from the lowest in scenario C1 to the highest incidences in scenario C4. We used an exponentially weighted multiplication factor with minimum values of 0.002, 0.004, 0.006 and 0.008 in August for scenarios C1–C4, respectively, increasing to peak values of 0.05, 0.10, 0.15 and 0.20 in January – March for these four scenarios. This multiplication factor was then multiplied by the estimated daily incidence of cough or fever in the UK for each month to provide hypothetical daily COVID-19 incidences for each month. An extended description of these methods can be found in Extended data, S3 9. These scenarios were selected to follow a similar epidemic curve shape to predictions reported in the Academy of Medical Sciences’ report “Preparing for a Challenging Winter 2020/21” 14, with the highest incidences in January and February 2021 and the peak incidence in our worst-case scenario (C4) equal to the peak incidence predicted in the report for a reproductive number R t=1.5 between September 2020 to July 2021. Based on estimates from the COVID Symptom Study app, 87.5% of these cases of COVID-19 were assumed to exhibit symptoms of cough, fever or loss of smell or taste 15 with the proportion of these symptomatic cases expected to request tests explored using the PROPTEST parameter. Total demand for swab tests due to baseline cough and fever cases and COVID-19 illnesses was calculated as:

The total predicted testing demand in each month was then calculated for each COVID-19 scenario (C1–C4).

Total UK testing demand in a low cough or fever incidence scenario. Estimated total UK testing demand was adjusted to explore the impact of a reduced incidence of baseline cough or fever cases relative to previous years due to social distancing and other COVID-19 public health interventions. Estimates of the relative reduction in monthly baseline cough or fever incidence for July – November 2020 compared to the corresponding months in the 2018–2019 Bug Watch cohort were available from the preliminary results of the ongoing Virus Watch cohort study (see www.ucl-virus-watch.net for more information about the study) in England (unpublished report, author: Robert Aldridge). These found that the median reduction in non-COVID-19 cough or fever incidence in these months relative to the Bug Watch baseline was 73% (range 34% – 81%). This was used to recalculate estimates of the total UK testing demand for each month assuming a 73% lower incidence of cough or fever relative to our historical baseline for each month.

All analyses were conducted using R version 3.6.3 16 using the R ‘ tidyverse’ packages version 1.3.0 17.

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.