behaviour booster vaccines and waning vaccine protection modelling the medium term CORD-Papers-2022-06-02 (Version 1)

Title: Behaviour booster vaccines and waning vaccine protection: modelling the medium-term dynamics of SARS-CoV-2 transmission in England
Abstract: England has experienced a heavy burden of COVID-19 with high infection levels observed throughout the summer months of 2021. Alongside the emergence of evidence suggesting that COVID-19 vaccine protection wanes over time booster vaccinations began for individuals aged 50 and above in September 2021. Using a model fitted to 18 months of epidemiological data we project potential dynamics of SARS-CoV-2 transmission in England to September 2022. We consider key uncertainties including behavioural change waning vaccine protection strategies for vaccination and the reintroduction of public health and social measures. We project the current wave of transmission will peak in Autumn 2021 with low levels of transmission in early 2022. The extent to which SARS-CoV-2 transmission resurges in 2022 depends largely on assumptions around waning vaccine protection and booster vaccinations. Widespread booster vaccinations or the reimposition of mild public health and social measures such as work-from-home policies could largely mitigate the wave of COVID-19 transmission projected to occur in England in Spring/Summer 2022.
Published: 2021-11-24
Journal: medRxiv
DOI: 10.1101/2021.11.22.21266584
DOI_URL: http://doi.org/10.1101/2021.11.22.21266584
Author Name: Barnard Rosanna C
Author link: https://covid19-data.nist.gov/pid/rest/local/author/barnard_rosanna_c
Author Name: Davies Nicholas G
Author link: https://covid19-data.nist.gov/pid/rest/local/author/davies_nicholas_g
Author Name: Jit Mark
Author link: https://covid19-data.nist.gov/pid/rest/local/author/jit_mark
Author Name: Edmunds W John
Author link: https://covid19-data.nist.gov/pid/rest/local/author/edmunds_w_john
sha: 97003f86cc7f1feccbbe8ebaafadd1210204831c
license: cc-by-nc-nd
license_url: https://creativecommons.org/licenses/by-nc-nd/4.0/
source_x: MedRxiv; Medline; PMC
source_x_url: https://www.medline.com/https://www.ncbi.nlm.nih.gov/pubmed/
pubmed_id: 34845459
pubmed_id_url: https://www.ncbi.nlm.nih.gov/pubmed/34845459
pmcid: PMC8629203
pmcid_url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8629203
url: http://medrxiv.org/cgi/content/short/2021.11.22.21266584v1?rss=1 https://www.ncbi.nlm.nih.gov/pubmed/34845459/ https://doi.org/10.1101/2021.11.22.21266584
has_full_text: TRUE
Keywords Extracted from Text Content: SARS-CoV-2 medRxiv preprint Figure 2 COVID-19 COVID-19 vaccine lockdown NHS COVID-19 vaccine lines COVID-19 dashboard 2 Office Vaccines First-dose UK Government COVID-19 Dashboard 2 SD/SD Alpha COVID-19 CO-CIN ICR UK Government's COVID-19 dashboard 2 first-dose Bangladesh 35 nCoV-19 vaccine AZD1222 medRxiv preprint Alpha Pillar 2 lockdowns Figure S2 AstraZeneca S5B REACT-2 12-19 adolescents UKHSA medRxiv preprint Figure S5 UK Biobank 20 patient Figure S9 BNT162b2 COVID-19 vaccines 6 vaccine lockdown pre-Alpha Delta B.1.617.2 B.1.1.7 Alpha UK Biobank 36 B.1.617.2 Delta Fig. 4 individuals people Fig. S9 Table) . 8th over-50s second-dose medRxiv AZ Survey ( children https://doi.org/10.1101/2021.11.22.21266584 doi Face LD/SD second-dose vaccine VE SARS-CoV-2 Figures 4, UK Government's COVID-19 VOCs JCVI PHE Oxford-AstraZeneca S3 pre-Alpha B.1.1.7 auto.arima coronavirus 2 UK Health Security Agency Alpha B.1.1.7 S7, S8 COVID-19 vaccines Fig. 2 Delta basecase SARS-CoV-2 38 ISARIC S6 UK COVID-19 vaccinations grocery 12-15-year-olds ≥85 Alpha. S8 ONS-CIS Pfizer/Moderna PHSMs medRxiv preprint Fig. 3D, S5 DE-MCMC Pfizer-BioNTech resurgences S7 Figure S10 S5A IFR viral-vector'-vaccines UK's Medicines medRxiv preprint Figure S1 National Statistics COVID-19 ChAdOx1 (AstraZeneca Pfizer/BioNTech Vaccine 27.76 S-gene UK's Joint IFR/IHR/ICR Delta B.1.617.2 VOCs left Alpha to Delta solid lines NHS line
Extracted Text Content in Record: First 5000 Characters:England has experienced a heavy burden of COVID-19, with high infection levels observed throughout the summer months of 2021. Alongside the emergence of evidence suggesting that COVID-19 vaccine protection wanes over time, booster vaccinations began for individuals aged 50 and above in September 2021. Using a model fitted to 18 months of epidemiological data, we project potential dynamics of SARS-CoV-2 transmission in England to September 2022. We consider key uncertainties including behavioural change, waning vaccine protection, strategies for vaccination, and the reintroduction of public health and social measures. We project the current wave of transmission will peak in Autumn 2021, with low levels of transmission in early 2022. The extent to which SARS-CoV-2 transmission resurges in 2022 depends largely on assumptions around waning vaccine protection and booster vaccinations. Widespread booster vaccinations or the reimposition of mild public health and social measures such as work-from-home policies could largely mitigate the wave of : medRxiv preprint Figure 2 . Mobility scenarios, transmission adjustments and overall transmission potential for the fitted model, shown from March 2020 to September 2022. Top: Historic Google Community Mobility data (grey) and assumed future mobility in England for no change (blue), a 3-month return to pre-pandemic baseline levels (red) and a 6-month return to pre-pandemic baseline levels (purple) scenarios used for model projections. Mobility indices are measured relative to baseline mobility levels recorded during early 2020, prior to the COVID-19 pandemic. The beginning of each lockdown and each roadmap Step is marked with a vertical dashed line and 'L' and 'S' labels, respectively. Middle: Fitted transmission adjustments by NHS England region and the average across regions (black), example projection for East of England (blue) and mean (black line) + interquartile range (red shaded) for projected transmission adjustments. Bottom: The "transmission potential" captures the overall impact of mobility and transmission adjustments on the time-varying potential for effective transmission, ignoring the impact of immunity and novel variants, though including the impact of school vacation periods. Eighteen months into the COVID-19 pandemic, 250 million confirmed cases and 5 million deaths have been attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide 1 . In England as of 17th November 2021, cumulative confirmed COVID-19 cases exceed 8 million, with more than 500,000 hospitalisations and 120,000 deaths within 28 days of a positive test being recorded, respectively 2 . Different variants of SARS-CoV-2 have emerged, with four (Alpha, Beta, Gamma and Delta) currently designated as variants of concern (VOC) associated with either increased transmissibility, severity, or changes in immunity by the World Health Organisation 3 . England saw the emergence and takeover of the Alpha B.1.1.7 variant in late 2020, which was subsequently overtaken by the Delta B.1.617.2 variant in Spring 2021. Various public health and social measures (PHSMs) have been implemented to suppress COVID-19 transmission in England, including national lockdowns, staged relaxations of lockdowns and tiered regional restrictions 4 , but all legal restrictions were completely lifted on 19th July 2021. Safe and effective COVID-19 vaccines have been developed at unprecedented speed, with four currently approved for use by the UK's Medicines and Healthcare products Regulatory Agency (MHRA). The COVID-19 vaccine rollout in England began on the 8th of December 2020 and to date more than 42 million people have received at least their first COVID-19 vaccine dose 2 . The initial rollout of vaccines followed guidance issued by the UK's Joint Committee on Vaccination and Immunisation (JCVI) 5 , with vaccine supply being targeted to health and social care workers and those in the highest risk categories first. Vaccines were then offered to sequentially younger age groups of adults (18 years and above). In August 2021, children aged 16 and 17 years old and clinically vulnerable children aged 12-15 were offered COVID-19 vaccines 6 . In September 2021, healthy 12-15-year-olds in England were offered their first COVID-19 vaccination, but to date, no such recommendation has been made for the second dose follow up 7 . A COVID-19 booster vaccination programme began on 24th September 2021, initially targeting the same priority groups that were first vaccinated. A full dose of the Pfizer/BioNTech or a half dose of the Moderna vaccine are recommended as a booster dose, regardless of what vaccine was received previously, to those at least 6 months after their primary course of vaccination. On 15th November 2021, the JCVI issued advice recommending that the widespread COVID-19 booster vaccination programme be extended to individuals aged 40-49 years 8 . In addition to a widespread booster vaccination programm
Keywords Extracted from PMC Text: Fig. S9 Table). REACT-2 study21 COVID-19 vaccine only7 PHSMs S8 S-gene Pfizer/BioNTech COVID-19 S6 algorithm28 people 18–29 " children Office Fig. 4 's auto.arima S7, S8 al.12 Bangladesh35 NHS UK Health Security Agency basecase France Fig. 2 Oxford-AstraZeneca patient's Survey (ONS-CIS)13,22 SARS-CoV-2 Alpha B.1.1.7 VOCs Pfizer/Moderna first-dose ICR left JCVI Face forecast30 COVID-19 vaccines resurgences UKHSA25 COVID-19 dashboard2 lockdown COVID-19 vaccinations first- individuals First-dose second-dose S5A JCVI guidance8 line England17 12–19 Fig. 3D, S5 epidemic15,16 UK countries32 UKHSA Delta B.1.617.2 VOCs ISARIC S5B Delta B.1.617.2 series"14 grocery CO-CIN IFR S3 Alpha Delta IFR/IHR/ICR pre-Alpha B.1.1.7 Oxford-AstraZeneca vaccine doses31 12–29 National Statistics COVID-19
Extracted PMC Text Content in Record: First 5000 Characters:Our compartmental model fits the observed dynamics of SARS-CoV-2 community transmission during the first, second and third waves of the COVID-19 epidemic in England between mid-February 2020 and October 2021 (Figs. 1 and S1), reproducing NHS England region-specific observed deaths, hospitalisations, hospital and ICU bed occupancy, PCR prevalence, and seropositivity. The model also captures the emergence and spread of the Alpha B.1.1.7 and Delta B.1.617.2 variants of concern in late 2020 and early 2021, fitting to the prevalence of S gene target failure (Fig. S2) and to the proportion of Delta sequenced cases (Fig. S3). Model estimates for increased transmissibility of Alpha relative to previously circulating SARS-CoV-2 variants and of Delta relative to Alpha are given in Table S1. To capture historic behavioural changes, the model uses Google Community Mobility indices over time to derive contact rates for each NHS England region modelled, based upon a measured relationship between Google Mobility indices and age-specific contact rates as measured by the CoMix study, and in combination with school attendance data and assumptions about school schedules (Fig. 2). The model also fits a time-varying "transmission adjustment" component for each NHS England region in order to capture additional variability in transmission that is not explained by the mobility data (see Methods). The fitted transmission adjustment can be seen in the middle row of Fig. 2; there are notable sharp peaks around Christmas 2020 and towards the end of Summer 2021, as well as a deep trough around the lockdown in early 2021. To project behavioural changes forwards from October 2021 to September 2022, we combine various assumptions on future mobility changes (Fig. 2) with simulated trajectories for future transmission adjustments based on the historic fitted transmission adjustment (full details are given in the Methods section). We present the majority of results here by plotting the median and interquantile ranges of a number of simulated future trajectories of SARS-CoV-2 transmission in England, but it is important to note that individual epidemic trajectories can fall outside of the model's projection intervals (Fig. 3A). Some individual epidemic trajectories are projected to result in rapid exponential rises in transmission with large peaks that may require PHSMs to be implemented in response. A comparison of the projected cumulative number of SARS-CoV-2 infections, hospital admissions and deaths between October 2021 and September 2022 across all the scenarios considered here is shown in Fig. 4, along with detailed results related to each type of uncertainty in the Supplementary material (Figs. S4–S9). Although this work investigates the consequences of behavioural change, booster vaccination policies and waning vaccine protection, it is important to note that PHSMs also have the ability to suppress projected rises in transmission (Figs. 3B, 4, S4). A complete list of scenarios considered and key assumptions for each scenario is given in the Supplementary material (Table S6). A key uncertainty is future behaviour and assumptions about future levels of mobility greatly influence the projected dynamics of SARS-CoV-2 transmission into 2022 (Figs. 3C, 4, S4). We consider three scenarios for future mobility (no change, a 3-month and a 6-month return to pre-pandemic baseline levels, shown in Fig. 2) to capture this uncertainty. All behavioural change scenarios considered project a peak in SARS-CoV-2 transmission in late 2021 followed by a decline to very low levels of transmission in early 2022 (Fig. S4). This is due to depletion of susceptible individuals due to a high force of infection in England during Autumn 2021. The scenario assuming no change in mobility projects that transmission remains at low levels through most of 2022, with early increases being projected by September 2022. The largest difference in projected outcomes lies between the no change and return to baseline scenarios (Figs. 3C, 4, S4). However, the timing and speed of the return to baseline levels of mobility is important; a 3-month return to baseline mobility results in transmission rising sooner in 2022 and remaining flatter through the projected time horizon, whereas a 6-month return to baseline mobility levels leads to a later rise in transmission but a higher peaking epidemic (Figs. 3C, S4). Over shorter timescales, a more gradual return to baseline mobility decreases the total number of infections, hospital admissions, and deaths, but over long timescales there is less of a difference between different rates of returning to baseline (Fig. S4 tables). Both of the return to baseline mobility scenarios result in very similar cumulative numbers of SARS-CoV-2 infections, hospital admissions and deaths by the end of September 2022 (Figs. 3C, 4, S4). These differences can be explained by interactions between waning, seasonality, and mobility rates. Other influential fac
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