Quantifying the effect of delaying the second COVID-19 vaccine dose in England: a mathematical modelling study

The impact of Covid-19 vaccination in Aotearoa New Zealand: A modelling study

Aotearoa New Zealand implemented a Covid-19 elimination strategy in 2020 and 2021, which enabled a large majority of the population to be vaccinated before being exposed to the virus. This strategy delivered one of the lowest pandemic mortality rates in the world. However, quantitative estimates of the population-level health benefits of vaccination are lacking. Here, we use a validated mathematical model of Covid-19 in New Zealand to investigate counterfactual scenarios with differing levels of vaccine coverage in different age and ethnicity groups. The model builds on earlier research by adding age- and time-dependent case ascertainment, the effect of antiviral medications, improved hospitalisation rate estimates, and the impact of relaxing control measures. The model was used for scenario analysis and policy advice for the New Zealand Government in 2022 and 2023. We compare the number of Covid-19 hospitalisations, deaths, and years of life lost in each counterfactual scenario to a baseline scenario that is fitted to epidemiological data between January 2022 and June 2023. Our results estimate that vaccines saved 6650 (95% credible interval [4424, 10180]) lives, and prevented 74500 [51000, 115400] years of life lost and 45100 [34400, 55600] hospitalisations during this 18-month period. Making the same comparison before the benefit of antiviral medications is accounted for, the estimated number of lives saved by vaccines increases to 7604 [5080, 11942]. Due to inequities in the vaccine rollout, vaccination rates among Māori were lower than in people of European ethnicity. Our results show that, if vaccination rates had been equitable, an estimated 11%-26% of the 292 Māori Covid-19 deaths that were recorded in this time period could have been prevented. We conclude that Covid-19 vaccination greatly reduced health burden in New Zealand and that equity needs to be a key focus of future vaccination programmes.

Covid19Vaxplorer: A free, online, user-friendly COVID-19 vaccine allocation comparison tool

There are many COVID-19 vaccines currently available, however, Low- and middle-income countries (LMIC) still have large proportions of their populations unvaccinated. Decision-makers must decide how to effectively allocate available vaccines (e.g. boosters or primary series vaccination, which age groups to target) but LMIC often lack the resources to undergo quantitative analyses of vaccine allocation, resulting in ad-hoc policies. We developed Covid19Vaxplorer (https://covid19vaxplorer.fredhutch.org/), a free, user-friendly online tool that simulates region-specific COVID-19 epidemics in conjunction with vaccination with the purpose of providing public health officials worldwide with a tool for vaccine allocation planning and comparison. We developed an age-structured mathematical model of SARS-CoV-2 transmission and COVID-19 vaccination. The model considers vaccination with up to three different vaccine products, primary series and boosters. We simulated partial immunity derived from waning of natural infection and vaccination. The model is embedded in an online tool, Covid19Vaxplorer that was optimized for its ease of use. By prompting users to fill information through several windows to input local parameters (e.g. cumulative and current prevalence), epidemiological parameters (e.g basic reproduction number, current social distancing interventions), vaccine parameters (e.g. vaccine efficacy, duration of immunity) and vaccine allocation (both by age groups and by vaccination status). Covid19Vaxplorer connects the user to the mathematical model and simulates, in real time, region-specific epidemics. The tool then produces key outcomes including expected numbers of deaths, hospitalizations and cases, with the possibility of simulating several scenarios of vaccine allocation at once for a side-by-side comparison. We provide two usage examples of Covid19Vaxplorer for vaccine allocation in Haiti and Afghanistan, which had as of Spring 2023, 2% and 33% of their populations vaccinated, and show that for these particular examples, using available vaccine as primary series vaccinations prevents more deaths than using them as boosters.

Using neural networks to calibrate agent based models enables improved regional evidence for vaccine strategy and policy

Distribution and administration strategy are critical to successful population immunization efforts. Agent-based modeling (ABM) can reflect the complexity of real-world populations and can experimentally evaluate vaccine strategy and policy. However, ABMs historically have been limited in their time-to-development, long runtime, and difficulty calibrating. Our team had several technical advances in the development of our GradABMs: a novel class of scalable, fast and differentiable simulations. GradABMs can simulate million-size populations in a few seconds on commodity hardware, integrate with deep neural networks and ingest heterogeneous sources. This allows for rapid and real-world sensitivity analyses. Our first epidemiological GradABM (EpiABMv1) enabled simulation interventions over real million-scale populations and was used in vaccine strategy and policy during the COVID-19 pandemic. Literature suggests decisions aided by evidence from these models saved thousands of lives. Our most recent model (EpiABMv2) extends EpiABMv1 to allow improved regional calibration using deep neural networks to incorporate local population data, and in some cases different policy recommendations versus our prior models. This is an important advance for our model to be more effective at vaccine strategy and policy decisions at the local public health level.

Covid19Vaxplorer: a free, online, user-friendly COVID-19 Vaccine Allocation Comparison Tool

Background

There are many COVID-19 vaccines currently available, however, Low- and middle-income countries (LMIC) still have large proportions of their populations unvaccinated. Decision-makers must decide how to effectively allocate available vaccines (e.g. boosters or primary series vaccination, which age groups to target) but LMIC often lack the resources to undergo quantitative analyses of vaccine allocation, resulting in ad-hoc policies. We developed Covid19Vaxplorer (https://covid19vaxplorer.fredhutch.org/), a free, user-friendly online tool that simulates region-specific COVID-19 epidemics in conjunction with vaccination with the purpose of providing public health officials worldwide with a tool for vaccine allocation planning and comparison.

Methods

We developed an age-structured mathematical model of SARS-CoV-2 transmission and COVID-19 vaccination. The model considers vaccination with up to three different vaccine products, primary series and boosters. We simulated partial immunity derived from waning of natural infection and vaccination. The model is embedded in an online tool, Covid19Vaxplorer that was optimized for its ease of use. By prompting users to fill information through several windows to input local parameters (e.g. cumulative and current prevalence), epidemiological parameters (e.g basic reproduction number, current social distancing interventions), vaccine parameters (e.g. vaccine efficacy, duration of immunity) and vaccine allocation (both by age groups and by vaccination status). Covid19Vaxplorer connects the user to the mathematical model and simulates, in real time, region-specific epidemics. The tool then produces key outcomes including expected numbers of deaths, hospitalizations and cases, with the possibility of simulating several scenarios of vaccine allocation at once for a side-by-side comparison.

Results

We provide two usage examples of Covid19Vaxplorer for vaccine allocation in Haiti and Afghanistan, which had as of Spring 2023 2% and 33% of their populations vaccinated, and show that for these particular examples, using available vaccine as primary series vaccinations prevents more deaths than using them as boosters. Covid19Vaxplorer allows users in 183 regions in the world to compare several vaccination strategies simultaneously, adjusting parameters to their local epidemics, infrastructure and logistics. Covid19Vaxplorer is an online, free, user-friendly tool that facilitates evidence-based decision making for vaccine distribution.

Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England

As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model and Bayesian inference framework to analyse epidemiological surveillance data from England. We quantified the impact of non-pharmaceutical interventions (NPIs), therapeutics, and vaccination on virus transmission and severity. Each successive variant had a higher intrinsic transmissibility. Omicron (BA.1) had the highest basic reproduction number at 8.3 (95% credible interval (CrI) 7.7-8.8). Varying levels of NPIs were crucial in controlling virus transmission until population immunity accumulated. Immune escape properties of Omicron decreased effective levels of immunity in the population by a third. Furthermore, in contrast to previous studies, we found Alpha had the highest basic infection fatality ratio (2.9%, 95% CrI 2.7-3.2), followed by Delta (2.2%, 95% CrI 2.0-2.4), Wildtype (1.2%, 95% CrI 1.1-1.2), and Omicron (0.7%, 95% CrI 0.6-0.8). Our findings highlight the importance of continued surveillance. Long-term strategies for monitoring and maintaining effective immunity against SARS-CoV-2 are critical to inform the role of NPIs to effectively manage future variants with potentially higher intrinsic transmissibility and severe outcomes.

Evaluation of Waning of SARS-CoV-2 Vaccine-Induced Immunity: A Systematic Review and Meta-analysis

Importance

Estimates of the rate of waning of vaccine effectiveness (VE) against COVID-19 are key to assess population levels of protection and future needs for booster doses to face the resurgence of epidemic waves.

Objective

To quantify the progressive waning of VE associated with the Delta and Omicron variants of SARS-CoV-2 by number of received doses.

Data Sources

PubMed and Web of Science were searched from the databases' inception to October 19, 2022, as well as reference lists of eligible articles. Preprints were included.

Study Selection

Selected studies for this systematic review and meta-analysis were original articles reporting estimates of VE over time against laboratory-confirmed SARS-CoV-2 infection and symptomatic disease.

Data Extraction and Synthesis

Estimates of VE at different time points from vaccination were retrieved from original studies. A secondary data analysis was performed to project VE at any time from last dose administration, improving the comparability across different studies and between the 2 considered variants. Pooled estimates were obtained from random-effects meta-analysis.

Main Outcomes and Measures

Outcomes were VE against laboratory-confirmed Omicron or Delta infection and symptomatic disease and half-life and waning rate associated with vaccine-induced protection.

Results

A total of 799 original articles and 149 reviews published in peer-reviewed journals and 35 preprints were identified. Of these, 40 studies were included in the analysis. Pooled estimates of VE of a primary vaccination cycle against laboratory-confirmed Omicron infection and symptomatic disease were both lower than 20% at 6 months from last dose administration. Booster doses restored VE to levels comparable to those acquired soon after the administration of the primary cycle. However, 9 months after booster administration, VE against Omicron was lower than 30% against laboratory-confirmed infection and symptomatic disease. The half-life of VE against symptomatic infection was estimated to be 87 days (95% CI, 67-129 days) for Omicron compared with 316 days (95% CI, 240-470 days) for Delta. Similar waning rates of VE were found for different age segments of the population.

Conclusions and Relevance

These findings suggest that the effectiveness of COVID-19 vaccines against laboratory-confirmed Omicron or Delta infection and symptomatic disease rapidly wanes over time after the primary vaccination cycle and booster dose. These results can inform the design of appropriate targets and timing for future vaccination programs.