Short-term Projections based on Early Omicron Variant Dynamics in England.

Throughout the ongoing COVID-19 pandemic, the worldwide transmission and replication of SARS-COV-2, the causative agent of COVID-19 disease, has resulted in the opportunity for multiple mutations to occur that may alter the virus transmission characteristics, the effectiveness of vaccines and the severity of disease upon infection. The Omicron variant (B.1.1.529) was first reported to the WHO by South Africa on 24 November 2021 and was declared a variant of concern by the WHO on 26 November 2021. The variant was first detected in the UK on 27 November 2021 and has since been reported in a number of countries globally where it is frequently associated with rapid increase in cases. Here we present analyses of UK data showing the earliest signatures of the Omicron variant and mathematical modelling that uses the UK data to simulate the potential impact of this variant in the UK. In order to account for the uncertainty in transmission advantage, vaccine escape and severity at the time of writing, we carry out a sensitivity analysis to assess the impact of these variant characteristics on future risk.

Vaccine breakthrough and the invasion dynamics of SARS-CoV-2 variants

Vaccination provides a powerful tool for mitigating and controlling the COVID-19 pandemic. However, a number of factors reduce these potential benefits. The first problem arises from heterogeneities in vaccine supply and uptake: from global inequities in vaccine distribution, to local variations in uptake derived from vaccine hesitancy. The second complexity is biological: though several COVID-19 vaccines offer substantial protection against infection and disease, breakthrough reinfection of vaccinees (and subsequent retransmission from these individuals) can occur, driven especially by new viral variants. Here, using a simple epidemiological model, we show that the combination of infection of remaining susceptible individuals and breakthrough infections of vaccinees can have significant effects in promoting infection of invading variants, even when vaccination rates are high and onward transmission from vaccinees relatively weak. Elaborations of the model show how heterogeneities in immunity and mixing between vaccinated and unvaccinated sub-populations modulate these effects, underlining the importance of quantifying these variables. Overall, our results indicate that high vaccination coverage still leaves no room for complacency if variants are circulating that can elude immunity, even if this happens at very low rates.

Vaccine escape in a heterogeneous population: insights for SARS-CoV-2 from a simple model

As a counter measure to the SARS-CoV-2 pandemic there has been swift development and clinical trial assessment of candidate vaccines, with subsequent deployment as part of mass vaccination campaigns. However, the SARS-CoV-2 virus has demonstrated the ability to mutate and develop variants, which can modify epidemiological properties and potentially also the effectiveness of vaccines. The widespread deployment of highly effective vaccines may rapidly exert selection pressure on the SARS-CoV-2 virus directed towards mutations that escape the vaccine induced immune response. This is particularly concerning whilst infection is widespread. By developing and analysing a mathematical model of two population groupings with differing vulnerability and contact rates, we explore the impact of the deployment of vaccine amongst the population on R, cases, disease abundance and vaccine escape pressure. The results from this model illustrate two insights (i) vaccination aimed at reducing prevalence could be more effective at reducing disease than directly vaccinating the vulnerable; (ii) the highest risk for vaccine escape can occur at intermediate levels of vaccination. This work demonstrates a key principle that the careful targeting of vaccines towards particular population groups could reduce disease as much as possible whilst limiting the risk of vaccine escape.