Study: Dynamics of Competing SARS-Cov-2 Variants During the Omicron Epidemic in England. Image Credit: Mayboon / Shutterstock.com

Additional SARS-CoV-2 variants and sporadic epidemics may become the ‘new normal’

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the coronavirus disease 2019 (COVID-19) pandemic, which has so far claimed more than 6.4 million deaths. Despite rigorous efforts to contain the transmission of the virus, SARS-CoV-2 spread rapidly and mutated several times. This led to the emergence of new variants of SARS-CoV-2 with higher transmissibility and immune evasion characteristics.

New The nature of communication journal study examines the dynamics of SARS-CoV-2 Omicron and other variants circulating in England since 23 November 2021, when Omicron was first detected.

Studies: Dynamics of competing SARS-Cov-2 variants during the Omicron epidemic in England. Image credit: Mayboon / Shutterstock.com

Introduction

The last SARS-CoV-2 variant (VOC) to be described is the Omicron variant (PANGO line B.1.1.529). This variant has many mutations in its spike protein, as well as in other viral proteins.

For example, the Omicron variant has 15 mutations in its receptor-binding domain (RBD), which binds to the host angiotensin-converting enzyme 2 (ACE2) receptor. These mutations change the sites where neutralizing antibodies bind to the RBD, which in turn allows Omicron to escape neutralization, even after vaccination or previous infection with older variants of SARS-CoV-2.

The result was an increasing number of reinfections and breakthrough infections. However, with the number of tests decreasing, coupled with the available test capacity currently at 100%, the true proportions of the Omicron wave remain unknown.

To overcome this problem, the current study used data from the Real-time Assessment of Community Transmission-1 (REACT-1), a cross-sectional test study conducted in England.

Study results

In the study samples, Omicron prevalence remained around 0.11% on 7 December 2022, which was about three weeks after the first confirmed case in England. At the same time, the Delta variant, which was the dominant circulating strain during the previous three months, had a prevalence of 1.3%.

Omicron strains appear to have been primarily imported or exported to the United States, Germany, and France.

About 50% of COVID-19 cases in England were due to Omicron by the end of next week. By December 23, 2021, 90% of cases were caused by Omicron.

By February 14, 2022, Omicron was responsible for nearly all cases. The last Delta-positive sample was also reported on this day.

Omikron cases increased by 0.2 per day from Nov 23, 2021 to Mar 1, 2022. On December 3, 2021, when the researchers of this study detected the first case of Omicron, the growth rate was 0.37. A little over a month later, it was only 0.1.

This may be due to the shorter production time for the Omicron, which is estimated to be 28% shorter than the Delta variant. A higher rate of spread of the virus among younger and less vaccinated age groups, who also mixed more in social circles, could also be a contributing factor.

By the end of 2021, about 7% of swabs were positive for Omicron; however, this prevalence decreased to less than 5% during January 2022. Later that month, the rate rose again to around 2.6% until early March 2022.

The reproduction number (Rt) was about two on 17 December 2022, which was two weeks after the onset of the Omicron wave in the UK. At this time, 90% of persons aged 12 years and older had been vaccinated with at least one dose of the COVID-19 vaccine, 82% with two doses, and 53% with three doses.

Rt subsequently declined as social interactions decreased. At the beginning of January 2022, Rt was under one.

At the end of January 2022, Rt increased to more than one and subsequently declined during February; however, it tended to rise during this month.

Despite significantly high levels of recent infections, the herd immunity threshold required to reduce prevalence has not yet been reached.”

In terms of the general population, the prevalence of Omicron increased across England to over 7% in North East England. However, its prevalence was less than 4% in East Anglia. London was associated with the oldest peak, which was probably because it was where the Omicron was first introduced.

Rt was highest for people aged five to 17 in January 2022. In other age groups, Rt quickly fell below one.

Omicron prevalence peaked in this group on January 28, 2022, at nearly 11%. This was compared to less than 8% on 1 January 2022 for people aged 18 to 34.

Individuals aged 55 years or older were associated with the lowest prevalence, consistent with their high vaccination coverage. Nevertheless, the Rt value in this group increased to 1.1 on March 1, 2022.

This demonstrates the limited effectiveness of the COVID-19 vaccine against Omicron infection.”

a Modeled prevalence of SARS-CoV-2 Omicron and Delta variants in England estimated using a Bayesian mixed-effects P-spline model.  Prevalence estimates are shown with central estimate (solid line) and 95% credible intervals (shaded area).  Daily weighted mean prevalence estimates (points) are shown with 95% confidence intervals (error bars).  b Modeled proportions of lineages identified as Omicron in England, estimated using Bayesian logistic regression (red) and Bayesian mixed-effects P-spline model (blue).  Estimates are shown with central estimate (solid line) and 95% confidence intervals (shaded area).  Daily estimates of the mean fraction of Omicron lines (points) are given with 95% confidence intervals (error bars).  c Daily growth rate of Omicron (purple), Delta (orange) and their additive difference (green) estimated from a Bayesian mixed-effects P-spline model.  Estimates are shown with central estimate (solid line) and 95% confidence intervals (shaded area).

AND Modeled prevalence of SARS-CoV-2 Omicron and Delta variants in England estimated using a Bayesian mixed-effects P-spline model. Prevalence estimates are shown with central estimate (solid line) and 95% credible intervals (shaded area). Daily weighted mean prevalence estimates (points) are shown with 95% confidence intervals (error bars). b Modeled proportions of lineages identified as Omicron in England, estimated using Bayesian logistic regression (red) and Bayesian mixed-effects P-spline model (blue). Estimates are shown with central estimate (solid line) and 95% confidence intervals (shaded area). Daily estimates of the mean fraction of Omicron lines (points) are given with 95% confidence intervals (error bars). C Daily growth rate of Omicron (purple), Delta (orange) and their additive difference (green) estimated from a mixed-effects Bayesian P-spline model. Estimates are shown with central estimate (solid line) and 95% confidence intervals (shaded area).

Competition for inferiority

Previous models have shown that the Omicron variants BA.1, BA.1.1 and BA.2 showed changing proportions during this period. Although BA.2 increased, the prevalence of BA.1 decreased.

At the peak of the Omicron wave on 30 December 2021, BA.1 accounted for 85% of cases compared to 15% and 0.2% for BA.1.1 and BA.2, respectively.

This trend reversed just two months later, with the prevalence of BA.1 falling to less than 10% of cases, while BA.1.1 and BA.2 increased to more than 20% and nearly 70%, respectively. These variants were responsible for the Omicron winter wave in England.

The daily growth rate of BA.2 and BA.1.1 was 0.133 and 0.42 times higher than BA.1, respectively, while BA.1 was 0.09 times higher than BA.1.1. Both variants are more portable than BA.1, with BA.2 spreading at the fastest rate of the three Omicron sub-variants.

BA.1.1 became dominant in some countries even before BA.1 was even established, indicating its superior fitness through a greater number of beneficial mutations.

The Rt for BA.2 was 1.17 compared to 0.77 for non-BA.2 Omicron variants on March 1, 2022. This supports the replicative suitability of BA.2.

BA.2 is also associated with the most specific symptoms of COVID-19, such as anosmia, ageusia, fever, and new prolonged cough in a higher proportion of patients compared to BA.1 infections.

Impacts

The current study used high-quality REACT-1 data to estimate the prevalence of Omicron infections. The researchers also describe the risk of exposure for Delta and Omicron infections, as well as for BA.1, BA.1.1, and BA.2 separately.

The dynamics of these different variants was reflected in their different rates of growth and prevalence over time, rather than treating them all as a single variant.

Further studies will need to investigate whether different lineages and sublineages have different cycle thresholds (Ct) for detection, which could change their observed prevalence. However, the study’s findings show that SARS-CoV-2 reaches a new level of fitness through the development of mutations that improve its immune evasion properties.

“Assuming the emergence of other different variants, occasional epidemics of a similar scale [as Omicron, which reached a record prevalence of 7% in England at one point] may become the “new normal”.”

Vaccine boosters and improvements to current COVID-19 vaccines to ensure immunity against these newer variants, as well as continuous surveillance, will be necessary to maintain public health.

Link to journal:

  • Eales, O., de Oliveira Martins, L., Page, AJ, et al. (2022). Dynamics of competing SARS-Cov-2 variants during the Omicron epidemic in England. Natural communication. doi:10.1038/s41467-022-32096-4.

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