#16,427
Researchers at the MRC Centre for Global Infectious Disease Analysis at Imperial College London have released a new report on the rapidly emerging Omicron variant, and while hospitalization data is incomplete, it suggests - at best - only limited changes in its severity compared to Delta.With the caveats that these findings are preliminary - are not yet peer-reviewed - and are based largely on mathematical modeling, they also find that Omicron substantially (but not completely) evades immunity gained from past infection and/or two doses of the vaccine, and is spreading much faster than Delta.
Although none of this comes as a complete surprise, this is still sobering news. We may still get lucky on the relative severity of Omicron, but so far the evidence is either incomplete or mixed.
First, a press release from Imperial Collage, followed by a link to the study.
Modelling suggests rapid spread of Omicron in England but same severity as Delta
by Emily Head, Dr Sabine L. van Elsland
17 December 2021
Omicron largely evades immunity from past infection or two vaccine doses according to Imperial's latest report.
The new report from the Imperial College London COVID-19 response team estimates that the risk of reinfection with the Omicron variant is 5.4 times greater than that of the Delta variant. This implies that the protection against reinfection by Omicron afforded by past infection may be as low as 19%.
Researchers estimate the growth and immune escape of the Omicron variant in England. They used data from the UKHSA and NHS for all PCR-confirmed SARS-CoV-2 cases in England who had taken a COVID test between November 29th and December 11th 2021.
This level of immune evasion means that Omicron poses a major, imminent threat to public health - Prof Neil Ferguson
The study includes people identified as having Omicron infection due to an S gene target failure (SGTF), as well as people with genotype data that confirmed Omicron infection. Overall, 196,463 people without S gene target failure (likely to be infected with another variant) and 11,329 cases with it (likely to be infected with Omicron) were included in the SGTF analysis, as well as 122,063 Delta and 1,846 Omicron cases in the genotype analysis.
Growth of Omicron
Firstly, the report looks at factors associated with testing positive for Omicron compared to non-Omicron (mostly Delta) cases. The results suggest that the proportion of Omicron among all COVID cases was doubling every 2 days up to December 11th, estimated from both S-gene Target Failure and genotype data. Based on these results they estimate that the reproduction number (R) of Omicron was above 3 over the period studied.
The distribution of Omicron by age, region and ethnicity currently differs markedly from Delta, with 18–29-year-olds, residents in the London region, and those of African ethnicity having significantly higher rates of infection with Omicron relative to Delta. London is substantially ahead of other English regions in Omicron frequency.
Omicron transmission is not yet uniformly distributed across the population. However, the researchers note that given its immune evasion, the age distribution of Omicron infection in the coming weeks may continue to differ from that of Delta.
The study finds no evidence of Omicron having lower severity than Delta, judged by either the proportion of people testing positive who report symptoms, or by the proportion of cases seeking hospital care after infection. However, hospitalisation data remains very limited at this time.
Reinfection rates
To assess the impact of Omicron on reinfection rates the researchers used genotype data, since even prior to Omicron, reinfection was correlated with negative S gene Target Failure data, likely due to random PCR target failure caused by the lower viral loads associated with reinfections.
Controlling for vaccine status, age, sex, ethnicity, asymptomatic status, region and specimen date, Omicron was associated with a 5.40 (95% CI: 4.38-6.63) fold higher risk of reinfection compared with Delta. To put this into context, in the pre-Omicron era, the UK “SIREN” study of COVID infection in healthcare workers estimated that prior infection afforded 85% protection against a second COVID infection over 6 months. The reinfection risk estimated in the current study suggests this protection has fallen to 19% (95%CI: 0-27%) against an Omicron infection.
Vaccine effectiveness against Omicron
The researchers found a significantly increased risk of developing a symptomatic Omicron case compared to Delta for those who were two or more weeks past their second vaccine dose, and two or more weeks past their booster dose (for AstraZeneca and Pfizer vaccines).
Depending on the estimates used for vaccine effectiveness against symptomatic infection from the Delta variant, this translates into vaccine effectiveness estimates against symptomatic Omicron infection of between 0% and 20% after two doses, and between 55% and 80% after a booster dose. Similar estimates were obtained using genotype data, albeit with greater uncertainty.
Prof Neil Ferguson from Imperial College London said: “This study provides further evidence of the very substantial extent to which Omicron can evade prior immunity given by both infection or vaccination. This level of immune evasion means that Omicron poses a major, imminent threat to public health.”
Prof Azra Ghani from Imperial College London said: “Quantifying reinfection risk and vaccine effectiveness against Omicron is essential for modelling the likely future trajectory of the Omicron wave and the potential impact of vaccination and other public health interventions.”
The work, which is not yet peer-reviewed, is presented in the latest report from the WHO Collaborating Centre for Infectious Disease Modelling within the MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London.
Since the emergence of the new coronavirus (COVID-19) in December 2019, the Imperial College COVID-19 Response Team has adopted a policy of immediately sharing research findings on the developing pandemic.
The link and summary to the full reports can be found at:
Report 49 - Growth, population distribution and immune escape of Omicron in England
16 December 2021
Authors: Neil Ferguson1, Azra Ghani, Anne Cori, Alexandra Hogan, Wes Hinsley, Erik Volz on behalf of the Imperial College COVID-19 response team
1Correspondence:
WHO Collaborating Centre for Infectious Disease Modelling, MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London.
Summary
To estimate the growth of the Omicron variant of concern (1) and its immune escape (2–9) characteristics, we analysed data from all PCR-confirmed SARS-CoV-2 cases in England excluding those with a history of recent international travel. We undertook separate analyses according to two case definitions. For the first definition, we included all cases with a definitive negative S-gene Target Failure (SGTF) result and specimen dates between 29/11/2021 and 11/12/2021 inclusive. For the second definition, we included cases with a positive genotype result and specimen date between 23/11/2021 and 11/12/2021 inclusive. We chose a later start date for the SGTF definition to ensure greater specificity of SGTF for Omicron.
We used logistic and Poisson regression to identify factors associated with testing positive for Omicron compared to non-Omicron (mostly Delta) cases. We explored the following predictors: day, region, symptomatic status, sex, ethnicity, age band and vaccination status. Our results suggest rapid growth of the frequency of the Omicron variant relative to Delta, with the exponential growth rate of its frequency estimated to be 0.34/day (95% CI: 0.33-0.35) [2.0 day doubling time] over the study period from both SGTF and genotype data. The distribution of Omicron by age, region and ethnicity currently differs markedly from Delta, with 18–29-year-olds, residents in the London region, and those of African ethnicity having significantly higher rates of infection with Omicron relative to Delta.
Hospitalisation and asymptomatic infection indicators were not significantly associated with Omicron infection, suggesting at most limited changes in severity compared with Delta.
To estimate the impact of Omicron on vaccine effectiveness (VE) for symptomatic infection we used conditional Poisson regression to estimate the hazard ratio of being an Omicron case (using SGTF definition) compared with Delta, restricting our analysis to symptomatic cases and matching by day, region, 10-year age band, sex and ethnicity. We found a significant increased risk of an Omicron case compared to Delta for those with vaccine status AZ 2+weeks post-dose 2 (PD2) , Pfizer 2+w PD2, AZ 2+w post-dose 3 (PD3) and PF 2+w PD3 vaccine states with hazard ratios of 1.86 (95%CI: 1.67-2.08), 2.68 (95%CI: 2.54-2.83), 4.32 (95%CI: 3.84-4.85) and 4.07 (95%CI: 3.66-4.51), respectively, where PD3 states are categorised by the dose 1/2 vaccine used. Depending on the Delta VE estimates used (10), these estimates translate into Omicron VE estimates of between 0% and 20% PD2 and between 55% and 80% PD3 against Omicron, consistent with other estimates (11). Similar estimates were obtained using genotype data, albeit with greater uncertainty.To assess the impact of Omicron on reinfection rates we relied on genotype data, since SGTF is associated with a higher observed rate of reinfection, likely due to reinfections typically having higher Ct values than primary infections and therefore being subject to a higher rate of random PCR target failure. Controlling for vaccine status, age, sex, ethnicity, asymptomatic status, region and specimen date and using conditional Poisson regression to predict reinfection status, Omicron was associated with a 5.41 (95% CI: 4.87-6.00) fold higher risk of reinfection compared with Delta. This suggests relatively low remaining levels of immunity from prior infection.
