Omicron (Purple) Now Dominant in US - Credit CDC
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It has been exactly 4 weeks since South Africa first alerted the world to a new COVID variant (see South African NICD Statement On B.1.1.529 Variant), which was quickly dubbed Omicron and classified as a VOC (Variant of Concern) by the WHO.
Since then, Omicron has demonstrated a remarkable transmissibility, and as become the dominant strain in the United States, and several European nations. On a more positive note, we've seen tantalizing reports - first out of South Africa, and now out of Europe - suggesting this variant may be less severe than Delta.
How much less severe is still up for debate, and if sufficient numbers of people are infected - even by a much milder virus than Delta - that could still produce a large number of hospitalizations and deaths. But any attenuation of its severity is welcome news.
And while Omicron might be the last act in COVID's pandemic play - leaving us with an endemic but less pathogenic virus in place - there are no guarantees that another, more problematic variant won't emerge.
Regardless, we still have the next few months to get through, which many experts still believe will be challenging, even if the virus is milder. We are apt to see the biggest surge of infections to date, with some projections (see IHME Forecast below) suggesting a doubling of infections over the next few months:
- Infections are predicted to increase: we will see about as many infections in the next 2-3 months as we have in the entire pandemic thus far.
- Fewer infections are likely to be detected: as a larger fraction of cases will be asymptomatic (about 90% as opposed to 40% of previous variants), fewer people will seek out testing and thus will not have their infections recorded.
- Overall hospitalizations and deaths will be lower than previous surges: the infection-hospitalization and infection-fatality rates of omicron are much lower than other variants like delta.
Yesterday, South Africa's NICD released their own (preprint) preliminary assessment on the clinical severity of Omicron, which suggests a 70% reduction in hospitalization over Omicron. They caution this may be due, in part, to high population immunity.
Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa
Nicole Wolter, Waasila Jassat, Sibongile Walaza, Richard Welch, Harry Moultrie, Michelle Groome, Daniel Gyamfi Amoako, Josie Everatt, Jinal N. Bhiman, Cathrine Scheepers, Naume Tebeila, Nicola Chiwandire, Mignon du Plessis, Nevashan Govender, Arshad Ismail, Allison Glass, Koleka Mlisana, Wendy Stevens, Florette K. Treurnicht, Zinhle Makatini, Nei-yuan Hsiao, Raveen Parboosing, Jeannette Wadula, Hannah Hussey, Mary-Ann Davies, Andrew Boulle, Anne von Gottberg, Cheryl Cohen
doi: https://doi.org/10.1101/2021.12.21.21268116
ABSTRACT
Background The SARS-CoV-2 Omicron variant of concern (VOC) almost completely replaced other variants in South Africa during November 2021, and was associated with a rapid increase in COVID-19 cases. We aimed to assess clinical severity of individuals infected with Omicron, using S Gene Target Failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy.
Methods We performed data linkages for (i) SARS-CoV-2 laboratory tests, (ii) COVID-19 case data, (iii) genome data, and (iv) the DATCOV national hospital surveillance system for the whole of South Africa. For cases identified using Thermo Fisher TaqPath COVID-19 PCR, infections were designated as SGTF or non-SGTF. Disease severity was assessed using multivariable logistic regression models comparing SGTF-infected individuals diagnosed between 1 October to 30 November to (i) non-SGTF in the same period, and (ii) Delta infections diagnosed between April and November 2021.
Results From 1 October through 6 December 2021, 161,328 COVID-19 cases were reported nationally; 38,282 were tested using TaqPath PCR and 29,721 SGTF infections were identified. The proportion of SGTF infections increased from 3% in early October (week 39) to 98% in early December (week 48). On multivariable analysis, after controlling for factors associated with hospitalisation, individuals with SGTF infection had lower odds of being admitted to hospital compared to non-SGTF infections (adjusted odds ratio (aOR) 0.2, 95% confidence interval (CI) 0.1-0.3).
Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ between SGTF-infected individuals compared to non-SGTF individuals diagnosed during the same time period (aOR 0.7, 95% CI 0.3-1.4). Compared to earlier Delta infections, after controlling for factors associated with severe disease, SGTF-infected individuals had a lower odds of severe disease (aOR 0.3, 95% CI 0.2-0.5).
Conclusion Early analyses suggest a reduced risk of hospitalisation among SGTF-infected individuals when compared to non-SGTF infected individuals in the same time period. Once hospitalised, risk of severe disease was similar for SGTF- and non-SGTF infected individuals, while SGTF-infected individuals had a reduced risk of severe disease when compared to earlier Delta-infected individuals. Some of this reduction is likely a result of high population immunity.
Report 50 - Hospitalisation risk for Omicron cases in England
Date: 22 December 2021
Authors: Neil Ferguson1, Azra Ghani, Wes Hinsley and Erik Volz on behalf of the Imperial College COVID-19 response team
1Correspondence: Prof Neil Ferguson
WHO Collaborating Centre for Infectious Disease Modelling, MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London.
Summary
(Excerpt)
Overall, we find evidence of a reduction in the risk of hospitalisation for Omicron relative to Delta infections, averaging over all cases in the study period. The extent of reduction is sensitive to the inclusion criteria used for cases and hospitalisation, being in the range 20-25% when using any attendance at hospital as the endpoint, and 40-45% when using hospitalisation lasting 1 day or longer or hospitalisations with the ECDS discharge field recorded as “admitted” as the endpoint (Table 1). These reductions must be balanced against the larger risk of infection with Omicron, due to the reduction in protection provided by both vaccination and natural infection. A previous infection reduces the risk of any hospitalisation by approximately 50% (Table 2) and the risk of a hospital stay of 1+ days by 61% (95%CI:55-65%) (before adjustments for under ascertainment of reinfections).
High historical infection attack rates and observed reinfection rates with Omicron mean it is necessary to correct hazard ratio estimates to accurately quantify intrinsic differences in severity between Omicron and Delta and to assess the protection afforded by past infection. The resulting adjustments are moderate (typically less than an increase of 0.2 in the hazard ratio for Omicron vs Delta and a reduction of approximately 0.1 in the hazard ratio for reinfections vs primary infections) but significant for evaluating severity overall. Using a hospital stay of 1+ days as the endpoint, the adjusted estimate of the relative risk of reinfections versus primary cases is 0.31, a 69% reduction in hospitalisation risk (Table 2).
Edinburgh Research ExplorerCitation for published version: Sheikh, A, Kerr, S, Woolhouse, M, McMenamin, J & Robertson, C 2021
Professor Aziz Sheikh MD, Usher Institute, University of Edinburgh, Edinburgh, UK Dr Steven Kerr PhD, Usher Institute, University of Edinburgh, Edinburgh, UK Professor Mark Woolhouse PhD, Usher Institute, University of Edinburgh, Edinburgh, UK Dr Jim McMenamin MBChB, Public Health Scotland, Glasgow, UK Professor Chris Robertson PhD, Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK On behalf of the EAVE II Collaborators
Summary
Background Since its emergence in November 2021 in southern Africa, the SARS-CoV-2 Omicron variant of concern (VOC) has rapidly spread across the world. There remain many unanswered questions about Omicron – in particular, in relation to its severity and the extent to which existing vaccines are effective in preventing COVID-19.
Methods Using the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance of COVID19 (EAVE II) platform, which comprises of linked primary care, vaccination, reverse transcriptase polymerase chain reaction (RT-PCR), sequencing, hospitalisation and mortality data on 5.4 million (99% of the population), we undertook a cohort analysis with a nested test negative design incident case control study covering the period November 1 to December 19, 2021 to provide initial estimates of Omicron severity and vaccine effectiveness (VE) against symptomatic disease. We used S gene status as a surrogate for Delta and Omicron VOCs, with S gene positive status indicating Delta whereas S gene negative indicated Omicron. Cox proportional hazard models were used to estimate the risk of COVID-19 hospitalisation adjusted for age, sex, socioeconomic status, vaccination status and clinical risk factors. Generalised additive logistic regression modelling with spline terms for age and sex were used to estimate VE relative to ≥25 weeks post second vaccine dose.
Findings The first case of Omicron confirmed by viral sequencing was recorded in Scotland on November 23, 2021, By December 19, 2021, there were 23,840 S gene negative cases. These S gene negative cases were predominantly in the age group 20-39 (11,732; 49.2%). The proportion of S gene negative cases that were possible reinfections was more than 10 times that of S gene positive (7.6% versus 0.7%). There were 15 hospital admissions in those S gene negative giving an adjusted observed/expected ratio of 0.32 (95% CI 0.19, 0.52). The third/booster vaccine dose was associated with a 57% (95% CI 55, 60) reduction in the risk of symptomatic S gene negative symptomatic infection relative to ≥25 weeks post second dose.
Interpretation These early national data suggest that Omicron is associated with a two-thirds reduction in the risk of COVID-19 hospitalisation when compared to Delta. Whilst offering the greatest protection against Delta, the third/booster dose of vaccination offers substantial additional protection against the risk of symptomatic COVID-19 for Omicron when compared to ≥25 weeks post second vaccine dose.
While all three reports cite a significant reduction in the risk for hospitalization with Omicron, there remains a wide range of opinion on how much of a reduction. When combined with some of the more aggressive infection projections, we could still see society severely impacted by Omicron.
Omicron is also continually evolving, and may pick up additional mutations that could either lessen, or increase, its impact over time. Some regions of the world may be harder hit than others, particularly in places where vaccination rates are low.
Some people online are dismissing Omicron as nothing but a `bad cold'. And for some (hopefully large) number of lucky individuals, that is likely to be true. But not everyone will come away unscathed, and deaths and hospitalization will continue.
Add in the knock on effects hundreds of millions of `mostly mild' infections on the global workforce - impacting essential services, the supply chain, and healthcare delivery - and the next few months are unlikely to be a walk in the park.
Still, the news is far better than it might have been. And for now, we appear to have caught a break.
