An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients

Abstract

Background:Whilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings.Methods:Here, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries.Results:Our analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61–0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population.Conclusions:Although clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome.Funding:Bronner P. Gonçalves, Peter Horby, Gail Carson, Piero L. Olliaro, Valeria Balan, Barbara Wanjiru Citarella, and research costs were supported by the UK Foreign, Commonwealth and Development Office (FCDO) and Wellcome [215091/Z/18/Z, 222410/Z/21/Z, 225288/Z/22/Z]; and Janice Caoili and Madiha Hashmi were supported by the UK FCDO and Wellcome [222048/Z/20/Z]. Peter Horby, Gail Carson, Piero L. Olliaro, Kalynn Kennon and Joaquin Baruch were supported by the Bill & Melinda Gates Foundation [OPP1209135]; Laura Merson was supported by University of Oxford’s COVID-19 Research Response Fund - with thanks to its donors for their philanthropic support. Matthew Hall was supported by a Li Ka Shing Foundation award to Christophe Fraser. Moritz U.G. Kraemer was supported by the Branco Weiss Fellowship, Google.org, the Oxford Martin School, the Rockefeller Foundation, and the European Union Horizon 2020 project MOOD (#874850). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Contributions from Srinivas Murthy, Asgar Rishu, Rob Fowler, James Joshua Douglas, François Martin Carrier were supported by CIHR Coronavirus Rapid Research Funding Opportunity OV2170359 and coordinated out of Sunnybrook Research Institute. Contributions from Evert-Jan Wils and David S.Y. Ong were supported by a grant from foundation Bevordering Onderzoek Franciscus; and Andrea Angheben by the Italian Ministry of Health “Fondi Ricerca corrente–L1P6” to IRCCS Ospedale Sacro Cuore–Don Calabria. The data contributions of J.Kenneth Baillie, Malcolm G. Semple, and Ewen M. Harrison were supported by grants from the National Institute for Health Research (NIHR; award CO-CIN-01), the Medical Research Council (MRC; grant MC_PC_19059), and by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with Public Health England (PHE) (award 200907), NIHR HPRU in Respiratory Infections at Imperial College London with PHE (award 200927), Liverpool Experimental Cancer Medicine Centre (grant C18616/A25153), NIHR Biomedical Research Centre at Imperial College London (award IS-BRC-1215-20013), and NIHR Clinical Research Network providing infrastructure support. All funders of the ISARIC Clinical Characterisation Group are listed in the appendix.

Lethality of SARS‐CoV‐2 infection—a comparative autopsy study focusing on COVID‐19 development and virus variants

“…in any of the omicron cases of our cohort 16 . Our observations are in concordance with clinical data associating an omicron infection with a milder disease course and low lethality 12,17,18 . Thus, the extent of lung injury is still an important denominator for patients’ prognosis and the clinical course of COVID‐19.…”

“…16 Our observations are in concordance with clinical data associating an omicron infection with a milder disease course and low lethality. 12,17,18 Thus, the extent of lung injury is still an important denominator for patients' prognosis and the clinical course of COVID-19. However, besides attenuation of viral pathogenicity, vaccination or resolved infection improved the specific immune status of the population, and improvement in disease management may also be an important factor for a better outcome of patients.…”

The viral fitness and intrinsic pathogenicity of dominant SARS-CoV-2 Omicron sublineages BA.1, BA.2, and BA.5

“…Recent clinical investigations revealed a decreased pathogenicity of BA.1 and BA.2 when compared to previous VOCs, 10 , 11 , 12 , 13 , 14 which are in agreement with previous in vitro and in vivo studies reported from us and others. 4 , 8 , 15 , 16 However, clinical severity of BA.5 and its related sublineages remain incompletely understood.…”

Divergent trajectory of replication and intrinsic pathogenicity of SARS-CoV-2 Omicron post-BA.2/5 subvariants in the upper and lower respiratory tract

“… 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 Subsequent Omicron subvariants emerged in waves, with a subvariant replacing the previous one every few months. We and others have evaluated the virological features, replication, and pathogenicity of these dominant Omicron subvariants, including BA.1, 6 , 7 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 42 , 43 , 44 , 45 , 46 BA.2, 23 , 24 , 25 , 26 , 35 , 47 , 48 , 49 and BA.5. 27 , 28 , 36 , 40 , 41 , 50 , 51 , 52 , 53 , 54 , 55 , 56 More recently, the emerged post-BA.2/5 subvariants were unable to successfully outcompete other subvariants to become the dominant Omicron lineage worldwide, leading to the cocirculation of multiple Omicron subvariants.…”