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


Bronner P Gonçalves, Matthew Hall, Waasila Jassat, Valeria Balan, Srinivas Murthy, Christiana Kartsonaki, Malcolm G Semple, Amanda Rojek, Joaquín Baruch, Luis Felipe Reyes, Abhishek Dasgupta, Jake Dunning, Barbara Wanjiru Citarella, Mark Pritchard, Alejandro Martín-Quiros, Uluhan Sili, J Kenneth Baillie, Diptesh Aryal, Yaseen Arabi, Aasiyah Rashan, Andrea Angheben, Janice Caoili, François Martin Carrier, Ewen M Harrison, Joan Gómez-Junyent, Claudia Figueiredo-Mello, James Joshua Douglas, Mohd Basri Mat Nor, Yock Ping Chow, Xin Ci Wong, Silvia Bertagnolio, Soe Soe Thwin, Anca Streinu-Cercel, Leonardo Salazar, Asgar Rishu, Rajavardhan Rangappa, David S Y Ong, Madiha Hashmi, Gail Carson, Janet Diaz, Rob Fowler, Moritz U G Kraemer, Evert-Jan Wils, Peter Horby, Laura Merson, Piero L Olliaro, ISARIC Clinical Characterisation Group [includes Husna Begum, Steve Webb]

Elife, 2022 Oct 5;11:e80556. DOI:

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.

Related Broad Research Areas