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A standardised protocol for relative SARS-CoV-2 variant severity assessment, applied to Omicron BA.1 and Delta in six European countries, October 2021 to February 2022
- Tommy Nyberg1 , Peter Bager2 , Ingrid Bech Svalgaard2 , Dritan Bejko3 , Nick Bundle4 , Josie Evans5 , Tyra Grove Krause2 , Jim McMenamin5 , Joël Mossong3 , Heather Mutch5 , Ajibola Omokanye4 , André Peralta-Santos6 , Pedro Pinto-Leite6 , Jostein Starrfelt7 , Simon Thelwall8 , Lamprini Veneti7 , Robert Whittaker7 , John Wood5 , Richard Pebody9,* , Anne M Presanis1,*
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View Affiliations Hide AffiliationsAffiliations: 1 MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom 2 Statens Serum Institut, Copenhagen, Denmark 3 Health Directorate, Luxembourg, Luxembourg 4 European Centre for Disease Prevention and Control, Stockholm, Sweden 5 Public Health Scotland, Glasgow, Scotland, United Kingdom 6 Directorate-General of Health, Lisbon, Portugal 7 Norwegian Institute of Public Health, Oslo, Norway 8 COVID-19 Vaccines and Epidemiology Division, UK Health Security Agency, London, United Kingdom 9 World Health Organization Regional Office for Europe, Copenhagen, Denmark * These authors contributed equally to this work and share last authorship.Tommy Nybergtommy.nyberg mrc-bsu.cam.ac.uk
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Citation style for this article: Nyberg Tommy, Bager Peter, Svalgaard Ingrid Bech, Bejko Dritan, Bundle Nick, Evans Josie, Krause Tyra Grove, McMenamin Jim, Mossong Joël, Mutch Heather, Omokanye Ajibola, Peralta-Santos André, Pinto-Leite Pedro, Starrfelt Jostein, Thelwall Simon, Veneti Lamprini, Whittaker Robert, Wood John, Pebody Richard, Presanis Anne M. A standardised protocol for relative SARS-CoV-2 variant severity assessment, applied to Omicron BA.1 and Delta in six European countries, October 2021 to February 2022. Euro Surveill. 2023;28(36):pii=2300048. https://doi.org/10.2807/1560-7917.ES.2023.28.36.2300048 Received: 19 Jan 2023; Accepted: 21 May 2023
Abstract
Several SARS-CoV-2 variants that evolved during the COVID-19 pandemic have appeared to differ in severity, based on analyses of single-country datasets. With decreased testing and sequencing, international collaborative studies will become increasingly important for timely assessment of the severity of new variants. Therefore, a joint WHO Regional Office for Europe and ECDC working group was formed to produce and pilot a standardised study protocol to estimate relative case-severity of SARS-CoV-2 variants during periods when two variants were co-circulating. The study protocol and its associated statistical analysis code was applied by investigators in Denmark, England, Luxembourg, Norway, Portugal and Scotland to assess the severity of cases with the Omicron BA.1 virus variant relative to Delta. After pooling estimates using meta-analysis methods (random effects estimates), the risk of hospital admission (adjusted hazard ratio (aHR) = 0.41; 95% confidence interval (CI): 0.31−0.54), admission to intensive care unit (aHR = 0.12; 95% CI: 0.05−0.27) and death (aHR = 0.31; 95% CI: 0.28−0.35) was lower for Omicron BA.1 compared with Delta cases. The aHRs varied by age group and vaccination status. In conclusion, this study demonstrates the feasibility of conducting variant severity analyses in a multinational collaborative framework and adds evidence for the reduced severity of the Omicron BA.1 variant.
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References
-
Bager P, Wohlfahrt J, Bhatt S, Stegger M, Legarth R, Møller CH, et al. , Omicron-Delta study group. Risk of hospitalisation associated with infection with SARS-CoV-2 omicron variant versus delta variant in Denmark: an observational cohort study. Lancet Infect Dis. 2022;22(7):967-76. https://doi.org/10.1016/S1473-3099(22)00154-2 PMID: 35468331
-
Lewnard JA, Hong VX, Patel MM, Kahn R, Lipsitch M, Tartof SY. Clinical outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) variant and BA.1/BA.1.1 or BA.2 subvariant infection in Southern California. Nat Med. 2022;28(9):1933-43. https://doi.org/10.1038/s41591-022-01887-z PMID: 35675841
-
Nyberg T, Ferguson NM, Nash SG, Webster HH, Flaxman S, Andrews N, et al. . Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study. Lancet. 2022;399(10332):1303-12. https://doi.org/10.1016/S0140-6736(22)00462-7 PMID: 35305296
-
Peralta-Santos A, Rodrigues EF, Moreno J, Ricoca V, Casaca P, Fernandes E, et al. Omicron (BA.1) SARS-CoV-2 variant is associated with reduced risk of hospitalization and length of stay compared with Delta (B.1.617.2). medRxiv. 2022:2022.01.20.22269406.
-
Sheikh A, Kerr S, Woolhouse M, McMenamin J, Robertson C, Simpson CR, et al. . Severity of omicron variant of concern and effectiveness of vaccine boosters against symptomatic disease in Scotland (EAVE II): a national cohort study with nested test-negative design. Lancet Infect Dis. 2022;22(7):959-66. https://doi.org/10.1016/S1473-3099(22)00141-4 PMID: 35468332
-
Ulloa AC, Buchan SA, Daneman N, Brown KA. Estimates of SARS-CoV-2 Omicron Variant Severity in Ontario, Canada. JAMA. 2022;327(13):1286-8. https://doi.org/10.1001/jama.2022.2274 PMID: 35175280
-
Veneti L, Bøås H, Bråthen Kristoffersen A, Stålcrantz J, Bragstad K, Hungnes O, et al. Reduced risk of hospitalisation among reported COVID-19 cases infected with the SARS-CoV-2 Omicron BA.1 variant compared with the Delta variant, Norway, December 2021 to January 2022. Euro Surveill. 2022;27(4):2200077. https://doi.org/10.2807/1560-7917.ES.2022.27.4.2200077 PMID: 35086614
-
Ward IL, Bermingham C, Ayoubkhani D, Gethings OJ, Pouwels KB, Yates T, et al. Risk of covid-19 related deaths for SARS-CoV-2 omicron (B.1.1.529) compared with delta (B.1.617.2): retrospective cohort study. BMJ. 2022;378:e070695. https://doi.org/10.1136/bmj-2022-070695 PMID: 35918098
-
Wolter N, Jassat W, Walaza S, Welch R, Moultrie H, Groome M, et al. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. Lancet. 2022;399(10323):437-46. https://doi.org/10.1016/S0140-6736(22)00017-4 PMID: 35065011
-
Bager P, Wohlfahrt J, Rasmussen M, Albertsen M, Krause TG. Hospitalisation associated with SARS-CoV-2 delta variant in Denmark. Lancet Infect Dis. 2021;21(10):1351. https://doi.org/10.1016/S1473-3099(21)00580-6 PMID: 34487704
-
Rodrigues EF, Moreno J, Leite PP, Casaca P, Nunes B, Gomes JP, et al. B.1.617.2 SARS-CoV-2 (Delta) variant is associated with increased risk of hospitalization and death compared with B.1.1.7 SARS-CoV-2 (Alpha) variant. medRxiv. 2022:2022.01.21.22268602 . https://doi.org/10.1101/2022.01.21.22268602
-
Sheikh A, McMenamin J, Taylor B, Robertson C, Public Health Scotland and the EAVE II Collaborators. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. Lancet. 2021;397(10293):2461-2. https://doi.org/10.1016/S0140-6736(21)01358-1 PMID: 34139198
-
Twohig KA, Nyberg T, Zaidi A, Thelwall S, Sinnathamby MA, Aliabadi S, et al. Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infect Dis. 2022;22(1):35-42. https://doi.org/10.1016/S1473-3099(21)00475-8 PMID: 34461056
-
Veneti L, Valcarcel Salamanca B, Seppälä E, Starrfelt J, Storm ML, Bragstad K, et al. No difference in risk of hospitalization between reported cases of the SARS-CoV-2 Delta variant and Alpha variant in Norway. Int J Infect Dis. 2022;115:178-84. https://doi.org/10.1016/j.ijid.2021.12.321 PMID: 34902584
-
Bager P, Wohlfahrt J, Fonager J, Rasmussen M, Albertsen M, Michaelsen TY, et al. Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study. Lancet Infect Dis. 2021;21(11):1507-17. https://doi.org/10.1016/S1473-3099(21)00290-5 PMID: 34171231
-
Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. , COVID study groups. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Euro Surveill. 2021;26(16):2100348. https://doi.org/10.2807/1560-7917.ES.2021.26.16.2100348 PMID: 33890566
-
Nyberg T, Twohig KA, Harris RJ, Seaman SR, Flannagan J, Allen H, et al. Risk of hospital admission for patients with SARS-CoV-2 variant B.1.1.7: cohort analysis. BMJ. 2021;373(1412):n1412. https://doi.org/10.1136/bmj.n1412 PMID: 34130987
-
Veneti L, Seppälä E, Larsdatter Storm M, Valcarcel Salamanca B, Alnes Buanes E, Aasand N, et al. Increased risk of hospitalisation and intensive care admission associated with reported cases of SARS-CoV-2 variants B.1.1.7 and B.1.351 in Norway, December 2020 -May 2021. PLoS One. 2021;16(10):e0258513. https://doi.org/10.1371/journal.pone.0258513 PMID: 34634066
-
Menni C, Valdes AM, Polidori L, Antonelli M, Penamakuri S, Nogal A, et al. Symptom prevalence, duration, and risk of hospital admission in individuals infected with SARS-CoV-2 during periods of omicron and delta variant dominance: a prospective observational study from the ZOE COVID Study. Lancet. 2022;399(10335):1618-24. https://doi.org/10.1016/S0140-6736(22)00327-0 PMID: 35397851
-
Vihta KD, Pouwels KB, Peto TEA, Pritchard E, House T, Studley R, et al. Omicron-Associated Changes in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Symptoms in the United Kingdom. Clin Infect Dis. 2023. https://doi.org/10.1093/cid/ciab945
-
Hui KPY, Ho JCW, Cheung MC, Ng KC, Ching RHH, Lai KL, et al. SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo. Nature. 2022;603(7902):715-20. https://doi.org/10.1038/s41586-022-04479-6 PMID: 35104836
-
Hughes TD, Subramanian A, Chakraborty R, Cotton SA, Herrera MDPG, Huang Y, et al. The effect of SARS-CoV-2 variant on respiratory features and mortality. Sci Rep. 2023;13(1):4503. https://doi.org/10.1038/s41598-023-31761-y PMID: 36934134
-
Woodbridge Y, Amit S, Huppert A, Kopelman NM. Viral load dynamics of SARS-CoV-2 Delta and Omicron variants following multiple vaccine doses and previous infection. Nat Commun. 2022;13(1):6706. https://doi.org/10.1038/s41467-022-33096-0 PMID: 36344489
-
Puhach O, Adea K, Hulo N, Sattonnet P, Genecand C, Iten A, et al. Infectious viral load in unvaccinated and vaccinated individuals infected with ancestral, Delta or Omicron SARS-CoV-2. Nat Med. 2022;28(7):1491-500. https://doi.org/10.1038/s41591-022-01816-0 PMID: 35395151
-
Collie S, Champion J, Moultrie H, Bekker L-G, Gray G. Effectiveness of BNT162b2 vaccine against Omicron variant in South Africa. N Engl J Med. 2022;386(5):494-6. https://doi.org/10.1056/NEJMc2119270 PMID: 34965358
-
Stowe J, Andrews N, Kirsebom F, Ramsay M, Bernal JL. Effectiveness of COVID-19 vaccines against Omicron and Delta hospitalisation, a test negative case-control study. Nat Commun. 2022;13(1):5736. https://doi.org/10.1038/s41467-022-33378-7 PMID: 36180428
-
Halford F, Nash S, Tessier E, Kall M, Dabrera G. Variation in reported SARS-CoV-2 cases after testing policy changes. Lancet Infect Dis. 2022;22(10):1418-9. https://doi.org/10.1016/S1473-3099(22)00572-2 PMID: 36027903
-
Norwegian Institute of Public Health (NIPH). Covid-19, influensa og andre luftveisinfeksjoner: Rapport – uke 41 og 42. [COVID-19, influenza and other respiratory infections: report – week 41 and 42]. Oslo: NIPH; 2022. Norwegian. Available from: https://www.fhi.no/publ/2020/koronavirus-ukerapporter/
-
Government of Portugal. Fim do estado de alerta. [End of alert status]. Lisbon: Government of Portugal; 2022. Portuguese. Available from: https://www.portugal.gov.pt/pt/gc23/comunicacao/noticia?i=fim-do-estado-de-alerta
-
Statens Serum Institut (SSI). Covid-19 nøgletal. [COVID-19 key figures]. Copenhagen: SSI; 2022 Danish. Available from: https://experience.arcgis.com/experience/aa41b29149f24e20a4007a0c4e13db1d
-
Spiess K, Gunalan V, Marving E, Nielsen SH, Jørgensen MGP, Fomsgaard AS, et al. , Danish COVID-19 Genome Consortium (DCGC). Rapid and flexible RT-qPCR surveillance platforms to detect SARS-CoV-2 mutations. Microbiol Spectr. 2023;11(1):e0359122. https://doi.org/10.1128/spectrum.03591-22 PMID: 36625603
-
Blomquist PB, Bridgen J, Bray N, O’Connell AM, West D, Groves N, et al. Enhancing epidemiological surveillance of the emergence of the SARS-CoV-2 Omicron variant using spike gene target failure data, England, 15 November to 31 December 2021. Euro Surveill. 2022;27(11):2200143. https://doi.org/10.2807/1560-7917.ES.2022.27.11.2200143 PMID: 35301981
-
Seaman SR, Nyberg T, Overton CE, Pascall DJ, Presanis AM, De Angelis D. Adjusting for time of infection or positive test when estimating the risk of a post-infection outcome in an epidemic. Stat Methods Med Res. 2022;31(10):1942-58. https://doi.org/10.1177/09622802221107105 PMID: 35695245
-
R Core Team. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2020. Available from: https://www.R-project.org
-
Whittaker R, Greve-Isdahl M, Bøås H, Suren P, Buanes EA, Veneti L. COVID-19 hospitalization among children <18 years by variant wave in Norway. Pediatrics. 2022;150(3):e2022057564. https://doi.org/10.1542/peds.2022-057564 PMID: 35916036
-
Wang L, Berger NA, Kaelber DC, Davis PB, Volkow ND, Xu R. Incidence rates and clinical outcomes of SARS-CoV-2 infection with the Omicron and Delta variants in children younger than 5 years in the US. JAMA Pediatr. 2022;176(8):811-3. https://doi.org/10.1001/jamapediatrics.2022.0945 PMID: 35363246
-
Clark M, Walker B, Bennett E, Herrick A, Kenny S, Gent N. Clinical characteristics of SARS-CoV-2 omicron infection in children under one year. SSRN. 2022 . https://doi.org/10.2139/ssrn.4013461
-
Griffith GJ, Morris TT, Tudball MJ, Herbert A, Mancano G, Pike L, et al. Collider bias undermines our understanding of COVID-19 disease risk and severity. Nat Commun. 2020;11(1):5749. https://doi.org/10.1038/s41467-020-19478-2 PMID: 33184277
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