On 26 November 2021, the World Health Organization (WHO) classified Omicron as a variant of concern (VOC), following its detection in South Africa showing significant genetic divergence from previously identified variants. This classification was established as per the WHO definition of variants, which are based on changes in virus characteristics regarding transmissibility, disease severity, immune escape, diagnostic or therapeutic escape, and an epidemiological impact suggesting an emerging risk to global public health. This classification represents a major worldwide challenge, meaning the emerging variant needs to be quickly detected and characterised.
Three days later, on November 29, the first case of this variant was confirmed in France, in Reunion Island (1). Santé publique France then set up dedicated surveillance for Omicron. On December 20, it represented 49% of cases in France (2) and was identified in 28 European countries. At the end of January 2022, Omicron was present in all EU/EEA countries and in 171 countries worldwide.
To this day, Omicron is present throughout the entire territory and now represents 99.9% of variants among the sequenced viruses1. In order to anticipate Omicron’s potential impact on the national health system, it was important to determine as soon as possible the characteristics of the first cases infected with this variant, in terms of demographics, travel history, clinical signs, vaccination status, etc.
The article that was just published in the journal Infectious Diseases Now presents these results for the first cases of Omicron detected in France.
Three questions to Anna Maisa and Guillaume Spaccaferri, Santé publique France
First of all, it is important to state the context at the time of the survey. The Delta variant was still dominant on the territory. We could see that Omicron cases were increasing in other countries, and had started to detect the first cases in France.
Although the data available from testing (SI-DEP), hospitalisation (SI-VIC) and vaccination (VAC-SI) databases are very rich in information for monitoring the epidemic, they remain rather limited concerning the characteristics of the cases due to the difficulty of performing real-time matching and the absence of clinical elements. In collaboration with the regional units of Santé publique France, we quickly decided to collect further details about the first cases that were not available in these databases. Our objective was to characterise the Omicron variant in order to anticipate its potential impact on the population and the health system.
The challenge was to collect all this information in a very short time, in the difficult context of the pandemic and the rapid increase in case numbers. Knowledge on the variant was accessible thanks to the sequencing of confirmed cases by the EMERGEN consortium (see box). Each person who was a confirmed Omicron case was contacted by epidemiologists from regional units of Santé publique France to answer a standardised survey. The collected information included travel history, clinical symptoms, comorbidities, previous SARS-CoV-2 infections and vaccination status. In this way, 468 Omicron cases were investigated during the study period (from 23/11/21 to 11/01/22), spanning almost the entire country (17 out of 18 regions).
Our investigation on these first 468 cases of Omicron in France showed that, although most of the cases (89%) were symptomatic, the symptoms were mild in the vast majority of cases. Loss of smell and taste, very common with other variants, were only rarely reported (8.3% and 9%, respectively). This was a major element, as it was previously one of the main symptoms that specifically suggested SARS-CoV-2 infection. Among the investigated cases, only 7 (2%) were hospitalised, and none were admitted to intensive care unit or had died. However, we must remain cautious while interpreting results because our study was based on a population composed of relatively young subjects (median age: 35 years) and a majority (64% of cases) was vaccinated with two doses, which also grants some protection against severe forms of the disease.
Since our study, several publications have shown that Omicron seems to have a reduced impact on the health system compared to Delta. In this respect, a study recently published by Santé publique France comparing the respective severity of these two variants concluded that the risk of experiencing a serious hospital event was lower for people infected with Omicron than those of the same age infected with Delta. However, this difference between variants diminished with age: this risk was divided by 9.1 for people aged 40–64 years infected with Omicron, by 5.3 for those aged 65–80 years, but only 2.0 for those aged 80 years and over (3).
When a new variant such as Omicron appears, rapid detection and characterisation of cases is essential. This helps to determine whether the new variant causes more severe or different symptoms than previous ones, more hospitalised cases or deaths. The effectiveness of current vaccines against emerging strains is also a crucial question. All this information is important for taking decisions regarding capacity and organisation of care, screening strategy and control measures.
The French public health system, including the screening and genomic surveillance laboratories brought together by the EMERGEN consortium (see box), alongside the local, regional and national authorities, have collectively demonstrated their ability to react and rapidly adapt when a new variant emerges. Since 18/02/2022, a Delta/Omicron recombinant now known as XD is under close observation by the consortium laboratories. Most of its genome corresponds to the Delta variant (sub-lineage AY.4), but a large portion of the S gene (coding for the Spike protein) corresponds to the Omicron variant (sub-lineage BA.1). On 8 March 2022, 27 sequences of this recombinant, which has been spreading at low levels for several weeks, were detected in France. To this day, very few data are available on its characteristics. Investigations are in progress.
The EMERGEN consortium (dedicated to EMERging pathogenic infections surveillance and research via microbial GENomic), coordinated by Santé publique France and the ANRS | Emerging Infectious Diseases, was created in January 2021 to launch a nationwide genomic surveillance system for SARS-CoV-2 infections. It is the first step (2 years) of work carried out by a sequencing network to support surveillance and research activities on emerging infectious diseases (viral, but also bacterial, fungal or parasitic). It combines surveillance activities conducted by Santé publique France and the National Reference Center for Respiratory Virus Infections, with research activities performed by the ANRS | Emerging Infectious Diseases. The objective is to monitor the genetic evolution of the SARS-CoV-2 virus to detect and characterise the emergence and spatio-temporal distribution of variants, i.e., viruses with mutations that may have functional consequences, such as infectivity, contagiousness, virulence or immune escape.
The EMERGEN project is based on a multidisciplinary consortium of complementary expertise: sample collection, sequencing preparation and execution, bioinformatics analysis of genomes, publication of data in national and international databases, analysis for surveillance purposes (Flash Surveys) or risk analysis (classification variants of concern, of interest or under monitoring), possible discovery and functional characterisation of new variants, and research on their epidemiological and functional impact.
For more information : https://www.santepubliquefrance.fr/emergen
1 Maisa A, Spaccaferri G, Fournier L, Schaeffer J, Deniau J, Rolland P, Coignard B; regional COVID-19 investigation team; EMERGEN consortium. First cases of Omicron in France are exhibiting mild symptoms, November 2021-January 2022. Infect Dis Now. 2022 Feb 12:S2666-9919(22)00036-7. doi: 10.1016/j.idnow.2022.02.003. Epub ahead of print. PMID: 35167979.
Other references cited :
(1) COVID-19. Point épidémiologique hebdomadaire, La Réunion, 16 décembre 2021. Santé publique France-Réunion.
(2) COVID-19. Point épidémiologique hebdomadaire. N°97, 06 janvier 2022.
(3) Severe hospital events following symptomatic infection with SARS-CoV-2 Omicron and Delta variants in France, December 2021 – January 2022: a retrospective, population-based, matched cohort study. Vincent Auvigne, Sophie Vaux, Yann Le Strat, Justine Schaeffer, Lucie Fournier, Cynthia Tamandjou, Charline Montagnat, Bruno Coignard, Daniel Levy-Bruhl, Isabelle Parent du Chatelet.