Link to Pubmed [PMID] – 32186279
Link to HAL – pasteur-04098591
Link to DOI – 10.1684/vir.2020.0825
Virologie, 2020, 24 (S1), pp.S3-S6. ⟨10.1684/vir.2020.0825⟩
Le 31 décembre 2019, les autorités chinoises informaient l’Organisation mondiale de la santé (OMS) de cas groupés de pneumonies d’étiologie inconnue ; la grande majorité des patients ayant été exposée à des animaux vivants d’un marché de la ville de Wuhan, en Chine. Le 7 janvier 2020, l’émergence d’un nouveau coronavirus était identifiée ; le virus 2019-nCoV déclaré comme l’agent responsable de cette nouvelle maladie respiratoire. Le partage immédiat par les autorités chinoises des séquences génomiques complètes du virus 2019-nCoV, via leur dépôt sur la plateforme Gisaid (Global Initiative on Sharing All Influenza Data) (initialement dédiée au suivi de l’évolution génétique des virus de la grippe), a permis aux divers laboratoires experts mondiaux de développer au plus vite des tests de détection de ce nouveau virus. L’épidémie a rapidement évolué, affectant d’autres régions de la Chine, et le 13 janvier 2020, la Thaïlande déclarait un premier cas importé de Wuhan. Le 27 janvier 2020, la surveillance épidémiologique internationale faisait état de 41 cas importés, 27 en Asie, 6 en Amérique du Nord, 5 en Océanie et 3 en Europe, tous en provenance de Chine. Le 30 janvier 2020, le directeur général de l’OMS déclarait l’épidémie de 2019-nCoV comme urgence de santé publique à portée internationale. Entre temps, le 24 janvier 2020, le ministère français chargé de la Santé avait confirmé trois premiers cas de patients infectés par le coronavirus de Wuhan. Les premiers cas en Europe ont été détectés en France par le Centre National de Référence (CNR) des Virus des infections respiratoires de l’Institut Pasteur ; les séquences du génome complet pour deux des premiers cas français ont été rapidement partagées via la plateforme Gisaid et les isolats viraux mis à disposition, dans le cadre de l’initiative European Virus Archive GLOBAL (EVAg). Le 12 février 2020, compte tenu du lien phylogénétique du virus 2019-nCoV avec le coronavirus responsable du syndrome respiratoire aigu sévère (SARS ayant causé une épidémie en 2002-2003) et d’autres coronavirus apparentés, le Comité international de taxonomie des virus (ICTV) attribuait la nouvelle dénomination SARS-CoV-2 au virus ; la maladie associée étant quant à elle nommée Covid-19, pour Coronavirus Infectious Disease 2019.
On December 31, 2019, Chinese authorities reported a cluster of pneumonia cases in Wuhan, China, most of which included patients who reported exposure to a seafood market selling live animals. Emergence of a new pathogenic zoonotic coronavirus (2019-nCoV) was suspected. By the 12th January 2020, several full genomic sequences were made available by Chinese authorities through the Global Initiative on Sharing All Influenza Data (GISAID) public platform [1] which was initially developed to share sequences and monitor the genetic evolution of influenza viruses. This enabled rapid development of specific RT-PCR methods for detection of 2019-nCoV. The outbreak rapidly evolved, affecting other parts of China. The 13 th January 2020, Thailand reported the first imported case from Wuhan. On 27 January 2020, forty-one travel-related cases were confirmed, all coming from China. Twenty-seven cases were imported to Asia, six to North America, five to Oceania, and three to Europe [2]. On 30 January 2020, the Director General of the World Health Organization (WHO) declared the outbreak of 2019-nCoV as a public health emergency of international concern. The first cases in the EU/EEA were confirmed in France the 24 th January 2020 at the National Reference Centre (NRC) for respiratory viruses (Institut Pasteur, Paris) and whole genome sequences from two of the first French cases were rapidly shared through the GISAID platform; virus isolates were shared through the European Virus Archive GLOBAL (EVAg) initiative as well [3]. The 12 th February 2020, based on its phylogenetic clustering with the SARS coronavirus which spread rapidly in 2002-2003 and other SARS-like coronaviruses, the novel coronavirus was named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses (ICTV) [4], while the disease associated with it is now referred to as Coronavirus Infectious Disease 2019 (COVID-19) [5]. Coronaviruses are large, enveloped, positive strand RNA viruses that can be divided into 4 genera: alpha, beta, delta, and gamma, of which alpha and beta CoVs are known to infect humans [6]. Four seasonal human coronaviruses (HCoVs 229E, NL63, OC43, and HKU1) are endemic globally and account for 10% to 30% of upper Respiratory Tract (upper RT) infections in adults. Coronaviruses are ecologically diverse, with the greatest variety seen in bats, suggesting bats as the reservoir for many of those viruses [7]. Peri-domestic mammals may serve as intermediate hosts, facilitating recombination and mutation events with increase of genetic diversity. Sequencing of SARS-CoV-2 has shown that it is highly similar to a known virus from a horseshoe bat (Rhinolofus affinis) found in China [8], and to viruses detected or isolated in Malayan pangolins (Manis javanica) that might have served as an intermediate amplifying host [9, 10]. Two emerging coronaviruses, SARS-CoV in 2002-2003 and Middle East Respiratory Syndrom (MERS)-CoV in 2012, caused severe respiratory syndrome in humans. Both are thought to have originated from the bat reservoir, after being hosted in their respective intermediate hosts palmed civets and dromedary