Mutations du virus Sars-CoV-2

Mutations du virus Sars-CoV-2

Sources : GISAID - Nextstrain

Phylogénie globale des séquences de Sars-CoV-2 sur Nextstrain. (Au 14/05/2020) Phylogénie des séquences Françaises. (Au 14/05/2020

- Mutations Sars-CoV-2 - Région Auvergne-Rhône-Alpes

- Mutations Sars-CoV-2 - Région Hauts-de-France

- Mutations Sars-CoV-2 - Région Ile de France

Article :

- Genetic diversity and evolution of SARS-CoV-2.

Tung Phan. Infect Genet Evol. 2020 Jul. Published online 2020 Feb 21.

"We performed genetic analyses of eighty-six complete or near-complete genomes of SARS-CoV-2 and revealed many mutations and deletions on coding and non-coding regions. These observations provided evidence of the genetic diversity and rapid evolution of this novel coronavirus."

"It is interesting that our nucleotide sequence alignment also revealed ninety-three mutations over the entire genomes of SARS-CoV-2. Forty-two missense mutations were identified in all the major non-structural and structural proteins, except the envelope protein. Twenty-nine missense mutations were in the ORF1ab polyprotein, eight in the spike surface glycoprotein, one in the matrix protein, and four in the nucleocapsid protein. Of note, three mutations (D³⁵⁴, Y³⁶⁴, and F³⁶⁷) located in the spike surface glycoprotein receptor-binding domain."

• Localisation des mutations. Lien distant
• Mutations dans la région Spike. Document local

Conclusion

"To date, a study on localization of amino acids involved in conformational changes of the SARS-CoV-2 spike surface glycoprotein structure is not available. The identification of these amino acids is of significance and should be investigated by further studies."

Article :

Patient-derived mutations impact pathogenicity of SARS-CoV-2.
Hangping Yao et ali. posted April 19, 2020. medRxiv preprint

La population étudiée :

The samples of the 11 patients involved in this study were collected during the early phase of the COVID-19 breakout in China, dates ranging from 1/22/2020 to 2/4/2020. 10 of the 11 patients had clear connections with Wuhan city, where the SARS-CoV-2 was originally identified.

• Caractéristiques épidémiologiques de l'échantillon. Document local
• Mutations observées (Faux-sens). Document local

Conclusion

"Current genomic survey data suggest that single nucleotide variants (SNVs) are abundant. However, no mutation has been directly linked with functional changes in viral pathogenicity."

Article :

- Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant.

Maria Pachetti et ali. J Transl Med. 2020; 18. Published online 2020 Apr 22

"We characterized 8 novel recurrent mutations of SARS-CoV-2, located at positions 1397, 2891, 14408, 17746, 17857, 18060, 23403 and 28881. Mutations in 2891, 3036, 14408, 23403 and 28881 positions are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America."

• Fréquence des mutations observées par zone géographique. Document local
• Evolution du nombre de mutations au cours du temps. Document local

Conclusion

"These findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern.The contribution of the mutated RdRp to this phenomenon needs to be investigated."

"It is also important to recognize whether the presence of some mutations might correlate with different SARS-CoV-2 mortality rates."

Article :

Introductions and early spread of SARS-CoV-2 in France

Fabiana Gambaro et ali. Posted April 29, 2020. medRxiv preprint.

"We sequenced 97 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from samples collected between January 24 and March 24, 2020 from infected patients in France."

• Répartition des mutations par région en France. Document local
• Pasteur - les 3 clades identifiés en France. Document local

Conclusion

"Phylogenetic analysis identified several early independent SARS-CoV-2 introductions without local transmission, highlighting the efficacy of the measures taken to prevent virus spread from symptomatic cases. In parallel, our genomic data reveals the later predominant circulation of a major clade in many French regions, and implies local circulation of the virus in undocumented infections prior to the wave of COVID-19 cases."