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Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa: An investigational study.
Travel Med Infect Dis. 2021 Mar-Apr; 40:101980.TM

Abstract

BACKGROUND

In Marseille, France, the COVID-19 incidence evolved unusually with several successive epidemic phases. The second outbreak started in July, was associated with North Africa, and involved travelers and an outbreak on passenger ships. This suggested the involvement of a new viral variant.

METHODS

We sequenced the genomes from 916 SARS-CoV-2 strains from COVID-19 patients in our institute. The patients' demographic and clinical features were compared according to the infecting viral variant.

RESULTS

From June 26th to August 14th, we identified a new viral variant (Marseille-1). Based on genome sequences (n = 89) or specific qPCR (n = 53), 142 patients infected with this variant were detected. It is characterized by a combination of 10 mutations located in the nsp2, nsp3, nsp12, S, ORF3a, ORF8 and N/ORF14 genes. We identified Senegal and Gambia, where the virus had been transferred from China and Europe in February-April as the sources of the Marseille-1 variant, which then most likely reached Marseille through Maghreb when French borders reopened. In France, this variant apparently remained almost limited to Marseille. In addition, it was significantly associated with a milder disease compared to clade 20A ancestor strains, in univariate analysis.

CONCLUSION

Our results demonstrate that SARS-CoV-2 can genetically diversify rapidly, its variants can diffuse internationally and cause successive outbreaks.

Authors+Show Affiliations

IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.Aix-Marseille Univ, Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France; Ecole Nationale Supérieure en Sciences de L'Aliment et des Industries Agroalimentaire, Alger, Algeria.Faculty of Sciences Ben M'sik, Hassan II University of Casablanca, Morocco.Faculty of Sciences Ben M'sik, Hassan II University of Casablanca, Morocco.Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Rufisque, Senegal.IHU Méditerranée Infection, Marseille, France.IHU Méditerranée Infection, Marseille, France.IHU Méditerranée Infection, Marseille, France.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France; French Armed Forces Center for Epidemiology and Public Health (CESPA), Marseille, France.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Rufisque, Senegal.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France. Electronic address: pierre-edouard.fournier@univ-amu.fr.IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France. Electronic address: didier.raoult@gmail.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

33535105

Citation

Colson, Philippe, et al. "Introduction Into the Marseille Geographical Area of a Mild SARS-CoV-2 Variant Originating From sub-Saharan Africa: an Investigational Study." Travel Medicine and Infectious Disease, vol. 40, 2021, p. 101980.
Colson P, Levasseur A, Gautret P, et al. Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa: An investigational study. Travel Med Infect Dis. 2021;40:101980.
Colson, P., Levasseur, A., Gautret, P., Fenollar, F., Thuan Hoang, V., Delerce, J., Bitam, I., Saile, R., Maaloum, M., Padane, A., Bedotto, M., Brechard, L., Bossi, V., Ben Khedher, M., Chaudet, H., Million, M., Tissot-Dupont, H., Lagier, J. C., Mboup, S., ... Raoult, D. (2021). Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa: An investigational study. Travel Medicine and Infectious Disease, 40, 101980. https://doi.org/10.1016/j.tmaid.2021.101980
Colson P, et al. Introduction Into the Marseille Geographical Area of a Mild SARS-CoV-2 Variant Originating From sub-Saharan Africa: an Investigational Study. Travel Med Infect Dis. 2021 Mar-Apr;40:101980. PubMed PMID: 33535105.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa: An investigational study. AU - Colson,Philippe, AU - Levasseur,Anthony, AU - Gautret,Philippe, AU - Fenollar,Florence, AU - Thuan Hoang,Van, AU - Delerce,Jeremy, AU - Bitam,Idir, AU - Saile,Rachid, AU - Maaloum,Mossaab, AU - Padane,Abdou, AU - Bedotto,Marielle, AU - Brechard,Ludivine, AU - Bossi,Vincent, AU - Ben Khedher,Mariem, AU - Chaudet,Hervé, AU - Million,Matthieu, AU - Tissot-Dupont,Hervé, AU - Lagier,Jean-Christophe, AU - Mboup,Souleymane, AU - Fournier,Pierre-Edouard, AU - Raoult,Didier, Y1 - 2021/01/31/ PY - 2020/12/22/received PY - 2021/01/20/revised PY - 2021/01/21/accepted PY - 2021/2/4/pubmed PY - 2021/4/28/medline PY - 2021/2/3/entrez KW - Covid-19 KW - Genome KW - Marseille-1 KW - SARS-CoV-2 KW - Travel KW - Variant SP - 101980 EP - 101980 JF - Travel medicine and infectious disease JO - Travel Med Infect Dis VL - 40 N2 - BACKGROUND: In Marseille, France, the COVID-19 incidence evolved unusually with several successive epidemic phases. The second outbreak started in July, was associated with North Africa, and involved travelers and an outbreak on passenger ships. This suggested the involvement of a new viral variant. METHODS: We sequenced the genomes from 916 SARS-CoV-2 strains from COVID-19 patients in our institute. The patients' demographic and clinical features were compared according to the infecting viral variant. RESULTS: From June 26th to August 14th, we identified a new viral variant (Marseille-1). Based on genome sequences (n = 89) or specific qPCR (n = 53), 142 patients infected with this variant were detected. It is characterized by a combination of 10 mutations located in the nsp2, nsp3, nsp12, S, ORF3a, ORF8 and N/ORF14 genes. We identified Senegal and Gambia, where the virus had been transferred from China and Europe in February-April as the sources of the Marseille-1 variant, which then most likely reached Marseille through Maghreb when French borders reopened. In France, this variant apparently remained almost limited to Marseille. In addition, it was significantly associated with a milder disease compared to clade 20A ancestor strains, in univariate analysis. CONCLUSION: Our results demonstrate that SARS-CoV-2 can genetically diversify rapidly, its variants can diffuse internationally and cause successive outbreaks. SN - 1873-0442 UR - https://www.unboundmedicine.com/medline/citation/33535105/Introduction_into_the_Marseille_geographical_area_of_a_mild_SARS_CoV_2_variant_originating_from_sub_Saharan_Africa:_An_investigational_study_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1477-8939(21)00021-1 DB - PRIME DP - Unbound Medicine ER -