Publications des scientifiques de l'IRD

Bedotto M., Fournier P. E., Houhamdi L., Levasseur A., Delerce J., Pinault L., Padane A., Chamieh A., Tissot-Dupont H., Brouqui P., Sokhna Cheikh, Azar E., Saile R., Mboup S., Bitam I., Colson P., Raoult D. (2021). Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant. Journal of Clinical Virology, 139, p. 104814 [4 p.]. ISSN 1386-6532.

Titre du document
Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant
Année de publication
2021
Type de document
Article référencé dans le Web of Science WOS:000652618600013
Auteurs
Bedotto M., Fournier P. E., Houhamdi L., Levasseur A., Delerce J., Pinault L., Padane A., Chamieh A., Tissot-Dupont H., Brouqui P., Sokhna Cheikh, Azar E., Saile R., Mboup S., Bitam I., Colson P., Raoult D.
Source
Journal of Clinical Virology, 2021, 139, p. 104814 [4 p.] ISSN 1386-6532
Introduction: The SARS-CoV-2 pandemic has been associated with the occurrence since summer 2020 of several viral variants that overlapped or succeeded each other in time. Those of current concern harbor mutations within the spike receptor binding domain (RBD) that may be associated with viral escape to immune responses. In our geographical area a viral variant we named Marseille-4 harbors a S477 N substitution in this RBD. Materials and methods: We aimed to implement an in-house one-step real-time reverse transcription-PCR (qPCR) assay with a hydrolysis probe that specifically detects the SARS-CoV-2 Marseille-4 variant. Results: All 6 cDNA samples from Marseille-4 variant strains identified in our institute by genome next-generation sequencing (NGS) tested positive using our Marseille-4 specific qPCR, whereas all 32 cDNA samples from other variants tested negative. In addition, 39/42 (93 %) respiratory samples identified by NGS as containing a Marseille-4 variant strain and 0/26 samples identified as containing non-Marseille-4 variant strains were positive. Finally, 2018/3960 (51%) patients SARS-CoV-2-diagnosed in our institute, 10/277 (3.6 %) respiratory samples collected in Algeria, and none of 207 respiratory samples collected in Senegal, Morocco, or Lebanon tested positive using our Marseille-4 specific qPCR. Discussion: Our in-house qPCR system was found reliable to detect specifically the Marseille-4 variant and allowed estimating it is involved in about half of our SARS-CoV-2 diagnoses since December 2020. Such approach allows the real-time surveillance of SARS-CoV-2 variants, which is warranted to monitor and assess their epidemiological and clinical characterics based on comprehensive sets of data.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Entomologie médicale / Parasitologie / Virologie [052]
Description Géographique
FRANCE ; MARSEILLE
Localisation
Fonds IRD [F B010081516]
Identifiant IRD
fdi:010081516
Contact