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SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding.
Dudouet, Pierre; Colson, Philippe; Aherfi, Sarah; Levasseur, Anthony; Beye, Mamadou; Delerce, Jeremy; Burel, Emilie; Lavrard, Philippe; Bader, Wahiba; Lagier, Jean-Christophe; Fournier, Pierre-Edouard; La Scola, Bernard; Raoult, Didier.
  • Dudouet P; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. pierre.dudouet@univ-amu.fr.
  • Colson P; Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005, Marseille, France. pierre.dudouet@univ-amu.fr.
  • Aherfi S; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Levasseur A; Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005, Marseille, France.
  • Beye M; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Delerce J; Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005, Marseille, France.
  • Burel E; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Lavrard P; Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005, Marseille, France.
  • Bader W; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Lagier JC; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Fournier PE; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • La Scola B; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Raoult D; Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France.
Sci Rep ; 12(1): 18721, 2022 Nov 04.
Article in English | MEDLINE | ID: covidwho-2106463
ABSTRACT
At the time of a new and unprecedented viral pandemic, many questions are being asked about the genomic evolution of SARS-CoV-2 and the emergence of different variants, leading to therapeutic and immune evasion and survival of this genetically highly labile RNA virus. The nasopharyngeal persistence of infectious virus beyond 17 days proves its constant interaction with the human immune system and increases the intra-individual mutational possibilities. We performed a prospective high-throughput sequencing study (ARTIC Nanopore) of SARS-CoV-2 from so-called "persistent" patients, comparing them with a non-persistent population, and analyzing the quasi-species present in a single sample at time t. Global intra-individual variability in persistent patients was found to be higher than in controls (mean 5.3%, Standard deviation 0.9 versus 4.6% SD 0.3, respectively, p < 0.001). In the detailed analysis, we found a greater difference between persistent and non-persistent patients with non-severe COVID 19, and between the two groups infected with clade 20A. Furthermore, we found minority N501Y and P681H mutation clouds in all patients, with no significant differences found both groups. The question of the SARS-CoV-2 viral variants' genesis remains to be further investigated, with the need to prevent new viral propagations and their consequences, and quasi-species analysis could be an important key to watch out.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Cohort study / Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: Sci Rep Year: 2022 Document Type: Article Affiliation country: S41598-022-22060-z

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Cohort study / Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: Sci Rep Year: 2022 Document Type: Article Affiliation country: S41598-022-22060-z