Setting-Up a Rapid SARS-CoV-2 Genome Assessment by Next-Generation Sequencing in an Academic Hospital Center (LPCE, Louis Pasteur Hospital, Nice, France).

Autor:	Hofman P; Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France., Bordone O; Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Chamorey E; Epidemiology and Biostatistics Unit, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France., Benzaquen J; Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France.; Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Schiappa R; Epidemiology and Biostatistics Unit, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France., Lespinet-Fabre V; Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Lanteri E; Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Brest P; Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France., Mograbi B; Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France., Maniel C; Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Tanga V; Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Allegra M; Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Salah M; Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Fayada J; Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Boutros J; Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Leroy S; Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Heeke S; Department of Thoracic H&N Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States., Hofman V; Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France., Marquette CH; Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France.; Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France., Ilié M; Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d'Azur, Nice, France.; Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne, Université Côte d'Azur, Nice, France.
Jazyk:	angličtina
Zdroj:	Frontiers in medicine [Front Med (Lausanne)] 2022 Jan 11; Vol. 8, pp. 730577. Date of Electronic Publication: 2022 Jan 11 (Print Publication: 2021).
DOI:	10.3389/fmed.2021.730577
Abstrakt:	Introduction: Aside from the reverse transcription-PCR tests for the diagnosis of the COVID-19 in routine clinical care and population-scale screening, there is an urgent need to increase the number and the efficiency for full viral genome sequencing to detect the variants of SARS-CoV-2. SARS-CoV-2 variants assessment should be easily, rapidly, and routinely available in any academic hospital. Materials and Methods: SARS-CoV-2 full genome sequencing was performed retrospectively in a single laboratory (LPCE, Louis Pasteur Hospital, Nice, France) in 103 SARS-CoV-2 positive individuals. An automated workflow used the Ion Ampliseq SARS-CoV-2 panel on the Genexus Sequencer. The analyses were made from nasopharyngeal swab (NSP) ( n = 64) and/or saliva ( n = 39) samples. All samples were collected in the metropolitan area of the Nice city (France) from September 2020 to March 2021. Results: The mean turnaround time between RNA extraction and result reports was 30 h for each run of 15 samples. A strong correlation was noted for the results obtained between NSP and saliva paired samples, regardless of low viral load and high (>28) Ct values. After repeated sequencing runs, complete failure of obtaining a valid sequencing result was observed in 4% of samples. Besides the European strain (B.1.160), various variants were identified, including one variant of concern (B.1.1.7), and different variants under monitoring. Discussion: Our data highlight the current feasibility of developing the SARS-CoV-2 next-generation sequencing approach in a single hospital center. Moreover, these data showed that using the Ion Ampliseq SARS-CoV-2 Assay, the SARS-CoV-2 genome sequencing is rapid and efficient not only in NSP but also in saliva samples with a low viral load. The advantages and limitations of this setup are discussed. Competing Interests: PH received honoraria from Thermo Fisher Scientific for participating in scientific meetings, outside this present work. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Hofman, Bordone, Chamorey, Benzaquen, Schiappa, Lespinet-Fabre, Lanteri, Brest, Mograbi, Maniel, Tanga, Allegra, Salah, Fayada, Boutros, Leroy, Heeke, Hofman, Marquette and Ilié.)
Databáze:	MEDLINE
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