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.
【저자키워드】 COVID-19, SARS-CoV-2, variants, next-generation sequencing (NGS), Genexus, 【초록키워드】 Saliva, feasibility, hospital, Sequencing, variant, SARS-CoV-2 variant, Diagnosis, reverse transcription-PCR, Laboratory, RNA extraction, Nasopharyngeal swab, Genome sequencing, Viral load, B.1.1.7, Next-generation sequencing, France, automated, correlation, Analysis, Efficiency, These data, Viral genome sequencing, limitation, material, routine clinical care, single hospital, variants of SARS-CoV-2, Complete, repeated, approach, European, highlight, SARS-CoV-2 positive individuals, detect, collected, was performed, Ion, Aside, Louis Pasteur, the SARS-CoV-2, the SARS-CoV-2 genome, 【제목키워드】 Rapid, France, assessment, center, Louis Pasteur,