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- Title
SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system.
- Authors
Rachiglio, Anna Maria; De Sabato, Luca; Roma, Cristin; Cennamo, Michele; Fiorenza, Mariano; Terracciano, Daniela; Pasquale, Raffaella; Bergantino, Francesca; Cavalcanti, Ernesta; Botti, Gerardo; Vaccari, Gabriele; Portella, Giuseppe; Normanno, Nicola
- Abstract
<bold>Background: </bold>Since the first complete genome sequencing of SARS-CoV-2 in December 2019, more than 550,000 genomes have been submitted into the GISAID database. Sequencing of the SARS-CoV-2 genome might allow identification of variants with increased contagiousness, different clinical patterns and/or different response to vaccines. A highly automated next generation sequencing (NGS)-based method might facilitate an active genomic surveillance of the virus.<bold>Methods: </bold>RNA was extracted from 27 nasopharyngeal swabs obtained from citizens of the Italian Campania region in March-April 2020 who tested positive for SARS-CoV-2. Following viral RNA quantification, sequencing was performed using the Ion AmpliSeq SARS-CoV-2 Research Panel on the Genexus Integrated Sequencer, an automated technology for library preparation and sequencing. The SARS-CoV-2 complete genomes were built using the pipeline SARS-CoV-2 RECoVERY (REconstruction of COronaVirus gEnomes & Rapid analYsis) and analysed by IQ-TREE software.<bold>Results: </bold>The complete genome (100%) of SARS-CoV-2 was successfully obtained for 21/27 samples. In particular, the complete genome was fully sequenced for all 15 samples with high viral titer (> 200 copies/µl), for the two samples with a viral genome copy number < 200 but greater than 20, and for 4/10 samples with a viral load < 20 viral copies. The complete genome sequences classified into the B.1 and B.1.1 SARS-CoV-2 lineages. In comparison to the reference strain Wuhan-Hu-1, 48 total nucleotide variants were observed with 26 non-synonymous substitutions, 18 synonymous and 4 reported in untranslated regions (UTRs). Ten of the 26 non-synonymous variants were observed in ORF1ab, 7 in S, 1 in ORF3a, 2 in M and 6 in N genes.<bold>Conclusions: </bold>The Genexus system resulted successful for SARS-CoV-2 complete genome sequencing, also in cases with low viral copies. The use of this highly automated system might facilitate the standardization of SARS-CoV-2 sequencing protocols and make faster the identification of novel variants during the pandemic.
- Subjects
CAMPANIA (Italy); SARS-CoV-2; NUCLEOTIDE sequencing; VIRAL genomes; COVID-19; VACCINE effectiveness; EXOMES; GENE libraries
- Publication
Journal of Translational Medicine, 2021, Vol 19, Issue 1, p1
- ISSN
1479-5876
- Publication type
journal article
- DOI
10.1186/s12967-021-02912-4