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10.1186/s12967-021-02912-4 http://scihub22266oqcxt.onion/10.1186/s12967-021-02912-4 34090468!8179693!34090468     free     free     free Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=34090468&cmd=llinks): Failed to open stream: HTTP request failed! 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SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system |pdf=|usr=}}{{34090468}} gab.com Text SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system JO: J Transl Med http://www.kidney.de/pget.php?&tw=1&pmid=34090468 #FOAvip BACKGROUND: 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. METHODS: 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. RESULTS: 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/microl), 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. CONCLUSIONS: 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. Twit Text FOAVip SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system ????J Transl Med http://www.kidney.de/pget.php?&tw=1&pmid=34090468 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=34090468 #FOAvip English Wikipedia <ref>{{Cite pmid|34090468}}</ref> SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system #MMPMID34090468 Rachiglio AM; De Sabato L; Roma C; Cennamo M; Fiorenza M; Terracciano D; Pasquale R; Bergantino F; Cavalcanti E; Botti G; Vaccari G; Portella G; Normanno N J Transl Med 2021[Jun]; 19 (1): 246 PMID34090468show ga BACKGROUND: 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. METHODS: 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. RESULTS: 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/microl), 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. CONCLUSIONS: 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. |*COVID-19[MESH] |*SARS-CoV-2[MESH] |High-Throughput Nucleotide Sequencing[MESH] |Humans[MESH] |Italy[MESH]SARS-CoV-2 complete genome sequencing from the Italian Campania region(epmc).pdf DeepDyve Pubget Overpricing