Table 2.
Classification of SARS-CoV-2, SARS-CoV, and MERS de novo assembled contigs using BLAST.
| Sample | Untargeted mNGS, or viral enrichment by capture probes | Total contigs ≥ 500bp |
Viral contigs ≥ 500bp |
Coronaviridae contig ≥ 500bp | Length of the longest Coronaviridae contig, bp | BLAST alignment length, bp | BLAST identity match, % | Subject taxonomy name | Release year of sequence of the species | Release year of sequence of the subject found |
|---|---|---|---|---|---|---|---|---|---|---|
| SARS-CoV-2 Patient A (Cq 20) |
Untargeted | 8,606 | 15 | 3 | 19,654 | 12,069 | 87.141 | Bat SARS SL CoVZC45 | 2003 | 2018 |
| Viral capturea | 8,232 | 51 | 31 | 5,811 | 5,820 | 90.567 | Bat SARS SL CoVZC45 | 2003 | 2018 | |
| SARS-CoV-2 Patient B (Cq 30) |
Untargeted | 2,815 | 31 | 16 | 2,503 | 2,456 | 91.450 | Bat SARS SL CoVZXC21 | 2003 | 2018 |
| Viral capturea | 2,110 | 39 | 13 | 4,866 | 4,856 | 92.360 | Bat SARS SL CoVZC45 | 2003 | 2018 | |
| SARS-CoV Frankfurt-1 (Cq 23) |
Untargeted | 3,836 | 10 | 1 | 29,692 | 1,236 | 72.411 | Bovine coronavirus isolate 4-17-03 | 2001 | 2018 |
| MERS-CoV EMC/2012 (Cq 22) |
Untargeted | 4,074 | 9 | 1 | 30,097 | 14,856 | 77.248 | Bat coronavirus HKU4-1 | 2006 | 2006 |
Table showing the total number of built contigs with a length > = 500bp, the number of these contigs where the hit with the lowest E-value would be a hit to viruses, the number of contigs where the hit with the lowest E-value would be a hit to Coronaviridae and of this last group the length of the longest contig, the alignment length, identity match, taxonomic name of BLAST result and the release years of sequences belonging to the species and subjects found by BLAST.
a
Enrichment by capture probes targeting vertebrate viruses designed in 2015