Table 2.
Virus and genome-specific comparison of the SISPA sequence data.
| Virus | Origin | Genome Segment/Gene | Sequence Length | Coverage | Identity | Indels | Substitutions | Ambiguities | Homopolymers Corrected | |
|---|---|---|---|---|---|---|---|---|---|---|
| NGS | SISPA | |||||||||
| CCHFV | Specimen 1 | L | 12,122 | 7347 | 60.6% | 99.8% | 4 | 2 | 3 | 22 |
| M | 5352 | − | − | − | − | − | − | |||
| S | 1573 | 1372 | 87.2% | 99.5% | 1 | 1 | 5 | 2 | ||
| Specimen 2 | L | 12,122 | 11,725 | 96.7% | 99.9% | 1 | 3 | 7 | 20 | |
| M | 5404 | 1878 | 34.7% | 99.6% | 5 | − | 3 | 5 | ||
| S | 1573 | 989 | 62.8% | 99.8% | 1 | − | − | 1 | ||
| Specimen 3 | L | 12,122 | 12,099 | 99.8% | 99.9% | − | 2 | 11 | ||
| M | 5352 | 5338 | 99.7% | 99.8% | 1 | 2 | 1 | 14 | ||
| S | 1573 | 1568 | 99.6% | 100% | − | − | − | 1 | ||
| Specimen 5 a | L | 12,121 | 12,116 | 99.9% | n.a. | − | n.a. | − | 11 | |
| M | 5332 | 5314 | 99.6% | n.a. | − | n.a. | 1 | 11 | ||
| S | 1621 | 1597 | 98.5% | n.a. | − | n.a. | 1 | 4 | ||
| JMTV | Specimen 4 | 1 (NSP1) | 2894 | 2732 | 94% | 99.9% | 1 | 1 | 1 | 6 |
| 2 (VP1) | 2549 | 2087 | 81.8% | 99.8% | − | 1 | 2 | 8 | ||
| 3 (NSP2) | 2643 | 2538 | 96.0% | 99.9% | − | 2 | − | 3 | ||
| 4 (VP2/3) | 2635 | 1547 | 58.7% | 99.2% | 4 | 5 | 2 | 4 | ||
| Specimen 6 b | 1 (NSP1) | 2894 | 2879 | 99.4% | 99.9% | 1 | 0.1 | − | 11 | |
| 2 (VP1) | 2549 | 2514 | 98.6% | 99.8% | − | 0.3 | − | 10 | ||
| 3 (NSP2) | 2643 | 2610 | 98.7% | 100% | − | − | − | 2 | ||
| 4 (VP2/3) | 2635 | 2592 | 98.3% | 99.8% | − | 0.4 | − | 5 | ||
n.a.: not available/not applicable; a no previously-available genome sequence data, coverage and identities are based on the most similar virus genome in GenBank b as compared to next generation sequencing (NGS) of the initial tick pool.