TABLE 5.
Identification of species of the genus Lyssavirus based on Lyssavirus sequences tiled on the PathogenID_v2.0 microarray and using the consensus sequence determination strategy
| Lyssavirus species (abbreviation), isolate, and parameter tested | Result obtained with analysis strategy of use of: |
||
|---|---|---|---|
| Prototype sequence only | Consensus sequence |
||
| Including all tiled sequences | Excluding prototype sequence | ||
| 1 (RABV) | |||
| 93127FRA | |||
| Base call ratea | 95.0 | 96.3 | 32.7 |
| BLAST scoreb | 791 | 801 | 38 |
| Accuracyc | 100 | 99.9 | 95.9 |
| 8764THA | |||
| Base call rate | 32.6 | 47.4 | 26.7 |
| BLAST score | 46 | 64 | 31 |
| Accuracy | 94.8 | 99.1 | 98.4 |
| 2 (LBV), 8619NIG | |||
| Base call rate | 96.6 | 96.4 | 28.1 |
| BLAST score | 816 | 814 | 39 |
| Accuracy | 99.9 | 99.9 | 97.7 |
| 3 (MOKV), 86100CAM | |||
| Base call rate | 56.3 | 67.4 | 28.4 |
| BLAST score | 66 | 112 | 64 |
| Accuracy | 98.2 | 99.8 | 98.5 |
| 4 (DUVV), 86132SA | |||
| Base call rate | 97.3 | 97.3 | 18.1 |
| BLAST score | 843 | 833 | 20 |
| Accuracy | 99.9 | 99.8 | 96.4 |
| 5 (EBLV-1), 8918FRA | |||
| Base call rate | 93.8 | 96.0 | 41.1 |
| BLAST score | 757 | 807 | 83 |
| Accuracy | 100 | 100 | 97.9 |
| 6 (EBLV-2), 9018HOL | |||
| Base call rate | 98.4 | 98.8 | 26.8 |
| BLAST score | 871 | 879 | 44 |
| Accuracy | 100 | 99.9 | 99.6 |
| 7 (ABLV), ABLV | |||
| Base call rate | 94.9 | 95.6 | 29.7 |
| BLAST score | 749 | 741 | 40 |
| Accuracy | 100 | 99.9 | 94.5 |
| 8e (DBLV), 0406SEN | |||
| Base call rate | NAd | 75.9 | NA |
| BLAST score | NA | 82 | NA |
| Accuracy | NA | 91.8 | NA |
| ?, WCBV | |||
| Base call rate | NA | 60.9 | NA |
| BLAST score | NA | 56 | NA |
| Accuracy | NA | 97.3 | NA |
Percentage of base calls generated from full-length tiled sequences.
BLAST score (bit score) obtained after BLAST query on a local viral and bacterial database using the consensus sequence determination strategy with m (minimum nucleotide length) = 12 and N (maximum undetermined nucleotide content) = 10. Default BLAST parameters, except for the minimum word length (7 nt), the expect threshold (increased from the default of 10 to 100,000), and the low complexity level filter (−F) turned off. All of the BLAST scores indicate correct identification at the species or isolate level (i.e., unique best hit corresponds to the expected species or isolate).
Percentage of nucleotides correctly identified, compared to the sequence obtained after classical sequencing of the corresponding Lyssavirus species tested.
NA, not applicable.
Tentative species.