The BLAST algorithm is used for sequence comparison, because of its advantages such as fast computation and accurate results in detecting local highly similar sequence regions. To overcome its inherent disadvantage (i.e. not a global alignment algorithm), we used a parameter called 'coverage' to detect gene-wide sequence similarity (25) . The default thresholds for identifying lineages were set to be 95% identity and 95% coverage. The user can reset the thresholds to any allowable value. The top BLAST results for a user-submitted query sequence are sorted by identity and coverage, and the best result is used to assign a lineage to the query sequence. If a result from BLAST falls below the thresholds, the lineage will be flagged with an asterisk ( Ã ).