Example 3 Alignment

Alignment of sequences that are too short to create a tree. Extensive contamination with pNL43 was detected by performing BLAST searches (indicated by yellow horizontal bars), and by using signature patterns that are characteristic for each patient. Although identity of one individual sequence to a lab strain would not conclusively prove contamination, all evidence taken together is very strong:

• the offending sequence in all cases was NL43
• NL43 was used in this laboratory
• all patients' sequences had clear characteristic signatures that were not shared by NL43.