At the institute where I work, we're sequencing H1N1 isolates from (IIRC) fifty UK patients. There are also emergency plans to start sequencing flu samples on a

At the institute where I work, we're sequencing H1N1 isolates from (IIRC) fifty UK patients. There are also emergency plans to start sequencing flu samples on a massive scale if it turns into a major epidemic. I would be astonished if large sequencing centres in other countries were not doing similar things. In other words: yes you're right, and it's already being done.