If anyone’s interested in looking at relationships between the new H1N1 and other influenza viruses, I’ve put up a (large!) table here showing relatives of each of the segments.
Knock yourselves out.
(This took me a good 15 minutes to produce, what with running the blast searches and writing the 15 lines of Python that parsed the output and printed out the table, so I hope you appreciate it.)
Impressive! Very interesting. And, I know you’ve brought this up before, but I think the media oftentimes lacks an appreciation of how small the sequence differences actually are between the strains, so this is a pretty cool demonstration of just that fact.
Thanks for that. Interesting. Do you know any of the background of the 100% homologous Auckland strain (this is NZ?). Is there any evidence it originated from the current North American outbreak?
This was a tourist from New Zealand returning from Mexico. It was one of the first non-American cases of this H1N1. I think there were 4 cases in New Zealand, and I think they were all acquired overseas (or on the flight home) — no evidence for community transmission within New Zealand.
I get the gist of what the table is showing, but I’m a bit confused on one thing. As I understand from reading your updates, there are no avian components to the “2009 H1N1″, but there are what I as a novice would consider some pretty high homologies with mallard, turkey, pintail, and several other avian references. If you could devote a couple of sentences on a future update explaining that, I’d appreciate it.
these duck-viruses from South Dakota are not “normal”. They are very close to
A/Wisconsin/10/1998 despite being
9 years later, so either there is some error
or the virus survived without replicating
which may sometimes happen but is rare.
In any case, it shouldn’t be viewed as a virus from 2007
Does this square with the NEJM report Thursday?
http://content.nejm.org/cgi/reprint/NEJMoa0903810.pdf