Comments on: Has the new H1N1 been hiding for 11 years? (No.)

By: PB

PB — Wed, 27 May 2009 08:19:02 +0000

Again, many thanx for this work. Perhaps at some point in the near future you could educate us uninformed folks about nomenclature. Assuming there is some underlying logic. What makes any given H1N1 genome a ‘swine’-designated sequence instead of a place-designated sequence? ie A/Brisbane/yada/yada(H1N1) versus A/swine/OH/yada/yada(H1N1). Is it an antigenic determination or a sequence signature or simply proximity to an actual porcine mammal(see I have avoided the ‘s’ word LOL)

By: iayork

iayork — Sat, 16 May 2009 03:40:49 +0000

Good point, especially about the flu database. That’s a fascinating article by Rabadan for several reasons.

By: Vincent Racaniello

Vincent Racaniello — Sat, 16 May 2009 03:19:51 +0000

Raul Rabadan tells me that the NA of the H1N1 is similar to Eurasian swine NAs that last circulated 10 years ago. And he also says that the swine flu database is sufficiently sparse for many countries that such comparisons aren’t valid. Plus, the flu database is full of errors (see his paper in J. Virol, 2008). So I suggest caution when using these sequences to make conclusions about the origin of influenza viruses.

By: gsgs

gsgs — Mon, 04 May 2009 15:00:36 +0000

seems that you are ignoring partial sequences.
Please include them.
The best matches are all from 1998/99 and not
from 2004-2007, where also some sequences are available. (segments 123458)

Except these South-Dakota ducks.

Moreover the expected number of mutations per year matches quite well with A/Wisconsin/10/1998,
so the new virus could be almost a direct descendent. (close relative)

By: dmv

dmv — Sun, 03 May 2009 15:51:23 +0000

jay:

I quote from a post over on Effect Measure:

‘But each isolate of this virus also has an “official” name or designation. One isolated from a Texas case has this name: A/Texas/05/2009(H1N1). The naming system looks complicated but it’s really quite simple. The A-part means that this is a flu virus of type A (rather than flu B or flu C). Texas is a location marker, which could be broad, like Texas, or more narrow, like the name of a city (e.g., Hong Kong). The 05 is the specimen identifier in the lab where it was isolated and 2009 is the year. If the virus had been isolated from a non-human animal, that would be included, e.g., A/Chicken/Shantou/4231/2003. And the H1N1 part is the subtype.’

The post is at this link: http://scienceblogs.com/effectmeasure/2009/04/swine_flu_a_virus_by_any_other.php

By: jay

jay — Sun, 03 May 2009 15:02:24 +0000