Comments on: More Swine Flu genome

By: RE

RE — Sun, 10 May 2009 04:45:54 +0000

Nice Work, But there a fundamental question that recombination will occur in gene level and not the protein (aminoacid) therefore It make more sense to use phylogenic tree or blast based on the genome sequence since the results of comparison by these two method are not completely identical, here are the closest match for canadian SW H1N1 that I found by simple blast. I look forward for your comments.

1 PB2 AF251434.1 (A/Swine/Minnesota/593/99 (H3N2))
AF251426.1 (A/Swine/Iowa/569/99 (H3N2))
AF251418.1 (A/Swine/Iowa/533/99 (H3N2))
AF251410.1 (A/Swine/Nebraska/209/98 (H3N2))
AY233387.1 (A/duck/NC/91347/01(H1N2))

2 PB1 AF342823.1 (A/Wisconsin/10/98 (H1N1))
AF250130.1 (A/Swine/Indiana/9K035/99 (H1N2))
AY233388.1 (A/duck/NC/91347/01(H1N2))
AF251429.1 (A/Swine/Minnesota/593/99 (H3N2))
AF251421.1 (A/Swine/Iowa/569/99 (H3N2))

3 PA CY033792.1 (A/pintail duck/South Dakota/Sg-00126/2007(H3N2))
AY233389.1 (A/duck/NC/91347/01(H1N2))
EF551052.1 (A/swine/North Carolina/2003(H3N2))
AF455722.1 (A/Swine/Illinois/100084/01 (H1N2))
AF251433.1 (A/Swine/Minnesota/593/99 (H3N2))

4 HA AF250124.1 (A/Swine/Indiana/9K035/99 (H1N2))
EF556201.1 (A/swine/Guangxi/17/2005(H1N2))
AY060047.1 (A/SW/MN/23124-T/01(H1N2))
AF455680.1 (A/Swine/Indiana/P12439/00(H1N2))
AY060050.1 (A/SW/MN/16419/01(H1N2))

5 NP AF251415.2 (A/Swine/Iowa/533/99 (H3N2))
AF251423.2 (A/Swine/Iowa/569/99 (H3N2))
EU798854.1 (A/swine/Korea/CY05/2007(H3N2))
EU798853.1 (A/swine/Korea/CY04/2007(H3N2))
AF251431.2 (A/Swine/Minnesota/593/99 (H3N2))

6 NA AF250366.2 (A/Swine/England/195852/92 (H1N1))
CY038009.1 (A/swine/England/WVL7/1992(H1N1))
CY038001.1 (A/swine/Spain/WVL6/1991(H1N1))
CY037908.1 (A/swine/England/WVL10/1993(H1N1))
AM920729.1 (A/swine/Germany/Vi5698/95(H1N1))

7 M AJ293925.1 (A/Hong Kong/1774/99(H3N2))
AY363575.1 (A/swine/Hong Kong/5212/99(H3N2))
AY363574.1 (A/swine/Hong Kong/5200/99(H3N2))
AY363573.1 (A/swine/Hong Kong/5190/99(H3N2))
DQ186981.1 (A/swine/Leipzig/145/92(H3N2))

8 NS EU735822.1 (A/turkey/OH/313053/2004(H3N2))
DQ150437.1 (A/swine/IN/PU542/04 (H3N1))
AF342817.1 (A/Wisconsin/10/98 (H1N1))
AF153262.1 (A/Swine/Minnesota/9088-2/98 (H3N2))
AF153261.1 (A/Swine/Texas/4199-2/98 (H3N2))

By: gsgs

gsgs — Sat, 02 May 2009 05:12:18 +0000

everything seems to go back to one ancestor
virus from this year. Presumably the one where
the reassortment happened

By: gsgs

gsgs — Sat, 02 May 2009 05:09:55 +0000

does Mexico only deposit her Sequences at GISAID ? Is it ethical to withhold them ?
Do they claim for some sort of “copyright” on
“their” viruses like Indonesia does for H5N1 ?

So we will always know who was the originator
of this mess when we get swine flu ….
A/Mexico/4482/2009 (H1N1)
A/Mexico/4486/2009 (H1N1)
A/Mexico/4108/2009 (H1N1)
A/Mexico/4115/2009 (H1N1)
A/Mexico/4603/2009 (H1N1)
A/Mexico/4604/2009 (H1N1)

By: Nulgod

Nulgod — Sat, 02 May 2009 02:34:57 +0000

what puzzle me is position 185, 331 & 391

By: Swine Flu Natural? « The Firing Squid

Swine Flu Natural? « The Firing Squid — Fri, 01 May 2009 00:27:41 +0000

[...] However, it should take a long time for three viruses to combine into one coat. Long enough for a precursor to have spread widely, causing animals to get sick so that they get tested, perhaps to the point that the new genome is detected in a laboratory, before a third virus is incorporated into the new strain. It should also be possible to find a virus having a combination of two of the three RNA strains somewhere else in the wild. This may have occurred already in pigs in Ohio (2007). There are doubts, however, that the Ohio outbreak is not a red herring, as is covered well here. [...]

By: David

David — Thu, 30 Apr 2009 19:02:22 +0000

Hi,

I’ve tried a similar analysis to Sandra’s, except using BLAST and maximum likelihood:

http://koppology.blogspot.com/2009/04/swine-flu-phylogeny-part-ii.html

I agree that there is not a particularly strong argument for the Ohio strain being particularly close. However, I have made other observations that I’ve detailed in the post — I think there is some tentative evidence for antigenic shift.

This is very much a first attempt, feedback would be appreciated.

By: iayork

iayork — Wed, 29 Apr 2009 16:52:14 +0000

I still think the most likely reason for the apparent difference in Mexico and the US is the missing denominator, rather than any host or environmental factor. That is, I suspect that the virus is much more widespread in Mexico City than the authorities know. Because they almost entirely tested severely ill hospitalized patients, it’s not surprising that they found high mortality rates; if they were also testing mild cases (as is happening in the US and elsewhere) I think they would likely find a very widespread infection with a low mortality rate.

But who knows.

By: Vincent Racaniello

Vincent Racaniello — Wed, 29 Apr 2009 16:46:28 +0000

I’ve compared the California and New York HA sequences, and they differ by only a few amino acids. If we assume that the NY strain came from Mexico, this would suggest that the Mexican strains are going to be similar. The increased severity (if that is really true) in Mexico is likely to be due to host factors. I notice a German sequence just came in – from a tourist who had traveled to Mexico. I’m going to do a quick alignment of that now. I wish I had more time to spend on this!

By: Daily News About Science : A few links about Science - Wednesday, 29 April 2009 05:09

Wed, 29 Apr 2009 13:26:19 +0000

[...] More Swine Flu genome [...]