CDC Release Swine Flu Sequences in Real Time

[HenryN]

CDC is releasing swine flu sequences in real time. Sequences from the following isolates have been placed on deposit at GISAID

Name - Host - Collection date

A/California/09/2009 7M 2009-04-15
A/Texas/05/2009 16M 2009-04-15
A/Texas/04/2009 16M 2009-04-14
A/California/07/2009 54M 2009-04-09
A/California/06/2009 41F 2009-04-16
A/California/05/2009 9F 2009-03-30
A/California/04/2009 10M 2009-04-01

[Laidback Al]

Re: CDC Release Swine Flu Sequences in Real Time

We seem to be missing a sample from the 16F (onset April 5, 2009), daughter of the 54M, both of whom were from San Diego County.

[gsgs]

Re: CDC Release Swine Flu Sequences in Real Time

any mentioning why gisaid ?
putting them at gisaid is not really "release"

some other country will hopefully release/publish them
but it gives delay

[HenryN]

Re: CDC Release Swine Flu Sequences in Real Time

any mentioning why gisaid ?
putting them at gisaid is not really "release"

some other country will hopefully release/publish them
but it gives delay

GISAID is a release.

[HenryN]

Re: CDC Release Swine Flu Sequences in Real Time

We seem to be missing a sample from the 16F (onset April 5, 2009), daughter of the 54M, both of whom were from San Diego County.

The sequences are being added as they become available. Initially there was just HA, NA, and M from California/4, which was followed by a full set (all 8 gene segments) from that isolate.
Today the ones I listed were added. Some are close to a full set, others, like California/9 just have an HA partial.
The sequences depend on isolating the virus and generating the sequences. Not all confirmed cases will generate virus.
I suspect the numbers will increase dramatically and the sequences are already sorting out.

Texas is distinct from California, and California is segregating out.

[gsgs]

Re: CDC Release Swine Flu Sequences in Real Time

then re-release it and post them here !
check their terms and conditions

are you the same niman who was shouting "free the sequences"
and critisizing WHO-private databases all the time ???

what changed ? Now you are one of those privilegies ?


the sequences will have to be published earlier or later,
this can't be kept secret.

[SophiaZoe]

Re: CDC Release Swine Flu Sequences in Real Time

I would be extremely interested in learning which genes are procine, which human, and of course, which avian.

[gsgs]

Re: CDC Release Swine Flu Sequences in Real Time

I assume it's 1,2,3,4,5,8 from US-swine and 6,7 from Eurasian swine (Thailand?)

US-swine(<1998) however is 1,3 avian, 2 human (1968), 45678 swine(<1918)

so segments 1,3 are still of avian characteristic after only 10years
and reporters misinterpreted this as quadruple reassortant

the gisaid people should know, but are they allowed to tell us ?

[gsgs]

Re: CDC Release Swine Flu Sequences in Real Time

> Due to the characteristics of his genome, the Mexican secretary
> of health assured that the virus was not developed in the country,
> but was brought by some traveller.

that's strange. What kind of characteristic could that be ?
And if he had the proof, then why withhold it ?

I doubt that the Mexican secretary of health is credible here.

[Legadillo]

Re: CDC Release Swine Flu Sequences in Real Time

Moved ...

[SophiaZoe]

Re: CDC Release Swine Flu Sequences in Real Time

I assume it's 1,2,3,4,5,8 from US-swine and 6,7 from Eurasian swine (Thailand?)

US-swine(<1998) however is 1,3 avian, 2 human (1968), 45678 swine(<1918)

so segments 1,3 are still of avian characteristic after only 10years
and reporters misinterpreted this as quadruple reassortant

the gisaid people should know, but are they allowed to tell us ?

Thanks GS! That helps. I assume your assumption is probably correct.

[Swissgirl]

Re: CDC Release Swine Flu Sequences in Real Time

CDC to Hold Briefing on Swine Flu
Today at 1:00pm (Est)

Health officials at the Centers for Disease Control and Prevention will hold a briefing at 1 P.M. Saturday at their headquarters in Atlanta concerning a new strain of Swine Flu.

The virus has killed dozens in Mexico and sickened several others in texas and california.

The Mexican government has closed museums, theaters and other public places and events in an effort to reduce the spread of Swine Flu.

Mexican Officials are encouraging people to stay home. But, if they have to go out, the Army has mobilized soldiers to give out masks to subway commuters.

[JJackson]

Re: CDC Release Swine Flu Sequences in Real Time

Has anyone got a link to public accessible/downloadable sequences?

Or, at the least, some information regarding where the GISAID sequences fit in phylogenic trees that I can compare with sequences I do have access to.

Or failing that just some sensible comments from anyone who has seen the sequences. i.e. beyond 'they have some human, avian and swine genes' (very helpful)

[flutrackers@cool.fr.nf]

Re: CDC Release Swine Flu Sequences in Real Time

Has anyone got a link to public accessible/downloadable sequences?

Or, at the least, some information regarding where the GISAID sequences fit in phylogenic trees that I can compare with sequences I do have access to.

Or failing that just some sensible comments from anyone who has seen the sequences. i.e. beyond 'they have some human, avian and swine genes' (very helpful)

Seconded. It be very very helpful.

[AlaskaDenise]

Re: CDC Release Swine Flu Sequences in Real Time

There may not yet be enough sequences to form any reasonable conclusions. Perhaps after the number of cases rises to the point where trends, etc. can be identified they will release significant sequences.

The labs may be overwhelmed.

.