July San Paolo Sequence Released

[Rwilmer]

Re: July San Paolo Sequence Released

Only the first change is human, but that is the only one that is "new". The other two are also in earlier 2009 pandemic sequences (but different combinations).

It is V252M that is not found in other pandemic swine sequences, but a single change can have a big effect.

From the quote I posted, it sounds like many family members died.

I don't see where many family members died, I only see the little 11 year old girl died in that family, in brazil.

[HenryN]

Re: July San Paolo Sequence Released

I don't see where many family members died, I only see the little 11 year old girl died in that family, in brazil.

I may have skimmed the reports too quickly. Many family members were infected, but I haven't found confirmation that they died (I saw tragedy and thought it refered to deaths of multiple family members).

"The family Laguna had eight other cases of swine flu confirmed: mother, father, younger brother, three cousins, grandmother and an aunt of the girl. The tragedy led the silence of their parents.

[HenryN]

Re: July San Paolo Sequence Released

I don't see where many family members died, I only see the little 11 year old girl died in that family, in brazil.

There were two additional deaths in Osasco, but no detail

http://flutracker.rhiza.com/flu/gmap0907280927.html?lat=-23.170663827102235&lon=-46.142578125&zoom=9

[HenryN]

Re: July San Paolo Sequence Released

I'm totally confused. How does V252M in Swine Flu have anything to do with 1918 H1N1? I see no comparison whatsoever with SC, BM, NY, etc. Are we looking at the same sequences?

The 2001 swine sequence from Hong Kong has V252M, but most or all others in the travel log (including the Peru seasonal sequences and the 1918 sequences have V252I).
The recombination happens at the nucleotide level, and the travel log represent nucleotide identity for the non-synonymous change, as well as the upstream region.

[gsgs]

Re: July San Paolo Sequence Released

do we have data from the other Brasil cases ?
Some sequences are Mexico-City , pre-Cancun and
some Cancun (with S220T in HA)

It could be that the Mexico-City strain is more virulent in average,
I think we should try to figure that out so other countries
can avoid it.

[HenryN]

Re: July San Paolo Sequence Released

do we have data from the other Brasil cases ?
Some sequences are Mexico-City , pre-Cancun and
some Cancun (with S220T in HA)

It could be that the Mexico-City strain is more virulent in average,
I think we should try to figure that out so other countries
can avoid it.

There is only one recent sequence from Brazil. The earlier seqeunces did not have V252M, but I suspect it is in Argentina. Almost all fatalities in Brazil are in the south

http://flutracker.rhiza.com/flu/gmap0907280927.html?lat=-24.54712317973075&lon=-50.9326171875&zoom=6

[HenryN]

Re: July San Paolo Sequence Released

do we have data from the other Brasil cases ?
Some sequences are Mexico-City , pre-Cancun and
some Cancun (with S220T in HA)

It could be that the Mexico-City strain is more virulent in average,
I think we should try to figure that out so other countries
can avoid it.

The travel log for the other non-synonymous change was posted earlier

gb|GQ402203.1| Influenza A virus (A/Canada-MB/RV1982/2009(H1N... 35.6 0.008
gb|GQ392029.1| Influenza A virus (A/Italy/127/2009(H1N1)) seg... 35.6 0.008
gb|GQ368664.1| Influenza A virus (A/Sao Paulo/2233/2009(H1N1)... 35.6 0.008
gb|GQ330653.1| Influenza A virus (A/Italy/56/2009(H1N1)) segm... 35.6 0.008
gb|GQ329076.1| Influenza A virus (A/Paris/2722/2009(H1N1)) se... 35.6 0.008
gb|CY041830.1| Influenza A virus (A/New York/3348/2009(H1N1))... 35.6 0.008
gb|CY041822.1| Influenza A virus (A/New York/3352/2009(H1N1))... 35.6 0.008
gb|CY041782.1| Influenza A virus (A/New York/3337/2009(H1N1))... 35.6 0.008
gb|GQ323551.1| Influenza A virus (A/Massachusetts/08/2009(H1N... 35.6 0.008
gb|GQ323451.1| Influenza A virus (A/Rhode Island/03/2009(H1N1... 35.6 0.008
gb|GQ323446.1| Influenza A virus (A/Maine/03/2009(H1N1)) segm... 35.6 0.008
gb|GQ287625.1| Influenza A virus (A/Tokushima/1/2009(H1N1)) s... 35.6 0.008
gb|GQ283493.1| Influenza A virus (A/Finland/555/2009(H1N1)) s... 35.6 0.008
gb|GQ232044.1| Influenza A virus (A/Rhode Island/02/2009(H1N1... 35.6 0.008
gb|GQ232007.1| Influenza A virus (A/Vermont/03/2009(H1N1)) se... 35.6 0.008
gb|GQ200287.1| Influenza A virus (A/Shandong/1/2009(H1N1)) se... 35.6 0.008
gb|GQ166222.1| Influenza A virus (A/Italy/07/2009(H1N1)) segm... 35.6 0.008

[HenryN]

Re: July San Paolo Sequence Released

Updated travel log

gb|GQ414768.1| Influenza A virus (A/Sao Paulo/43812/2009(H1N1... 32.2 11
gb|GQ229293.1| Influenza A virus (A/swine/Hong Kong/NS1659/20... 32.2 11
gb|EU521831.1| Influenza A Virus (A/Yurimaguas/FLU4785/2006(H... 32.2 11
gb|EU521815.1| Influenza A Virus (A/Chanchamayo/FLU4292/2006(... 32.2 11
gb|EU521813.1| Influenza A Virus (A/Chanchamayo/FLU4036/2006(... 32.2 11
gb|EU521812.1| Influenza A Virus (A/Chanchamayo/FLU4032/2006(... 32.2 11
gb|EU521807.1| Influenza A virus (A/Chanchamayo/FLU3954/2006(... 32.2 11
gb|DQ431990.1| Influenza A virus (A/swine/Taiwan/CO935/2004(H... 32.2 11
gb|DQ447187.1| Influenza A virus (A/swine/Taiwan/CO935/2004(H... 32.2 11
gb|AY060041.1| Influenza A virus (A/SW/NE/21147/01(H1N2)) hem... 32.2 11
gb|CY009332.1| Influenza A virus (A/Fort Worth/50(H1N1)) segm... 32.2 11
gb|CY008988.1| Influenza A virus (A/Denver/57(H1N1)) segment ... 32.2 11
gb|AY377929.1| Influenza A virus (A/swine/Taichung/200-8/2002... 32.2 11
gb|AF117241.1|AF117241 Influenza A virus (A/South Carolina/1/... 32.2 11
dbj|D00837.1|FLA39HA Influenza A virus (A/swine/Cambridge/193... 32.2 11
dbj|AB043486.1| Influenza A virus (A/Saga/2/1957(H1N1)) HA ge... 32.2 11
dbj|AB043485.1| Influenza A virus (A/Meguro/1/1956(H1N1)) HA ... 32.2 11
dbj|AB043484.1| Influenza A virus (A/Yamagishi/55(H1N1)) HA g... 32.2 11
dbj|AB043483.1| Influenza A virus (A/Taiwan/13/1954(H1N1)) HA... 32.2 11
dbj|AB043482.1| Influenza A virus (A/Kojiya/1/1952(H1N1)) HA ... 32.2 11
gb|AF116576.1|AF116576 Influenza A virus (A/New_York/1/18(H1N... 32.2 11
gb|AF116575.1|AF116575 Influenza A virus (A/Brevig_Mission/1/... 32.2 11
gb|U04859.1|IAU04859 Influenza A virus (H1N1) A/swine/Cambrid... 32.2 11

[HenryN]

Re: July San Paolo Sequence Released

Updated travel log 2

gb|GQ414768.1| Influenza A virus (A/Sao Paulo/43812/2009(H1N1... 38.2 0.19
gb|GQ411907.1| Influenza A virus (A/Shanghai/143T/2009(H1N1))... 38.2 0.19
gb|GQ402203.1| Influenza A virus (A/Canada-MB/RV1982/2009(H1N... 38.2 0.19
gb|GQ392029.1| Influenza A virus (A/Italy/127/2009(H1N1)) seg... 38.2 0.19
gb|GQ368664.1| Influenza A virus (A/Sao Paulo/2233/2009(H1N1)... 38.2 0.19
gb|GQ330653.1| Influenza A virus (A/Italy/56/2009(H1N1)) segm... 38.2 0.19
gb|GQ329076.1| Influenza A virus (A/Paris/2722/2009(H1N1)) se... 38.2 0.19
gb|CY041830.1| Influenza A virus (A/New York/3348/2009(H1N1))... 38.2 0.19
gb|CY041822.1| Influenza A virus (A/New York/3352/2009(H1N1))... 38.2 0.19
gb|CY041782.1| Influenza A virus (A/New York/3337/2009(H1N1))... 38.2 0.19
gb|GQ323551.1| Influenza A virus (A/Massachusetts/08/2009(H1N... 38.2 0.19
gb|GQ323451.1| Influenza A virus (A/Rhode Island/03/2009(H1N1... 38.2 0.19
gb|GQ323446.1| Influenza A virus (A/Maine/03/2009(H1N1)) segm... 38.2 0.19
gb|GQ287625.1| Influenza A virus (A/Tokushima/1/2009(H1N1)) s... 38.2 0.19
gb|GQ283493.1| Influenza A virus (A/Finland/555/2009(H1N1)) s... 38.2 0.19
gb|GQ232044.1| Influenza A virus (A/Rhode Island/02/2009(H1N1... 38.2 0.19
gb|GQ232007.1| Influenza A virus (A/Vermont/03/2009(H1N1)) se... 38.2 0.19
gb|GQ200287.1| Influenza A virus (A/Shandong/1/2009(H1N1)) se... 38.2 0.19
gb|GQ166222.1| Influenza A virus (A/Italy/07/2009(H1N1)) segm... 38.2 0.19

[HenryN]

Re: July San Paolo Sequence Released

Updated travel log 3

gb|GQ414768.1| Influenza A virus (A/Sao Paulo/43812/2009(H1N1... 34.2 2.9
gb|GQ377095.1| Influenza A virus (A/California/24/2009(H1N1))... 34.2 2.9
gb|GQ359765.1| Influenza A virus (A/Stockholm/31/2009(H1N1)) ... 34.2 2.9
gb|GQ292961.1| Influenza A virus (A/Mexico City/22/2009(H1N1)... 34.2 2.9
gb|GQ229293.1| Influenza A virus (A/swine/Hong Kong/NS1659/20... 34.2 2.9
gb|GQ232085.1| Influenza A virus (A/Guangdong/02/2009(H1N1)) ... 34.2 2.9
gb|GQ223435.1| Influenza A virus (A/Guangdong/05/2009(H1N1)) ... 34.2 2.9
gb|GQ132144.1| Influenza A virus (A/Canada-ON/RV1529/2009(H1N... 34.2 2.9

[HenryN]

Re: July San Paolo Sequence Released

Note that the 2001 Hong Kong swine has 2 of the 3 polymorphisms (no random mutations required).

[HenryN]

Re: July San Paolo Sequence Released

Updated travel log 2

gb|GQ414768.1| Influenza A virus (A/Sao Paulo/43812/2009(H1N1... 38.2 0.19
gb|GQ411907.1| Influenza A virus (A/Shanghai/143T/2009(H1N1))... 38.2 0.19
gb|GQ402203.1| Influenza A virus (A/Canada-MB/RV1982/2009(H1N... 38.2 0.19
gb|GQ392029.1| Influenza A virus (A/Italy/127/2009(H1N1)) seg... 38.2 0.19
gb|GQ368664.1| Influenza A virus (A/Sao Paulo/2233/2009(H1N1)... 38.2 0.19
gb|GQ330653.1| Influenza A virus (A/Italy/56/2009(H1N1)) segm... 38.2 0.19
gb|GQ329076.1| Influenza A virus (A/Paris/2722/2009(H1N1)) se... 38.2 0.19
gb|CY041830.1| Influenza A virus (A/New York/3348/2009(H1N1))... 38.2 0.19
gb|CY041822.1| Influenza A virus (A/New York/3352/2009(H1N1))... 38.2 0.19
gb|CY041782.1| Influenza A virus (A/New York/3337/2009(H1N1))... 38.2 0.19
gb|GQ323551.1| Influenza A virus (A/Massachusetts/08/2009(H1N... 38.2 0.19
gb|GQ323451.1| Influenza A virus (A/Rhode Island/03/2009(H1N1... 38.2 0.19
gb|GQ323446.1| Influenza A virus (A/Maine/03/2009(H1N1)) segm... 38.2 0.19
gb|GQ287625.1| Influenza A virus (A/Tokushima/1/2009(H1N1)) s... 38.2 0.19
gb|GQ283493.1| Influenza A virus (A/Finland/555/2009(H1N1)) s... 38.2 0.19
gb|GQ232044.1| Influenza A virus (A/Rhode Island/02/2009(H1N1... 38.2 0.19
gb|GQ232007.1| Influenza A virus (A/Vermont/03/2009(H1N1)) se... 38.2 0.19
gb|GQ200287.1| Influenza A virus (A/Shandong/1/2009(H1N1)) se... 38.2 0.19
gb|GQ166222.1| Influenza A virus (A/Italy/07/2009(H1N1)) segm... 38.2 0.19

Sequences with mixtures at this position include

A/Canada-MB/RV2020/2009
A/Canada-MB/RV2013/2009
A/Canada-MB/RV1977/2009
A/Canada-MB/RV2023/2009
A/Canada-MB/RV1964/2009

[Rwilmer]

Re: July San Paolo Sequence Released

So this mutation found was V252M, and not V252I, found in 1918?

[HenryN]

Re: July San Paolo Sequence Released

So this mutation found was V252M, and not V252I, found in 1918?

The nucleotide change responsible for V252M is as indicated in the travel log (and is in the 1918 isolates).

[Rwilmer]

Re: July San Paolo Sequence Released

The problem is that is was bad a biology in high school so I really don't understand any of this. Especially deoxyribonucleic acid.