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I Have Some Questions About Sequences

M

mixin

Well-known member
I went through all the Novel H1N1 sequences at Genbank and here are my questions:

* I noticed some of the numbers are not in sync with the collection dates. Here is an example:
California/09/2009 04-15-09 M 7
California/10/2009 04-08-09 F
Who names the genomes? And when?

* I noticed some of the sequences had this notation:
Antigen_character : A/CALIFORNIA/07/2009-LIKE (H1N1)V
Do all the genomes have this character, or only the ones noted?
Why is this significant?

* Could someone explain these?:
A/reassortant/IDCDC-RG15(Texas/05/2009 x Puerto Rico/8/1934
A/reassortant/NYMC X-179A(California/07/2009 x NYMC X-157
A/resassortant/IVR-153(A/California/07/2009 x IVR-6)

* The number system is confusing. Here is the first from Paris:
Paris/2573/2009 04-29-09 F 24 Ile-de-France
The number is 2573. Is that the number of tests they've done this year?
Or is it chosen some other way?

* Mexico (and others) appear to have different naming systems within their country.
Here are a couple from Mexico:
Mexico/InDRE4114/2009
Monterrey/2/2009 05-08-09 M Nuevo Leon
Mexico/47N/2009 04-25-09 M 5 Mexico City
If I'm coming to the correct conclusion, then any with the "Monterrey' name comes from the Nuevo Leon region and the "Mexico" sequences come from the Mexico City area.
Why can't we find out where the "InDre" sequences are from?

* I found this odd one in the Tennessee list:
Tennessee/1-560/2009 05-01-09 (Memphis)
Tennessee/05/2009 04-28-09 M 13
The 1-560 is the only 1 in all the US sequences I looked at that was not named like the others. What's different about this one?

If anyone wants to look at my complete list, it's at gs's forum
http://www.setbb.com/phpbb/viewtopic.php?t=753&mforum=fluwiki2
 
Re: I Have Some Questions About Sequences

> I Have Some Questions About Sequences

> I went through all the Novel H1N1 sequences at Genbank and here are my questions:

> * I noticed some of the numbers are not in sync with the collection dates. Here is an example:
> California/09/2009 04-15-09 M 7
> California/10/2009 04-08-09 F
> Who names the genomes? And when?

I assume samples are collected and first frozen. Then in some intervals they are examed
and what comes first out of the freezer gets the first number.

>* I noticed some of the sequences had this notation:
> Antigen_character : A/CALIFORNIA/07/2009-LIKE (H1N1)V
> Do all the genomes have this character, or only the ones noted?
> Why is this significant?

sometimes they are curious and compare the new found sequences to existing
sequences

> * Could someone explain these?:
> A/reassortant/IDCDC-RG15(Texas/05/2009 x Puerto Rico/8/1934
> A/reassortant/NYMC X-179A(California/07/2009 x NYMC X-157
> A/resassortant/IVR-153(A/California/07/2009 x IVR-6)

some viruses are preserved and available for laboratories. The 1934 virus is commonly used,
also because it grows well in eggs , I think. The Calif./07 was one of the earliest
manynamesflu-strains collected in USA and chosen for vaccine, replicated, prepared,
sent to other laboratories.

>* The number system is confusing. Here is the first from Paris:
> Paris/2573/2009 04-29-09 F 24 Ile-de-France
> The number is 2573. Is that the number of tests they've done this year?
> Or is it chosen some other way?

presumably the number of tests this year. But this includes seasonal flu and who knows
what else

> * Mexico (and others) appear to have different naming systems within their country.
> Here are a couple from Mexico:
> Mexico/InDRE4114/2009
> Monterrey/2/2009 05-08-09 M Nuevo Leon
> Mexico/47N/2009 04-25-09 M 5 Mexico City

presumably different groups collecting the viruses, different laboratories
sequencing them and/or submitting to genbank. Often some groups are preparing
papers about the sequences which then are published in some medical journals.
I assume they get money for the publishing or it helps for their reputation, their career.

>If I'm coming to the correct conclusion, then any with the "Monterrey' name comes
> from the Nuevo Leon region and the "Mexico" sequences come from the Mexico City
> area. Why can't we find out where the "InDre" sequences are from?

Monterrey is a town in Mexico, presumably in the province "Nuevo Leon". The provinces
are responsible to report the cases to the central government.
Some should also be from Oaxaca, 4108 should be from Veracruz province
InDRE is
Instituto de Diangnostico y Referencia Epidemiologicos (inDRE), Canada/Mexico
they sent some sequences to Canada in the early days

> * I found this odd one in the Tennessee list:
> Tennessee/1-560/2009 05-01-09 (Memphis)
> Tennessee/05/2009 04-28-09 M 13
> The 1-560 is the only 1 in all the US sequences I looked at that was not named like the others.
> What's different about this one?

Maybe St.Jude's ? St.Jude's is in Memphis AFAIK. Usually US-sequencing is done by CDC

> If anyone wants to look at my complete list, it's at gs's forum
> http://www.setbb.com/phpbb/viewtopic...forum=fluwiki2

thanks. I plan to copy it to H5N1-experts later
 
Re: I Have Some Questions About Sequences

mixin said:
I went through all the Novel H1N1 sequences at Genbank and here are my questions:

* I noticed some of the numbers are not in sync with the collection dates. Here is an example:
California/09/2009 04-15-09 M 7
California/10/2009 04-08-09 F
Who names the genomes? And when?

- Usually the institution which done the test named the strains. California refers to the isolation place. 09 refers to isolate number. 2009 refers to year collected. For human isolate, we don't put the host type.

* I noticed some of the sequences had this notation:
Antigen_character : A/CALIFORNIA/07/2009-LIKE (H1N1)V
Do all the genomes have this character, or only the ones noted?
Why is this significant?

-Probably they tested this isolate as 2009 H1N1 like by PCR. But some confusion might occur, and sequences haven't been confirmed. To avoid misdiagnosis, they prefer to name it that way.

* Could someone explain these?:
A/reassortant/IDCDC-RG15(Texas/05/2009 x Puerto Rico/8/1934
A/reassortant/NYMC X-179A(California/07/2009 x NYMC X-157
A/resassortant/IVR-153(A/California/07/2009 x IVR-6)

- As I mentioned before, the naming of influenza A virus will started with A/host type/place/isolate code/year.

-In this case, the isolate refers to mixed strains. This must have been sequenced compeletely. I'm not sure why they didn't put the host type instead.

* The number system is confusing. Here is the first from Paris:
Paris/2573/2009 04-29-09 F 24 Ile-de-France
The number is 2573. Is that the number of tests they've done this year?
Or is it chosen some other way?

-Usually the code number refers to isolate number. But numbers are not always showing the number of patients. It could be number of the kind of isolate. For example, throat swab of Mr A, numbered as 1. But the nasal swab of Mr A, numbered as 2. Et cetera.

* Mexico (and others) appear to have different naming systems within their country.
Here are a couple from Mexico:
Mexico/InDRE4114/2009
Monterrey/2/2009 05-08-09 M Nuevo Leon
Mexico/47N/2009 04-25-09 M 5 Mexico City
If I'm coming to the correct conclusion, then any with the "Monterrey' name comes from the Nuevo Leon region and the "Mexico" sequences come from the Mexico City area.
Why can't we find out where the "InDre" sequences are from?

- Probably the isolates were confirmed and uploaded by different institution/laboratory. Each institution has their own naming categories. InDre4114 is the lab code. We can find some isolates with lab name on it, for example A/Indonesia/CDC.../2005 (H5N1)

* I found this odd one in the Tennessee list:
Tennessee/1-560/2009 05-01-09 (Memphis)
Tennessee/05/2009 04-28-09 M 13
The 1-560 is the only 1 in all the US sequences I looked at that was not named like the others. What's different about this one?

- Again, probably they came from different diagnostic lab.

If anyone wants to look at my complete list, it's at gs's forum
http://www.setbb.com/phpbb/viewtopic.php?t=753&mforum=fluwiki2
Click to expand...


I hope this can help. Maybe not :D
 
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