HIV and H1N1 Genome Map

[greenprogrammin]

I have been wanting to study the HIV genome map and match known sequences.

 

Has anyone done this?

 

I was looking at some H1N1 sequences back a while a go. I have not found the map to understand the genome...

 

Does anyone know if there is a H1N1 Genome Map laying around anywhere?

 

I'm trying to get involved in current events... I would like to talk about these genomes and stuff later.

 

I think I found the HIV genome map on NIAD but I havn't checked around for the H1N1 map.

 

Also, This is my first post to this forum and I just wanted to start a thread...

 

Thanx

Edited November 1, 2009 by greenprogrammin

[CharonY]

What do you mean with genome map? The annotated sequence has been published earlier.

[Genecks]

Maybe Pubmed?

 

pubmed.gov > search > dropdown genome

 

Also, don't use thanx.

 

In the 2009 flu pandemic, the virus isolated from patients in the United States was found to be made up of genetic elements from four different flu viruses – North American swine influenza, North American avian influenza, human influenza, and swine influenza virus typically found in Asia and Europe – "an unusually mongrelised mix of genetic sequences."[12] This new strain appears to be a result of reassortment of human influenza and swine influenza viruses, in all four different strains of subtype H1N1.

 

http://en.wikipedia.org/wiki/H1n1#2009_A.28H1N1.29_pandemic

 

 

On April 24, the U.S. Centers for Disease Control and Prevention (CDC) determined that seven samples from suspected cases in Mexico matched the strain that had infected patients in Texas and California with no known linkages to animals or one another; the strain appeared to be spreading from human to human.[43][44] The CDC determined that the strain contained genes from four different flu viruses – North American swine influenza, North American avian influenza, human influenza, and swine influenza virus typically found in Asia and Europe – "an unusually mongrelised mix of genetic sequences."[45][46] A CDC investigative team arrived in Mexico City on April 25 to work with Mexican counterparts to study the virus.[47]

 

http://en.wikipedia.org/wiki/2009_A/H1N1#Genetics

 

 

April 29, 2009

Q: Have you completely sequenced this virus?

 

R.D.: Yes, 2 weeks ago. Very soon after we received specimens from California and Texas. Hemagglutinin, neuraminidase, and matrix, the three genes that have the most public health interest, were sequenced, and then the whole genome was completed.

 

http://blogs.sciencemag.org/scienceinsider/2009/04/exclusive-cdc-h.html

 

Where, CharonY?

Does it have an actual genome or just cited bits and pieces?

 

Along with the actual spread of viral infections, availabilities

of 2009 swine H1N1 specific sequences deposited to NCBI's database GenBank also rapidly

proliferated starting early April through July, 2009. Laboratories of worldwide origins using

mostly Sanger-Dideoxy-terminator sequencing method sequenced most of 2009 novel H1N1 sequences.

Based on the up to date sequence comparisons, it is clear that not all deposited 2009 swine H1N1

sequences were identical. However, it was uncertain whether the differences of those supposedly

identical/similar causative agents were due to various clinical relevancies, i.e., severe or

mild infections. Or it was also possible that different sequences were actually derived from

different sequencing schemes using various RT-PCR amplification primers and protocols employed

by wide-range laboratories all over the world.

http://binf.gmu.edu/colloq/houng.txt

 

http://www.ncbi.nlm.nih.gov/genomes/FLU/help.html#genomeset

Edited November 1, 2009 by Genecks

[greenprogrammin]

CharonY:

This is similar to what I was looking for:

://www.hiv.lanl.gov/content/sequence/HIV/MAP/landmark.html

The above is for the HIV Genome. I'm looking for the H1N1 genome map.

 

Genecks:

Thanks for the details on the ScienceMag entries.

I'll post details later if I find it.

 

good night!

Edited November 2, 2009 by greenprogrammin

[CharonY]

You have to keep in mind that the H1N1 variant is just a different Influenza A strain. The basic sequence has long been published. You are probably more interested in more detailed analyses of the differences between the strains. There are a couple out there including the one posted here:

 

http://www.scienceforums.net/forum/showthread.php?t=41872&highlight=h1n1

 

Also for starters you may want to check a recent review. The author was Schnitzler, I do not know the complete reference off the top of my head, though.

[greenprogrammin]

This is what I have for the HIV Genome Map.

I can see the gene layout.

://www.hiv.lanl.gov/content/sequence/HIV/MAP/landmark.html

I'm looking for this for the H1N1 Virus.

 

I guess I could look for Influenza A gene map instead...

 

Thanks for the thought and the quick replies!

[greenprogrammin]

I guess this genome is a little different. Looks like there are 8 segments.

Some really good reading on this is found on the link below.

Look under the nucleic acid section of the description by the International Commitee on Taxonomy of Viruses (ICTV).

 

Description of Influenza A

://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/00.046.0.01.htm

 

also:

 

Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.

://www.ncbi.nlm.nih.gov/pubmed/16208317

Edited November 2, 2009 by greenprogrammin
Consecutive posts merged.

[gsgs]

I've been downloading sequences from genbank and building

and analysing flu-databases. Anyone interested to share tasks,

exchange tools,data ?

 

I also downloaded all the 14 virus-files in Feb. , >300MB

 

I extracted and aligned 399 HIV-1 C and made a mutation picture

 

 

I'm currently extracting Dengue viruses

 

 

(I haven't done anything but flu until last week)