...asked Joe. Answer: only a few days to sequence, clean up the data, and submit to NCBI. Seven H1N1 swine flu sequences are up (H/T Jonathan Eisen). I've not had a chance to crack anything open yet, but I hope to see some analysis from more of the genomics geeks soon...However, one bummer is that they don't have any from the Mexico cases available--and particularly, any sequence data from any of the fatal cases. These will be helpful to see if there are any point mutations that could possibly account for a virulence difference between the Mexican and US cases. (Unlikely, I'd guess, but it would be nice to check it out...)
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It's not even three months since the first H1N1 swine flu cases were diagnosed in San Diego, but already there is a significant amount of science published on the subject. Lots of genetic sequences from various isolates, clinical descriptions of hospitalized and fatal cases and now animal…
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What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu?
If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer.
Activity 4. Picking influenza sequences and comparing them with phylogenetic trees
We can get the…
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Clinician call:
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Well, that answers that question, I'll ask a harder one next time! :-P
Thanks!
Just read on Huffington Post there is a sample of an early case of the swine flu from a 4 year old boy in Mexico.
Thanks.
I appreciate your many posts on the swine flu; what is going on, and both what we do know and what remains uncertain. IMHO knowledge, even when the facts are grim, remains the best cure for the irrational fears that crop up when things aren't understood and rumors proliferate.
I've compared Influenza A H1N1 (swine flu) virus segment 4 hemagglutinin (HA) gene coding variation in isolates from different regions. This protein plays the most significant role in cell entry. It is interesting to note that at three of the four locations of variation the Texas and California_05 sequences match better than the two California sequences.
At codon/amino acid 8:
A_Calfornia_05_2009_H1N1="Methionine"
A_Calfornia_04_2009_H1N1="Leucine"
A_Texas_05_2009_H1N1="Leucine"
At codon/amino acid 87:
A_Calfornia_05_2009_H1N1="Serine"
A_Calfornia_04_2009_H1N1="Proline"
A_Texas_05_2009_H1N1="Serine"
At codon/amino acid 176:
A_Calfornia_05_2009_H1N1="Threonine"
A_Calfornia_04_2009_H1N1="Alanine"
A_Texas_05_2009_H1N1="Alanine"
At codon/amino acid 274:
A_Calfornia_05_2009_H1N1="Isoleucine"
A_Calfornia_04_2009_H1N1="Valine"
A_Texas_05_2009_H1N1="Valine"
Source for 4 year old boy sample:
http://www.chron.com/disp/story.mpl/world/6395793.html
Technology will save us. It took 31 days to sequence the SARS virus in 2003, but only a few days in 2009 to do the swine flu virus.
By 2015, it will take less than 1 day.
Read here about the all-important Impact of Computing, and how such problems get solved progressively faster.
Far too cute to be a professor.....
It already takes less than a day. I'm a molecular biologist and know about these things.
Yep, Jerry's right--this is the whole time to sequence, make sure there are no discrepancies or errors in the raw sequence (which can require sequencing a second time, depending on the quality of your data), and get it uploaded to NCBI. The sequencing part of it can be one of the fastest steps, depending on what type of machine you have.
So soon, the 'less than a day' step will be just hours, and then minutes. Moore's Law at work.
GK,
If anything the computational side of things holds things up actually, certainly for the larger genomes I know more about; the sequencing itself is very fast. (I'm a freelance/consulting computational biologist by the way.) This may change when single-pass sequencing of whole genomes is common: some researchers are trying to work up to sequencing entire chromosomes as one long sequence. (Surely we're already there with viruses, after all their "chromosomes" are tiny.) On top of that, they are looking at doing individual chromosomes, rather than a mixture of many.