...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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Tara C. Smith is an Assistant Professor of Epidemiology. Her research involves a number of pathogens at the animal-human nexus. She also writes for The Panda's Thumb and previously for WIRED SCIENCE's Correlations. Please note the views expressed on this site are Dr. Smith's alone and may not be representative of the groups mentioned above.
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Infectious Disease Series
« Swine flu--still spreading | Main | Swine flu and snake oil »
How long does it take to sequence an influenza virus?
Category: General Epidemiology • General biology • Infectious disease • Influenza • Outbreak • Public health • Various viruses
Posted on: April 28, 2009 1:50 AM, by Tara C. Smith
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Comments
Well, that answers that question, I'll ask a harder one next time! :-P
Thanks!
Posted by: Joe | April 28, 2009 2:32 AM
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.
Posted by: Elizabeth | April 28, 2009 5:03 AM
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.
Posted by: Art | April 28, 2009 8:27 AM
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"
Posted by: Superkuh | April 28, 2009 10:18 AM
Source for 4 year old boy sample:
http://www.chron.com/disp/story.mpl/world/6395793.html
Posted by: phytosleuth | April 28, 2009 11:00 AM
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.
Posted by: GK | April 28, 2009 2:54 PM
Far too cute to be a professor.....
Posted by: GK | April 28, 2009 3:05 PM
It already takes less than a day. I'm a molecular biologist and know about these things.
Posted by: JerryG | April 28, 2009 5:40 PM
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.
Posted by: Tara C. Smith | April 28, 2009 5:47 PM
So soon, the 'less than a day' step will be just hours, and then minutes. Moore's Law at work.
Posted by: GK | April 28, 2009 6:29 PM
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.
Posted by: BioinfoTools | April 28, 2009 7:40 PM