Posts Tagged ‘Research’

Analysis of a scientific H1N1 sequencing article

November 8, 2009

I came across this article written in April 2009. I do not have an extensive background in chemistry or biology and I do not claim to be able to understand this article completely.

Here is a link to the entire article:
Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites
See the abstract below:

Some of the points I found interesting ( and be sure to comment if I am incorrect:

  • The virus was able to be sequenced and put in a database within 2 weeks of the outbreak in Mexico.
  • The researchers thought it interesting that this new virus was more similar to H5N1 avian flu than to H1N1 already in the Americas.
  • They also compared similarities to the 1918 flu which has been dug up from cadavers, sequenced and put into a bio informatics database. They found 21 differences.
  • The primary purpose of the article was to determine if the current antiviral drugs will still work with this new strain, and they conclude that so far they will.
  • They discuss the how (fast, much?) the current virus it currently mutating and are concerned that the places it is mutating will make antibodies and vaccines less effective.
  • One of the links H1N1 Model in the article was to a molecule modeling program that show mutations between this current virus and 1918 and avian virus. It also showed current mutations as recent as Oct 23. It seems to me that there are a lot of mutations but few on the difference sites.
  • The researchers are all in Singapore. One of the reviewers is in Bethesda MD

My questions:

  • Are only 21 differences (out of 380 or so) significant and indicate this is very close to 1918 flu and/or avian flu?
  • This only concerns the neuraminidase portion of the virus, which I gather is an important protein. Is this the important part or can viruses differ in other areas not covered by this paper?
  • Abstract

    In this work, we study the consequences of sequence variations of the “2009 H1N1” (swine or Mexican flu) influenza A virus strain neuraminidase for drug treatment and vaccination. We find that it is phylogenetically more closely related to European H1N1 swine flu and H5N1 avian flu rather than to the H1N1 counterparts in the Americas. Homology-based 3D structure modeling reveals that the novel mutations are preferentially located at the protein surface and do not interfere with the active site. The latter is the binding cavity for 3 currently used neuraminidase inhibitors: oseltamivir (Tamiflu┬«), zanamivir (Relenza┬«) and peramivir; thus, the drugs should remain effective for treatment. However, the antigenic regions of the neuraminidase relevant for vaccine development, serological typing and passive antibody treatment can differ from those of previous strains and already vary among patients.er

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