Swine flu has only half genetic markers seen in previous pandemic strains


Swine flu has only half genetic markers seen in previous pandemic strains

The new H1N1 "swine flu" strain that is spreading around the world and is nearly at pandemic alert level, has only half the key genetic markers found in previous pandemic strains, said US researchers yesterday.

Jonathan Allen and Tom Slezak from Lawrence Livermore National Laboratory, a US Department of Energy lab in Livermore, California, and colleagues, published a study in the open access journal BMC Microbiology 2 weeks ago describing how they found 34 conserved amino acid markers from past pandemic flu strains.

Since then they have analyzed sequences from the new H1N1 virus and found that it has only half of the 34 markers.

However, Slezak cautioned that while their finding sugggests that the current H1N1 strain lacks many of the attributes that made previous outbreaks deadly, the lack of similarity to those strains does not mean that it will not be a major problem.

Allen and Sleazak also said more research was needed before we can say how dangerous the new strain might actually be.

In their original study, Allen and Sleazak and colleagues used reverse engineering principles to search for class specific amino acid mutations conserved in past pandemics.

To do this they used "proteomes" of past pandemic virus strains: a preteome is the entire collection of amino acids that is made when all the genes in an organism are expressed. So in effect what they did was scan all the building blocks of proteins that all the genes of previous pandemic strains expressed and looked for repeated patterns across the strains.

They found 34 amino acid markers that were linked to host specificity and high mortality. Some of the markers meant little on their own, but when combined with "other mutations they improved class prediction", they found.

"Evolutionary pathways involving H1N1 human and swine strains mixed with avian strains show the potential to acquire the pandemic markers with a double reassortment and one or two amino acid mutations," they wrote.

The findings may have important implications for how surveillance tools could track new mutations more effectively and illustrate the "potential for reassortment and mutation events to lead to new circulating influenza strains," said Allen and Sleazak.

"Conserved amino acid markers from past influenza pandemic strains."

Jonathan E Allen, Shea N Gardner, Elizabeth A Vitalis, and Tom R Slezak.

BMC Microbiology2009, 9:77

Published: 22 April 2009

doi:10.1186/1471-2180-9-77

Additional source: Biomed Central.

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