The Flu Formerly Known as Swine

Friday, October 29, 2010 // Uncategorized

4/30/2009 9:44:18 PM

This is taken from Pro Med Digest.  I was introduced to it by a patient who was a graduate student in microbiology.  It is a nonprofit service that shares information on the emergence of diseases of plants and animals around the world.  They usually send me multiple updates throughout the day.  The first part has to do with the change in the official name of Swine Flu to Influenza A (H1N1).  This will help those countries like Russia that think that the virus is spread by pork ingestion.  Following that there is a discussion of the origins of the virus.  It appears that it has elements of previous swine viruses, but does not appear to presently infect pigs.

Pork: The Other White Meat

Note: It is now apparent that the 2009 influenza A (H1N1) virus
currently circulating in humans, though genetically linked to swine
influenza viruses, has not been found in swine and that swine do not
appear to be involved in the ongoing epidemic.  For that reason, and
in keeping with usage by WHO and other agencies, ProMED will drop the
term “swine flu” from our coverage.  We expect the term will continue
to be used by the media and in common usage for some time. – Mod.LM]

This is a discussion of the origins of the virus:

The origin of the recent swine influenza A(H1N1) virus infecting humans
– ———————————
By: V Trifonov1, H Khiabanian1, B Greenbaum1,2, R Rabadan 1 At: 1
Department of Biomedical Informatics, Center for Computational
Biology and Bioinformatics, Columbia University College of Physicians
and Surgeons, New York, United States, and 2 The Simons Center for
Systems Biology, Institute for Advanced Study, Princeton, United

Preliminary analysis of the genome of the new H1N1 influenza A virus
responsible for the current pandemic indicates that all genetic
segments are related closest to those of common swine influenza

A new H1N1 influenza A virus has been identified in Mexico and has
spread rapidly to other regions around the world. The World Health
Organization in collaboration with many other national and
international agencies is working efficiently to evaluate, diagnose
and implement measures to contain the spread of this virus. Among the
many efforts is the timely release of the genomic sequences from
different viral isolates [1]. This is allowing thousands of
scientists to participate in the endeavor.

There have been some questions raised about the origin of the new
strain. Influenza A is a single stranded RNA virus with 8 different
segments. When 2 viruses co-infect the same cell, new viruses can be
produced that contain segments from both parental strains.

By using sequences collected in public databases, we can identify the
closest relatives of the new strain found in Mexico and construct
clusters and phylogenetic trees. Sequence alignment and similarity,
cluster analyses by principal component analysis and phylogenetic
tree all point to similar results.

Our preliminary analyses show that the closest relatives to this new
strain are found in swine, and occasionally in turkeys. Six segments
of the virus are related to swine viruses from North America and the
other 2 (NA and M) from swine viruses isolated in Europe/Asia. The
closest clusters (for the HA segment) in the NCBI data base are North
America swine influenza A(H1N2) and H3N2s. The closest relatives of
the neuraminidase (NA) gene of the new virus, are influenza A
isolates from 1992. As more data becomes accessible, the evolution of
this gene could be clarified.

The North American ancestors are related to the multiple
reassortants, H1N2 and H3N2 swine viruses isolated in North America
since 1998 [2,3]. In particular, the swine H3N2 isolates from 1998
were a triple reassortment of human, swine and avian origin.

Therefore, this preliminary analysis suggests at least 2 swine
ancestors to the current H1N1, one of them related to the triple
reassortant viruses isolated in North America in 1998. So far, the
new strain has not been reported in pigs. It is not clear whether
this is due to insufficient surveillance of the swine population or
whether this virus has been generated in a very recent reassortment


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