Recombinomics | Elegant Evolution

Home Founder What's New In The News Consulting

H1N1 Consulting

Paradigm Shift

Viral Evolution

Intervention Monitoring

Vaccine Screening

Vaccine Development

Expression Profiling

Drug Discovery

Custom Therapies


Audio:Aug18 Sep5 Sep15 Nov17  RSS Feed twitter News Now                         


Curious CIDRAP Comments On Swine H3N2pdm11 Matches NOT
Recombinomics Commentary 21:30
November 30, 2011

An informal analysis by the USDA's Agricultural Research Service has found that 8 of about 30 swine H3N2 viruses in the GenBank database have the pandemic H1N1 matrix gene so far, said the USDA official, who requested anonymity. "More detailed analyses of these and other samples continue," the official added.

The significance of the above comment from a CIDRAP update is clear. 

A re-analysis of the 30 trH3N2 sequences listed in the Oct 26 analysis identified two 2010 isolates that were inadvertantly absent from the retest, and these two isolates,
A/swine/Iowa/A01049035/2010 and A/swine/Iowa/A01049034/2010, increased the number of public H3N2 sequences at Genbank with H1N1pdm09 M gene to eight.
Recombinomics apologizes for the confusion created by the prior commentary.

The two 2010 sequences were virtually identical to each other, and the HA and NA genes did not match the human H3N2pdm11 sequences.  Recently, sequences for the other five genes were released and all were H3N2 swine related but only the NP matched H3N2pdm11.  Thus, the two isolates had a constellation of seven trH3N2 genes with H1N1 pdm09, but only one of the seven was the same lineage as H3N2pdm09.

An Oct 4 analysis identified five trH3N2 isolates with the H1N1pdm09 M gene, (A/swine/Texas/A01049555/2011, A/swine/Texas/A01049556/2011, A/swine/Iowa/A01049750/2011, A/swine/Texas/A01049914/2011, A/swine/Texas/A01049915/2011) but all five sets of sequences (HA, NA, MP) were virtually identical to each other, but neither the HA nor the NA sequences were closely related to the human H3N2pdm11 sequences.

Last week a single set of sequences from New York,
A/swine/NY/A01104005/2011, was released.  The release was unusual because it was not part of a larger release, and sequences from all eight gene segments were included.  That sequence had the H1N1pdm09 M gene, and all seven of the other genes matched the 10 human H3N2pdm11 sequences.

Thus, the public portion of Genbank has 31 sets of swine trH3N2 sequences from samples collected since October 24, 2010, and one of those sequences matches the 10 human H3N2pdm11 sequences.

Media Link 

Recombinomics Presentations

Recombinomics Publications

Recombinomics Paper at Nature Precedings

Home | Founder | What's New | In The News | Contact Us

© 2011 Recombinomics.  All rights reserved.