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:Sep5 Sep15 Nov17 Dec1 RSS Feed twitter News Now                         


trH1N2 HA NA MP Matches With Ohio H3N2pdm11 Parent
Recombinomics Commentary 19:30
December 08, 2011

The recently released H1N2 swine sequences from Ohio, A/swine/Ohio/FAH10-1/2010. included three gene segments (PB1, NA, MP) which matched H3N2pdm11, which was present in all ten trH3N2 human cases identified in 2011.  The matches in NA of A/Pennsylvania/14/2010 were noted for South Dakota swine sequences from 2010, as was the match of the M gene with H1N1pdm09.  More recently, H1N2 sequences released by the USDA also contained NA and MP matches with H3N2pdm11 (which also had the NA gene from A/Pennsylvania/14/2010), but these sequences only covered 3 of the 8 gene segments.

An analysis of H1N2 sequences are Genbank, which were collected after the start of the 2009 pandemic identified an increasing frequency of isolates with H1N1pdm M gene.  A further analysis identified a subset of 30 isolates which had an H1N1pdm M gene, as well as an NA sequence that matched the lineage in H3N2pdm11.

Since the Ohio H1N2 sequence also had an H3N2pdm11match for PB1, the Genbank sequences were analyzed for an H1 match with , and 21 isolates were identified which matched the HA, NA, and MP lineage found in ohio (see list below), supporting widespread donor sequences in swine, which had all three gene segments acquired by H3N2pdm11.  These matches included the 2010 isolates from South Dakota and Iowa. Indicating these donor sequences have been circulating in swine since late 2010, but the only H3N2pdm11 swine match was in a sample collected September 13 in New York, A/swine/NY/A01104005/2011.
The detection of a large number of H1N2 donor sequences throughout the Midwest, beginning in late 2010, suggests that the absence of H3N2pdm11 in swine isolates collected prior to the detection in humans in Indian and Pennsylvania supports spread in humans, leading to reassortants which exchange genes within the H3N2pdm11 sub-clade, which preserves the same lineages for all 8 gene segments.

The sequence identities in all 10 human H3N2pdm11  isolates, and paucity of such sequences in swine, signals a need for more aggressive surveillance in humans, including sequencing of influenza A positive samples from children under the age of ten.

HA, NA and MP Related To sw/OH/FAH10-1/10
HQ833566 A/swine/Ohio/FAH10-1/2010
CY078421 A/swine/South Dakota/2/2010
CY078424 A/swine/South Dakota/3/2010
JN652499 A/swine/Iowa/A01049846/2011
JN652420 A/swine/Iowa/A01049722/2011
JN652421 A/swine/Iowa/A01049723/2011
JN652422 A/swine/Iowa/A01049724/2011
JN652423 A/swine/Iowa/A01049728/2011
JN652516 A/swine/Indiana/A01049953/2011
JN652498 A/swine/Indiana/A01049794/2011
JN162060 A/swine/Iowa/A01049450/2011
JN652418 A/swine/Iowa/A01049718/2011
JN652503 A/swine/Iowa/A01049887/2011
JN652413 A/swine/Iowa/A01049646/2011
JN652514 A/swine/Iowa/A01049951/2011
CY081566 A/swine/South Dakota/4/2010
JN652518 A/swine/Indiana/A01049964/2011
CY099367 A/swine/Illinois/A00907647/2011
JN652517 A/swine/Minnesota/A01049956/2011
JF812285 A/swine/Iowa/A01049071/2010
JN652502 A/swine/Illinois/A01049872/2011
JN652501 A/swine/Illinois/A01049871/2011

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.