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Commentary
Increasing
H1N1pdm09 M Gene In US trH1N2 Swine
Recombinomics Commentary 22:30
December 07, 2011
The USDA and agencies which research animal disease have released a series of swine sequences. The vast majority of the USDA sequences cover 3 of the 8 genes (HA, NA, MP). Many of these sequences have acquired an H1N1pdm09 M gene, and a subset of those isolates also have an N2 sequence that is closely related to the sequence in H3N2pdm11.
A recent paper had noted the dramatic increase in genetic stability in swine isolates containing the H1N1pdm09 M gene. The isolates in the paper were largely H1N2 isolates from early 2010. Below is a list of H1N2 sequences at GISAID (and Genbank) collected since the start of the 2009 pandemic, which include a M gene sequence.
The list includes the collection date, demonstrating a significant increase in collections in the first five months of 2011, as well as an increasing frequency of isolates with a H1N1pdm09 M gene. Although the sequence data on the isolates below, full sequences from the earlier isolates, identified multiple genes acquired from H1N1pdm09, signaling a high frequency of reassortment.
An increase in trH3N2 swine isolates with H1N2pdm09 M gene was noted previously, which created a number of distinct constellations.
However, in spite of the large number of trH1N2 and trH3N2 sequences with H1N1pdm09 M gene, all 2011 human isolates have the same constellation and lineage, although there is reassortment within the H3N2pdm11 sub-clade, signaling adaptation and evolution in humans, leading to the same constellation and lineage in all 10 human cases, identified in four states over a four month period.
trH1N2 w/ H1N1pdm09 M gene in bold Collection date
A/swine/Illinois/A00907647/2011 07-08
A/swine/Michigan/A01202035/2011 05-26
A/swine/Michigan/A01202036/2011 05-26
A/swine/Michigan/A01202037/2011 05-26
A/swine/Iowa/A01049970/2011 05-16
A/swine/Indiana/A01049964/2011 05-11
A/swine/Illinois/A01049967/2011 05-11
A/swine/Illinois/A01049968/2011 05-11
A/swine/Illinois/A01049969/2011 05-11
A/swine/Minnesota/A01049956/2011 05-10
A/swine/Iowa/A01049951/2011 05-09
A/swine/Illinois/A01049952/2011 05-09 A/swine/Indiana/A01049953/2011 05-07
A/swine/Iowa/A01049887/2011 04-26
A/swine/Iillinois/A01049871/2011 04-19
A/swine/Iillinois/A01049872/2011 04-19
A/swine/Iowa/A01049863/2011 04-18
A/swine/Iowa/A01049864/2011 04-18
A/swine/Iowa/A01049846/2011 04-13
A/swine/Iowa/A01049858/2011 04-10
A/swine/Indiana/A01049794/2011 04-06
A/swine/Iowa/A01049765/2011 03-29
A/swine/Iowa/A01049766/2011 03-29
A/swine/Iowa/A01049755/2011 03-28
A/swine/Iowa/A01049726/2011 03-22
A/swine/Iowa/A01049722/2011 03-22
A/swine/Iowa/A01049723/2011 03-22
A/swine/Iowa/A01049724/2011 03-22
A/swine/Iowa/A01049728/2011 03-22
A/swine/Iowa/A01049718/2011 03-21
A/swine/Iowa/A01049661/2011 03-08
A/swine/Iowa/A01049648/2011 03-07
A/swine/Iowa/A01049640/2011 03-07
A/swine/Iowa/A01049645/2011 03-07
A/swine/Iowa/A01049643/2011 03-07
A/swine/Iowa/A01049646/2011 03-07
A/swine/South Dakota/6/2011 02-25
A/swine/South Dakota/5/2011 02-25
A/swine/Iowa/A01049525/2011 02-08
A/swine/Iowa/A01049506/2011 02-04
A/swine/Oklahoma/A01049500/2011 02-03
A/swine/Iowa/A01049450/2011 01-19
A/swine/South Dakota/4/2010 12-28
A/swine/Iowa/A01049228/2010 12-06
A/swine/Illinois/A01049164/2010 12-01
A/swine/ South Dakota/3/2010 11-23
A/swine/South Dakota/2/2010 11-23
A/swine/North Carolina/A0109085/2010 11-16
A/swine/Illinois/A01049074/2010 11-16
A/swine/Iowa/A01049071/2010 11-16
A/swine/Iowa/A01049062/2010 11-16
A/swine/Iowa/A01049060/2010 11-16
A/swine/North Carolina/226126/2010 09-08
A/swine/North Carolina/226125/2010 09-08
A/swine/North Carolina/226124/2010 09-08
A/swine/Oklahoma/44837-5/2010 07-19
A/swine/Minnesota/239106/2010 05-05
A/swine/North Carolina/239108/2010 04-21
A/swine/Indiana/240218/2010 02-21
A/swine/Minnesota/340304/2010 01-01
A/swine/North Carolina/44837-4/2009 12-21
A/swine/Minnesota/44837-3/2009 11-23
A/swine/SD/31813/2009 11-20
A/swine/North Carolina/44837-2/2009 11-15
A/swine/South Dakota/152B/2009 09-04
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