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Increasing H1N1pdm09 M Gene In US trH1N2 Swine
Recombinomics Commentary 22:30
December 07, 2011

The recently released swine trH1N2 set of sequences from Ohio, A/swine/Ohio/FAH10-1/2010, contained the three genes acquired by the emerging human 2010 trH3N2 contagion.  The resulting reassortant has 5 genes (PB2, PA, HA, NP, NS) from the dominant human trH3N2 and 3 genes from the swine trH1N2, to produce H3N2pdm11, which has been isolated from all ten 2011 confirmed cases, as well as one isolate from a pig in New York.

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
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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