Rhiza Labs FluTracker Forum

Commentary

http://www.recombinomics.com/News/09091 ... ilent.html

_________________
www.twitter.com/hniman

descends in 1,2,3,4,6 from the Canadian variant
A/Sw/Ontario/33853/2005(H3N2) - like

5,8 are less clear - Ontario/2005 or USA/1998
another introduction ? I'll check



http://webcache.googleusercontent.com/s ... 05&ct=clnk

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rather than Ontario, these new sequences seem to descend
pretty much directly from the similar
A/turkey/Ohio/313053/2004(H3N2)
in segments 1,2,3,4,5,6,8

which was still another independent reassortment
see the above paper

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no patents on genes, publish the GISAID sequences !

Most of the closely related sequences are human cases from 2010 and are at GISAID (sequences were released a year ago). However, Genbank has a full set of sequences for Kansas/13/2009, as well as the Pennsylvania swine from 2010 (NA sequences are close to A/Pennsylvania/14/2010 and latest cases). There are additional recent swine sequences that are much closer than the Canadian swine from 2005.

The relationship of the latest genes to prior sequences was described last month and well reflected in blast data for IN/08/11 as well as the latest sequences on this thread.
You are living in the past.

_________________
www.twitter.com/hniman

You really are missing the point, in part because you don't look at the human sequences at GISAID. The 2011 and 2010 HUMAN cases are clearly clustering together on phylogentic branches that have few if any swine sequences. The constellation of M from H1N1 with 7 trH3N2 genes is a more recent example (only seen in human 2011 sequences), but the other genes include the recent HUMAN cases.

Data from 2004 and 2005 really have little relevance to the emerging trH3N2 which has evolved into a significant human contagion.

_________________
www.twitter.com/hniman

OK, I corrected the ancestor as A/turkey/Ohio/313053/1004(H3N2)

Kansas/13/2009 goes also back to the turkey, but different
from the 2011 constellation

common ancestor Kansas/13/2009 and 2011H3N2 in
segments 1,2 is ~2006
in segment 3 is ~2007
in segments 4 is ~2003
in segment 5 is ~2008
in segment 8 is ~2009
in segment 6 is ~2001

so apparantly quite some reassortment of similar viruses

_________________
no patents on genes, publish the GISAID sequences !

you're not saying, these evolve in humans ?
Even seasonal flu dies each year in USA.

So, do they evolve in swine or maybe even turkey ?
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well, humans had contact to swine, not turkeys,
so obviously swine

_________________
no patents on genes, publish the GISAID sequences !

No, they are passing H2H and clustering quite clearly in humans. There is some swine, but the human cases clearly outnumber swine, even after increased swine surveillance. The phylogenetic data are quite striking.

_________________
www.twitter.com/hniman

The 2010 case in Pennsylvania is one example where swine may play a role. That patient, A/Pennsylvania/14/2010 denied contact with swine, but his sequences are close to 2010 swine sequences from PA, so they may have led to infection of a contact of the infected the confirmed case. The NA from that case and those swine has been acquired by the 2011 trH3N2 in the four confirmed cases. Thus, the swine may play a role, but the role involves 2010 sequences, not sequences from 2004 or 2005. Same is true for the M gene segment which is like 2009 pandemc H1N1 isolates. The PB1 is also found in swine, but swine since 2007. There number of TRIG sequences in swine is high, but the recent sequences are driving the changes, not reassortment with 2004 and 2005 sequences.

_________________
www.twitter.com/hniman

OK, I included swine H3N2 2003-2011 in my list.
Lots of reassortments.

I'm not sure yet about the number of introductions
from human segments into swine.

human cases outnumber swine ? But so many swine sequences
with frequent reassortment and only sporadic human cases.

looking for the closest human segments now ...

_________________
no patents on genes, publish the GISAID sequences !

segments 1,3,5,6,8 are very close to A/Sw/PA/62170-x/2010/10/25
segment 2 to A/Sw/MN/1300/2007/01/31
segment 4 to A/Sw/IN/A01049091/2010/11/18

_________________
no patents on genes, publish the GISAID sequences !