Rhiza Labs FluTracker Forum

You need to read the commentaries. You seem to be more lost than usual (which isn't easy).

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www.twitter.com/hniman

I bet there will be no H3N2 pandemic in the next 10 years.
Do you accept the bet ?

I offer 1:2

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no patents on genes, publish the GISAID sequences !

Please.

_________________
www.twitter.com/hniman

You are more lost than ever. The CDC is already testing a pandemic H3N2 vaccine (A/Minnesota/11/2010) and has already acknowledged that the seasonal H3N2 vaccine will be of little use. Your recommendation of use of a human target from 1996 is nonsense and displays a profound lack of knowledge of the current pandemic, which the CDC has yet to acknowledge, but is quite clear from the sequence data of recent trH3N2 isolates, as well as the appearance of unsubtypables and dominance of H3N2 (trH3N2 being reported as seasonal H3N2).

You should stick to the babble boards. Your lack of background / understanding is glaringly clear and quite remarkable.

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www.twitter.com/hniman

Commentary

http://www.recombinomics.com/News/09101 ... demic.html

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www.twitter.com/hniman

Here is a quick review of the H3N2 problems. Samples are typically tested for influenza A or B and those that are influenza A positive are then tested for H1 or H3 using reagents directed against human sequences. Consequently trH3 frequently tests positive because the trH3 traces back to a seasonal H3N2 infection in swine in the 1990's.

trH3N2 can be easily detected in an antigen characterization test or by sequencing, but both assay involving isolation of the virus, which is frequently limited to CDC testing. In samples that have technical difficulties in the growth of the virus, like A/Pennsylvania/40/2010, discovery that it is trH3N2 can take many months (PA/40/10 was reported as a trH3N2 5 months after sample collection). Thus, many samples like PA/40 are listed as seasonal H3N2 and not tested further.

This problem can be overcome by simply testing the sample in a PCR test that is directed against swine H3 sequences, as was done for A/Pennsylvania/09/2011, which was unsubtypable in the standard serotyping test.

Thus, in the absence of PCR testing, there are SERIOUS issues with the recent influenza A positive samples which have not been sub-typed or which have been reported as seasonal H3N2.

_________________
www.twitter.com/hniman

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http://www.ncbi.nlm.nih.gov/pubmed/21900876
Swine-Origin (H3N2) Infection in 2 Children --- Indiana and Pennsylvania, July--August 2011.

http://www.ncbi.nlm.nih.gov/pubmed/21880744
The M segment of the 2009 new pandemic H1N1 influenza virus is critical for its high transmission efficiency in the guinea pig model.

Cross-protective immunity to influenza pH1N1 2009 viruses induced by seasonal A(H3N2)
virus is mediated by virus-specific T cells.

Virulence and genetic compatibility of polymerase reassortant viruses derived from the pandemic (H1N1) 2009 influenza virus and circulating influenza A viruses.
reassortment between the pandemic A/California/04/09 (CA04, H1N1) and current human and animal influenza viruses produced variants possessing a broad spectrum of pathogenicity in the mouse model.
Although most polymerase reassortants had attenuated pathogenicity (including those containing seasonal human H3N2 and high-pathogenicity H5N1 virus segments) compared to that of the parental CA04 (H1N1) virus, some recombinants had significantly enhanced virulence. Unexpectedly, one of the five highly virulent reassortants contained a A/Swine/Korea/JNS06/04(H3N2)-like PB2 gene with no known virulence factors

Modifications in the polymerase genes of a swine-like triple-reassortant influenza virus to generate live attenuated vaccines against 2009 pandemic H1N1 viruses.
modified A/turkey/OH/313053/04 (H3N2) (ty/04), (LAIV). this vaccine is highly attenuated in mice
A single immunization with the ty/04 att-based vaccines conferred complete protection against a lethal H1N1pdm virus infection in mice

Immunity to pre-1950 H1N1 influenza viruses confers cross-protection against the pandemic swine-origin 2009 A (H1N1) influenza virus.

Alternative live-attenuated influenza vaccines based on modifications in the polymerase genes protect against epidemic and pandemic flu.

Prime-boost immunization with HA/C3d DNA followed by a recombinant pseudorabies virus boost enhanced protective immunity against H3N2 swine influenza virus in mice.


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no patents on genes, publish the GISAID sequences !

differences to IN/08 of selected related viruses in per mille in the 8 segments

frequent reassortment is apparent

277 >A/Indiana/08_b/2011/07/27
 12: 50, 47, 43, 57, 24, 36,121, 21   A/Sw/NC/2003//
 31: 48, 42, 42, 60, 38, 77,128, 37   A/Sw/Korea/JNS06/2004//
 41: 32, 23, 20, 34, 26, 41,120, 21   A/Sw/Alberta/14722/2005//
 42:---,---,---, 40,---, 30,---,---   A/Sw/Alberta/Biovet1/05//
 45: 25, 26, 20, 40, 25, 36,120, 21   A/Sw/British Columbia/28103/2005//
 62: 51, 40, 43,103, 32, 74,119, 21   A/Sw/Korea/CAN04/2005//
 66: 29, 24, 22, 33, 26, 38,120, 20   A/Sw/Manitoba/12707/2005//
 84: 25, 22, 20, 33, 25, 38,120, 20   A/Sw/Ontario/33853/2005//
 85:---,---,---, 39,---, 30,---,---   A/Sw/Ontario/Biovet1/05//
102:---,---,---,---,---,---,---, 23   A/Sw/NC/25464/2005/05/
105: 27, 24, 20, 41, 26, 38,120, 20   A/Sw/Quebec/4001/2005/07/12
109: 26, 24,---, 37,---,---,---,---   A/Sw/Minnesota/SG-00234/2005/08/18
127: 50, 39, 42,103, 32, 74,120, 20   A/Sw/Korea/CAS09/2006//
133: 30, 31, 22, 43,---,---,---,---   A/Sw/Minnesota/SG-00242/2006/10/12
137: 19,---, 13,---,---,---,---,---   A/Sw/Minnesota/SG-00243/2006/11/17
138: 31, 28, 23, 42, 26, 47,123, 22   A/Sw/Minnesota/65767/2006/12/26
140: 18, 26, 13, 40, 12, 45,120, 25   A/Sw/Minnesota/66853/2006/12/26
141: 36, 55, 38, 39, 32, 40,117, 11   A/Sw/Minnesota/66960/2006/12/26
148: 50, 39, 43, 89, 31, 72,121, 75   A/Sw/Korea/CY04/2007//
153: 29, 27, 21, 41, 30, 43,121, 23   A/Sw/Minnesota/1145/2007//
157: 31, 29, 22, 41, 30, 44,117, 23   A/Sw/Oklahoma/008722/2007//
158: 30, 26, 23, 44, 52, 88,122, 27   A/Sw/Oklahoma/011506/2007//
165: 19, 26, 15, 41, 12, 43,121, 65   A/Sw/Minnesota/578/2007/01/24
166: 19, 16, 12, 35, 17, 41,121, 25   A/Sw/Minnesota/1300/2007/01/31
192: 21, 21, 16, 40, 35, 43,119, 28   A/Sw/NC/R08-001877-D08-013371/2008 //
199: 34, 38, 30, 48, 23, 23,120, 28   A/Sw/Kansas/015252/2009//
200: 34, 39, 31, 50, 22, 24,120, 23   A/Sw/Oklahoma/001142/2009//
206: 34, 32, 30, 48, 32, 53,122, 28   A/Sw/QC/382/2009/05/08
213:---,---,---, 13,---,---,---,---   A/Sw/Minnesota/02948/2009/05/19
214: 41, 32, 31, 42, 36, 53,123, 26   A/Sw/QC/414/2009/05/22
215: 36, 31, 32, 48, 34, 48,125, 32   A/Sw/QC/1840-2/2009/05/28
223: 40, 36, 62, 45, 50, 53,  5, 35   A/Sw/Minnesota/239105/2009/11/24
243: 18, 36, 16, 61, 20, 59,126, 19   A/Sw/Pennsylvania/057108-1/2010/09/20
244:  8, 25,  5, 44,  6,  2,124,  2   A/Sw/Pennsylvania/62170-1/2010/10/25
245:  8, 30,  5, 49,  7,  4,124,  4   A/Sw/Pennsylvania/62170-2/2010/10/25
246:  8, 24,  5, 44,  6,  2,124,  2   A/Sw/Pennsylvania/62170-3/2010/10/25
247:  8, 31,  5, 46,  6,  5,124,  2   A/Sw/Pennsylvania/62170-4/2010/10/25
248: 70, 84, 64, 48, 55, 53,  7, 54   A/Sw/Quebec/1257777/2010/11/08
249: 74, 63, 65, 54, 53, 59,  5, 53   A/Sw/Quebec/1257774/2010/11/09
254:---,---,---,  5,---,  4,121,---   A/Sw/Indiana/A01049091/2010/11/18
270:---,---,---,  5,---,  3,121,---   A/Sw/NC/A01049436/2011/01/19
271: 25, 22, 20, 33, 25, 38,120, 20   A/Sw/Ontario/33853/2005
272: 40, 34, 33, 92, 28, 64,117, 23   A/Sw/Index/triple-reassortant/1998
273:  1,  1,  0,  1,  4,  7,  2,  1   A/Pennsylvania/09/2011/08/20
274:  1,  0,  0,  0,  1,  0,  1,  1   A/Pennsylvania/11/2011/08/25
275:---,---,---,  2,---,---,  0,  1   A/Pennsylvania/10/2011/08/26
276:  0,  0,  0,  0,  0,  0,  2,  0   A/Indiana/08_a/2011/07/27
277:  0,  0,  0,  0,  0,  0,  0,  0   A/Indiana/08_b/2011/07/27
278: 23, 20, 17, 33, 24, 34,120, 20   A/turkey/Ohio/313053_b/2004
279: 23, 21, 17, 32, 24, 34,120, 17   A/turkey/Ohio/313053_a/2004
280:---,---,---,---,---,---, 79,---   A/turkey/Ohio/313053_c/2004
281: 23, 21, 17, 48,  8, 52,118,  2   A/Kansas/13/2009/07/27

_________________
no patents on genes, publish the GISAID sequences !

The data on the trH3N2 sequences is really related to the 2011 human sequences above and the 2010 human sequences at GISAID (other than M).

_________________
www.twitter.com/hniman

These are a bunch of random citations.

The keys for the trH3N2's is the acquisition of M from pandemic H1N1 as well as the internal genes closely related to the Huron Fair cluster (A/Ohio/01/2007 and A/Ohio/02/2007), but none of this has anything to do with unsubtypables, which are all about surveillance/detection/reporting and immunological escape via H3 and N2.

_________________
www.twitter.com/hniman