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PostPosted: Sat Jun 18, 2011 5:51 pm 
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niman wrote:
niman wrote:
Japan's NIID has recently released (at GISAID) HA and NA sequences from 2011. Phylogenetic analysis identifies clonal expansion of H1N1 with H274Y.

Transmitting sub-clade has S188T and A200T.

Transmitting H274Y in DE and MD is also on an S188T background

http://www.recombinomics.com/News/05111 ... DE_MD.html

http://www.recombinomics.com/News/05111 ... Spike.html

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PostPosted: Sat Jun 18, 2011 9:33 pm 
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Commentary

http://www.recombinomics.com/News/06191 ... _2011.html

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PostPosted: Sun Jun 19, 2011 12:59 am 
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niman wrote:
Recent NA sequences from Japan with H274Y

EPI318171 A/HOKKAIDO/12/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318168 A/NIIGATA/51/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318167 A/KOBE/537/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318165 A/IWATE/1008/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318161 A/KAGAWA/2/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318154 A/HIROSHIMA/45/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318152 A/HIROSHIMA/49/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318149 A/WAKAYAMA/23/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318139 A/NIIGATA/62/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318133 A/SAPPORO/19/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318131 A/YAMAGUCHI/35/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI305490 A/HIROSHIMA/17/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI305475 A/YOKOHAMA/29/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)

10 of the sequences, collected between Dec 22, 2010 and Feb 2, 2011 map to the same branch and, as indicated by names below, are widely distributed throughout Japan signaling clonal expansion:
A/HIROSHIMA/17/2011
A/WAKAYAMA/23/2011
A/SAPPORO/19/2011
A/NIIGATA/51/2011
A/HOKKAIDO/12/2011
A/YOKOHAMA/29/2011
A/NIIGATA/62/2011
A/KOBE/537/2011
A/YAMAGUCHI/35/2010
A/HIROSHIMA/49/2011

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PostPosted: Sun Jun 19, 2011 1:01 am 
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niman wrote:
niman wrote:
Recent NA sequences from Japan with H274Y

EPI318171 A/HOKKAIDO/12/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318168 A/NIIGATA/51/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318167 A/KOBE/537/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318165 A/IWATE/1008/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318161 A/KAGAWA/2/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318154 A/HIROSHIMA/45/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318152 A/HIROSHIMA/49/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318149 A/WAKAYAMA/23/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318139 A/NIIGATA/62/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318133 A/SAPPORO/19/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI318131 A/YAMAGUCHI/35/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI305490 A/HIROSHIMA/17/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)
EPI305475 A/YOKOHAMA/29/2011 (A/H1N1 swl) segment 6 (NA) 27.0 6.505485e+00 14/14 (100%)

10 of the sequences, collected between Dec 22, 2010 and Feb 2, 2011 map to the same branch and, as indicated by names below, are widely distributed throughout Japan signaling clonal expansion:
A/HIROSHIMA/17/2011
A/WAKAYAMA/23/2011
A/SAPPORO/19/2011
A/NIIGATA/51/2011
A/HOKKAIDO/12/2011
A/YOKOHAMA/29/2011
A/NIIGATA/62/2011
A/KOBE/537/2011
A/YAMAGUCHI/35/2010
A/HIROSHIMA/49/2011

The clonal expansion is inconsistant with figures cited by WHO

http://www.who.int/csr/disease/influenz ... index.html

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PostPosted: Sun Jun 19, 2011 7:45 am 
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niman wrote:
niman wrote:
10 of the sequences, collected between Dec 22, 2010 and Feb 2, 2011 map to the same branch and, as indicated by names below, are widely distributed throughout Japan, signaling clonal expansion:

A/HIROSHIMA/17/2011
A/WAKAYAMA/23/2011
A/SAPPORO/19/2011
A/NIIGATA/51/2011
A/HOKKAIDO/12/2011
A/YOKOHAMA/29/2011
A/NIIGATA/62/2011
A/KOBE/537/2011
A/YAMAGUCHI/35/2010
A/HIROSHIMA/49/2011

The clonal expansion is inconsistant with figures cited by WHO

http://www.who.int/csr/disease/influenz ... index.html

The above sequences were generated by NIID (and 8 of the 10 were from Jan, 2011 collections), who reported an H274Y rate of 1.5% in January. That rate jumped to 4.8% in Feb and 5.8% in Mar, but is likely a gross undercount due to the WHO "agreement" to count samples with H274Y levels below 50% was wild type. Moreover, clonal expansion would NOT require Tamiflu selection, so the citation of linkage to treatment also remains HIGHLY suspect (most samples are collected PRIOR to treatment and therefore post collection Tamiflu treatment would be an irrelevent fact that could be used to misclassify samples and create the WHO H274Y reports claiming a high linkage to treatment, which lack credibility).

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PostPosted: Sun Jun 19, 2011 8:34 am 
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WHO data, including NIID figures

Image

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PostPosted: Sun Jun 19, 2011 10:03 am 
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niman wrote:
WHO data, including NIID figures

Image

The comments below from the latest WHO report are inconsistant with the sequences released by NIID at GISAID:

Based on available data, among Japanese oseltamivir resistant viruses, the vast majority were from cases treated or prophylaxed with oseltamivir.

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PostPosted: Sun Jun 19, 2011 11:04 am 
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niman wrote:
niman wrote:
WHO data, including NIID figures

Image

The comments below from the latest WHO report are inconsistant with the sequences released by NIID at GISAID:

Based on available data, among Japanese oseltamivir resistant viruses, the vast majority were from cases treated or prophylaxed with oseltamivir.

The NIID sequences are from H274Y clonally expanding in communities throughout Japan and are NOT linked to Tamiflu treatment.

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PostPosted: Sun Jun 19, 2011 11:48 am 
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Location: Pittsburgh, PA USA
Commentary

http://www.recombinomics.com/News/06191 ... n_WHO.html

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PostPosted: Mon Jun 20, 2011 9:05 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 28257
Location: Pittsburgh, PA USA
Commentary

http://www.recombinomics.com/News/06201 ... cerns.html

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