Rhiza Labs FluTracker Forum

triple reassortants had functional PB1-F2 AFAIR
this was lost then in mexflu and this was seen as a reason
for reduced virulence and a concern that
a functional PB1-F2 might be acquired

_________________
no patents on genes, publish the GISAID sequences !

PB1 is human and traces back to the early/mid 1990's as do all PB1's in triple reassortants. The polymerase complex of human PB1 and avian PB2/PA goes back to the 1990's. The point mutation that causes truncation in F2 is a separate issue.

_________________
www.twitter.com/hniman

A/swine/Korea/4779/2010 has pandemic NS. The rest are swine triple reasssortant gene segments so it should have a full PB1-F2. Same is true for A/swine/Korea/4383/2010. A/swine/Korea/5008/2010 also has TR swine PB1-F2 but MP and NS are pandemic H1N1.

_________________
www.twitter.com/hniman

so no mexflu HA,NA with full PB1-F2 yet

_________________
no patents on genes, publish the GISAID sequences !

239105: oomomomo
239106: momhmomm
A1047604:mmmhmo?m
A1047613:oooOoc?o
226128:oomOmcmm


m:mexflu
o:Ontario/33853/2005(H3N2)
O:Ohio/511445/2007(H1N1)
c:Iowa/CEID23/H1N1(human)



s:swine
t:triple-reassortant

A/Sw/Korea/4941/2010/04: mmmmstmm
A/Sw/Korea/4940/2010 : mmmmmtmm
A/Sw/Korea/4779/2010 : tttttttm
A/Sw/Korea/4382/2009/12 : mmmtmtmm
A/Sw/Korea/5008/2010 : ttttmttm
A/Sw/Korea/4383/2009 : tttttttm

A/Sw/Thailand/2010/01 : mmmmmemm

A/Sw/Quebec/1265553/2010 : mmmtmtmm
A/mink/Nova Scotia/1265707/2010 : mmmtmtmm

_________________
no patents on genes, publish the GISAID sequences !

There are multiple isolates from Minnesota with pandemic H1N1 genes
Top 100 NP matches for A/swine/Minnesota/A01047604/2010(H1N2)

HQ840328.1 Influenza A virus (A/swine/Minnesota/165A/2009(H1N1)) segment 5 nucleocapsid protein (NP) gene, complete cds 2628 2628 100% 0.0 98%
HQ840295.1 Influenza A virus (A/swine/Minnesota/074A/2009(H1N1)) segment 5 nucleocapsid protein (NP) gene, complete cds 2628 2628 100% 0.0 98%
HQ840287.1 Influenza A virus (A/swine/Minnesota/074A/2009(H1N1)) segment 5 nucleocapsid protein (NP) gene, complete cds 2628 2628 100% 0.0 98%
CY061989.1 Influenza A virus (A/New York/7019/2009(H1N1)) segment 5, complete sequence 2628 2628 100% 0.0 98%
CY057777.1 Influenza A virus (A/Wisconsin/629-D00802/2009(H1N1)) segment 5, complete sequence 2628 2628 100% 0.0 98%
HQ840320.1 Influenza A virus (A/swine/Minnesota/165A/2009(H1N1)) segment 5 nucleocapsid protein (NP) gene, complete cds 2625 2625 100% 0.0 98%
CY086921.1 Influenza A virus (A/swine/Minnesota/239105/2009(H3N2)) nucleocapsid protein (NP) gene, complete cds 2623 2623 100% 0.0 98%
HQ840312.1 Influenza A virus (A/swine/Minnesota/136B/2009(H1N1)) segment 5 nucleocapsid protein (NP) gene, complete cds 2623 2623 100% 0.0 98%
HQ840307.1 Influenza A virus (A/swine/Minnesota/130A/2009(H1N1)) segment 5 nucleocapsid protein (NP) gene, complete cds 2623 2623 100% 0.0 98%
HQ840299.1 Influenza A virus (A/swine/Minnesota/130A/2009(H1N1)) segment 5 nucleocapsid protein (NP) gene, complete cds 2623 2623 100% 0.0 98%
CY069109.1 Influenza A virus (A/Guam/NHRC0028/2009(H1N1)) segment 5, complete sequence 2623 2623 100% 0.0 98%
CY069085.1 Influenza A virus (A/Guam/NHRC0025/2009(H1N1)) segment 5, complete sequence 2623 2623 100% 0.0 98%
CY057953.1 Influenza A virus (A/Wisconsin/629-D00050/2009(H1N1)) segment 5, complete sequence 2623 2623 100% 0.0 98%
CY057945.1 Influenza A virus (A/Wisconsin/629-D00629/2009(H1N1)) segment 5, complete sequence 2623 2623 100% 0.0 98%
CY057769.1 Influenza A virus (A/Wisconsin/629-D01346/2009(H1N1)) segment 5, complete sequence 2623 2623 100% 0.0 98%
CY057441.1 Influenza A virus (A/Wisconsin/629-D01522/2009(H1N1)) segment 5, complete sequence 2623 2623 100% 0.0 98%
CY057369.1 Influenza A virus (A/Wisconsin/629-D00643/2009(H1N1)) segment 5, complete sequence 2623 2623 100% 0.0 98%
CY057014.1 Influenza A virus (A/Wisconsin/629-D02041/2009(H1N1)) segment 5, complete sequence 2623 2623 100% 0.0 98%
CY051786.1 Influenza A virus (A/New York/4844/2009(H1N1)) segment 5, complete sequence 2623 2623 100% 0.0 98%
GQ392021.1 Influenza A virus (A/Moscow/IIV04/2009(H1N1)) segment 5 nucleocapsid protein (NP) gene, complete cds 2623 2623 100% 0.0 98%
CY087011.1 Influenza A virus (A/New York/3565/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY086996.1 Influenza A virus (A/New York/3251/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY086988.1 Influenza A virus (A/New York/3250/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY086980.1 Influenza A virus (A/New York/3217/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY086972.1 Influenza A virus (A/New York/3198/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY086929.1 Influenza A virus (A/swine/Minnesota/239106/2010(H1N2)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY084449.1 Influenza A virus (A/New York/6902/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083716.1 Influenza A virus (A/Madrid/INS112/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083664.1 Influenza A virus (A/San Diego/INS41/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083650.1 Influenza A virus (A/District of Columbia/INS22/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083568.1 Influenza A virus (A/Lima/WRAIR8511F/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083512.1 Influenza A virus (A/Piura/WRAIR1694P/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083416.1 Influenza A virus (A/San Diego/WRAIR1666P/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083392.1 Influenza A virus (A/San Diego/WRAIR1663P/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083384.1 Influenza A virus (A/San Diego/WRAIR1662P/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083360.1 Influenza A virus (A/San Diego/WRAIR1658P/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083257.1 Influenza A virus (A/San Diego/WRAIR1642P/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083233.1 Influenza A virus (A/Guam/WRAIR1510P/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083225.1 Influenza A virus (A/California/WRAIR1507P/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083121.1 Influenza A virus (A/Quito/WRAIR0617T/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083105.1 Influenza A virus (A/Piura/WRAIR0603F/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083097.1 Influenza A virus (A/Lima/WRAIR0519F/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083081.1 Influenza A virus (A/Bogota/WRAIR0440T/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY083049.1 Influenza A virus (A/Lima/WRAIR0285F/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY081545.1 Influenza A virus (A/Cambodia/NHRCC00008/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY081537.1 Influenza A virus (A/Cambodia/NHRCC00007/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY081529.1 Influenza A virus (A/Cambodia/NHRCC00006/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY081521.1 Influenza A virus (A/Cambodia/NHRCC00005/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY081513.1 Influenza A virus (A/Cambodia/NHRCC00004/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY081505.1 Influenza A virus (A/Cambodia/NHRCC00003/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY081497.1 Influenza A virus (A/Cambodia/NHRCC00002/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY081489.1 Influenza A virus (A/Cambodia/NHRCC00001/2009(H1N1)) nucleocapsid protein (NP) gene, complete cds 2619 2619 100% 0.0 98%
CY074079.1 Influenza A virus (A/Argentina/HNRG84/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY074072.1 Influenza A virus (A/Argentina/HNRG83/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY074051.1 Influenza A virus (A/Argentina/HNRG5/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY074043.1 Influenza A virus (A/Argentina/HNRG45/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY074033.1 Influenza A virus (A/Argentina/HNRG36/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY074023.1 Influenza A virus (A/Argentina/HNRG32/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY074013.1 Influenza A virus (A/Argentina/HNRG21/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY074003.1 Influenza A virus (A/Argentina/HNRG14/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY073996.1 Influenza A virus (A/Argentina/HNRG107/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY073982.1 Influenza A virus (A/Argentina/HNRG105/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY073975.1 Influenza A virus (A/Argentina/HNRG104/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY073419.1 Influenza A virus (A/San Diego/WR1640P/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY073255.1 Influenza A virus (A/Athens/WRAIR2962N/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY073127.1 Influenza A virus (A/Mexico City/WRAIR1773T/2010(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY073026.1 Influenza A virus (A/Hong Kong/WRAIR0114T/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY073018.1 Influenza A virus (A/Hong Kong/WRAIR0113N/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY072929.1 Influenza A virus (A/Managua/4063.01/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY072889.1 Influenza A virus (A/Managua/12.01/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY072721.1 Influenza A virus (A/Managua/3359.01/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY072665.1 Influenza A virus (A/Managua/2339.03/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY072657.1 Influenza A virus (A/Managua/4570.01/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY072409.1 Influenza A virus (A/Athens/INS334/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY072337.1 Influenza A virus (A/Newark/INS319/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY072289.1 Influenza A virus (A/Warsaw/INS313/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071739.1 Influenza A virus (A/Mexico City/WR1701T/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY071587.1 Influenza A virus (A/Amman/WR1335T/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY071579.1 Influenza A virus (A/South Carolina/WR1326P/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY071571.1 Influenza A virus (A/South Carolina/WR1325P/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY071563.1 Influenza A virus (A/South Carolina/WR1324P/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY071547.1 Influenza A virus (A/California/WR1323P/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY071539.1 Influenza A virus (A/California/WR1321P/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY071507.1 Influenza A virus (A/California/WR1317P/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY071395.1 Influenza A virus (A/Hong Kong/WR0114N/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%
CY071370.1 Influenza A virus (A/Newark/INS429/2010(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071338.1 Influenza A virus (A/Bangkok/INS425/2010(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071322.1 Influenza A virus (A/Athens/INS421/2010(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071314.1 Influenza A virus (A/Athens/INS420/2010(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071298.1 Influenza A virus (A/Athens/INS417/2010(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071282.1 Influenza A virus (A/Athens/INS413/2010(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071130.1 Influenza A virus (A/Athens/INS383/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071050.1 Influenza A virus (A/New York/NHRC0004/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071042.1 Influenza A virus (A/New York/NHRC0003/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071026.1 Influenza A virus (A/New York/NHRC0001/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY071010.1 Influenza A virus (A/Guam/NHRC0031/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY070994.1 Influenza A virus (A/Guam/NHRC0029/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY070986.1 Influenza A virus (A/Guam/NHRC0007/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY070978.1 Influenza A virus (A/Guam/NHRC0006/2009(H1N1)) segment 5, complete sequence 2619 2619 100% 0.0 98%
CY069642.1 Influenza A virus (A/Singapore/527/2009(H1N1)) segment 5 sequence 2619 2619 100% 0.0 98%

_________________
www.twitter.com/hniman

isn't that very dangerous ?

_________________
no patents on genes, publish the GISAID sequences !

Swine jumping to humans and then back to swine is a VERY dangerous situation, no WHO proclamations on the pandemic end required.

The recent Costa Rica swine sequences have MANY RBD changes and the possiblity of similar chnages in the fatal and severe cases in Mexico and Venzuela are quite real.

http://www.recombinomics.com/News/02101 ... Swine.html

http://www.recombinomics.com/News/02141 ... Swine.html

_________________
www.twitter.com/hniman