Rhiza Labs FluTracker Forum

GISAID
EPI282705 A/Ankara/WRAIR1440T/2009 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI282681 A/Ankara/WRAIR1426N/2009 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI277801 A/Ankara/WR1429T/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065

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GISAID
EPI304250 A/Canada-ON/RV2966/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI304186 A/Canada-ON/RV2912/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI297859 A/Hemsbury/1948 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI297734 A/Netherlands/001S1/1948 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI296641 A/Thailand/SN_0116/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI296406 A/Thailand/Siriraj-01/2007 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI295627 A/Slovakia/1634/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI295625 A/Slovakia/1626/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI295623 A/Slovakia/1625/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI295621 A/Slovakia/1624/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI295619 A/Slovakia/1623/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI281760 A/Texas/AF2627/2009 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI281700 A/South Carolina/AF2562/2009 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI281272 A/swine/Iowa/02039/2008 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI279891 A/Hong Kong/2200/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI278566 A/Slovakia/1580/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI278564 A/Slovakia/838/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI276799 A/Japan/AF2263/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI276369 A/ENG/1067/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI276317 A/ENG/720/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI276310 A/ENG/715/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI276226 A/Connecticut/AF2153/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI276199 A/California/AF2124/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI272381 A/Bellamy/42 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI272379 A/Puerto Rico/8/34 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI272377 A/WS/33 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI272375 A/NWS/33 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI270599 A/California/VRDL130/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI269536 A/swine/Iowa/03010/2010 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI262463 A/swine/Iowa/02997/2010 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI259432 A/swine/Iowa/02998/2010 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI258040 A/Heilongjiang-Jianhua/SWL18/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI256029 A/Ostrava 221/10 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI255640 A/swine/Hong Kong/2314/2009 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI252962 A/Texas/JMS395/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI252954 A/Texas/JMS394/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI252273 A/Puerto Rico/8/34/PY102-V1 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI252272 A/Puerto Rico/8/1934 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI252271 A/Puerto Rico/8/34 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI252235 A/Puerto Rico/8/34/Mount Sinai (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI252234 A/Puerto Rico/8/34 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI248570 A/Almaty/32/1998 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI246150 A/Yamagata/13/2008 (A/H1N1 seasonal) segment 6 (NA) 27.0 6.04065
EPI245781 A/ENG/639/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI244467 A/swine/Pingtung/64-25/2007 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI244466 A/swine/Pingtung/64-26/2007 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI244465 A/swine/Pingtung/64-29/2007 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI244047 A/OSAKA/2190/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI243208 A/swine/29/1937 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI242890 A/WS/1933 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI242886 A/NWS/33 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI242756 A/swine/Northern Ireland/1938 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI242754 A/swine/Cambridge/1939 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI242623 A/swine/NI/1938 (A/H1) segment 4 (HA) 27.0 6.04065
EPI242603 A/swine/Cambridge/39 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI242590 A/swine/1931 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI242406 A/lvPR8/34 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI242398 A/hvPR8/34 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI242092 A/WSN/33 (A/H0 seasonal) segment 4 (HA) 27.0 6.04065
EPI242085 A/WSN/1933 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI242077 A/WSN/1933 TS61 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI242061 A/VM113-V1 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI242056 A/United Kingdom/1/1933 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI242024 A/Puerto Rico/8-1-MA/1934 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI241907 A/NWS/G70C (A/H1N9) segment 4 (HA) 27.0 6.04065
EPI241906 A/NWS-Tokyo (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI241905 A/NWS-Mvi (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI241904 A/NWS-G70c (A/H1N9) segment 4 (HA) 27.0 6.04065
EPI241899 A/NWS-F (A/H1N2 seasonal) segment 4 (HA) 27.0 6.04065
EPI241888 A/Melbourne/1-MA/1946 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI241058 A/Puerto Rico/8-1/1934 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI241050 A/Phila/1935 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI240999 A/Melbourne/1/1946 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI240997 A/Marton/43 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI240958 A/Iowa/1943 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI240957 A/Huston/43 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI240898 A/Henry/1936 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI240872 A/DSP/43 (A/H0 seasonal) segment 4 (HA) 27.0 6.04065
EPI240847 A/Alaska/1935 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI240837 A/AA/Marton/1943 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI240829 A/AA/Huston/1945 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI236372 A/swine/Cotes dArmor/48376/2002 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI236037 A/lake ice/Lake Park/Siberia/9.9/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236035 A/lake ice/Lake Park/Siberia/9.5/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236034 A/lake ice/Lake Park/Siberia/9.4/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236033 A/lake ice/Lake Park/Siberia/9.2/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236032 A/lake ice/Lake Park/Siberia/8.8/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236030 A/lake ice/Lake Park/Siberia/8.5/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236029 A/lake ice/Lake Park/Siberia/8.2/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236024 A/lake ice/Lake Park/Siberia/7.4/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236014 A/lake ice/Lake Park/Siberia/5.6b/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236012 A/lake ice/Lake Park/Siberia/5.5b/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236007 A/lake ice/Lake Park/Siberia/4.9/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236006 A/lake ice/Lake Park/Siberia/4.8/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236005 A/lake ice/Lake Park/Siberia/4.6/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236003 A/lake ice/Lake Park/Siberia/4.2/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236002 A/lake ice/Lake Park/Siberia/4.10/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236001 A/lake ice/Lake Park/Siberia/4.1/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI236000 A/lake ice/Lake Park/Siberia/23.9/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235996 A/lake ice/Lake Park/Siberia/21.3/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235987 A/lake ice/Lake Park/Siberia/18.4/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235979 A/lake ice/Lake Park/Siberia/16.9/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235978 A/lake ice/Lake Park/Siberia/16.6/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235971 A/lake ice/Lake Park/Siberia/13.9/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235970 A/lake ice/Lake Park/Siberia/13.7/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235968 A/lake ice/Lake Park/Siberia/13.5/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235967 A/lake ice/Lake Park/Siberia/13.4/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235965 A/lake ice/Lake Park/Siberia/13.2/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI235964 A/lake ice/Lake Park/Siberia/13.10/2002 (A/H1) segment 4 (HA) 27.0 6.04065
EPI234590 A/swine/SD/31813/2009 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI234428 A/swine/Malaysia/3966/1984 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI232931 A/KOBE/92404/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI231302 A/Ontario/RV3226/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI230642 A/Wilson-Smith/33 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI230631 A/Wilson-Smith/1933 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI230626 A/Weiss/43 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI230593 A/Melbourne/35 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI230541 A/Bel/1942 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI227708 A/Michigan/25/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI227628 A/Bermuda/9261/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI225738 A/swine/Cotes dArmor/0123/2006 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI225737 A/swine/Cotes dArmor/0113/2006 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI222610 A/swine/Cotes dArmor/0040/2007 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI217322 A/SC/9/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI210905 A/TOTTORI/72/2008 (A/H1 seasonal) segment 6 (NA) 27.0 6.04065
EPI210794 A/HOKKAIDO/19/2009 (A/H1 seasonal) segment 6 (NA) 27.0 6.04065
EPI190159 A/Hong Kong/179/2008 (A/H1N1 seasonal) segment 6 (NA) 27.0 6.04065
EPI186625 A/swine/Morbihan/0028/2007 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI185269 A/Taiwan/VGHYM0122-01/1990 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI178476 A/Israel/644/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI176775 A/Puerto Rico/8-SV3/1934 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI176767 A/Puerto Rico/8-SV1/1934 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI175402 A/swine/Pingtung/92-2/2003 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI162018 A/Lyon/1350/2007 (A/H1N1 seasonal) segment 6 (NA) 27.0 6.04065
EPI161892 A/Hong Kong/179/2008 (A/H1N1 seasonal) segment 6 (NA) 27.0 6.04065
EPI159360 A/Puerto Rico/8/1934 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI157931 A/Lyon/1350/2007 (A/H1N1 seasonal) segment 6 (NA) 27.0 6.04065
EPI133952 A/Hawaii/28/2007 (A/H1N1 seasonal) segment 6 (NA) 27.0 6.04065
EPI131598 A/Mongolia/111/91 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI131596 A/Mongolia/153/88 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI131282 A/PR/8/34 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI130751 A/swine/Iowa/15/30 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI130667 A/Tokyo/3/67 (A/H1N2 seasonal) segment 4 (HA) 27.0 6.04065
EPI130571 A/swine/St-Hyacinthe/148/1990 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI124024 A/swine/Iowa/15/1930 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI116891 A/Bangkok/569/98 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI115405 A/Puerto Rico/8/34 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI103016 A/swine/Taiwan/CO935/2004 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI102972 A/swine/Taiwan/CO935/2004 (A/H1N2) segment 4 (HA) 27.0 6.04065
EPI74156 A/swine/Ohio/23/1935 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI63011 A/Auckland/606/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI55237 A/Canterbury/05/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI46288 A/Waikato/92/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI33819 A/Canterbury/152/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI32368 A/Canterbury/79/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI32349 A/Canterbury/71/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI32330 A/Canterbury/70/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI32273 A/Canterbury/65/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI32102 A/South Canterbury/159/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI31969 A/Canterbury/73/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI31874 A/Canterbury/48/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI31836 A/Canterbury/45/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI31684 A/Canterbury/24/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI31627 A/Canterbury/19/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI31608 A/Canterbury/17/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI31190 A/Canterbury/76/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI29937 A/Puerto Rico/8/34 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI25489 A/swine/Korea/S175/2004 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI25445 A/swine/Korea/S10/2004 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI16512 A/London/1/1919 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI16510 A/London/1/1918 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI12643 A/Iceland/25/2000 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI12575 A/Trieste/21/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI12571 A/Greece/158/2001 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI11310 A/Buenos Aires/344/99 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI11308 A/Buenos Aires/6177/99 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI11302 A/Buenos Aires/T118/97 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI11300 A/Buenos Aires/T114/97 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI11298 A/Buenos Aires/A64/97 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI5571 A/South Carolina/1/18 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI5569 A/New_York/1/18 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI5567 A/Brevig Mission/1/1918 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI4899 A/swine/Iowa/15/30 (A/H1N1) segment 4 (HA) 27.0 6.04065
EPI4160 A/Taiwan/112/1996 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065
EPI583 A/Tokyo/62/1999 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.04065

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GISAID

EPI295732 A/England/4500186/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065
EPI231507 A/Brazil/7450/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.04065

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The GISAID pedigrees were added to show that most of these shared polymorphisms are EXTREMELY rare in the database, yet are found in 2 or 3 sequences from the swine herd in a discordant pattern. These newly acquired polymorphisms are NOT explained by "random mutation", as put forward by the flat earth society members, including the CDC and WHO consultants.

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The discordant pattern seen in the HA sequences extends to the NA sequences. Once again there are multiple synonymous and non-synonymous polymorphisms found in all six NA sequences, but there are two additional polymorphisms appended onto this well defined background. Both are present in A/swine/Costa Rica/000125-3/2010 but one is shared with A/swine/Costa Rica/000125-19, while the other is shared with A/swine/Costa Rica/000125-14/2010 and A/swine/Costa Rica/000125-16/2010, which eliminates clonal expansion and supports recombination (see pedigrees below).

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C531T

JF279898.1 Influenza A virus (A/swine/Costa Rica/000125-19/2010(H1N1)) segment 6
JF279886.1 Influenza A virus (A/swine/Costa Rica/000125-3/2010(H1N1)) segment 6
EPI303660 A/Canada-MB/RV2110/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI303644 A/Canada-MB/RV2105/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI303149 A/Canada-MB/RV1976/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI301664 A/swine/Germany-NW/R708/10 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI300798 A/Taiwan/14/2009 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI299617 A/Switzerland/5165/2010 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI299610 A/Switzerland/9356/2009 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI295628 A/Slovakia/1634/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI295626 A/Slovakia/1626/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI295624 A/Slovakia/1625/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI295622 A/Slovakia/1624/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI295620 A/Slovakia/1623/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI295600 A/Austria/532579/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI278648 A/swine/Germany-SH/R402/10 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI278642 A/swine/Germany-NI/R258/09 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI278639 A/swine/Germany-NI/R248/09 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI278637 A/swine/Germany-NI/R211/09 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI278619 A/Kansas/05/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI278565 A/Slovakia/1580/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI273031 A/swine/Gent/130/2002 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI273030 A/swine/Gent/06/2001 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI273028 A/swine/Gent/112/2007 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI273027 A/swine/Gent/106/2007 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI273026 A/swine/Gent/83/2006 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI273025 A/swine/Gent/132/2005 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI259556 A/Ytml/NIV9438/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI257387 A/Chongqing-Wuxi/SWL3120/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI257331 A/Chongqing-Wuxi/SWL3118/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI256245 A/Beijing-Huairou/SWL1998/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI256241 A/Beijing-Huairou/SWL11001/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI254876 A/New York/2963/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI252548 A/Ontario/9698/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI248508 A/swine/Germany-NW/IDT2889/04 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI248506 A/swine/Germany-SN/siv-leipz8826/09 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI248504 A/swine/Germany-SN/siv-leipz6340/09 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI248502 A/swine/Germany-SN/siv-leipz243/09 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI248492 A/swine/Germany-BB/leipz11308/09 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI248484 A/swine/Germany-SH/R1737/09 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI248476 A/turkey/Germany-NI/R778/09 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI240167 A/mallard/Marquenterre/Z237/1983 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI237248 A/California/VRDL6/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI232390 A/swine/Germany/SIV05/2007 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI231139 A/mallard/Korea/L08-8/2008 (A/H6N1) segment 6 (NA) 27.0 6.04065
EPI225741 A/swine/Cotes dArmor/0190/2006 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI217065 A/North Carolina/35/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI194268 A/Uruguay/755/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI186623 A/swine/Cotes d'Armor/016007/2005 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI186622 A/swine/Cotes d'Armor/002007/2006 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI186621 A/swine/Cotes d'Armor/0227/2005 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI186620 A/swine/Cotes d'Armor/0136_18/2006 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI181272 A/swine/Greven/IDT2889/2004 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI181265 A/swine/Ennigerloh/IDT5803/2006 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI181264 A/swine/Haseluenne/IDT2617/03 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI181263 A/swine/Haseluenne/IDT2617/03 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI181262 A/swine/Haseluenne/IDT2617/03 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI175370 A/swine/Hungary/19774/2006 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI161647 A/swine/Italy/247578/2004 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI161646 A/swine/Italy/65296/2004 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI161645 A/swine/Italy/53949/2004 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI120449 A/swine/Italy/66945/2006 (A/H3N1) segment 6 (NA) 27.0 6.04065
EPI32639 A/swine/Spain/53207/2004 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI32620 A/swine/Spain/51915/2003 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI16638 A/mallard/Stralsund/41-6/81 (A/H2N1) segment 6 (NA) 27.0 6.04065

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C693T (A231V)

JF279895.1 Influenza A virus (A/swine/Costa Rica/000125-16/2010(H1N1)) segment 6
JF279889.1 Influenza A virus (A/swine/Costa Rica/000125-14/2010(H1N1)) segment 6
JF279886.1 Influenza A virus (A/swine/Costa Rica/000125-3/2010(H1N1)) segment 6
EPI301406 A/England/142/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI283641 A/Barcelona/INS378/2009 (A/H1N1) segment 6 (NA) 27.0 6.04065
EPI278820 A/Arizona/07/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI278517 A/Ukraine/131/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI273905 A/Kenya/915/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI258035 A/Xinjiang-Tianshan/SWL1119/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI257627 A/Liaoning-Heping/SWL1606/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI256373 A/Beijing-Huairou/SWL11005/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI256345 A/Beijing-Huairou/SWL11032/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI256105 A/Beijing-Huairou/SWL1856/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI254892 A/New York/3230/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI254680 A/Seoul/7/2010 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI235501 A/Sumy/795/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI234544 A/Russia/171/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI232211 A/Cherkasy/346/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI232207 A/Cherkasy/333/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI227733 A/Nevada/18/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065
EPI217379 A/Catalonia/S1620/2009 (A/H1N1 swl) segment 6 (NA) 27.0 6.04065

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The discordance seen in HA and NA sequences also extends to MP. There is only one polymorphisms that is found in multiple sequences (other than those in all six) and it is shared between a different combination of isolates, as seen in pedigree below

C7T

JF279902.1 Influenza A virus (A/swine/Costa Rica/000125-20/2010(H1N1)) segment 7
JF279899.1 Influenza A virus (A/swine/Costa Rica/000125-19/2010(H1N1)) segment 7
JF279890.1 Influenza A virus (A/swine/Costa Rica/000125-14/2010(H1N1)) segment 7
EPI280543 A/mallard/Nevada/450206-4/2006 (A/H5N2) segment 7 (MP) 27.0 6.04065
EPI275254 A/glaucous gull/Alaska/44198-027/2006 (A/H16N3) segment 7 (MP) 27.0 6.04065
EPI243214 A/X-31 (A/H3N2) segment 7 (MP) 27.0 6.04065
EPI238928 A/mallard/Minnesota/29/1998 (A/H6N8) segment 7 (MP) 27.0 6.04065
EPI238422 A/chicken/Jiangsu/1/1999 (A/H9N2) segment 7 (MP) 27.0 6.04065
EPI236229 A/northern pintail/Texas/282/2002 (A/H6N1) segment 7 (MP) 27.0 6.04065
EPI235788 A/chicken/Jiangsu/1/2002 (A/H9N2) segment 7 (MP) 27.0 6.04065
EPI191086 A/duck/Zhejiang/3/2002 (A/H9N2) segment 7 (MP) 27.0 6.04065
EPI159149 A/mallard/MN/323/1999 (A/H4N8) segment 7 (MP) 27.0 6.04065
EPI142117 A/Hong Kong/CUHK18358/1998 (A/H3N2) segment 7 (MP) 27.0 6.04065
EPI142095 A/Hong Kong/CUHK10276/1998 (A/H3N2) segment 7 (MP) 27.0 6.04065
EPI127890 A/Hong Kong/CUHK18358/1998 (A/H3N2) segment 7 (MP) 27.0 6.04065
EPI127846 A/Hong Kong/CUHK10276/1998 (A/H3N2) segment 7 (MP) 27.0 6.04065
EPI77466 A/mallard/Maryland/1235/2006 (A/H3N6) segment 7 (MP) 27.0 6.04065
EPI32446 A/New York/607/1995 (A/H1N1 seasonal) segment 7 (MP) 27.0 6.04065
EPI17516 A/Taiwan/3/71 (A/H3N2) segment 7 (MP) 27.0 6.04065
EPI4645 A/Chicken/New Jersey/15086-3/94 (A/H7N3) segment 7 (MP) 27.0 6.04065

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As a quick summery, the USDA released a series of six isolates from a swine herd in Costa Rica from samples collected in November, 2010. Each of the gene segments had multiple markers found in all six isoaltes (HA, NA. MP) but all three genes had additional markers shared between various subsets of the six isolates.

These combinations were discordant in all three genes, strongly supporting recombination between the six isoaltes which each other. The number of examples of discordance effectively elimates a "random mutation" explanation as well as a "lab error" explanation and thoroughly discredits the "random mutation" paradigm propgated by the CDC and WHO consultants (and some posters who spread the nonsense on Internet message boards).

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Commentary

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

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