An automated global clade classification tool for H1 hemagglutinin genes from swine influenza A viruses

Transcription

1 An automated global clade classification tool for H1 hemagglutinin genes from swine influenza A viruses Yun Zhang J. Craig Venter Institute June 25, 2017

2 Outline A web-based, automated H1 clade classification tool Comprehensive H1 clade annotations in IRD H1 clade based analysis and visualization

3 Genetic Diversity of Swine Influenza A Viruses Swine H1 has diversified into 3 genetic lineages classical swine H1 from 1918 Spanish flu a, b, g, H1N1pdm09 human seasonal lineage d, H1 hu N2, A/swine/Italy/4675/2003 Eurasian avian lineage H1 av N1 Challenges inconsistent naming conventions limited global data

4 Global Swine H1 Classification Nomenclature

5 A LEGEND US C ade B Global Swine H1 HA Phylogeny B GU Influenza A Virus A/chicken/Scotland/1959 H5N Chicken/Avian -N/A- United Kingdom -N/A- -N/A- Outgroup Outgroup CY Influenza A Virus A/swine/JY2/1931(H1N1) H1N Swine -N/A- Unknown -N/A- -N/A- alpha 1A.1 EU Influenza A Virus A/swine/Iowa/1945 H1N Swine North America USA Iowa -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Ohio/23/1935 H1N Swine North America USA Ohio -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Wisconsin/2/1970 H1N Swine North America USA Wisconsin -N/A- alpha 1A.1 EU Influenza A Virus A/swine/Iowa/1973 H1N Swine North America USA Iowa -N/A- alpha 1A.1 AB Influenza A Virus A/swine/Saraburi/NIAH /2009 H1N1 11/2009 Swine Asia Thailand -N/A- -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Wisconsin/11/1980 H1N Swine North America USA Wisconsin -N/A- alpha 1A.1 JN Influenza A Virus A/swine/Korea/VDS3/2009 H1N1 09/2009 Swine Asia South Korea -N/A alpha 1A.1.1 JF Influenza A Virus A/swine/QC/370/2009 H1N1 05/08/2009 Swine North America Canada -N/A alpha 1A.1.1 JF Influenza A Virus A/swine/QC/1697-2/2009 H1N1 05/15/2009 Swine North America Canada -N/A alpha 1A.1.1 JF Influenza A Virus A/swine/QC/729-B/2009 H1N1 09/04/2009 Swine North America Canada -N/A alpha 1A.1.1 CY Influenza A Virus A/swine/Manitoba/D0290/2013 H1N2 11/20/2013 Swine North America Canada -N/A alpha 1A.1.1 CY Influenza A Virus A/swine/Manitoba/D0378/2015 H1N2 04/14/2015 Swine North America Canada -N/A alpha 1A.1.1 CY Influenza A Virus A/swine/Manitoba/D0175/2012 H1N1 10/23/2012 Swine North America Canada -N/A alpha 1A.1.1 CY Influenza A Virus A/swine/Hong Kong/1304/2003 H1N2 09/28/2003 Swine Asia Hong Kong -N/A- -N/A- alpha 1A.1.1 FJ Influenza A Virus A/swine/Taichung/E3/1992(H1N1) H1N1 09/08/1992 Swine Asia Taiwan -N/A- -N/A- alpha 1A.1.1 CY Influenza A Virus A/swine/Iowa/1/1986 H1N Swine North America USA Iowa -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Iowa/1/1985 H1N Swine North America USA Iowa -N/A- alpha 1A.1 KJ Influenza A Virus A/swine/Thailand/CU-S3350N/2012 H1N1 02/13/2012 Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 KM Influenza A Virus A/swine/Thailand/CU-S3631N/2012 H1N2 12/06/2012 Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 AB Influenza A Virus A/swine/Ratchaburi/NIAH1481/2000 H1N Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 KC Influenza A Virus A/swine/Thailand/CU-SPL4/2010 H1N1 08/10/2010 Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 KJ Influenza A Virus A/swine/Thailand/CU-S3340N/2012 H1N1 01/24/2012 Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 GQ Influenza A Virus A/swine/Hong Kong/NS837/2001(H1N1) H1N1 04/09/2001 Swine Asia Hong Kong -N/A- -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Iowa/24297/1991 H1N Swine North America USA Iowa -N/A- alpha 1A.1 CY Influenza A Virus A/swine/California/T /1991 H1N Swine North America USA California -N/A- alpha 1A.1 KF Influenza A Virus A/swine/Beijing/216/1992(H1N1) H1N Swine Asia China -N/A- -N/A- alpha-beta-gamma2-like 1A.1.3 CY Influenza A Virus A/swine/Hong Kong/1286/1993 H1N1 11/29/1993 Swine Asia Hong Kong -N/A- -N/A- alpha-beta-gamma2-like 1A.1.3 CY Influenza A Virus A/swine/Hong Kong/NS143/2000 H1N1 09/15/2000 Swine Asia Hong Kong -N/A- -N/A- alpha-beta-gamma2-like 1A.1.3 CY Influenza A Virus A/swine/Hong Kong/NS1680/2001 H1N1 12/28/2001 Swine Asia Hong Kong -N/A- -N/A- alpha 1A.1.3 JN Influenza A Virus A/swine/Guangdong/603/2010(H1N2) H1N2 02/27/2010 Swine Asia China -N/A- -N/A- alpha 1A.1.3 KM Influenza A Virus A/swine/Guangdong/NS3155/2012 H1N2 09/13/2012 Swine Asia China -N/A- -N/A- alpha 1A.1.3 CY Influenza A Virus A/swine/Hong Kong/2503/1994 H1N1 04/25/1994 Swine Asia Hong Kong -N/A- -N/A- alpha-beta-gamma2-like 1A.1 GU Influenza A Virus A/swine/Guangdong/446/2006(H1N1) H1N Swine Asia China -N/A- -N/A- alpha 1A.1 FJ Influenza A Virus A/swine/Guangdong/1/2005 H1N Swine Asia China -N/A- -N/A- alpha 1A.1 KU Influenza A Virus A/swine/Mexico/AVX3/2011 H1N1 03/18/2011 Swine North America Mexico -N/A- -N/A- gamma2-beta-like 1A.3.1 KU Influenza A Virus A/swine/Mexico/AVX42/2012 H1N1 11/26/2012 Swine North America Mexico -N/A- -N/A- gamma2-beta-like 1A.3.1 KU Influenza A Virus A/swine/Mexico/AVX11/2012 H1N1 03/13/2012 Swine North America Mexico -N/A- -N/A- gamma2-beta-like 1A.3.1 CY Influenza A Virus A/swine/Minnesota/SG1470/2004 H1N1 08/13/2004 Swine North America USA Minnesota -N/A- beta 1A.2 KU Influenza A Virus A/swine/Oklahoma/A /2016 H1N1 01/22/2016 Swine North America USA Oklahoma beta 1A.2 KF Influenza A Virus A/swine/Nebraska/A /2013 H1N1 09/05/2013 Swine North America USA Nebraska -N/A- beta 1A.2 KC Influenza A Virus A/swine/Nebraska/A /2012 H1N1 11/27/2012 Swine North America USA Nebraska beta 1A.2 AF Influenza A Virus A/Swine/Iowa/930/01 H1N Swine North America USA Iowa -N/A- beta 1A.2 AF Influenza A Virus A/Swine/Minnesota/55551/00 H1N Swine North America USA Minnesota -N/A- beta 1A.2 CY Influenza A Virus A/swine/North Carolina/47834/2000 H1N Swine North America USA North Carolina -N/A- beta 1A.2 CY Influenza A Virus A/swine/North Carolina/7571/2003 H1N Swine North America USA North Carolina -N/A- gamma2 1A.3 CY Influenza A Virus A/swine/North Carolina/01169/2006 H1N2 06/22/2006 Swine North America USA North Carolina -N/A- gamma2 1A.3 CY Influenza A Virus A/swine/Tennessee/00264/2004 H1N1 03/11/2004 Swine North America USA Tennessee gamma2 1A.3 JQ Influenza A Virus A/swine/Minnesota/A /2011 H1N2 01/27/2011 Swine North America USA Minnesota gamma2 1A.3.2 CY Influenza A Virus A/swine/Texas/SG1187/2004 H1N1 02/25/2004 Swine North America USA Texas gamma2 1A.3.2 CY Influenza A Virus A/swine/Texas/00525/2005 H1N1 03/08/2005 Swine North America USA Texas gamma2 1A.3.2 KC Influenza A Virus A/swine/Illinois/A /2012 H1N1 10/2012 Swine North America USA Illinois gamma2 1A.3.2 JQ Influenza A Virus A/swine/Oklahoma/A /2011 H1N1 03/24/2011 Swine North America USA Oklahoma gamma2 1A.3.2 CY Influenza A Virus A/swine/Texas/00195/2003 H1N1 10/15/2003 Swine North America USA Texas gamma2 1A.3.2 CY Influenza A Virus A/swine/North Carolina/18161/2002 H1N Swine North America USA North Carolina -N/A- gamma2 1A.3.3 CY Influenza A Virus A/swine/Kentucky/SG1167/2003 H1N1 01/22/2003 Swine North America USA Kentucky gamma-npdm-like 1A.3.3 AF Influenza A Virus A/Swine/Indiana/9K035/99 H1N Swine North America USA Indiana -N/A- gamma 1A AF Influenza A Virus A/Swine/Illinois/100085A/01 H1N Swine North America USA Illinois -N/A- gamma 1A KJ Influenza A Virus A/swine/Indiana/13TOSU1052/2013 H1N2 07/01/2013 Swine North America USA Indiana -N/A- gamma 1A KX Influenza A Virus A/swine/Illinois/A /2016 H1N1 03/10/2016 Swine North America USA Illinois gamma 1A KT Influenza A Virus A/swine/Iowa/A /2015 H1N1 08/13/2015 Swine North America USA Iowa -N/A- gamma 1A CY Influenza A Virus A/swine/Korea/1130/2009 H1N2 01/2009 Swine Asia South Korea -N/A gamma 1A AF Influenza A Virus A/Swine/Ohio/891/01 H1N Swine North America USA Ohio -N/A- gamma 1A AF Influenza A Virus A/Swine/Indiana/P12439/00 H1N Swine North America USA Indiana -N/A- npdm 1A.3.3 KU Influenza A Virus A/swine/Mexico/AVX27/2012 H1N1 08/02/2012 Swine North America Mexico -N/A- -N/A- npdm 1A HQ Influenza A Virus A/swine/Iowa/ /2009(H1N1) H1N1 11/08/2009 Swine North America USA Iowa npdm 1A JF Influenza A Virus A/swine/Costa Rica/ /2010 H1N1 11/01/2010 Swine North America Costa Rica -N/A- -N/A- npdm 1A KC Influenza A Virus A/swine/Freren/IDT /2011 H1N2 08/31/2011 Swine Europe Germany -N/A- -N/A- npdm 1A CY Influenza A Virus A/swine/Pennsylvania/A /2011 H1N1 02/14/2011 Swine North America USA Pennsylvania npdm 1A HQ Influenza A Virus A/swine/IL/ /2010(H1N1) H1N1 06/02/2010 Swine North America USA Illinois -N/A- npdm 1A KU Influenza A Virus A/swine/Nebraska/A /2016 H1N1 01/15/2016 Swine North America USA Nebraska npdm 1A CY Influenza A Virus A/Wisconsin/629-D00839/2009(H1N1) H1N1 09/22/2009 Human North America USA Wisconsin npdm NA JF Influenza A Virus A/swine/MB/36/2009 H1N1 10/06/2009 Swine North America Canada -N/A npdm 1A KM Influenza A Virus A/swine/Guangxi/NS2777/2010 H1N2 11/07/2010 Swine Asia China -N/A- -N/A- npdm 1A.3.3 KM Influenza A Virus A/swine/Guangxi/2891/2011 H1N2 10/09/2011 Swine Asia China -N/A- -N/A- npdm 1A.3.3 GQ Influenza A Virus A/swine/Hong Kong/1562/2005(H1N2) H1N2 11/11/2005 Swine Asia Hong Kong -N/A- -N/A- npdm 1A CY Influenza A Virus A/swine/Hong Kong/NS252/2009 H1N2 03/19/2009 Swine Asia Hong Kong -N/A- -N/A- npdm 1A KM Influenza A Virus A/swine/Guangdong/3583/2011 H1N2 10/27/2011 Swine Asia China -N/A- -N/A- npdm 1A GQ Influenza A Virus A/swine/Hong Kong/NS623/2002(H1N2) H1N2 07/09/2002 Swine Asia Hong Kong -N/A- -N/A- npdm 1A CY Influenza A Virus A/swine/Hong Kong/NS30/2004 H1N2 01/06/2004 Swine Asia Hong Kong -N/A- -N/A- npdm 1A EF Influenza A Virus A/swine/Guangxi/13/2006 H1N Swine Asia China -N/A- -N/A- npdm 1A KM Influenza A Virus A/swine/Hong Kong/4083/2011 H1N2 10/20/2011 Swine Asia Hong Kong -N/A- -N/A- npdm 1A GQ Influenza A Virus A/swine/Hong Kong/78/2003(H1N2) H1N2 01/23/2003 Swine Asia Hong Kong -N/A- -N/A- gamma-npdm-like 1A.3.3 AF Influenza A Virus A/Brevig Mission/1/1918 H1N Human North America USA Alaska -N/A- Other Other-Human D00837 Influenza A Virus A/swine/Cambridge/1939 H1N Swine Europe United Kingdom -N/A- -N/A- ND Other-Human CY Influenza A Virus A/Memphis/49/1983 H1N Human North America USA Tennessee -N/A- Other Other-Human CY Influenza A Virus A/Baylor/4052/1981 H1N Human North America USA Texas -N/A- Other Other-Human CY Influenza A Virus A/Memphis/29/1983 H1N Human North America USA Tennessee -N/A- Other Other-Human CY Influenza A Virus A/New Zealand/7/1983 H1N Human Oceania New Zealand -N/A- -N/A- Other Other-Human CY Influenza A Virus A/Texas/2922-3/1986 H1N Human North America USA Texas -N/A- delta-like Other-Human-1B.2 DQ Influenza A Virus A/Taiwan/01/1986 H1N Human Asia Taiwan -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Siena/4/1987(H1N1) H1N Human Europe Italy -N/A- -N/A- delta-like Other-Human-1B.2 JX Influenza A Virus A/Florida/2/1993(H1N1) H1N Human North America USA Florida -N/A- delta-like Other-Human-1B.2 JX Influenza A Virus A/Wellington/47/1992 H1N Human Oceania New Zealand -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Moscow/13/1998 H1N Human Europe Russia -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Malaysia/06768/1995 H1N1 05/16/1995 Human Asia Malaysia -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/New York/633/1995 H1N1 12/15/1995 Human North America USA New York delta-like Other-Human-1B.2 CY Influenza A Virus A/Texas/36/91 H1N Human North America USA Texas -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Beijing/262/1995 H1N Human Asia China -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Shanghai/2/1997 H1N Human Asia China -N/A- -N/A- delta-like Other-Human-1B.2 GU Influenza A Virus A/swine/Fujian/0325/2008 H1N1 03/25/2008 Swine Asia China -N/A- -N/A- delta-like Other-Human-1B.2 EU Influenza A Virus A/Denmark/3/2001 H1N Human Europe Denmark -N/A- -N/A- delta-like Other-Human-1B.2 KU Influenza A Virus A/swine/Mexico/AVX7/2011 H1N2 03/18/2011 Swine North America Mexico -N/A- -N/A- delta-like Other-Human-1B.2 KU Influenza A Virus A/swine/Mexico/AVX49/2013 H1N2 03/25/2013 Swine North America Mexico -N/A- -N/A- delta-like Other-Human-1B.2 KP Influenza A Virus A/Canterbury/23/2000 H1N1 08/03/2000 Human Oceania New Zealand -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Auckland/579/2000 H1N1 08/30/2000 Human Oceania New Zealand -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/swine/Hong Kong/1435/2006 H1N1 10/12/2006 Swine Asia Hong Kong -N/A- -N/A- delta-like Other-Human-1B.2 AB Influenza A Virus A/swine/Binh Doung/02_16/2010 H1N Swine Asia Viet Nam -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/HaNoi/BM898/2003 H1N1 10/14/2003 Human Asia Viet Nam -N/A- -N/A- delta2-delta-like Other-Human-1B.2 CY Influenza A Virus A/New York/221/2003 H1N1 03/21/2003 Human North America USA New York delta2 Other-Human-1B.2 CY Influenza A Virus A/Hanoi/ISBM31/2005 H1N1 04/08/2005 Human Asia Viet Nam -N/A- -N/A- delta2 Other-Human-1B.2 CY Influenza A Virus A/swine/Argentina/CIP051-BsAs76/2009 H1N1 10/2009 Swine South America Argentina -N/A- -N/A- delta2 Other-Human-1B.2 KR Influenza A Virus A/swine/Argentina/CIP051-C05-M1-1/2012 H1N2 12/05/2012 Swine South America Argentina -N/A- -N/A- delta2 Other-Human-1B.2 HQ Influenza A Virus A/swine/Minnesota/6004-1/2009 H1N1 11/19/2009 Swine North America USA Minnesota delta2 Other-Human-1B.2 KP Influenza A Virus A/Iowa/02/2006 H1N1 12/29/2006 Human North America USA Iowa delta2 NA EU Influenza A Virus A/Iowa/02/2006 H1N1 12/29/2006 Human North America USA Iowa delta2 Other-Human-1B.2 CY Influenza A Virus A/swine/North Carolina/01550/2007 H1N1 04/04/2007 Swine North America USA North Carolina delta2 1B.2.1 KU Influenza A Virus A/swine/Indiana/A /2016 H1N2 01/07/2016 Swine North America USA Indiana delta2 1B.2.1 KU Influenza A Virus A/swine/North Carolina/A /2016 H1N2 01/28/2016 Swine North America USA North Carolina delta2 1B.2.1 KT Influenza A Virus A/swine/North Carolina/A /2015 H1N2 05/06/2015 Swine North America USA North Carolina delta2 1B.2.1 KU Influenza A Virus A/swine/North Carolina/A /2015 H1N2 10/22/2015 Swine North America USA North Carolina delta2 1B.2.1 FJ Influenza A Virus A/swine/IL/00685/2005(H1N1) H1N Swine North America USA Illinois -N/A- delta2 1B.2.1 CY Influenza A Virus A/swine/North Carolina/00839/2005(H1N1) H1N1 10/27/2005 Swine North America USA North Carolina delta2 1B.2.1 HQ Influenza A Virus A/swine/Indiana/0582-3/2009 H1N2 08/04/2009 Swine North America USA Indiana delta2 1B.2.1 CY Influenza A Virus A/swine/North Carolina/ /2005 H1N Swine North America USA North Carolina -N/A- delta2 1B.2.1 KP Influenza A Virus A/swine/Brazil/G2P2/2013(H1N2) H1N2 06/05/2013 Swine South America Brazil -N/A- -N/A- delta-like 1B.2.2 KM Influenza A Virus A/swine/Brazil/ /2011 H1N2 07/06/2011 Swine South America Brazil -N/A- -N/A- delta-like 1B.2.2 KF Influenza A Virus A/swine/Brazil/31_11_1/2011 H1N2 02/25/2011 Swine South America Brazil -N/A- -N/A- delta-like 1B.2.2 CY Influenza A Virus A/swine/Argentina/CIP051-StaFeN2/2010 H1N2 05/2010 Swine South America Argentina -N/A- -N/A- delta-like 1B.2.2 DQ Influenza A Virus A/swine/Ontario/48235/04 H1N Swine North America Canada -N/A- -N/A- delta-like 1B.2.2 JN Influenza A Virus A/swine/Iowa/A /2011 H1N2 03/29/2011 Swine North America USA Iowa delta-like 1B.2.2 JX Influenza A Virus A/swine/Oklahoma/A /2012 H1N2 09/2012 Swine North America USA Oklahoma -N/A- delta1 1B.2.2 JQ Influenza A Virus A/swine/Minnesota/0745/2010 H1N2 03/03/2010 Swine North America USA Minnesota delta1 1B KC Influenza A Virus A/swine/Illinois/A /2012 H1N2 10/26/2012 Swine North America USA Illinois delta1 1B KT Influenza A Virus A/swine/Iowa/A /2015 H1N2 09/23/2015 Swine North America USA Iowa -N/A- delta1 1B KF Influenza A Virus A/swine/North Carolina/A /2013 H1N2 11/2013 Swine North America USA North Carolina delta1 1B KF Influenza A Virus A/swine/Kansas/A /2013 H1N2 10/14/2013 Swine North America USA Kansas delta1 1B KT Influenza A Virus A/swine/Iowa/A /2015 H1N2 09/09/2015 Swine North America USA Iowa -N/A- delta1 1B KF Influenza A Virus A/swine/Nebraska/A /2013 H1N2 09/09/2013 Swine North America USA Nebraska -N/A- delta1 1B JN Influenza A Virus A/swine/Arkansas/A /2011 H1N2 05/03/2011 Swine North America USA Arkansas delta1 1B HQ Influenza A Virus A/swine/Minnesota/0913-1/2009 H1N2 09/16/2009 Swine North America USA Minnesota delta1 1B CY Influenza A Virus A/swine/Oklahoma/ /2008(H1N2) H1N Swine North America USA Oklahoma -N/A- delta1 1B HM Influenza A Virus A/swine/Minnesota/03023/2010(H1N2) H1N2 04/26/2010 Swine North America USA Minnesota delta1 1B JN Influenza A Virus A/swine/Oklahoma/A /2011 H1N2 02/03/2011 Swine North America USA Oklahoma delta1 1B JX Influenza A Virus A/swine/Minnesota/A /2009 H1N2 12/28/2009 Swine North America USA Minnesota delta1 1B HQ Influenza A Virus A/swine/Minnesota/8721-1/2010 H1N2 04/14/2010 Swine North America USA Minnesota delta1 1B KF Influenza A Virus A/swine/Iowa/13C094/2013 H1N2 03/26/2013 Swine North America USA Iowa delta1 1B KT Influenza A Virus A/swine/Iowa/A /2015 H1N2 09/01/2015 Swine North America USA Iowa -N/A- delta1 1B KU Influenza A Virus A/swine/Nebraska/A /2015 H1N2 09/02/2015 Swine North America USA Nebraska -N/A- delta1 1B KX Influenza A Virus A/swine/Illinois/A /2016 H1N2 03/15/2016 Swine North America USA Illinois delta1 1B KU Influenza A Virus A/swine/Oklahoma/A /2016 H1N2 01/22/2016 Swine North America USA Oklahoma delta1 1B KJ Influenza A Virus A/swine/Kansas/A /2014 H1N2 04/01/2014 Swine North America USA Kansas delta1 1B KU Influenza A Virus A/swine/Illinois/A /2015 H1N2 11/30/2015 Swine North America USA Illinois delta1 1B CY Influenza A Virus A/swine/Minnesota/02324/2008 H1N2 09/10/2008 Swine North America USA Minnesota -N/A- delta1 1B CY Influenza A Virus A/swine/England/00003/2009 H1N2 01/12/2009 Swine Europe United Kingdom -N/A delta-like 1B.2.2 AF Influenza A Virus A/swine/Scotland/410440/94 H1N Swine Europe United Kingdom -N/A- -N/A- Other 1B.1 AF Influenza A Virus A/swine/England/438207/94 H1N Swine Europe United Kingdom -N/A- -N/A- Other 1B.1 CY Influenza A Virus A/swine/England/40280/1996 H1N2 07/09/1996 Swine Europe United Kingdom -N/A- -N/A- Other 1B.1.1 CY Influenza A Virus A/swine/England/448813/1994 H1N2 04/24/1994 Swine Europe United Kingdom -N/A Other 1B.1.1 KR Influenza A Virus A/swine/Scotland/51190/1999 H1N2 09/30/1999 Swine Europe United Kingdom -N/A- -N/A- Other 1B.1.1 CY Influenza A Virus A/swine/England/88761/1997 H1N2 02/03/1997 Swine Europe United Kingdom -N/A Other 1B.1.1 KR Influenza A Virus A/swine/England/038712/2012 H1N2 12/05/2012 Swine Europe United Kingdom -N/A Other 1B.1.1 JF Influenza A Virus A/swine/England/1428/2009 H1N2 12/08/2009 Swine Europe United Kingdom -N/A Other 1B.1.1 JF Influenza A Virus A/swine/England/1157/2009 H1N2 10/05/2009 Swine Europe United Kingdom -N/A Other 1B.1.1 KR Influenza A Virus A/swine/England/058879/2011 H1N2 05/16/2011 Swine Europe United Kingdom -N/A Other 1B.1.1 CY Influenza A Virus A/swine/England/002295/2002 H1N2 12/04/2002 Swine Europe United Kingdom -N/A Other 1B.1.1 KR Influenza A Virus A/swine/England/463180/1994 H1N2 05/12/1994 Swine Europe United Kingdom -N/A Other 1B.1.2 HQ Influenza A Virus A/swine/Italy/3592/1999 H1N Swine Europe Italy -N/A- -N/A- Other 1B CY Influenza A Virus A/swine/Italy/172336/2001 H1N Swine Europe Italy -N/A- -N/A- Other 1B HQ Influenza A Virus A/swine/Italy/70757/2009 H1N Swine Europe Italy -N/A- -N/A- Other 1B KF Influenza A Virus A/swine/Italy/20333/2006 H1N Swine Europe Italy -N/A- -N/A- Other 1B KR Influenza A Virus A/swine/France/Cotes GU Influenza A Virus A/chicken/Scotland/1959 H5N Chicken/Avian -N/A- United Kingdom -N/A- -N/A- Outgroup Outgroup CY Influenza A Virus A/swine/JY2/1931(H1N1) H1N Swine -N/A- Unknown -N/A- -N/A- alpha 1A.1 EU Influenza A Virus A/swine/Iowa/1945 H1N Swine North America USA Iowa -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Ohio/23/1935 H1N Swine North America USA Ohio -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Wisconsin/2/1970 H1N Swine North America USA Wisconsin -N/A- alpha 1A.1 EU Influenza A Virus A/swine/Iowa/1973 H1N Swine North America USA Iowa -N/A- alpha 1A.1 AB Influenza A Virus A/swine/Saraburi/NIAH /2009 H1N1 11/2009 Swine Asia Thailand -N/A- -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Wisconsin/11/1980 H1N Swine North America USA Wisconsin -N/A- alpha 1A.1 JN Influenza A Virus A/swine/Korea/VDS3/2009 H1N1 09/2009 Swine Asia South Korea -N/A alpha 1A.1.1 JF Influenza A Virus A/swine/QC/370/2009 H1N1 05/08/2009 Swine North America Canada -N/A alpha 1A.1.1 JF Influenza A Virus A/swine/QC/1697-2/2009 H1N1 05/15/2009 Swine North America Canada -N/A alpha 1A.1.1 JF Influenza A Virus A/swine/QC/729-B/2009 H1N1 09/04/2009 Swine North America Canada -N/A alpha 1A.1.1 CY Influenza A Virus A/swine/Manitoba/D0290/2013 H1N2 11/20/2013 Swine North America Canada -N/A alpha 1A.1.1 CY Influenza A Virus A/swine/Manitoba/D0378/2015 H1N2 04/14/2015 Swine North America Canada -N/A alpha 1A.1.1 CY Influenza A Virus A/swine/Manitoba/D0175/2012 H1N1 10/23/2012 Swine North America Canada -N/A alpha 1A.1.1 CY Influenza A Virus A/swine/Hong Kong/1304/2003 H1N2 09/28/2003 Swine Asia Hong Kong -N/A- -N/A- alpha 1A.1.1 FJ Influenza A Virus A/swine/Taichung/E3/1992(H1N1) H1N1 09/08/1992 Swine Asia Taiwan -N/A- -N/A- alpha 1A.1.1 CY Influenza A Virus A/swine/Iowa/1/1986 H1N Swine North America USA Iowa -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Iowa/1/1985 H1N Swine North America USA Iowa -N/A- alpha 1A.1 KJ Influenza A Virus A/swine/Thailand/CU-S3350N/2012 H1N1 02/13/2012 Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 KM Influenza A Virus A/swine/Thailand/CU-S3631N/2012 H1N2 12/06/2012 Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 AB Influenza A Virus A/swine/Ratchaburi/NIAH1481/2000 H1N Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 KC Influenza A Virus A/swine/Thailand/CU-SPL4/2010 H1N1 08/10/2010 Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 KJ Influenza A Virus A/swine/Thailand/CU-S3340N/2012 H1N1 01/24/2012 Swine Asia Thailand -N/A- -N/A- alpha 1A.1.2 GQ Influenza A Virus A/swine/Hong Kong/NS837/2001(H1N1) H1N1 04/09/2001 Swine Asia Hong Kong -N/A- -N/A- alpha 1A.1 CY Influenza A Virus A/swine/Iowa/24297/1991 H1N Swine North America USA Iowa -N/A- alpha 1A.1 CY Influenza A Virus A/swine/California/T /1991 H1N Swine North America USA California -N/A- alpha 1A.1 KF Influenza A Virus A/swine/Beijing/216/1992(H1N1) H1N Swine Asia China -N/A- -N/A- alpha-beta-gamma2-like 1A.1.3 CY Influenza A Virus A/swine/Hong Kong/1286/1993 H1N1 11/29/1993 Swine Asia Hong Kong -N/A- -N/A- alpha-beta-gamma2-like 1A.1.3 CY Influenza A Virus A/swine/Hong Kong/NS143/2000 H1N1 09/15/2000 Swine Asia Hong Kong -N/A- -N/A- alpha-beta-gamma2-like 1A.1.3 CY Influenza A Virus A/swine/Hong Kong/NS1680/2001 H1N1 12/28/2001 Swine Asia Hong Kong -N/A- -N/A- alpha 1A.1.3 JN Influenza A Virus A/swine/Guangdong/603/2010(H1N2) H1N2 02/27/2010 Swine Asia China -N/A- -N/A- alpha 1A.1.3 KM Influenza A Virus A/swine/Guangdong/NS3155/2012 H1N2 09/13/2012 Swine Asia China -N/A- -N/A- alpha 1A.1.3 CY Influenza A Virus A/swine/Hong Kong/2503/1994 H1N1 04/25/1994 Swine Asia Hong Kong -N/A- -N/A- alpha-beta-gamma2-like 1A.1 GU Influenza A Virus A/swine/Guangdong/446/2006(H1N1) H1N Swine Asia China -N/A- -N/A- alpha 1A.1 FJ Influenza A Virus A/swine/Guangdong/1/2005 H1N Swine Asia China -N/A- -N/A- alpha 1A.1 KU Influenza A Virus A/swine/Mexico/AVX3/2011 H1N1 03/18/2011 Swine North America Mexico -N/A- -N/A- gamma2-beta-like 1A.3.1 KU Influenza A Virus A/swine/Mexico/AVX42/2012 H1N1 11/26/2012 Swine North America Mexico -N/A- -N/A- gamma2-beta-like 1A.3.1 KU Influenza A Virus A/swine/Mexico/AVX11/2012 H1N1 03/13/2012 Swine North America Mexico -N/A- -N/A- gamma2-beta-like 1A.3.1 CY Influenza A Virus A/swine/Minnesota/SG1470/2004 H1N1 08/13/2004 Swine North America USA Minnesota -N/A- beta 1A.2 KU Influenza A Virus A/swine/Oklahoma/A /2016 H1N1 01/22/2016 Swine North America USA Oklahoma beta 1A.2 KF Influenza A Virus A/swine/Nebraska/A /2013 H1N1 09/05/2013 Swine North America USA Nebraska -N/A- beta 1A.2 KC Influenza A Virus A/swine/Nebraska/A /2012 H1N1 11/27/2012 Swine North America USA Nebraska beta 1A.2 AF Influenza A Virus A/Swine/Iowa/930/01 H1N Swine North America USA Iowa -N/A- beta 1A.2 AF Influenza A Virus A/Swine/Minnesota/55551/00 H1N Swine North America USA Minnesota -N/A- beta 1A.2 CY Influenza A Virus A/swine/North Carolina/47834/2000 H1N Swine North America USA North Carolina -N/A- beta 1A.2 CY Influenza A Virus A/swine/North Carolina/7571/2003 H1N Swine North America USA North Carolina -N/A- gamma2 1A.3 CY Influenza A Virus A/swine/North Carolina/01169/2006 H1N2 06/22/2006 Swine North America USA North Carolina -N/A- gamma2 1A.3 CY Influenza A Virus A/swine/Tennessee/00264/2004 H1N1 03/11/2004 Swine North America USA Tennessee gamma2 1A.3 JQ Influenza A Virus A/swine/Minnesota/A /2011 H1N2 01/27/2011 Swine North America USA Minnesota gamma2 1A.3.2 CY Influenza A Virus A/swine/Texas/SG1187/2004 H1N1 02/25/2004 Swine North America USA Texas gamma2 1A.3.2 CY Influenza A Virus A/swine/Texas/00525/2005 H1N1 03/08/2005 Swine North America USA Texas gamma2 1A.3.2 KC Influenza A Virus A/swine/Illinois/A /2012 H1N1 10/2012 Swine North America USA Illinois gamma2 1A.3.2 JQ Influenza A Virus A/swine/Oklahoma/A /2011 H1N1 03/24/2011 Swine North America USA Oklahoma gamma2 1A.3.2 CY Influenza A Virus A/swine/Texas/00195/2003 H1N1 10/15/2003 Swine North America USA Texas gamma2 1A.3.2 CY Influenza A Virus A/swine/North Carolina/18161/2002 H1N Swine North America USA North Carolina -N/A- gamma2 1A.3.3 CY Influenza A Virus A/swine/Kentucky/SG1167/2003 H1N1 01/22/2003 Swine North America USA Kentucky gamma-npdm-like 1A.3.3 AF Influenza A Virus A/Swine/Indiana/9K035/99 H1N Swine North America USA Indiana -N/A- gamma 1A AF Influenza A Virus A/Swine/Illinois/100085A/01 H1N Swine North America USA Illinois -N/A- gamma 1A KJ Influenza A Virus A/swine/Indiana/13TOSU1052/2013 H1N2 07/01/2013 Swine North America USA Indiana -N/A- gamma 1A KX Influenza A Virus A/swine/Illinois/A /2016 H1N1 03/10/2016 Swine North America USA Illinois gamma 1A KT Influenza A Virus A/swine/Iowa/A /2015 H1N1 08/13/2015 Swine North America USA Iowa -N/A- gamma 1A CY Influenza A Virus A/swine/Korea/1130/2009 H1N2 01/2009 Swine Asia South Korea -N/A gamma 1A AF Influenza A Virus A/Swine/Ohio/891/01 H1N Swine North America USA Ohio -N/A- gamma 1A AF Influenza A Virus A/Swine/Indiana/P12439/00 H1N Swine North America USA Indiana -N/A- npdm 1A.3.3 KU Influenza A Virus A/swine/Mexico/AVX27/2012 H1N1 08/02/2012 Swine North America Mexico -N/A- -N/A- npdm 1A HQ Influenza A Virus A/swine/Iowa/ /2009(H1N1) H1N1 11/08/2009 Swine North America USA Iowa npdm 1A JF Influenza A Virus A/swine/Costa Rica/ /2010 H1N1 11/01/2010 Swine North America Costa Rica -N/A- -N/A- npdm 1A KC Influenza A Virus A/swine/Freren/IDT /2011 H1N2 08/31/2011 Swine Europe Germany -N/A- -N/A- npdm 1A CY Influenza A Virus A/swine/Pennsylvania/A /2011 H1N1 02/14/2011 Swine North America USA Pennsylvania npdm 1A HQ Influenza A Virus A/swine/IL/ /2010(H1N1) H1N1 06/02/2010 Swine North America USA Illinois -N/A- npdm 1A KU Influenza A Virus A/swine/Nebraska/A /2016 H1N1 01/15/2016 Swine North America USA Nebraska npdm 1A CY Influenza A Virus A/Wisconsin/629-D00839/2009(H1N1) H1N1 09/22/2009 Human North America USA Wisconsin npdm NA JF Influenza A Virus A/swine/MB/36/2009 H1N1 10/06/2009 Swine North America Canada -N/A npdm 1A KM Influenza A Virus A/swine/Guangxi/NS2777/2010 H1N2 11/07/2010 Swine Asia China -N/A- -N/A- npdm 1A.3.3 KM Influenza A Virus A/swine/Guangxi/2891/2011 H1N2 10/09/2011 Swine Asia China -N/A- -N/A- npdm 1A.3.3 GQ Influenza A Virus A/swine/Hong Kong/1562/2005(H1N2) H1N2 11/11/2005 Swine Asia Hong Kong -N/A- -N/A- npdm 1A CY Influenza A Virus A/swine/Hong Kong/NS252/2009 H1N2 03/19/2009 Swine Asia Hong Kong -N/A- -N/A- npdm 1A KM Influenza A Virus A/swine/Guangdong/3583/2011 H1N2 10/27/2011 Swine Asia China -N/A- -N/A- npdm 1A GQ Influenza A Virus A/swine/Hong Kong/NS623/2002(H1N2) H1N2 07/09/2002 Swine Asia Hong Kong -N/A- -N/A- npdm 1A CY Influenza A Virus A/swine/Hong Kong/NS30/2004 H1N2 01/06/2004 Swine Asia Hong Kong -N/A- -N/A- npdm 1A EF Influenza A Virus A/swine/Guangxi/13/2006 H1N Swine Asia China -N/A- -N/A- npdm 1A KM Influenza A Virus A/swine/Hong Kong/4083/2011 H1N2 10/20/2011 Swine Asia Hong Kong -N/A- -N/A- npdm 1A GQ Influenza A Virus A/swine/Hong Kong/78/2003(H1N2) H1N2 01/23/2003 Swine Asia Hong Kong -N/A- -N/A- gamma-npdm-like 1A.3.3 AF Influenza A Virus A/Brevig Mission/1/1918 H1N Human North America USA Alaska -N/A- Other Other-Human D00837 Influenza A Virus A/swine/Cambridge/1939 H1N Swine Europe United Kingdom -N/A- -N/A- ND Other-Human CY Influenza A Virus A/Memphis/49/1983 H1N Human North America USA Tennessee -N/A- Other Other-Human CY Influenza A Virus A/Baylor/4052/1981 H1N Human North America USA Texas -N/A- Other Other-Human CY Influenza A Virus A/Memphis/29/1983 H1N Human North America USA Tennessee -N/A- Other Other-Human CY Influenza A Virus A/New Zealand/7/1983 H1N Human Oceania New Zealand -N/A- -N/A- Other Other-Human CY Influenza A Virus A/Texas/2922-3/1986 H1N Human North America USA Texas -N/A- delta-like Other-Human-1B.2 DQ Influenza A Virus A/Taiwan/01/1986 H1N Human Asia Taiwan -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Siena/4/1987(H1N1) H1N Human Europe Italy -N/A- -N/A- delta-like Other-Human-1B.2 JX Influenza A Virus A/Florida/2/1993(H1N1) H1N Human North America USA Florida -N/A- delta-like Other-Human-1B.2 JX Influenza A Virus A/Wellington/47/1992 H1N Human Oceania New Zealand -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Moscow/13/1998 H1N Human Europe Russia -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Malaysia/06768/1995 H1N1 05/16/1995 Human Asia Malaysia -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/New York/633/1995 H1N1 12/15/1995 Human North America USA New York delta-like Other-Human-1B.2 CY Influenza A Virus A/Texas/36/91 H1N Human North America USA Texas -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Beijing/262/1995 H1N Human Asia China -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Shanghai/2/1997 H1N Human Asia China -N/A- -N/A- delta-like Other-Human-1B.2 GU Influenza A Virus A/swine/Fujian/0325/2008 H1N1 03/25/2008 Swine Asia China -N/A- -N/A- delta-like Other-Human-1B.2 EU Influenza A Virus A/Denmark/3/2001 H1N Human Europe Denmark -N/A- -N/A- delta-like Other-Human-1B.2 KU Influenza A Virus A/swine/Mexico/AVX7/2011 H1N2 03/18/2011 Swine North America Mexico -N/A- -N/A- delta-like Other-Human-1B.2 KU Influenza A Virus A/swine/Mexico/AVX49/2013 H1N2 03/25/2013 Swine North America Mexico -N/A- -N/A- delta-like Other-Human-1B.2 KP Influenza A Virus A/Canterbury/23/2000 H1N1 08/03/2000 Human Oceania New Zealand -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/Auckland/579/2000 H1N1 08/30/2000 Human Oceania New Zealand -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/swine/Hong Kong/1435/2006 H1N1 10/12/2006 Swine Asia Hong Kong -N/A- -N/A- delta-like Other-Human-1B.2 AB Influenza A Virus A/swine/Binh Doung/02_16/2010 H1N Swine Asia Viet Nam -N/A- -N/A- delta-like Other-Human-1B.2 CY Influenza A Virus A/HaNoi/BM898/2003 H1N1 10/14/2003 Human Asia Viet Nam -N/A- -N/A- delta2-delta-like Other-Human-1B.2 CY Influenza A Virus A/New York/221/2003 H1N1 03/21/2003 Human North America USA New York delta2 Other-Human-1B.2 CY Influenza A Virus A/Hanoi/ISBM31/2005 H1N1 04/08/2005 Human Asia Viet Nam -N/A- -N/A- delta2 Other-Human-1B.2 CY Influenza A Virus A/swine/Argentina/CIP051-BsAs76/2009 H1N1 10/2009 Swine South America Argentina -N/A- -N/A- delta2 Other-Human-1B.2 KR Influenza A Virus A/swine/Argentina/CIP051-C05-M1-1/2012 H1N2 12/05/2012 Swine South America Argentina -N/A- -N/A- delta2 Other-Human-1B.2 HQ Influenza A Virus A/swine/Minnesota/6004-1/2009 H1N1 11/19/2009 Swine North America USA Minnesota delta2 Other-Human-1B.2 KP Influenza A Virus A/Iowa/02/2006 H1N1 12/29/2006 Human North America USA Iowa delta2 NA EU Influenza A Virus A/Iowa/02/2006 H1N1 12/29/2006 Human North America USA Iowa delta2 Other-Human-1B.2 CY Influenza A Virus A/swine/North Carolina/01550/2007 H1N1 04/04/2007 Swine North America USA North Carolina delta2 1B.2.1 KU Influenza A Virus A/swine/Indiana/A /2016 H1N2 01/07/2016 Swine North America USA Indiana delta2 1B.2.1 KU Influenza A Virus A/swine/North Carolina/A /2016 H1N2 01/28/2016 Swine North America USA North Carolina delta2 1B.2.1 KT Influenza A Virus A/swine/North Carolina/A /2015 H1N2 05/06/2015 Swine North America USA North Carolina delta2 1B.2.1 KU Influenza A Virus A/swine/North Carolina/A /2015 H1N2 10/22/2015 Swine North America USA North Carolina delta2 1B.2.1 FJ Influenza A Virus A/swine/IL/00685/2005(H1N1) H1N Swine North America USA Illinois -N/A- delta2 1B.2.1 CY Influenza A Virus A/swine/North Carolina/00839/2005(H1N1) H1N1 10/27/2005 Swine North America USA North Carolina delta2 1B.2.1 HQ Influenza A Virus A/swine/Indiana/0582-3/2009 H1N2 08/04/2009 Swine North America USA Indiana delta2 1B.2.1 CY Influenza A Virus A/swine/North Carolina/ /2005 H1N Swine North America USA North Carolina -N/A- delta2 1B.2.1 KP Influenza A Virus A/swine/Brazil/G2P2/2013(H1N2) H1N2 06/05/2013 Swine South America Brazil -N/A- -N/A- delta-like 1B.2.2 KM Influenza A Virus A/swine/Brazil/ /2011 H1N2 07/06/2011 Swine South America Brazil -N/A- -N/A- delta-like 1B.2.2 KF Influenza A Virus A/swine/Brazil/31_11_1/2011 H1N2 02/25/2011 Swine South America Brazil -N/A- -N/A- delta-like 1B.2.2 CY Influenza A Virus A/swine/Argentina/CIP051-StaFeN2/2010 H1N2 05/2010 Swine South America Argentina -N/A- -N/A- delta-like 1B.2.2 DQ Influenza A Virus A/swine/Ontario/48235/04 H1N Swine North America Canada -N/A- -N/A- delta-like 1B.2.2 JN Influenza A Virus A/swine/Iowa/A /2011 H1N2 03/29/2011 Swine North America USA Iowa delta-like 1B.2.2 JX Influenza A Virus A/swine/Oklahoma/A /2012 H1N2 09/2012 Swine North America USA Oklahoma -N/A- delta1 1B.2.2 JQ Influenza A Virus A/swine/Minnesota/0745/2010 H1N2 03/03/2010 Swine North America USA Minnesota delta1 1B KC Influenza A Virus A/swine/Illinois/A /2012 H1N2 10/26/2012 Swine North America USA Illinois delta1 1B KT Influenza A Virus A/swine/Iowa/A /2015 H1N2 09/23/2015 Swine North America USA Iowa -N/A- delta1 1B KF Influenza A Virus A/swine/North Carolina/A /2013 H1N2 11/2013 Swine North America USA North Carolina delta1 1B KF Influenza A Virus A/swine/Kansas/A /2013 H1N2 10/14/2013 Swine North America USA Kansas delta1 1B KT Influenza A Virus A/swine/Iowa/A /2015 H1N2 09/09/2015 Swine North America USA Iowa -N/A- delta1 1B KF Influenza A Virus A/swine/Nebraska/A /2013 H1N2 09/09/2013 Swine North America USA Nebraska -N/A- delta1 1B JN Influenza A Virus A/swine/Arkansas/A /2011 H1N2 05/03/2011 Swine North America USA Arkansas delta1 1B HQ Influenza A Virus A/swine/Minnesota/0913-1/2009 H1N2 09/16/2009 Swine North America USA Minnesota delta1 1B CY Influenza A Virus A/swine/Oklahoma/ /2008(H1N2) H1N Swine North America USA Oklahoma -N/A- delta1 1B HM Influenza A Virus A/swine/Minnesota/03023/2010(H1N2) H1N2 04/26/2010 Swine North America USA Minnesota delta1 1B JN Influenza A Virus A/swine/Oklahoma/A /2011 H1N2 02/03/2011 Swine North America USA Oklahoma delta1 1B JX Influenza A Virus A/swine/Minnesota/A /2009 H1N2 12/28/2009 Swine North America USA Minnesota delta1 1B HQ Influenza A Virus A/swine/Minnesota/8721-1/2010 H1N2 04/14/2010 Swine North America USA Minnesota delta1 1B KF Influenza A Virus A/swine/Iowa/13C094/2013 H1N2 03/26/2013 Swine North America USA Iowa delta1 1B KT Influenza A Virus A/swine/Iowa/A /2015 H1N2 09/01/2015 Swine North America USA Iowa -N/A- delta1 1B KU Influenza A Virus A/swine/Nebraska/A /2015 H1N2 09/02/2015 Swine North America USA Nebraska -N/A- delta1 1B KX Influenza A Virus A/swine/Illinois/A /2016 H1N2 03/15/2016 Swine North America USA Illinois delta1 1B KU Influenza A Virus A/swine/Oklahoma/A /2016 H1N2 01/22/2016 Swine North America USA Oklahoma delta1 1B KJ Influenza A Virus A/swine/Kansas/A /2014 H1N2 04/01/2014 Swine North America USA Kansas delta1 1B KU Influenza A Virus A/swine/Illinois/A /2015 H1N2 11/30/2015 Swine North America USA Illinois delta1 1B CY Influenza A Virus A/swine/Minnesota/02324/2008 H1N2 09/10/2008 Swine North America USA Minnesota -N/A- delta1 1B CY Influenza A Virus A/swine/England/00003/2009 H1N2 01/12/2009 Swine Europe United Kingdom -N/A delta-like 1B.2.2 AF Influenza A Virus A/swine/Scotland/410440/94 H1N Swine Europe United Kingdom -N/A- -N/A- Other 1B.1 AF Influenza A Virus A/swine/England/438207/94 H1N Swine Europe United Kingdom -N/A- -N/A- Other 1B.1 CY Influenza A Virus A/swine/England/40280/1996 H1N2 07/09/1996 Swine Europe United Kingdom -N/A- -N/A- Other 1B.1.1 CY Influenza A Virus A/swine/England/448813/1994 H1N2 04/24/1994 Swine Europe United Kingdom -N/A Other 1B.1.1 KR Influenza A Virus A/swine/Scotland/51190/1999 H1N2 09/30/1999 Swine Europe United Kingdom -N/A- -N/A- Other 1B.1.1 CY Influenza A Virus A/swine/England/88761/1997 H1N2 02/03/1997 Swine Europe United Kingdom -N/A Other 1B.1.1 KR Influenza A Virus A/swine/England/038712/2012 H1N2 12/05/2012 Swine Europe United Kingdom -N/A Other 1B.1.1 JF Influenza A Virus A/swine/England/1428/2009 H1N2 12/08/2009 Swine Europe United Kingdom -N/A Other 1B.1.1 JF Influenza A Virus A/swine/England/1157/2009 H1N2 10/05/2009 Swine Europe United Kingdom -N/A Other 1B.1.1 KR Influenza A Virus A/swine/England/058879/2011 H1N2 05/16/2011 Swine Europe United Kingdom -N/A Other 1B.1.1 CY Influenza A Virus A/swine/England/002295/2002 H1N2 12/04/2002 Swine Europe United Kingdom -N/A Other 1B.1.1 KR Influenza A Virus A/swine/England/463180/1994 H1N2 05/12/1994 Swine Europe United Kingdom -N/A Other 1B.1.2 HQ Influenza A Virus A/swine/Italy/3592/1999 H1N Swine Europe Italy -N/A- -N/A- Other 1B CY Influenza A Virus A/swine/Italy/172336/2001 H1N Swine Europe Italy -N/A- -N/A- Other 1B HQ Influenza A Virus A/swine/Italy/70757/2009 H1N Swine Europe Italy -N/A- -N/A- Other 1B KF Influenza A Virus A/swine/Italy/20333/2006 H1N Swine Europe Italy -N/A- -N/A- Other 1B KR Influenza A Virus A/swine/France/CotesdArmor-0198/2011 H1N2 04/11/2011 Swine Europe France -N/A Other 1B KC Influenza A Virus A/swine/France/ /2012 H1N Swine Europe France -N/A- -N/A- Other 1B KJ Influenza A Virus A/swine/France/ /2012 H1N2 11/16/2012 Swine Europe France -N/A Other 1B KC Influenza A Virus A/swine/France/ /2011 H1N2 03/07/2011 Swine Europe France -N/A Other 1B CY Influenza A Virus A/swine/Cotes d'armor/1174/2009 H1N Swine Europe France -N/A- -N/A- Other 1B CY Influenza A Virus A/swine/Cotes d'armor/790/1997 H1N Swine Europe France -N/A- -N/A- Other 1B EU Influenza A Virus A/swine/Bakum/1832/2000 H1N Swine Europe Germany -N/A- -N/A- Other 1B AJ Influenza A Virus A/swine/Italy/1081/00 H1N Swine Europe Italy -N/A- -N/A- Other 1B KR Influenza A Virus A/swine/Netherlands/De-Lutte-167A/2012 H1N2 04/25/2012 Swine Europe Netherlands -N/A Other 1B CY Influenza A Virus A/swine/Spain/40564/2002(H1N2) H1N Swine Europe Spain -N/A- -N/A- Other 1B CY Influenza A Virus A/swine/Gent/177/2002 H1N Swine Europe Belgium -N/A- -N/A- Other 1B KR Influenza A Virus A/swine/Belgium/Oostkamp-26/2012 H1N2 01/12/2012 Swine Europe Belgium -N/A Other 1B KR Influenza A Virus A/swine/Spain/29257/2012 H1N2 01/30/2012 Swine Europe Spain -N/A Other 1B.1.2 KR Influenza A Virus A/swine/Spain/29262/2012 H1N2 01/31/2012 Swine Europe Spain -N/A Other 1B.1.2 AF Influenza A Virus A/swine/England/690421/95 H1N Swine Europe United Kingdom -N/A- -N/A- Other 1B.1.2 KR Influenza A Virus A/swine/Denmark/ /2011 H1N Swine Europe Denmark -N/A- -N/A- Other 1C.2 KR Influenza A Virus A/swine/Denmark/ /2011 H1N Swine Europe Denmark -N/A- -N/A- Other 1C.2 CY Influenza A Virus A/swine/Lutol/3/2000(H1N1) H1N Swine Europe Poland -N/A- -N/A- Other 1C.2.3 CY Influenza A Virus A/swine/Finnistere/800/2004 H1N Swine Europe France -N/A- -N/A- Other 1C.2.3 CY Influenza A Virus A/swine/Hong Kong/NS129/2003 H1N1 02/06/2003 Swine Asia Hong Kong -N/A- -N/A- Other 1C.2.3 KM Influenza A Virus A/swine/Guangxi/3612/2011 H1N1 12/11/2011 Swine Asia China -N/A- -N/A- Other 1C.2.3 KM Influenza A Virus A/swine/Hong Kong/126/2012 H1N1 01/05/2012 Swine Asia Hong Kong -N/A- -N/A- Other 1C.2.3 KM Influenza A Virus A/swine/Hong Kong/NS967/2012 H1N1 03/15/2012 Swine Asia Hong Kong -N/A- -N/A- Other 1C.2.3 AM Influenza A Virus A/swine/Germany/SEk1178/2000 H1N Swine Europe Germany -N/A- -N/A- Other 1C.2.2 GQ Influenza A Virus A/swine/Haseluenne/IDT2617/2003 H1N1 10/09/2003 Swine Europe Germany -N/A Other 1C.2.2 JQ Influenza A Virus A/swine/Spain/16/2009 H1N1 07/2009 Swine Europe Spain -N/A Other 1C.2.2 KU Influenza A Virus A/Poland/wild boar/ /2013 H1N1 12/12/2013 Swine Europe Poland -N/A Other 1C.2.2 KR Influenza A Virus A/swine/Germany/Reinberg-IDT /2012 H1N1 01/02/2012 Swine Europe Germany -N/A Other 1C.2.2 CY Influenza A Virus A/swine/Spain/50047/2003 H1N Swine Europe Spain -N/A- -N/A- Other 1C.2.2 GQ Influenza A Virus A/swine/Greven/IDT2889/2004 H1N1 01/07/2004 Swine Europe Germany -N/A Other 1C.2.1 KJ Influenza A Virus A/swine/Italy/50814/2012 H1N1 01/2012 Swine Europe Italy -N/A Other 1C.2.1 KR Influenza A Virus A/swine/Belgium/Lichtervelde-57/2013 H1N1 03/01/2013 Swine Europe Belgium -N/A Other 1C.2.1 CY Influenza A Virus A/swine/Italy/ /2003 H1N Swine Europe Italy -N/A- -N/A- Other 1C.2.1 CY Influenza A Virus A/swine/Spain/51915/2003 H1N Swine Europe Spain -N/A- -N/A- Other 1C.2.1 KR Influenza A Virus A/swine/Netherlands/Wijhe-371/2012 H1N1 10/24/2012 Swine Europe Netherlands -N/A Other 1C.2.1 JX Influenza A Virus A/swine/Spain/03/2008 H1N1 06/01/2008 Swine Europe Spain -N/A- -N/A- Other 1C.2.1 KR Influenza A Virus A/swine/Denmark/ /2010 H1N2 05/28/2010 Swine Europe Denmark -N/A Other 1C.2 KC Influenza A Virus A/swine/Denmark/ /2004 H1N Swine Europe Denmark -N/A- -N/A- Other 1C.2 KC Influenza A Virus A/swine/Denmark/ /2003 H1N Swine Europe Denmark -N/A- -N/A- Other 1C.2 KR Influenza A Virus A/swine/Denmark/ /2009 H1N1 04/2009 Swine Europe Denmark -N/A Other 1C.2 KC Influenza A Virus A/swine/Denmark/ /2004 H1N Swine Europe Denmark -N/A- -N/A- Other 1C.2 FJ Influenza A Virus A/swine/Belgium/1/1998 H1N Swine Europe Belgium -N/A- -N/A- Other 1C.2 CY Influenza A Virus A/swine/Denmark/WVL9/1993 H1N Swine Europe Denmark -N/A- -N/A- Other 1C.2 KR Influenza A Virus A/swine/England/267/2007 H1N1 02/22/2007 Swine Europe United Kingdom -N/A Other 1C.1 CY Influenza A Virus A/swine/England/453/2006 H1N1 05/05/2006 Swine Europe United Kingdom -N/A Other 1C.1 KR Influenza A Virus A/swine/England/024079/2013 H1N1 08/21/2013 Swine Europe United Kingdom -N/A- -N/A- Other 1C.1 CY Influenza A Virus A/swine/England/26029/1998 H1N1 06/17/1998 Swine Europe United Kingdom -N/A- -N/A- Other 1C.1 CY Influenza A Virus A/swine/Spain/WVL6/1991 H1N Swine Europe Spain -N/A- -N/A- Other 1C.1 AJ Influenza A Virus A/swine/Italy/1498-2/97 H1N Swine Europe Italy -N/A- -N/A- Other 1C.1 AM Influenza A Virus A/swine/Germany/Vi5698/1995 H1N Swine Europe Germany -N/A- -N/A- Other 1C.1 KJ Influenza A Virus A/swine/Germany/S27/1981 H1N Swine Europe Germany -N/A- -N/A- Other 1C.1 AF Influenza A Virus A/swine/Netherlands/3/80 H1N Swine Europe Netherlands -N/A- -N/A- Other 1C.1 KJ Influenza A Virus A/swine/Arnsberg/1/1979 H1N1 12/07/1979 Swine Europe Germany -N/A Other 1C.1 KT Influenza A Virus A/duck/Schleswig/21/1979 H1N Duck/Avian Europe Germany -N/A- -N/A- Other Other-Avian KT Influenza A Virus A/coot/Schleswig/2/1980 H1N Common Coot/Avian Europe Germany -N/A- -N/A- Other Other-Avian D00839 Influenza A Virus A/duck/HK/196/1977 H Duck/Avian Asia Hong Kong -N/A- -N/A- Other Other-Avian GU Influenza A Virus A/mallard/Marquenterre/Z237/1983(H1N1) H1N Mallard/Avian Europe France -N/A- -N/A- Other Other-Avian AB Influenza A Virus A/duck/Miyagi/66/1977 H1N Duck/Avian Asia Japan -N/A- -N/A- Other Other-Avian KP Influenza A Virus A/duck/Hainan/Q221/2012 H1N Duck/Avian Asia China -N/A- -N/A- Other Other-Avian KP Influenza A Virus A/duck/Fujian/89/2013 H1N Duck/Avian Asia China -N/A- -N/A- Other Other-Avian EF Influenza A Virus A/chicken/Hong Kong/14/1976 H1N Chicken/Avian Asia Hong Kong -N/A- -N/A- Other Other-Avian CY Influenza A Virus A/duck/Victoria/2b/1980 H1N Duck/Avian Oceania Australia -N/A- -N/A- Other Other-Avian CY Influenza A Virus A/thick-billed murre/alaska/335/1976 H1N Murre/Avian North America USA Alaska -N/A- Other Other-Avian CY Influenza A Virus A/blue-winged teal/wisconsin/336/1976 H1N Blue-Winged Teal/Avian North America USA Wisconsin -N/A- Other Other-Avian CY Influenza A Virus A/mallard/ALB/201/1998 H1N1 08/11/1998 Mallard/Avian North America Canada -N/A- -N/A- Other Other-Avian AF Influenza A Virus A/turkey/Minnesota/1661/81 H1N Turkey/Avian North America USA Minnesota -N/A- Other Other-Avian CY Influenza A Virus A/mallard/Alberta/119/1998 H1N1 08/06/1998 Mallard/Avian North America Canada -N/A- -N/A- Other Other-Avian CY Influenza A Virus A/ruddy turnstone/new Jersey/AI09-618/2009 H1N9 05/26/2009 Ruddy Turnstone/Avian North America USA New Jersey Other Other-Avian CY Influenza A Virus A/blue-winged teal/illinois/12os4788/2012 H1N1 10/20/2012 Blue-Winged Teal/Avian North America USA Illinois Other Other-Avian Loading Influenza Research Database... About Us Community Announcements Links Resources Support Best-known H1 tree H1 reference tree 0.1 LEGEND G oba C ade 1A 1B Proposed by influenza experts Anderson TK, Macken CA, Lewis NS, Scheuermann RH, Van Reeth K, Brown IH, Swenson SL, Simon G, Saito T, Berhane Y, Ciacci-Zanella J, Pereda A, Davis CT, Donis RO, Webby RJ, Vincent AL (2016) A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses. msphere. doi: /mSphere Best-known H1 tree Swine, human & avian 7070 H1 sequences H1 reference tree 239 H1s 1C Sign Out yun.zhang@jcvi.org Benefits Reflect the evolution of swine IAV in a global context A unified nomenclature system

6 Global Swine H1 Classification & IRD

7 Loading Influenza About Research Us Community Database... Announcements Links Resources Support Sign Out SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA HELP Search Search our comprehensive database for: Sequences & Strains Animal Surveillance Sequence Feature Variant Types Immune epitope data 3D protein structures Host Factor Data Antiviral Drugs Browse All Search Types Highlights Start Analysis Tutorial Analyze Analyze data online: Sequence Alignment Phylogenetic Tree Sequence Variation (SNP) Metadata driven Comparative Analysis HPAI H5N1 Clade Classification Swine H1 Clade Classification BLAST Browse All Tools Phylogenetic Trees IRD uses PhyML (Guindon and Gascuel, 2003) and offers multiple evolutionary models to infer phylogenies. Decoration options let you color tree leaves by metadata. Export image and legend, or download trees as Newick or PhyloXml files for other viewing software. Key Highlights: Quick Tree produces an accurate topology for > 1,000 sequences. Custom Tree lets you choose an evolutionary model and parameter values. ModelCompare (Custom Tree) suggests an evolutionary model to best fit the data. Specify metadata for the leaves (strain name, etc.) Save to Workbench Use your workbench to: Store and share data Combine working sets Integrate your data with IRD data Store and share analyses Custom search alert What's New with Flu Global Swine H1 Classification In collaboration with Tavis Anderson and Amy Vincent at USDA, the newly proposed Global Swine H1 Classification scheme has been implemented in IRD. Major functions include: Clade classification of all H1 sequences in IRD regardless of host. Sequence search based on H1 clade annotations. Clade assignment tool for user provided H1 sequences. Phylogenetic tree decoration based on H1 clade annotations. Comparison of H1 sequences by Meta CATS using H1 clade metadata. Public influenza virus database and analysis resource Tight integration of a wide variety of different data types Novel derived data only available in IRD A broad array of analysis and visualization tools Individual personal online workbenches Large user community 1534 sessions/week (2017 average) 41% from U.S. 59% international (UK, China, Japan, India, Germany, South Korea, Canada, etc.) 529 citations in scientific publications (20JUN2017)

8 4/18/2017 Influenza Research Database - Swine H1 Clade Classification H1 Clade Classification Tool Loading Influenza Research Database... About Us Community Announcements Links Resources Support SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA Workbench Sign In HELP Home Swine H1 Clade Classification Swine H1 Clade Classification Tool The swine H1 clade classification tool classifies the clade of the HA/H1 viruses from any host and for any NA subtype, with reference to the global swine H1 clade scheme (Anderson et al., 2016 ) the US swine H1 classification scheme. This tool infers the clade for a query sequence from its position within the reference tree. It is a collaboration between Catherine Macken at IRD and Tavis Anderson and others at the USDA. SOP for global swine H1 clade classification Global Swine H1 Clade Classification Reference Tree Global Swine H1 Clade Classification Reference Sequences SOP for US swine H1 clade classification US Swine H1 Clade Classification Reference Tree Description of US clades with name that include " like" Sequences from other serotypes of HA, or other segments will yield unpredictable and likely incorrect results. If unsure of your sequence's segment or serotype, we suggest you use the IRD Sequence Annotation Tool (Analyze & Visualize > Annotate Nucleotide Sequences). ANALYSIS NAME 6/21/2017 Influenza Research Database - Swine H1 Clade Classification INPUT SEQUENCES Analyze my custom sequences only. Upload a file containing my sequences in FASTA Paste sequences in FASTA format. format. Loading Influenza AboutResearch Us Community Database... Announcements Links Resources Support Sign Out Analyze my custom sequences and associated metadata with IRD sequences. Clear SEARCH DATA ANALYZE & VISUALIZE WORKBENCH yun.zhang@jcvi.org Run SUBMIT DATA HELP Release Date: Mar 16, 2017 Home Swine H1 Clade Classification Results This system is provided for authorized users only. Anyone using this system expressly consents to monitoring while using the system. Improper use of this system may be referred to law enforcement officials. This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute, and Vecna Technologies. Swine H1 Clade Classification Report Save Analysis Download Raw Result Sequence Identifier Global Swine H1 Clade Classification (SOP) Clade Assignment Unified Tree Tree Viewer US Swine H1 Clade Classification (SOP) Clade Assignment Unified Tree Tree Viewer KP B.2.1 Download View Tree delta2 Download View Tree KX B.2.1 Download View Tree delta2 Download View Tree

9 Comprehensive H1 Clade Annotations in IRD Strain Information *1 Complete Genome Set: Organism Name: Strain Name: Subtype: Global Swine H1 Clade (SOP): US Swine H1 Clade(SOP): 2009 Pandemic H1N1 like (SOP)?: Yes Influenza A Virus A/Minnesota/14/2012 View Strain Details H1N2 1B delta1 Mixed Positive and Negative Segments 1C.2.1 1C.2.3 1B.2.1 1B B Other-Human- 1B.2 1A (pdm09) 1A H1 viruses of all hosts 1A 1B 1C Other

10 Sequence Search by H1 Clade Nucleotide Sequence Search Search for influenza sequences, proteins, and strains using two types of searches. Use the advanced search to allow you to refine your search with the more fine grained search, and you can pick your viewing options. Results matching your criteria: 1,514 DATA TYPE COMPLETE GENOME HOST GEOGRAPHIC GROUPING Genome Segments Protein Strain VIRUS TYPE A B C Provisional Influenza D (PMID: ) SUBTYPE * Use comma to separate multiple entries. Ex: H1N1, H7, H3N2. STRAIN NAME Complete Genome Only SELECT SEGMENTS Complete? All PB2 PB1 PA HA NP NA MP NS CLADE CLASSIFICATION Swine North America South America COUNTRY Choose a Country... CLADE CLASSIFICATION None Global H1 Clade (SOP) 1B.2.2 1B B B.2.2 like * Use comma to separate multiple entries. Ex: A/chicken/Israel/1055/2008, A/chicken/Laos/16/2008. None Global H1 Clade (SOP) 1B.2.2 1B B B.2.2 like US H1 Clade (SOP) DATE RANGE From: YYYY To: YYYY To add month to search, see Advance Options: Month Range US H1 Clade (SOP) H5 Clade (SOP) 2009 ph1n1 Sequence Similarity (SOP) H5 Clade (SOP) 2009 ph1n1 Sequence Similarity (SOP) ADVANCED OPTIONS Show All Tip: To select multiple or deselect, Ctrl click (Windows) or Cmd click (MacOS) Clear Search

11 Data Analysis and Visualization Based on H1 Clade Metadata-driven Comparative Analysis Tool (meta-cats) - Setup Subset Mouse click on the sequences to select them, Ctrl and/or shift key enable the multiple selection. After selecting the sequences, click on "Add" to move into the group. "Remove" will send the selected sequences back to the main list. Auto grouping on: Global Swine H1 Clade Group1: 1A Group2: 1A MAIN LIST OF SEQUENCES HA N/A N/A A/swine/Iowa/A /2017 ARJ63955 HA N/A N/A A/swine/Iowa/A /2017 ARU07169 LIST OF SEQUENCES GROUP 1 Add Remove HA N/A N/A A/Wisconsin/88/2016 APH11078 HA N/A N/A A/Montana/54/2016 APH11102 HA N/A N/A A/Montana/51/2016 APH11145 HA N/A N/A A/California/138/2016 APH11198 HA N/A N/A A/Wyoming/31/2016 APH11241 HA N/A N/A A/Delaware/29/2016 APO20313 HA N/A N/A A/Pennsylvania/91/2016 APO sequences LIST OF SEQUENCES GROUP 2 Christian Zmasek. Archaeopteryx.js. Monday 9:45-10 pm, Viral evolution and Ecology I - W37-10 Add Remove HA N/A N/A A/swine/South Dakota/A /2016 APF29921 HA N/A N/A A/swine/Iowa/A /2016 APG56845 HA N/A N/A A/swine/Iowa/A /2016 APG56857 HA N/A N/A A/swine/North Carolina/A /2016 APG56863 HA N/A N/A A/swine/Iowa/A /2016 APG56871 HA N/A N/A A/swine/Iowa/A /2016 APG56875 HA N/A N/A A/swine/Minnesota/A /2016 APG56827 Clear 126 sequences Run

12 Summary A web-based, automated H1 clade classification tool Comprehensive H1 clade annotations H1 clade based analysis and visualization

13 Acknowledgements Amy Vincent Tavis Anderson Thomas Smith Ed Klem IRD You Catherine Macken Richard Scheuermann Nicola Lewis