Swine H1 Clade ASV2017 web - Influenza Research …...An automated global clade classification tool for H1 hemagglutinin genes from swine influenza A viruses Yun Zhang J. Craig Venter

An automated global clade classification tool for H1 hemagglutinin genes from

swine influenza A viruses

Yun ZhangJ. Craig Venter Institute

June 25, 2017

Outline

A web-based, automated H1 clade classification tool

Comprehensive H1 clade annotations in IRD

H1 clade based analysis and visualization

Swine H1 has diversified into 3 genetic lineagesclassical swine H1 from 1918 Spanish flu

• a, b, g, H1N1pdm09 human seasonal lineage

• d, H1huN2, A/swine/Italy/4675/2003Eurasian avian lineage

• H1avN1

Challengesinconsistent naming conventionslimited global data

Genetic Diversity of Swine Influenza A Viruses

Global Swine H1 Classification Nomenclature

Global Swine H1 HA PhylogenyProposed by influenza expertsAnderson 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: 10.1128/mSphere.00275-16

Best-known H1 treeSwine, human & avian7070 H1 sequences

H1 reference tree239 H1s

BenefitsReflect the evolution of swine IAV in a global contextA unified nomenclature system

Best-known H1 tree

A B C

Sequence Identifier

Global Swine H1 Clade Classification (SOP) US Swine H1 Clade Classification (SOP)

Clade Assignment Unified Tree Tree Viewer Clade Assignment Unified Tree Tree Viewer

2016054341 1B.2.2.1 Download View Tree delta1 Download View Tree

400183 1B.2.1 Download View Tree delta2 Download View Tree

63709BNot H1 Sequence. Unable to determine classification.

Not H1 Sequence. Unable to determine classification.

33325Not H1 Sequence. Unable to determine classification.


Swine H1 Clade Classification Report

Loading Influenza Research Database...

Release Date: Sep 29, 2016

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 lawenforcement officials.This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272201400028C and is a collaboration between NorthropGrumman Health IT, J. Craig Venter Institute, and Vecna Technologies.

Save Analysis Download Raw Result


Sequence Identifier Clade Assignment Unified Tree Tree Viewer

2016054341|HA|swine|USA|Indiana|2016 delta1 Download View Tree

402352|HA|swine|Mexico||2010 npdm Download View Tree

63709A|HA|swine|USA|North_Carolina|2015 gamma Download View Tree

400183|HA|swine|USA|Iowa|2015 delta2 Download View Tree


17581|HA|swine|USA|Illinois|2015 Not H1 Sequence Unable to determine classification

404009|HA|swine|Canada|Alberta|2015 Not H1 Sequence Unable to determine classification

63709B|HA|swine|USA|North_Carolina|2015 Not H1 Sequence Unable to determine classification

33325|HA|swine|USA|Missouri|2015 Not H1 Sequence Unable to determine classification

Home Swine H1 Clade Classification Results

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• Rename “Swine H1 Clade” to “US Swine H1 Clade”• Add SOP for US Swine H1 Clade• Add “Global Swine H1 Clade (SOP)”

GU052518|Influenza A Virus|A/chicken/Scotland/1959|H5N1|1959|Chicken/Avian|-N/A-|United Kingdom|-N/A-|-N/A-|Outgroup|OutgroupCY147406|Influenza A Virus|A/swine/JY2/1931(H1N1)|H1N1|1931|Swine|-N/A-|Unknown|-N/A-|-N/A-|alpha|1A.1EU139824|Influenza A Virus|A/swine/Iowa/1945|H1N1|1945|Swine|North America|USA|Iowa|-N/A-|alpha|1A.1CY027291|Influenza A Virus|A/swine/Ohio/23/1935|H1N1|1935|Swine|North America|USA|Ohio|-N/A-|alpha|1A.1

CY022437|Influenza A Virus|A/swine/Wisconsin/2/1970|H1N1|1970|Swine|North America|USA|Wisconsin|-N/A-|alpha|1A.1EU139826|Influenza A Virus|A/swine/Iowa/1973|H1N1|1973|Swine|North America|USA|Iowa|-N/A-|alpha|1A.1

AB620186|Influenza A Virus|A/swine/Saraburi/NIAH116625-17/2009|H1N1|11/2009|Swine|Asia|Thailand|-N/A-|-N/A-|alpha|1A.1CY022421|Influenza A Virus|A/swine/Wisconsin/11/1980|H1N1|1980|Swine|North America|USA|Wisconsin|-N/A-|alpha|1A.1

JN043430|Influenza A Virus|A/swine/Korea/VDS3/2009|H1N1|09/2009|Swine|Asia|South Korea|-N/A-|08-09|alpha|1A.1.1JF713826|Influenza A Virus|A/swine/QC/370/2009|H1N1|05/08/2009|Swine|North America|Canada|-N/A-|08-09|alpha|1A.1.1JF713904|Influenza A Virus|A/swine/QC/1697-2/2009|H1N1|05/15/2009|Swine|North America|Canada|-N/A-|08-09|alpha|1A.1.1JF714129|Influenza A Virus|A/swine/QC/729-B/2009|H1N1|09/04/2009|Swine|North America|Canada|-N/A-|08-09|alpha|1A.1.1CY194974|Influenza A Virus|A/swine/Manitoba/D0290/2013|H1N2|11/20/2013|Swine|North America|Canada|-N/A-|13-14|alpha|1A.1.1CY195551|Influenza A Virus|A/swine/Manitoba/D0378/2015|H1N2|04/14/2015|Swine|North America|Canada|-N/A-|14-15|alpha|1A.1.1CY194365|Influenza A Virus|A/swine/Manitoba/D0175/2012|H1N1|10/23/2012|Swine|North America|Canada|-N/A-|12-13|alpha|1A.1.1

CY085590|Influenza A Virus|A/swine/Hong Kong/1304/2003|H1N2|09/28/2003|Swine|Asia|Hong Kong|-N/A-|-N/A-|alpha|1A.1.1FJ752514|Influenza A Virus|A/swine/Taichung/E3/1992(H1N1)|H1N1|09/08/1992|Swine|Asia|Taiwan|-N/A-|-N/A-|alpha|1A.1.1

CY028788|Influenza A Virus|A/swine/Iowa/1/1986|H1N1|1986|Swine|North America|USA|Iowa|-N/A-|alpha|1A.1CY022317|Influenza A Virus|A/swine/Iowa/1/1985|H1N1|1985|Swine|North America|USA|Iowa|-N/A-|alpha|1A.1

KJ162037|Influenza A Virus|A/swine/Thailand/CU-S3350N/2012|H1N1|02/13/2012|Swine|Asia|Thailand|-N/A-|-N/A-|alpha|1A.1.2KM355368|Influenza A Virus|A/swine/Thailand/CU-S3631N/2012|H1N2|12/06/2012|Swine|Asia|Thailand|-N/A-|-N/A-|alpha|1A.1.2

AB434288|Influenza A Virus|A/swine/Ratchaburi/NIAH1481/2000|H1N1|2000|Swine|Asia|Thailand|-N/A-|-N/A-|alpha|1A.1.2KC610049|Influenza A Virus|A/swine/Thailand/CU-SPL4/2010|H1N1|08/10/2010|Swine|Asia|Thailand|-N/A-|-N/A-|alpha|1A.1.2KJ162044|Influenza A Virus|A/swine/Thailand/CU-S3340N/2012|H1N1|01/24/2012|Swine|Asia|Thailand|-N/A-|-N/A-|alpha|1A.1.2

GQ229261|Influenza A Virus|A/swine/Hong Kong/NS837/2001(H1N1)|H1N1|04/09/2001|Swine|Asia|Hong Kong|-N/A-|-N/A-|alpha|1A.1CY027155|Influenza A Virus|A/swine/Iowa/24297/1991|H1N1|1991|Swine|North America|USA|Iowa|-N/A-|alpha|1A.1CY028780|Influenza A Virus|A/swine/California/T9001707/1991|H1N1|1991|Swine|North America|USA|California|-N/A-|alpha|1A.1KF057118|Influenza A Virus|A/swine/Beijing/216/1992(H1N1)|H1N1|1992|Swine|Asia|China|-N/A-|-N/A-|alpha-beta-gamma2-like|1A.1.3CY085073|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

CY085350|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.1.3CY085478|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

JN375115|Influenza A Virus|A/swine/Guangdong/603/2010(H1N2)|H1N2|02/27/2010|Swine|Asia|China|-N/A-|-N/A-|alpha|1A.1.3KM029815|Influenza A Virus|A/swine/Guangdong/NS3155/2012|H1N2|09/13/2012|Swine|Asia|China|-N/A-|-N/A-|alpha|1A.1.3

CY087088|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.1GU086033|Influenza A Virus|A/swine/Guangdong/446/2006(H1N1)|H1N1|2006|Swine|Asia|China|-N/A-|-N/A-|alpha|1A.1FJ536842|Influenza A Virus|A/swine/Guangdong/1/2005|H1N1|2005|Swine|Asia|China|-N/A-|-N/A-|alpha|1A.1

KU976666|Influenza A Virus|A/swine/Mexico/AVX3/2011|H1N1|03/18/2011|Swine|North America|Mexico|-N/A-|-N/A-|gamma2-beta-like|1A.3.1KU976612|Influenza A Virus|A/swine/Mexico/AVX42/2012|H1N1|11/26/2012|Swine|North America|Mexico|-N/A-|-N/A-|gamma2-beta-like|1A.3.1KU976570|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

CY159249|Influenza A Virus|A/swine/Minnesota/SG1470/2004|H1N1|08/13/2004|Swine|North America|USA|Minnesota|-N/A-|beta|1A.2KU752363|Influenza A Virus|A/swine/Oklahoma/A01730424/2016|H1N1|01/22/2016|Swine|North America|USA|Oklahoma|15-16|beta|1A.2KF712462|Influenza A Virus|A/swine/Nebraska/A01399492/2013|H1N1|09/05/2013|Swine|North America|USA|Nebraska|-N/A-|beta|1A.2KC445220|Influenza A Virus|A/swine/Nebraska/A01277829/2012|H1N1|11/27/2012|Swine|North America|USA|Nebraska|12-13|beta|1A.2

AF455679|Influenza A Virus|A/Swine/Iowa/930/01|H1N2|2001|Swine|North America|USA|Iowa|-N/A-|beta|1A.2AF455678|Influenza A Virus|A/Swine/Minnesota/55551/00|H1N2|2000|Swine|North America|USA|Minnesota|-N/A-|beta|1A.2CY098476|Influenza A Virus|A/swine/North Carolina/47834/2000|H1N1|2000|Swine|North America|USA|North Carolina|-N/A-|beta|1A.2CY040545|Influenza A Virus|A/swine/North Carolina/7571/2003|H1N1|2003|Swine|North America|USA|North Carolina|-N/A-|gamma2|1A.3CY157935|Influenza A Virus|A/swine/North Carolina/01169/2006|H1N2|06/22/2006|Swine|North America|USA|North Carolina|-N/A-|gamma2|1A.3

CY157743|Influenza A Virus|A/swine/Tennessee/00264/2004|H1N1|03/11/2004|Swine|North America|USA|Tennessee|03-04|gamma2|1A.3JQ906888|Influenza A Virus|A/swine/Minnesota/A01201429/2011|H1N2|01/27/2011|Swine|North America|USA|Minnesota|10-11|gamma2|1A.3.2

CY159613|Influenza A Virus|A/swine/Texas/SG1187/2004|H1N1|02/25/2004|Swine|North America|USA|Texas|03-04|gamma2|1A.3.2CY159761|Influenza A Virus|A/swine/Texas/00525/2005|H1N1|03/08/2005|Swine|North America|USA|Texas|04-05|gamma2|1A.3.2

KC134375|Influenza A Virus|A/swine/Illinois/A01203922/2012|H1N1|10/2012|Swine|North America|USA|Illinois|12-13|gamma2|1A.3.2JQ922326|Influenza A Virus|A/swine/Oklahoma/A01134908/2011|H1N1|03/24/2011|Swine|North America|USA|Oklahoma|10-11|gamma2|1A.3.2

CY157631|Influenza A Virus|A/swine/Texas/00195/2003|H1N1|10/15/2003|Swine|North America|USA|Texas|03-04|gamma2|1A.3.2CY098516|Influenza A Virus|A/swine/North Carolina/18161/2002|H1N1|2002|Swine|North America|USA|North Carolina|-N/A-|gamma2|1A.3.3CY157647|Influenza A Virus|A/swine/Kentucky/SG1167/2003|H1N1|01/22/2003|Swine|North America|USA|Kentucky|02-03|gamma-npdm-like|1A.3.3

AF250124|Influenza A Virus|A/Swine/Indiana/9K035/99|H1N2|1999|Swine|North America|USA|Indiana|-N/A-|gamma|1A.3.3.3AF455681|Influenza A Virus|A/Swine/Illinois/100085A/01|H1N2|2001|Swine|North America|USA|Illinois|-N/A-|gamma|1A.3.3.3

KJ640283|Influenza A Virus|A/swine/Indiana/13TOSU1052/2013|H1N2|07/01/2013|Swine|North America|USA|Indiana|-N/A-|gamma|1A.3.3.3KX036706|Influenza A Virus|A/swine/Illinois/A01733206/2016|H1N1|03/10/2016|Swine|North America|USA|Illinois|15-16|gamma|1A.3.3.3KT767634|Influenza A Virus|A/swine/Iowa/A02025552/2015|H1N1|08/13/2015|Swine|North America|USA|Iowa|-N/A-|gamma|1A.3.3.3

CY107827|Influenza A Virus|A/swine/Korea/1130/2009|H1N2|01/2009|Swine|Asia|South Korea|-N/A-|08-09|gamma|1A.3.3.3AF455675|Influenza A Virus|A/Swine/Ohio/891/01|H1N2|2001|Swine|North America|USA|Ohio|-N/A-|gamma|1A.3.3.3AF455680|Influenza A Virus|A/Swine/Indiana/P12439/00|H1N2|2000|Swine|North America|USA|Indiana|-N/A-|npdm|1A.3.3

KU976628|Influenza A Virus|A/swine/Mexico/AVX27/2012|H1N1|08/02/2012|Swine|North America|Mexico|-N/A-|-N/A-|npdm|1A.3.3.2HQ424885|Influenza A Virus|A/swine/Iowa/44837-1/2009(H1N1)|H1N1|11/08/2009|Swine|North America|USA|Iowa|09-10|npdm|1A.3.3.2

JF279888|Influenza A Virus|A/swine/Costa Rica/000125-14/2010|H1N1|11/01/2010|Swine|North America|Costa Rica|-N/A-|-N/A-|npdm|1A.3.3.2KC222556|Influenza A Virus|A/swine/Freren/IDT13837-1/2011|H1N2|08/31/2011|Swine|Europe|Germany|-N/A-|-N/A-|npdm|1A.3.3.2CY114996|Influenza A Virus|A/swine/Pennsylvania/A01134526/2011|H1N1|02/14/2011|Swine|North America|USA|Pennsylvania|10-11|npdm|1A.3.3.2HQ291549|Influenza A Virus|A/swine/IL/27486-2/2010(H1N1)|H1N1|06/02/2010|Swine|North America|USA|Illinois|-N/A-|npdm|1A.3.3.2KU666855|Influenza A Virus|A/swine/Nebraska/A01729687/2016|H1N1|01/15/2016|Swine|North America|USA|Nebraska|15-16|npdm|1A.3.3.2

CY057462|Influenza A Virus|A/Wisconsin/629-D00839/2009(H1N1)|H1N1|09/22/2009|Human|North America|USA|Wisconsin|08-09|npdm|NAJF714082|Influenza A Virus|A/swine/MB/36/2009|H1N1|10/06/2009|Swine|North America|Canada|-N/A-|09-10|npdm|1A.3.3.2KM027967|Influenza A Virus|A/swine/Guangxi/NS2777/2010|H1N2|11/07/2010|Swine|Asia|China|-N/A-|-N/A-|npdm|1A.3.3KM028087|Influenza A Virus|A/swine/Guangxi/2891/2011|H1N2|10/09/2011|Swine|Asia|China|-N/A-|-N/A-|npdm|1A.3.3

GQ229333|Influenza A Virus|A/swine/Hong Kong/1562/2005(H1N2)|H1N2|11/11/2005|Swine|Asia|Hong Kong|-N/A-|-N/A-|npdm|1A.3.3.1CY085998|Influenza A Virus|A/swine/Hong Kong/NS252/2009|H1N2|03/19/2009|Swine|Asia|Hong Kong|-N/A-|-N/A-|npdm|1A.3.3.1KM027639|Influenza A Virus|A/swine/Guangdong/3583/2011|H1N2|10/27/2011|Swine|Asia|China|-N/A-|-N/A-|npdm|1A.3.3.1

GQ229365|Influenza A Virus|A/swine/Hong Kong/NS623/2002(H1N2)|H1N2|07/09/2002|Swine|Asia|Hong Kong|-N/A-|-N/A-|npdm|1A.3.3.1CY085622|Influenza A Virus|A/swine/Hong Kong/NS30/2004|H1N2|01/06/2004|Swine|Asia|Hong Kong|-N/A-|-N/A-|npdm|1A.3.3.1EF556199|Influenza A Virus|A/swine/Guangxi/13/2006|H1N2|2006|Swine|Asia|China|-N/A-|-N/A-|npdm|1A.3.3.1

KM028935|Influenza A Virus|A/swine/Hong Kong/4083/2011|H1N2|10/20/2011|Swine|Asia|Hong Kong|-N/A-|-N/A-|npdm|1A.3.3.1GQ229309|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

AF116575|Influenza A Virus|A/Brevig Mission/1/1918|H1N1|1918|Human|North America|USA|Alaska|-N/A-|Other|Other-HumanD00837|Influenza A Virus|A/swine/Cambridge/1939|H1N1|1939|Swine|Europe|United Kingdom|-N/A-|-N/A-|ND|Other-Human

CY019755|Influenza A Virus|A/Memphis/49/1983|H1N1|1983|Human|North America|USA|Tennessee|-N/A-|Other|Other-HumanCY021029|Influenza A Virus|A/Baylor/4052/1981|H1N1|1981|Human|North America|USA|Texas|-N/A-|Other|Other-HumanCY017235|Influenza A Virus|A/Memphis/29/1983|H1N1|1983|Human|North America|USA|Tennessee|-N/A-|Other|Other-HumanCY020189|Influenza A Virus|A/New Zealand/7/1983|H1N1|1983|Human|Oceania|New Zealand|-N/A-|-N/A-|Other|Other-HumanCY020565|Influenza A Virus|A/Texas/2922-3/1986|H1N1|1986|Human|North America|USA|Texas|-N/A-|delta-like|Other-Human-1B.2DQ508873|Influenza A Virus|A/Taiwan/01/1986|H1N1|1986|Human|Asia|Taiwan|-N/A-|-N/A-|delta-like|Other-Human-1B.2CY045852|Influenza A Virus|A/Siena/4/1987(H1N1)|H1N1|1987|Human|Europe|Italy|-N/A-|-N/A-|delta-like|Other-Human-1B.2JX477159|Influenza A Virus|A/Florida/2/1993(H1N1)|H1N1|1993|Human|North America|USA|Florida|-N/A-|delta-like|Other-Human-1B.2JX477164|Influenza A Virus|A/Wellington/47/1992|H1N1|1992|Human|Oceania|New Zealand|-N/A-|-N/A-|delta-like|Other-Human-1B.2CY125084|Influenza A Virus|A/Moscow/13/1998|H1N1|1998|Human|Europe|Russia|-N/A-|-N/A-|delta-like|Other-Human-1B.2CY117691|Influenza A Virus|A/Malaysia/06768/1995|H1N1|05/16/1995|Human|Asia|Malaysia|-N/A-|-N/A-|delta-like|Other-Human-1B.2CY016963|Influenza A Virus|A/New York/633/1995|H1N1|12/15/1995|Human|North America|USA|New York|95-96|delta-like|Other-Human-1B.2

CY009316|Influenza A Virus|A/Texas/36/91|H1N1|1991|Human|North America|USA|Texas|-N/A-|delta-like|Other-Human-1B.2CY033614|Influenza A Virus|A/Beijing/262/1995|H1N1|1995|Human|Asia|China|-N/A-|-N/A-|delta-like|Other-Human-1B.2CY125076|Influenza A Virus|A/Shanghai/2/1997|H1N1|1997|Human|Asia|China|-N/A-|-N/A-|delta-like|Other-Human-1B.2GU646016|Influenza A Virus|A/swine/Fujian/0325/2008|H1N1|03/25/2008|Swine|Asia|China|-N/A-|-N/A-|delta-like|Other-Human-1B.2EU097934|Influenza A Virus|A/Denmark/3/2001|H1N1|2001|Human|Europe|Denmark|-N/A-|-N/A-|delta-like|Other-Human-1B.2

KU976716|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.2KU976748|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

KP456570|Influenza A Virus|A/Canterbury/23/2000|H1N1|08/03/2000|Human|Oceania|New Zealand|-N/A-|-N/A-|delta-like|Other-Human-1B.2CY022149|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

CY086839|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.2AB628080|Influenza A Virus|A/swine/Binh Doung/02_16/2010|H1N2|2010|Swine|Asia|Viet Nam|-N/A-|-N/A-|delta-like|Other-Human-1B.2

CY104020|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.2CY002984|Influenza A Virus|A/New York/221/2003|H1N1|03/21/2003|Human|North America|USA|New York|02-03|delta2|Other-Human-1B.2CY104822|Influenza A Virus|A/Hanoi/ISBM31/2005|H1N1|04/08/2005|Human|Asia|Viet Nam|-N/A-|-N/A-|delta2|Other-Human-1B.2CY075856|Influenza A Virus|A/swine/Argentina/CIP051-BsAs76/2009|H1N1|10/2009|Swine|South America|Argentina|-N/A-|-N/A-|delta2|Other-Human-1B.2KR863479|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

HQ896649|Influenza A Virus|A/swine/Minnesota/6004-1/2009|H1N1|11/19/2009|Swine|North America|USA|Minnesota|09-10|delta2|Other-Human-1B.2KP457752|Influenza A Virus|A/Iowa/02/2006|H1N1|12/29/2006|Human|North America|USA|Iowa|06-07|delta2|NAEU100706|Influenza A Virus|A/Iowa/02/2006|H1N1|12/29/2006|Human|North America|USA|Iowa|06-07|delta2|Other-Human-1B.2CY159409|Influenza A Virus|A/swine/North Carolina/01550/2007|H1N1|04/04/2007|Swine|North America|USA|North Carolina|06-07|delta2|1B.2.1

KU598293|Influenza A Virus|A/swine/Indiana/A01729197/2016|H1N2|01/07/2016|Swine|North America|USA|Indiana|15-16|delta2|1B.2.1KU752378|Influenza A Virus|A/swine/North Carolina/A01730690/2016|H1N2|01/28/2016|Swine|North America|USA|North Carolina|15-16|delta2|1B.2.1KT000052|Influenza A Virus|A/swine/North Carolina/A02077509/2015|H1N2|05/06/2015|Swine|North America|USA|North Carolina|14-15|delta2|1B.2.1KU160750|Influenza A Virus|A/swine/North Carolina/A01945825/2015|H1N2|10/22/2015|Swine|North America|USA|North Carolina|15-16|delta2|1B.2.1

FJ638298|Influenza A Virus|A/swine/IL/00685/2005(H1N1)|H1N1|2005|Swine|North America|USA|Illinois|-N/A-|delta2|1B.2.1CY099151|Influenza A Virus|A/swine/North Carolina/00839/2005(H1N1)|H1N1|10/27/2005|Swine|North America|USA|North Carolina|05-06|delta2|1B.2.1HQ896632|Influenza A Virus|A/swine/Indiana/0582-3/2009|H1N2|08/04/2009|Swine|North America|USA|Indiana|08-09|delta2|1B.2.1

CY098509|Influenza A Virus|A/swine/North Carolina/38448-1/2005|H1N1|2005|Swine|North America|USA|North Carolina|-N/A-|delta2|1B.2.1KP027593|Influenza A Virus|A/swine/Brazil/G2P2/2013(H1N2)|H1N2|06/05/2013|Swine|South America|Brazil|-N/A-|-N/A-|delta-like|1B.2.2KM507519|Influenza A Virus|A/swine/Brazil/185-11-7/2011|H1N2|07/06/2011|Swine|South America|Brazil|-N/A-|-N/A-|delta-like|1B.2.2KF680296|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.2.2CY075864|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

DQ280236|Influenza A Virus|A/swine/Ontario/48235/04|H1N2|2004|Swine|North America|Canada|-N/A-|-N/A-|delta-like|1B.2.2JN652497|Influenza A Virus|A/swine/Iowa/A01049766/2011|H1N2|03/29/2011|Swine|North America|USA|Iowa|10-11|delta-like|1B.2.2JX975013|Influenza A Virus|A/swine/Oklahoma/A01203865/2012|H1N2|09/2012|Swine|North America|USA|Oklahoma|-N/A-|delta1|1B.2.2JQ023762|Influenza A Virus|A/swine/Minnesota/0745/2010|H1N2|03/03/2010|Swine|North America|USA|Minnesota|09-10|delta1|1B.2.2.2KC333087|Influenza A Virus|A/swine/Illinois/A01271513/2012|H1N2|10/26/2012|Swine|North America|USA|Illinois|12-13|delta1|1B.2.2.2KT924274|Influenza A Virus|A/swine/Iowa/A01795227/2015|H1N2|09/23/2015|Swine|North America|USA|Iowa|-N/A-|delta1|1B.2.2.2

KF922774|Influenza A Virus|A/swine/North Carolina/A01290725/2013|H1N2|11/2013|Swine|North America|USA|North Carolina|13-14|delta1|1B.2.2.2KF922759|Influenza A Virus|A/swine/Kansas/A01290646/2013|H1N2|10/14/2013|Swine|North America|USA|Kansas|13-14|delta1|1B.2.2.2KT867232|Influenza A Virus|A/swine/Iowa/A02076974/2015|H1N2|09/09/2015|Swine|North America|USA|Iowa|-N/A-|delta1|1B.2.2.2KF697082|Influenza A Virus|A/swine/Nebraska/A01399636/2013|H1N2|09/09/2013|Swine|North America|USA|Nebraska|-N/A-|delta1|1B.2.2.2

JN652509|Influenza A Virus|A/swine/Arkansas/A01049917/2011|H1N2|05/03/2011|Swine|North America|USA|Arkansas|10-11|delta1|1B.2.2.2HQ896639|Influenza A Virus|A/swine/Minnesota/0913-1/2009|H1N2|09/16/2009|Swine|North America|USA|Minnesota|08-09|delta1|1B.2.2.2CY045599|Influenza A Virus|A/swine/Oklahoma/010226-17/2008(H1N2)|H1N2|2008|Swine|North America|USA|Oklahoma|-N/A-|delta1|1B.2.2.2HM570049|Influenza A Virus|A/swine/Minnesota/03023/2010(H1N2)|H1N2|04/26/2010|Swine|North America|USA|Minnesota|09-10|delta1|1B.2.2.2JN652405|Influenza A Virus|A/swine/Oklahoma/A01049500/2011|H1N2|02/03/2011|Swine|North America|USA|Oklahoma|10-11|delta1|1B.2.2.2JX657805|Influenza A Virus|A/swine/Minnesota/A01076183/2009|H1N2|12/28/2009|Swine|North America|USA|Minnesota|09-10|delta1|1B.2.2.1HQ896666|Influenza A Virus|A/swine/Minnesota/8721-1/2010|H1N2|04/14/2010|Swine|North America|USA|Minnesota|09-10|delta1|1B.2.2.1KF704120|Influenza A Virus|A/swine/Iowa/13C094/2013|H1N2|03/26/2013|Swine|North America|USA|Iowa|12-13|delta1|1B.2.2.1KT825123|Influenza A Virus|A/swine/Iowa/A01770929/2015|H1N2|09/01/2015|Swine|North America|USA|Iowa|-N/A-|delta1|1B.2.2.1KU198904|Influenza A Virus|A/swine/Nebraska/A01940285/2015|H1N2|09/02/2015|Swine|North America|USA|Nebraska|-N/A-|delta1|1B.2.2.1KX036670|Influenza A Virus|A/swine/Illinois/A01733533/2016|H1N2|03/15/2016|Swine|North America|USA|Illinois|15-16|delta1|1B.2.2.1KU695705|Influenza A Virus|A/swine/Oklahoma/A01730089/2016|H1N2|01/22/2016|Swine|North America|USA|Oklahoma|15-16|delta1|1B.2.2.1

KJ777467|Influenza A Virus|A/swine/Kansas/A01377287/2014|H1N2|04/01/2014|Swine|North America|USA|Kansas|13-14|delta1|1B.2.2.1KU379643|Influenza A Virus|A/swine/Illinois/A01896080/2015|H1N2|11/30/2015|Swine|North America|USA|Illinois|15-16|delta1|1B.2.2.1

CY099207|Influenza A Virus|A/swine/Minnesota/02324/2008|H1N2|09/10/2008|Swine|North America|USA|Minnesota|-N/A-|delta1|1B.2.2.1CY115896|Influenza A Virus|A/swine/England/00003/2009|H1N2|01/12/2009|Swine|Europe|United Kingdom|-N/A-|08-09|delta-like|1B.2.2

AF085413|Influenza A Virus|A/swine/Scotland/410440/94|H1N2|1994|Swine|Europe|United Kingdom|-N/A-|-N/A-|Other|1B.1AF085414|Influenza A Virus|A/swine/England/438207/94|H1N2|1994|Swine|Europe|United Kingdom|-N/A-|-N/A-|Other|1B.1CY116159|Influenza A Virus|A/swine/England/40280/1996|H1N2|07/09/1996|Swine|Europe|United Kingdom|-N/A-|-N/A-|Other|1B.1.1CY116198|Influenza A Virus|A/swine/England/448813/1994|H1N2|04/24/1994|Swine|Europe|United Kingdom|-N/A-|93-94|Other|1B.1.1

KR700342|Influenza A Virus|A/swine/Scotland/51190/1999|H1N2|09/30/1999|Swine|Europe|United Kingdom|-N/A-|-N/A-|Other|1B.1.1CY116323|Influenza A Virus|A/swine/England/88761/1997|H1N2|02/03/1997|Swine|Europe|United Kingdom|-N/A-|96-97|Other|1B.1.1

KR700493|Influenza A Virus|A/swine/England/038712/2012|H1N2|12/05/2012|Swine|Europe|United Kingdom|-N/A-|12-13|Other|1B.1.1JF297998|Influenza A Virus|A/swine/England/1428/2009|H1N2|12/08/2009|Swine|Europe|United Kingdom|-N/A-|09-10|Other|1B.1.1JF297997|Influenza A Virus|A/swine/England/1157/2009|H1N2|10/05/2009|Swine|Europe|United Kingdom|-N/A-|09-10|Other|1B.1.1KR699860|Influenza A Virus|A/swine/England/058879/2011|H1N2|05/16/2011|Swine|Europe|United Kingdom|-N/A-|10-11|Other|1B.1.1

CY115912|Influenza A Virus|A/swine/England/002295/2002|H1N2|12/04/2002|Swine|Europe|United Kingdom|-N/A-|02-03|Other|1B.1.1KR700601|Influenza A Virus|A/swine/England/463180/1994|H1N2|05/12/1994|Swine|Europe|United Kingdom|-N/A-|93-94|Other|1B.1.2HQ660233|Influenza A Virus|A/swine/Italy/3592/1999|H1N2|1999|Swine|Europe|Italy|-N/A-|-N/A-|Other|1B.1.2.2CY116487|Influenza A Virus|A/swine/Italy/172336/2001|H1N1|2001|Swine|Europe|Italy|-N/A-|-N/A-|Other|1B.1.2.2

HQ660238|Influenza A Virus|A/swine/Italy/70757/2009|H1N2|2009|Swine|Europe|Italy|-N/A-|-N/A-|Other|1B.1.2.2KF305978|Influenza A Virus|A/swine/Italy/20333/2006|H1N2|2006|Swine|Europe|Italy|-N/A-|-N/A-|Other|1B.1.2.2KR700193|Influenza A Virus|A/swine/France/CotesdArmor-0198/2011|H1N2|04/11/2011|Swine|Europe|France|-N/A-|10-11|Other|1B.1.2.3KC295233|Influenza A Virus|A/swine/France/22-120255/2012|H1N2|2012|Swine|Europe|France|-N/A-|-N/A-|Other|1B.1.2.3KJ128311|Influenza A Virus|A/swine/France/22-120390/2012|H1N2|11/16/2012|Swine|Europe|France|-N/A-|12-13|Other|1B.1.2.3KC345629|Influenza A Virus|A/swine/France/22-110153/2011|H1N2|03/07/2011|Swine|Europe|France|-N/A-|10-11|Other|1B.1.2.3

CY116367|Influenza A Virus|A/swine/Cotes d'Armor/1174/2009|H1N2|2009|Swine|Europe|France|-N/A-|-N/A-|Other|1B.1.2.3CY116410|Influenza A Virus|A/swine/Cotes d'Armor/790/1997|H1N2|1997|Swine|Europe|France|-N/A-|-N/A-|Other|1B.1.2.3EU053148|Influenza A Virus|A/swine/Bakum/1832/2000|H1N2|2000|Swine|Europe|Germany|-N/A-|-N/A-|Other|1B.1.2.1AJ344010|Influenza A Virus|A/swine/Italy/1081/00|H1N2|2000|Swine|Europe|Italy|-N/A-|-N/A-|Other|1B.1.2.1

KR700883|Influenza A Virus|A/swine/Netherlands/De-Lutte-167A/2012|H1N2|04/25/2012|Swine|Europe|Netherlands|-N/A-|11-12|Other|1B.1.2.1CY116550|Influenza A Virus|A/swine/Spain/40564/2002(H1N2)|H1N2|2002|Swine|Europe|Spain|-N/A-|-N/A-|Other|1B.1.2.1CY116442|Influenza A Virus|A/swine/Gent/177/2002|H1N2|2002|Swine|Europe|Belgium|-N/A-|-N/A-|Other|1B.1.2.1

KR699932|Influenza A Virus|A/swine/Belgium/Oostkamp-26/2012|H1N2|01/12/2012|Swine|Europe|Belgium|-N/A-|11-12|Other|1B.1.2.1KR700177|Influenza A Virus|A/swine/Spain/29257/2012|H1N2|01/30/2012|Swine|Europe|Spain|-N/A-|11-12|Other|1B.1.2KR700592|Influenza A Virus|A/swine/Spain/29262/2012|H1N2|01/31/2012|Swine|Europe|Spain|-N/A-|11-12|Other|1B.1.2

AF085415|Influenza A Virus|A/swine/England/690421/95|H1N2|1995|Swine|Europe|United Kingdom|-N/A-|-N/A-|Other|1B.1.2KR700057|Influenza A Virus|A/swine/Denmark/10-1958-1/2011|H1N2|2011|Swine|Europe|Denmark|-N/A-|-N/A-|Other|1C.2KR700049|Influenza A Virus|A/swine/Denmark/10-1725-1/2011|H1N2|2011|Swine|Europe|Denmark|-N/A-|-N/A-|Other|1C.2

CY116531|Influenza A Virus|A/swine/Lutol/3/2000(H1N1)|H1N1|2000|Swine|Europe|Poland|-N/A-|-N/A-|Other|1C.2.3CY116356|Influenza A Virus|A/swine/Finnistere/800/2004|H1N1|2004|Swine|Europe|France|-N/A-|-N/A-|Other|1C.2.3CY085550|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

KM028327|Influenza A Virus|A/swine/Guangxi/3612/2011|H1N1|12/11/2011|Swine|Asia|China|-N/A-|-N/A-|Other|1C.2.3KM029167|Influenza A Virus|A/swine/Hong Kong/126/2012|H1N1|01/05/2012|Swine|Asia|Hong Kong|-N/A-|-N/A-|Other|1C.2.3KM029311|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

AM920737|Influenza A Virus|A/swine/Germany/SEk1178/2000|H1N2|2000|Swine|Europe|Germany|-N/A-|-N/A-|Other|1C.2.2GQ161124|Influenza A Virus|A/swine/Haseluenne/IDT2617/2003|H1N1|10/09/2003|Swine|Europe|Germany|-N/A-|03-04|Other|1C.2.2JQ301929|Influenza A Virus|A/swine/Spain/16/2009|H1N1|07/2009|Swine|Europe|Spain|-N/A-|08-09|Other|1C.2.2KU517792|Influenza A Virus|A/Poland/wild boar/1951718/2013|H1N1|12/12/2013|Swine|Europe|Poland|-N/A-|13-14|Other|1C.2.2KR700366|Influenza A Virus|A/swine/Germany/Reinberg-IDT14457-1/2012|H1N1|01/02/2012|Swine|Europe|Germany|-N/A-|11-12|Other|1C.2.2

CY009892|Influenza A Virus|A/swine/Spain/50047/2003|H1N1|2003|Swine|Europe|Spain|-N/A-|-N/A-|Other|1C.2.2GQ161156|Influenza A Virus|A/swine/Greven/IDT2889/2004|H1N1|01/07/2004|Swine|Europe|Germany|-N/A-|03-04|Other|1C.2.1

KJ847576|Influenza A Virus|A/swine/Italy/50814/2012|H1N1|01/2012|Swine|Europe|Italy|-N/A-|11-12|Other|1C.2.1KR700891|Influenza A Virus|A/swine/Belgium/Lichtervelde-57/2013|H1N1|03/01/2013|Swine|Europe|Belgium|-N/A-|12-13|Other|1C.2.1

CY116466|Influenza A Virus|A/swine/Italy/151672-3/2003|H1N1|2003|Swine|Europe|Italy|-N/A-|-N/A-|Other|1C.2.1CY010572|Influenza A Virus|A/swine/Spain/51915/2003|H1N1|2003|Swine|Europe|Spain|-N/A-|-N/A-|Other|1C.2.1

KR700869|Influenza A Virus|A/swine/Netherlands/Wijhe-371/2012|H1N1|10/24/2012|Swine|Europe|Netherlands|-N/A-|12-13|Other|1C.2.1JX908073|Influenza A Virus|A/swine/Spain/03/2008|H1N1|06/01/2008|Swine|Europe|Spain|-N/A-|-N/A-|Other|1C.2.1KR066556|Influenza A Virus|A/swine/Denmark/101081-2/2010|H1N2|05/28/2010|Swine|Europe|Denmark|-N/A-|09-10|Other|1C.2KC900284|Influenza A Virus|A/swine/Denmark/13160-1/2004|H1N1|2004|Swine|Europe|Denmark|-N/A-|-N/A-|Other|1C.2KC900282|Influenza A Virus|A/swine/Denmark/13772-1/2003|H1N1|2003|Swine|Europe|Denmark|-N/A-|-N/A-|Other|1C.2

KR066560|Influenza A Virus|A/swine/Denmark/10913-1/2009|H1N1|04/2009|Swine|Europe|Denmark|-N/A-|08-09|Other|1C.2KC900270|Influenza A Virus|A/swine/Denmark/13184-1/2004|H1N1|2004|Swine|Europe|Denmark|-N/A-|-N/A-|Other|1C.2

FJ805962|Influenza A Virus|A/swine/Belgium/1/1998|H1N1|1998|Swine|Europe|Belgium|-N/A-|-N/A-|Other|1C.2CY038023|Influenza A Virus|A/swine/Denmark/WVL9/1993|H1N1|1993|Swine|Europe|Denmark|-N/A-|-N/A-|Other|1C.2

KR700640|Influenza A Virus|A/swine/England/267/2007|H1N1|02/22/2007|Swine|Europe|United Kingdom|-N/A-|06-07|Other|1C.1CY116206|Influenza A Virus|A/swine/England/453/2006|H1N1|05/05/2006|Swine|Europe|United Kingdom|-N/A-|05-06|Other|1C.1

KR701057|Influenza A Virus|A/swine/England/024079/2013|H1N1|08/21/2013|Swine|Europe|United Kingdom|-N/A-|-N/A-|Other|1C.1CY116074|Influenza A Virus|A/swine/England/26029/1998|H1N1|06/17/1998|Swine|Europe|United Kingdom|-N/A-|-N/A-|Other|1C.1

CY037999|Influenza A Virus|A/swine/Spain/WVL6/1991|H1N1|1991|Swine|Europe|Spain|-N/A-|-N/A-|Other|1C.1AJ344019|Influenza A Virus|A/swine/Italy/1498-2/97|H1N1|1997|Swine|Europe|Italy|-N/A-|-N/A-|Other|1C.1AM920728|Influenza A Virus|A/swine/Germany/Vi5698/1995|H1N1|1995|Swine|Europe|Germany|-N/A-|-N/A-|Other|1C.1

KJ889364|Influenza A Virus|A/swine/Germany/S27/1981|H1N1|1981|Swine|Europe|Germany|-N/A-|-N/A-|Other|1C.1AF091314|Influenza A Virus|A/swine/Netherlands/3/80|H1N1|1980|Swine|Europe|Netherlands|-N/A-|-N/A-|Other|1C.1KJ889300|Influenza A Virus|A/swine/Arnsberg/1/1979|H1N1|12/07/1979|Swine|Europe|Germany|-N/A-|79-80|Other|1C.1KT715450|Influenza A Virus|A/duck/Schleswig/21/1979|H1N1|1979|Duck/Avian|Europe|Germany|-N/A-|-N/A-|Other|Other-AvianKT715445|Influenza A Virus|A/coot/Schleswig/2/1980|H1N1|1980|Common Coot/Avian|Europe|Germany|-N/A-|-N/A-|Other|Other-AvianD00839|Influenza A Virus|A/duck/HK/196/1977|H1|1977|Duck/Avian|Asia|Hong Kong|-N/A-|-N/A-|Other|Other-Avian

GU066779|Influenza A Virus|A/mallard/Marquenterre/Z237/1983(H1N1)|H1N1|1983|Mallard/Avian|Europe|France|-N/A-|-N/A-|Other|Other-AvianAB271113|Influenza A Virus|A/duck/Miyagi/66/1977|H1N1|1977|Duck/Avian|Asia|Japan|-N/A-|-N/A-|Other|Other-Avian

KP658029|Influenza A Virus|A/duck/Hainan/Q221/2012|H1N2|2012|Duck/Avian|Asia|China|-N/A-|-N/A-|Other|Other-AvianKP658037|Influenza A Virus|A/duck/Fujian/89/2013|H1N8|2013|Duck/Avian|Asia|China|-N/A-|-N/A-|Other|Other-Avian

EF679200|Influenza A Virus|A/chicken/Hong Kong/14/1976|H1N1|1976|Chicken/Avian|Asia|Hong Kong|-N/A-|-N/A-|Other|Other-AvianCY094927|Influenza A Virus|A/duck/Victoria/2b/1980|H1N1|1980|Duck/Avian|Oceania|Australia|-N/A-|-N/A-|Other|Other-AvianCY179139|Influenza A Virus|A/thick-billed murre/Alaska/335/1976|H1N6|1976|Murre/Avian|North America|USA|Alaska|-N/A-|Other|Other-Avian

CY178994|Influenza A Virus|A/blue-winged teal/Wisconsin/336/1976|H1N1|1976|Blue-Winged Teal/Avian|North America|USA|Wisconsin|-N/A-|Other|Other-AvianCY004507|Influenza A Virus|A/mallard/ALB/201/1998|H1N1|08/11/1998|Mallard/Avian|North America|Canada|-N/A-|-N/A-|Other|Other-Avian

AF091310|Influenza A Virus|A/turkey/Minnesota/1661/81|H1N1|1981|Turkey/Avian|North America|USA|Minnesota|-N/A-|Other|Other-AvianCY136973|Influenza A Virus|A/mallard/Alberta/119/1998|H1N1|08/06/1998|Mallard/Avian|North America|Canada|-N/A-|-N/A-|Other|Other-Avian

CY146085|Influenza A Virus|A/ruddy turnstone/New Jersey/AI09-618/2009|H1N9|05/26/2009|Ruddy Turnstone/Avian|North America|USA|New Jersey|08-09|Other|Other-AvianCY186648|Influenza A Virus|A/blue-winged teal/Illinois/12OS4788/2012|H1N1|10/20/2012|Blue-Winged Teal/Avian|North America|USA|Illinois|12-13|Other|Other-Avian

0.1









































































0.1

LEGENDUS Clade

LEGENDGlobal Clade

A B C

Sequence Identifier

Global Swine H1 Clade Classification (SOP) US Swine H1 Clade Classification (SOP)


2016054341 1B.2.2.1 Download View Tree delta1 Download View Tree

400183 1B.2.1 Download View Tree delta2 Download View Tree

63709BNot H1 Sequence. Unable to determine classification.


33325Not H1 Sequence. Unable to determine classification.




Release Date: Sep 29, 2016

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 lawenforcement officials.This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272201400028C and is a collaboration between NorthropGrumman Health IT, J. Craig Venter Institute, and Vecna Technologies.



Sequence Identifier Clade Assignment Unified Tree Tree Viewer


402352|HA|swine|Mexico||2010 npdm Download View Tree

63709A|HA|swine|USA|North_Carolina|2015 gamma Download View Tree

400183|HA|swine|USA|Iowa|2015 delta2 Download View Tree


17581|HA|swine|USA|Illinois|2015 Not H1 Sequence - Unable to determine classification

404009|HA|swine|Canada|Alberta|2015 Not H1 Sequence - Unable to determine classification

63709B|HA|swine|USA|North_Carolina|2015 Not H1 Sequence - Unable to determine classification

33325|HA|swine|USA|Missouri|2015 Not H1 Sequence - Unable to determine classification




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• Rename “Swine H1 Clade” to “US Swine H1 Clade”• Add SOP for US Swine H1 Clade• Add “Global Swine H1 Clade (SOP)”









































































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LEGENDUS Clade

LEGENDGlobal Clade

1B

1C

1A

H1 reference tree

Global Swine H1 Classification & IRD

www.fludb.orgPublic influenza virus database and analysis resource

Tight integration of a wide variety of different data types

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6/20/2017 Influenza Research Database - Influenza genome database with visualization and analysis tools

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What's New with FluGlobal Swine H1 Classification In collaboration with Tavis Anderson and AmyVincent at USDA, the newly proposed GlobalSwine H1 Classification scheme has beenimplemented in IRD. Major functions include:

Clade classification of all H1 sequences inIRD regardless of host.

Sequence search based on H1 cladeannotations.

Clade assignment tool for userprovided H1sequences.

Phylogenetic tree decoration based on H1clade annotations.

Comparison of H1 sequences by MetaCATSusing H1 clade metadata.

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IRD Workshop Dates: February 25, 2017 Location: 2017 American Association of SwineVeterinarians Annual Meeting, Denver, Colorado

Influenza Vaccines for the World – IVW 2017 Dates: April 1921, 2017 Location: Lausanne, Switzerland

IRD/VPR Handson Workshop Dates: May 29, 2017 Location: Erasmus University Medical Center,Netherlands

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Matrix Protein 2 extracellular domain (M2e) is a

candidate for developing a universal Influenza A

vaccine. However poor immunogenicity presents a

roadblock. Two recently published platforms for

delivering M2e epitopes show promise. Recombinant adenoviruses displaying matrix 2

ectodomain epitopes (M2e) on their fiber proteins

as universal influenza vaccines.Tang et al.introduced conserved M2e epitopes into the HI loop ofchimpanzee adenovirus fiber protein. The insertion waswell tolerated and M2e epitopes were expressed on thevirion surface. One recombinant adenovirus, AdC68F3M2e(H1H5H7), induced robust M2especificantibody responses in BALB/c mice and conferredefficient protection against homologous andheterologous virus challenges. Consensus M2e peptide conjugated to gold

nanoparticles confers protection against H1N1,

H3N2 and H5N1 influenza A viruses. Tao, et al.

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Data Summary Updated June 18, 2017



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H1 Clade Classification Tool4/18/2017 Influenza Research Database - Swine H1 Clade Classification

https://www.fludb.org/brc/h1CladeClassifier.spg?method=ShowCleanInputPage&decorator=influenza 1/1


Release Date: Mar 16, 2017

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. HHSN272201400028C and is a collaboration between Northrop

Grumman Health IT, J. Craig Venter Institute, and Vecna Technologies.

ANALYSIS NAME

Analyze my custom sequences only. Upload a file containing my sequences in FASTA format.

Paste sequences in FASTA format.

Analyze my custom sequences and associated metadata with IRDsequences.

INPUT SEQUENCES

RunClear

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 collaborationbetween 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 youuse the IRD Sequence Annotation Tool (Analyze & Visualize > Annotate Nucleotide Sequences).

Home Swine H1 Clade Classification


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6/21/2017 Influenza Research Database - Swine H1 Clade Classification

https://www.fludb.org/brc/h1CladeClassifier.spg?decorator=influenza&method=RetrieveResults&ticketNumber=HC_813246458358# 1/1


Release Date: May 23, 2017

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 lawenforcement officials. This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272201400028C and is a collaboration between NorthropGrumman Health IT, J. Craig Venter Institute, and Vecna Technologies.



Sequence Identifier Global Swine H1 Clade Classification (SOP) US Swine H1 Clade Classification (SOP)


KP461621 1B.2.1 Download View Tree delta2 Download View Tree

KX151021 1B.2.1 Download View Tree delta2 Download View Tree




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Comprehensive H1 Clade Annotations in IRD

4/18/2017 Influenza Research Database - A/Minnesota/14/2012 - HA Hemagglutinin - KJ620415

https://www.fludb.org/brc/fluSegmentDetails.spg?ncbiGenomicAccession=KJ620415&decorator=influenza 1/3


Download Generate PDF Add to Working Set Identify Similar Sequences (BLAST) Send Comments to Curator

Complete Genome Set: Yes

Organism Name: Influenza A Virus

Strain Name: A/Minnesota/14/2012 View Strain Details

Subtype: H1N2

Global Swine H1 Clade(SOP):

1B.2.2.2

US Swine H1 Clade(SOP): delta1

2009 Pandemic H1N1like(SOP) ?:

Mixed Positive and Negative Segments

Host: Human

Collection Date: 12/2012

Flu Season (SOP): 1213

Isolation Country: USA

GenBank SubmissionDate:

04/19/2014

NCBI Taxon ID: 1479037

GenBank Header Notes:

GenBank Accession Numbers KJ620412KJ620419 represent sequences from the 8segments of Influenza A virus(A/Minnesota/14/2012(H1N2)).##AssemblyDataSTART## AssemblyMethod :: Lasergene DNA Star v. 10Sequencing Technology :: ABI 3730xl DNAAnalyzers ##AssemblyDataEND##

SNP (SOP)SNP Details

Consensus # insertions comparedwith consensus

# deletions comparedwith consensus

# mismatches comparedwith consensus

Host: Human; Subtype: H1N2; Segment: 4 0 0 68

Influenza Segment/Protein Details

Segment: KJ620415

Strain Information | Segment Information | SNP Details | Annotation | References | Data Sources |

Protein: HA Hemagglutinin

Protein Information | Isoelectric Pt/Molecular Weight | Pfam Domain | Pfam Motifs | Predicted Epitopes | Gene Ontologies | Database Cross References | Our curation pipeline has not identified potential sequence artifacts in KJ620415 by alignment to A/4/H1 profile.

Strain Information*1

Segment Information*1

Genbank Source SequenceAccession:

KJ620415

Definition: Influenza A virus (A/Minnesota/14/2012(H1N2)) segment 4hemagglutinin (HA) gene, complete cds.

Authors: Duff,M.A., Ma,J., Ma,J., Hesse,R.A., Sloan,H. and Ma,W.

Segment Number: 4

Segment Length: 1698

Complete Coding Sequence: Complete

2009 Pandemic H1N1like (SOP) ? No

Sequence: View Sequence and design PCR primers

Segment Annotation*1Protein Name Complete Sequence CDS Start CDS End Protein Length (aa) Source View Sequence and Design Primers

HA Hemagglutinin Complete 1 1698 565 GenBank Nucleotide

Home Swine H1... Results Strain Details (A/Minnesota/14/2012) Segment Details (A/Minnesota/14/2012 Seg. 4)


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1A 1B 1C Other

1A.3.3.2 (pdm09)1A.3.3.3

…

1B.2.11B.2.2.11B.2.2.2

Other-Human-1B.2 …

1C.2.11C.2.3

…

22167 H1 viruses of all hosts

Sequence Search by H1 Clade6/20/2017 Influenza Research Database - Sequence Search

https://www.fludb.org/brc/influenza_sequence_search_segment_display.spg?method=ModifySearch&selectionContext=1498011283147 1/1




DATA TYPEGenome SegmentsProteinStrain

VIRUS TYPEABCProvisional Influenza D

(PMID:24595369)

SUBTYPE

* Use comma to separate multipleentries.Ex: H1N1, H7, H3N2.

STRAIN NAME

* Use comma to separate multipleentries. Ex: A/chicken/Israel/1055/2008,A/chicken/Laos/16/2008.

DATE RANGEFrom: YYYY To: YYYY

To add month to search, seeAdvance Options: Month Range

Complete Genome Only

COMPLETE GENOME

SELECT SEGMENTS Complete?

All PB2 PB1 PA HA NP NA MP NS

CLADE CLASSIFICATION None Global H1 Clade (SOP)

US H1 Clade (SOP) H5 Clade (SOP) 2009 pH1N1 Sequence Similarity

(SOP)

HOST GEOGRAPHIC GROUPING

COUNTRY

ADVANCED OPTIONS

SearchClear

Results matching your criteria: 1,514

Tip: To select multiple or deselect, Ctrlclick (Windows) or Cmdclick (MacOS)

Show All

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 grainedsearch, and you can pick your viewing options.

1B.2.2 1B.2.2.1

1B.2.2.2 1B.2.2like

Swine North America

South America

Choose a Country...

Home Nucleotide Sequence Search



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6/20/2017 Influenza Research Database - Sequence Search

https://www.fludb.org/brc/influenza_sequence_search_segment_display.spg?method=ModifySearch&selectionContext=1498011283147 1/1




DATA TYPEGenome SegmentsProteinStrain

VIRUS TYPEABCProvisional Influenza D

(PMID:24595369)

SUBTYPE

* Use comma to separate multipleentries.Ex: H1N1, H7, H3N2.

STRAIN NAME

* Use comma to separate multipleentries. Ex: A/chicken/Israel/1055/2008,A/chicken/Laos/16/2008.

DATE RANGEFrom: YYYY To: YYYY

To add month to search, seeAdvance Options: Month Range

Complete Genome Only

COMPLETE GENOME

SELECT SEGMENTS Complete?

All PB2 PB1 PA HA NP NA MP NS

CLADE CLASSIFICATION None Global H1 Clade (SOP)

US H1 Clade (SOP) H5 Clade (SOP) 2009 pH1N1 Sequence Similarity

(SOP)

HOST GEOGRAPHIC GROUPING

COUNTRY

ADVANCED OPTIONS

SearchClear

Results matching your criteria: 1,514

Tip: To select multiple or deselect, Ctrlclick (Windows) or Cmdclick (MacOS)

Show All

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 grainedsearch, and you can pick your viewing options.

1B.2.2 1B.2.2.1

1B.2.2.2 1B.2.2like

Swine North America

South America

Choose a Country...

Home Nucleotide Sequence Search



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Data Analysis and Visualization Based on H1 Clade

6/21/2017 Influenza Research Database - Metadata-driven Comparative Analysis Tool (meta-CATS) - Setup Subset

https://www.fludb.org/brc/mgc.spg 1/1




113 sequencesAdd | Remove

126 sequencesAdd | Remove

RunClear

MAIN LIST OF SEQUENCESHA|N/A|N/A|A/swine/Iowa/A01932394/2017|ARJ63955HA|N/A|N/A|A/swine/Iowa/A02214243/2017|ARU07169

LIST OF SEQUENCES GROUP 1

LIST OF SEQUENCES GROUP 2

HA|N/A|N/A|A/Wisconsin/88/2016|APH11078HA|N/A|N/A|A/Montana/54/2016|APH11102HA|N/A|N/A|A/Montana/51/2016|APH11145HA|N/A|N/A|A/California/138/2016|APH11198HA|N/A|N/A|A/Wyoming/31/2016|APH11241HA|N/A|N/A|A/Delaware/29/2016|APO20313HA|N/A|N/A|A/Pennsylvania/91/2016|APO20335

HA|N/A|N/A|A/swine/South Dakota/A01678471/2016|APF29921HA|N/A|N/A|A/swine/Iowa/A01782389/2016|APG56845HA|N/A|N/A|A/swine/Iowa/A01782580/2016|APG56857HA|N/A|N/A|A/swine/North Carolina/A01782500/2016|APG56863HA|N/A|N/A|A/swine/Iowa/A01782237/2016|APG56871HA|N/A|N/A|A/swine/Iowa/A01782394/2016|APG56875HA|N/A|N/A|A/swine/Minnesota/A01782585/2016|APG56827

Metadata-driven Comparative Analysis Tool (meta-CATS) - Setup SubsetMouse 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 CladeGroup1: 1A.3.3.2 113

Group2: 1A.3.3.3 126

Home Protein Sequence Search Results Metadatadriven Comparative Analysis Tool for Sequences (metaCATS)



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Christian Zmasek. Archaeopteryx.js. Monday 9:45-10 pm, Viral evolution and Ecology I - W37-10

Summary

A web-based, automated H1 clade classification tool

Comprehensive H1 clade annotations

H1 clade based analysis and visualization

Acknowledgements

Amy VincentTavis Anderson

Catherine Macken

Nicola Lewis

Thomas SmithEd Klem

Richard Scheuermann

IRD You

Documents

Swine H1 Clade ASV2017 web - Influenza Research …...An automated global clade classification tool for H1 hemagglutinin genes from swine influenza A viruses Yun Zhang J. Craig Venter