Dr. Mike Murtaugh - PRRS '174' - What are we learning about PRRSV evolution and characterization of new emerging strains of PRRSV?

Information about Dr. Mike Murtaugh - PRRS '174' - What are we learning about PRRSV...

Published on January 17, 2016

Author: trufflemedia

Source: slideshare.net

Content

1. PRRSV Evolution and New, Emerging Strains 11/20/2015 These producers are willing to share their premises IDs and  pathogen status in the interests of national disease control. Regional Projects: N212 MN, PA, and SE IA Michael Murtaugh Xiong Wang Mohammad Alkhamis Bob Morrison Andres Perez University of Minnesota

2. There are Two General Types of PRRSV Type 1 (European) Type 2 (North American) ORF5 Dendrogram

3. PRRSV2/USA/MN17A/2012 PRRSV2/USA/MN17B/2013 PRRSV2/USA/MN16/2011 PRRSV2/USA/MN2/2012 PRRSV2/USA/1-2-3Yeske PRRSV2/Illinois/XW073/2011/ORF5PRRSV2/Indiana/XW071/2010/ORF5PRRSV2/USA/IA12/2012 PRRSV2/USA/NADC30/2008 PRRSV2/CHN/HENAN-HEB PRRSV2/Indiana/XW087/2013/ORF5 PRRSV2/Indiana/XW085/2011/ORF5 PRRSV2/Indiana/XW075/2011/ORF5 PRRSV2/Indiana/XW076/2012/ORF5 PRRSV2/USA/MN6/2012 PRRSV2/USA/MN7/2012 PRRSV2/USA/MN5/2012 PRRSV2/USA/MN414/2014 PRRSV2/USA/MN4/2012 PRRSV2/Indiana/XW077/2012/ORF5 PRRSV2/Iowa/XW091/2013/ORF5 PRRSV2/USA/BI-Sample2 PRRSV2/USA/AL27 PRRSV2/USA/EP37 PRRSV2/USA/MN3/2012 PRRSV2/Michigan/XW090/2011/ORF5 PRRSV2/Indiana/XW070/2009/ORF5 PRRSV2/Indiana/XW069/2009/ORF5 PRRSV2/KOR/CA-2/2013 PRRSV2/USA/Iowa21/2015/ORF5 PRRSV2/USA/Hawkeye7_Before PRRSV2/USA/MN184A PRRSV2/USA/Biss_After PRRSV2/USA/Hawkeye4_After PRRSV2/Indiana/XW052/2012/ORF5 PRRSV2/Indiana/XW053/2012/ORF5 PRRSV2/Indiana/XW084/2011/ORF5 IAF-Klop CAN L1 PRRSV2/USA/NC174/2015/ORF5 PRRSV2/USA/MN1/2012PRRSV2/USA/Hawkeye2_Before PRRSV2/USA/QUAL2_After PRRSV2/USA/Hawkeye4_Before PRRSV2/Indiana/XW065/2007/ORF5 PRRSV2/Indiana/XW060/2006/ORF5 PRRSV2/Indiana/XW064/2007/ORF5 PRRSV2/Indiana/XW055/2012/ORF5 PRRSV2/Indiana/XW059/2006/ORF5 PRRSV2/Indiana/XW056/2012/ORF5 PRRSV2/Indiana/XW089/2011/ORF5 PRRSV2/Michigan/XW074/2011/ORF5 PRRSV2/Indiana/XW054/2012/ORF5 PRRSV2/Indiana/XW081/2013/ORF5 PRRSV2/Minnesota/XW095/2007/ORF5 PRRSV2/USA/BonHomme(Spronk) PRRSV2/USA/MN11A/2012 PRRSV2/USA/MN15/2012 PRRSV2/USA/JA1262 PRRSV2/Indiana/XW079/2013/ORF5 PRRSV2/USA/MN9A/2012 02SP3THAL1 98-3298L1 IAF-EXP91CANL1 FF41-7-2 PRRSV2/Indiana/XW063/2007/ORF5 HU1021012 PRRSV2/Indiana/XW066/2008/ORF5 PRRSV2/Indiana/XW078/2013/ORF5 PRRSV2/Indiana/XW057/2013/ORF5 PRRSV2/Indiana/XW088/2007/ORF5 PRRSV2/Indiana/XW093/2013/ORF5 PRRSV2/CHN/QY2010/2010 PRRSV2/CHN/SH1211/2012 PRRSV2/Indiana/XW086/2011/ORF5 FJ-1CHNL3 Jyn1JPNL5.1 PRRSV2/Indiana/XW066/2008/ORF5 A11-57151-5-2 PA8L5.1 MLVPRRS2-5-2 U-USPOLL5.1 PRRSV2/Indiana/XW067/2008/ORF5 PRRSV2/Indiana/XW072/2011/ORF5 LU534AUTL5.1 PRRSV2/Illinois/XW051/2011/ORF5PRRSV2/USA/ISU-P PRRSV2/DEN/DK-2010-10-4-1/2010 PRRSV2/Indiana/XW061/2006/ORF5 PRRSV2/Indiana/XW062/2006/ORF5 PRRSV2/Michigan/XW094/2006/ORF5 PRRSV2/CHN/HZ-31/2012 PRRSV2/DEN/DK-2004-2-1/200430352-3MIL5.2 ISU55L5.2 PRRSV2/KOR/LMY/2002 NADC-8L5.2 PRRSV2/USA/MtEcho 34075NEL6 PrimePacNeb-1L7 5591 NCL9 PRRSV2/USA/CleenyWest PRRSV2/USA/JZ8 PRRSV2/USA/JZ2 PRRSV2/Indiana/XW082/2008/ORF5 PRRSV2/Indiana/XW068/2008/ORF5 MN30100 1-4-2 2000-5424 L917198-6 L9 PRRSV2/Indiana/XW092/2013/ORF5PRRSV2/USA/NC16845/2006PRRSV2/Indiana/XW083/2010/ORF5 02-01676 L9 2000-52502 L8 98-6470-1 L9 NADC20 PRRSV2/Indiana/XW050/2013/ORF5 ATP PRRS 1-4-2 PRRSV2/USA/JA142/2004 98-31701-1 L8 Fostera PRRS 1-3-2 PRRSV2/Indiana/XW080/2013/ORF5 24901 GTM L8 PRRSV2/USA/E32 SDSU-73 L8 CH-1a L8 PRRSV2/CHN/Em2007/2007 PRRSV2/CHN/SHB/2005 PRRSV2/CHN/GD3/2005 PRRSV2/CHN/HB-1/2001 PRRSV2/CHN/HK4/2003 PRRSV2/CHN/NVDC-GD2-2011/2011 PRRSV2/VIE/SRV07/2007 PRRSV2/CHN/NVDC-JS2-2011/2011 PRRSV2/CHN/09HUB7/2009 PRRSV2/VIE/07QN/2007 PRRSV2/CHN/09HUN1/2009 PRRSV2/CHN/09BJ/2009 PRRSV2/CHN/09HEB/2009 PRRSV2/LAO/10-LW8-1/2010 PRRSV2/CHN/JX PRRSV2/CHN/GD-2011/2011PRRSV2/VIE/10-10QN/2010 0.02 Lineage 1 Lineage 2Lineage 5.1 Lineage 5.2 Lineage 6,7 Lineage 9 Lineage 8 Type 2 PRRSV Diversity ORF5

4. PRRSV2/USA/MN17A/2012 PRRSV2/USA/MN17B/2013 PRRSV2/USA/MN16/2011 PRRSV2/USA/MN2/2012 PRRSV2/USA/1-2-3Yeske PRRSV2/Illinois/XW073/2011/ORF5PRRSV2/Indiana/XW071/2010/ORF5PRRSV2/USA/IA12/2012 PRRSV2/USA/NADC30/2008 PRRSV2/CHN/HENAN-HEB PRRSV2/Indiana/XW087/2013/ORF5 PRRSV2/Indiana/XW085/2011/ORF5 PRRSV2/Indiana/XW075/2011/ORF5 PRRSV2/Indiana/XW076/2012/ORF5 PRRSV2/USA/MN6/2012 PRRSV2/USA/MN7/2012 PRRSV2/USA/MN5/2012 PRRSV2/USA/MN414/2014 PRRSV2/USA/MN4/2012 PRRSV2/Indiana/XW077/2012/ORF5 PRRSV2/Iowa/XW091/2013/ORF5 PRRSV2/USA/BI-Sample2 PRRSV2/USA/AL27 PRRSV2/USA/EP37 PRRSV2/USA/MN3/2012 PRRSV2/Michigan/XW090/2011/ORF5 PRRSV2/Indiana/XW070/2009/ORF5 PRRSV2/Indiana/XW069/2009/ORF5 PRRSV2/KOR/CA-2/2013 PRRSV2/USA/Iowa21/2015/ORF5 PRRSV2/USA/Hawkeye7_Before PRRSV2/USA/MN184A PRRSV2/USA/Biss_After PRRSV2/USA/Hawkeye4_After PRRSV2/Indiana/XW052/2012/ORF5 PRRSV2/Indiana/XW053/2012/ORF5 PRRSV2/Indiana/XW084/2011/ORF5 IAF-Klop CAN L1 PRRSV2/USA/NC174/2015/ORF5 PRRSV2/USA/MN1/2012PRRSV2/USA/Hawkeye2_Before PRRSV2/USA/QUAL2_After PRRSV2/USA/Hawkeye4_Before PRRSV2/Indiana/XW065/2007/ORF5 PRRSV2/Indiana/XW060/2006/ORF5 PRRSV2/Indiana/XW064/2007/ORF5 PRRSV2/Indiana/XW055/2012/ORF5 PRRSV2/Indiana/XW059/2006/ORF5 PRRSV2/Indiana/XW056/2012/ORF5 PRRSV2/Indiana/XW089/2011/ORF5 PRRSV2/Michigan/XW074/2011/ORF5 PRRSV2/Indiana/XW054/2012/ORF5 PRRSV2/Indiana/XW081/2013/ORF5 PRRSV2/Minnesota/XW095/2007/ORF5 PRRSV2/USA/BonHomme(Spronk) PRRSV2/USA/MN11A/2012 PRRSV2/USA/MN15/2012 PRRSV2/USA/JA1262 PRRSV2/Indiana/XW079/2013/ORF5 PRRSV2/USA/MN9A/2012 02SP3THAL1 98-3298L1 IAF-EXP91CANL1 FF41-7-2 PRRSV2/Indiana/XW063/2007/ORF5 HU1021012 PRRSV2/Indiana/XW066/2008/ORF5 PRRSV2/Indiana/XW078/2013/ORF5 PRRSV2/Indiana/XW057/2013/ORF5 PRRSV2/Indiana/XW088/2007/ORF5 PRRSV2/Indiana/XW093/2013/ORF5 PRRSV2/CHN/QY2010/2010 PRRSV2/CHN/SH1211/2012 PRRSV2/Indiana/XW086/2011/ORF5 FJ-1CHNL3 Jyn1JPNL5.1 PRRSV2/Indiana/XW066/2008/ORF5 A11-57151-5-2 PA8L5.1 MLVPRRS2-5-2 U-USPOLL5.1 PRRSV2/Indiana/XW067/2008/ORF5 PRRSV2/Indiana/XW072/2011/ORF5 LU534AUTL5.1 PRRSV2/Illinois/XW051/2011/ORF5PRRSV2/USA/ISU-P PRRSV2/DEN/DK-2010-10-4-1/2010 PRRSV2/Indiana/XW061/2006/ORF5 PRRSV2/Indiana/XW062/2006/ORF5 PRRSV2/Michigan/XW094/2006/ORF5 PRRSV2/CHN/HZ-31/2012 PRRSV2/DEN/DK-2004-2-1/200430352-3MIL5.2 ISU55L5.2 PRRSV2/KOR/LMY/2002 NADC-8L5.2 PRRSV2/USA/MtEcho 34075NEL6 PrimePacNeb-1L7 5591 NCL9 PRRSV2/USA/CleenyWest PRRSV2/USA/JZ8 PRRSV2/USA/JZ2 PRRSV2/Indiana/XW082/2008/ORF5 PRRSV2/Indiana/XW068/2008/ORF5 MN30100 1-4-2 2000-5424 L917198-6 L9 PRRSV2/Indiana/XW092/2013/ORF5PRRSV2/USA/NC16845/2006PRRSV2/Indiana/XW083/2010/ORF5 02-01676 L9 2000-52502 L8 98-6470-1 L9 NADC20 PRRSV2/Indiana/XW050/2013/ORF5 ATP PRRS 1-4-2 PRRSV2/USA/JA142/2004 98-31701-1 L8 Fostera PRRS 1-3-2 PRRSV2/Indiana/XW080/2013/ORF5 24901 GTM L8 PRRSV2/USA/E32 SDSU-73 L8 CH-1a L8 PRRSV2/CHN/Em2007/2007 PRRSV2/CHN/SHB/2005 PRRSV2/CHN/GD3/2005 PRRSV2/CHN/HB-1/2001 PRRSV2/CHN/HK4/2003 PRRSV2/CHN/NVDC-GD2-2011/2011 PRRSV2/VIE/SRV07/2007 PRRSV2/CHN/NVDC-JS2-2011/2011 PRRSV2/CHN/09HUB7/2009 PRRSV2/VIE/07QN/2007 PRRSV2/CHN/09HUN1/2009 PRRSV2/CHN/09BJ/2009 PRRSV2/CHN/09HEB/2009 PRRSV2/LAO/10-LW8-1/2010 PRRSV2/CHN/JX PRRSV2/CHN/GD-2011/2011PRRSV2/VIE/10-10QN/2010 0.02 Lineage 1 Lineage 2Lineage 5.1 Lineage 5.2 Lineage 6,7 Lineage 9 Lineage 8 1-8-4 1-7-4 2-5-2 1-4-2 1-4-2 HP PRRS Type 2 PRRSV Diversity ORF5

5. PRRSV2/CHN/DC/2010 PRRSV2/LAO/10-LW8-1/2010 PRRSV2/CHN/GX10-48/2006 PRRSV2/CHN/10-10BJ-1/2010 PRRSV2/CHN/10-10SD/2010PRRSV2/CHN/09JS/2009PRRSV2/CHN/09HEN1/2009PRRSV2/CHN/GD-2011/2011PRRSV2/CHN/10HD-GD/2010PRRSV2/CHN/10-10JX/2010 PRRSV2/CHN/BJ1102/2011 PRRSV2/CHN/WUH3/2008 PRRSV2/CHN/09DB2/2009 PRRSV2/CHN/10-10JL/2010 PRRSV2/CHN/09HUN1/2009 PRRSV2/CHN/11GZ-GD/2011 PRRSV2/CHN/SX-1/2009 PRRSV2/CHN/09SD/2009 PRRSV2/CHN/09SC/2009 PRRSV2/CHN/SX2009/2009 PRRSV2/CHN/SD0901 PRRSV2/CHN/09BJ/2009 PRRSV2/CHN/ZP-1/2009 PRRSV2/CHN/BJ/2007 PRRSV2/CHN/XJu-1/2012 PRRSV2/CHN/BJsy06/2006 PRRSV2/CHN/NX06 PRRSV2/CHN/NVDC-GD2-2011/2011 PRRSV2/CHN/SD16/2012 PRRSV2/CHN/07HEN/2007 PRRSV2/CHN/HUN2/2006 PRRSV2/CHN/JXM80/2008 PRRSV2/CHN/HEB1/2006 PRRSV2/CHN/SD-CXA/2009 PRRSV2/CHN/NVDC-JS2-2011/2011 PRRSV2/CHN/GX1002/2010 PRRSV2/CHN/JL-0412/2012 PRRSV2/CHN/KP PRRSV2/CHN/YD/2009 PRRSV2/VIE/10-10QN/2010 PRRSV2/CHN/LN/2006 PRRSV2/CHN/HV PRRSV2/CHN/AH0701/2007PRRSV2/CHN/GDQJ/2007PRRSV2/CHN/08SDWF/2008 PRRSV2/CHN/JXA1/2006 PRRSV2/VIE/07QN/2007 PRRSV2/CHN/07BJ/2007 PRRSV2/CHN/Henan-A8/2013 PRRSV2/CHN/SDA3/2011 PRRSV2/VIE/SRV07/2007 PRRSV2/CHN/CWZ-1-F3/2008 PRRSV2/CHN/GX09-16/2009 PRRSV2/CHN/CG/2007 PRRSV2/CHN/GDQY/2007 PRRSV2/CHN/SH1211/2012 PRRSV2/CHN/HZ-31/2012 PRRSV2/CHN/NJ-1106/2012 PRRSV2/CHN/NT0801/2008 PRRSV2/CHN/GD3/2005 PRRSV2/CHN/BJ0706/2007 PRRSV2/CHN/HK4/2003 PRRSV2/CHN/SHB/2005 PRRSV2/CHN/HK12/2004 PRRSV2/CHN/HB-1(sh)/2001 PRRSV2/CHN/LN1101 PRRSV2/CHN/Em2007/2007 PRRSV2/CHN/CH-1a/1999 PRRSV2/CHN/CH-1R PRRSV2/CHN/GM2/2011 PRRSV2/CHN/QY2010/2010 PRRSV2/USA/MN30100 PRRSV2/USA/NC16845/2006 PRRSV2/USA/Ingelvac_ATP PRRSV2/USA/INGELVAC_ATP PRRSV2/USA/JA142/2004 PRRSV2/USA/MtEcho PRRSV2/USA/NVSL97-7985/1997 PRRSV2/USA/SDSU73PRRSV2/USA/E32 PRRSV2/USA/JZ1 PRRSV2/USA/CleenyWest PRRSV2/USA/JZ8 PRRSV2/USA/JZ2 PRRSV2/USA/QUAL2_After PRRSV2/USA/FF4_After PRRSV2/USA/FF3_Before PRRSV2/USA/Flagship_Before PRRSV2/USA/Prime_Pac/1996 PRRSV2/KOR/LMY/2002 PRRSV2/USA/ISU-P PRRSV2/DEN/DK-2004-2-1/2004 PRRSV2/DEN/DK-2008-10-1-3/2008 PRRSV2/DEN/DK-2003-2-3/2003PRRSV2/CHN/HN1 PRRSV2/DEN/DK-2010-10-4-1/2010 PRRSV2/DEN/DK-2011-88005-A8-Pl/2011 PRRSV2/DEN/DK-2012-01-11-3/2012 PRRSV2/USA/QUAL1_Before PRRSV2/USA/1784(IA) PRRSV2/DEN/DK-1997-19407B/1997 PRRSV2/KOR/PL97-1/1997 PRRSV2/USA/VR2332/1995 PRRSV2/USA/SD95-21/1995 PRRSV2/USA/VR2332 PRRSV2/CHN/YN-2011/2011 PRRSV2/USA/MLV PRRSV2/CHN/GS2004/2004 PRRSV2/CHN/SD1-100 PRRSV2/CHN/DY/2007 PRRSV2/HUN/Hungary102/2012 PRRSV2/KOR/CA-2/2013 PRRSV2/USA/Biss_After PRRSV2/USA/Biss_Before PRRSV2/USA/Lewis_After PRRSV2/USA/Lewis_Before PRRSV2/USA/MFF_After PRRSV2/USA/MN184B PRRSV2/USA/MN/MN184C PRRSV2/USA/MN184APRRSV2/USA/FF2_AfterPRRSV2/USA/Flagship_AfterPRRSV2/USA/Iowa21/2015 15036 lfv_free PRRSV2/USA/Hawkeye4_After PRRSV2/USA/Hawkeye7_After PRRSV2/USA/Hawkeye2_After PRRSV2/USA/North_Carolina59/2015 15059 lfv_free PRRSV2/USA/K9/2009 PRRSV2/USA/NADC30/2008 PRRSV2/CHN/HENAN-HEB PRRSV2/CHN/HENAN-XINX/2013 PRRSV2/USA/BonHomme(Spronk) PRRSV2/USA/MN11A/2012 PRRSV2/USA/MN14/2012 PRRSV2/USA/MN15/2012 PRRSV2/USA/JA1262 PRRSV2/USA/MN9A/2012 PRRSV2/USA/IA12/2012 PRRSV2/USA/IL8/2012 PRRSV2/USA/MN2/2012 PRRSV2/USA/MN414/2014 PRRSV2/USA/MN1/2012 PRRSV2/USA/MN3/2012 PRRSV2/USA/MN7/2012 PRRSV2/USA/AL27 PRRSV2/USA/EP37 PRRSV2/USA/BI-Sample1 PRRSV2/USA/BI-Sample2 PRRSV2/USA/MN4/2012 PRRSV2/USA/K10/2010 PRRSV2/USA/MN5/2012 PRRSV2/USA/1-2-3Yeske PRRSV2/USA/MN16/2011 PRRSV2/USA/MN17A/2012 PRRSV2/USA/MN17B/2013 0.02 Type 2 PRRSV Diversity Whole Genome HP PRRS Ingelvac MLV Reisolates Conclusions: Genbank sampling is highly biased. No naming system.

6. Mlu I HincII Sac II 1 8 4 1 18 2 2 5 2 1 26 2 ORF5 0 100 200 300 400 500 600 Here are some common PRRSV RFLP types

7. Table 1. PRRS virus Restriction Fragment Length Polymorphism (RFLP) cut sites MluI Digestion = A^CGCGT HincII Digestion = GT(CT)^(AG)AC SacII Digestion = CCGC^GG RFLP # Cut Sites RFLP # Cut Sites RFLP # Cut Sites 1 - 1 - 1 - 2 408 2 88 2 24 3 336 3 219 3 555 4 532 4 88, 219 4 24, 555 5 360 5 24, 582 6 88, 360 6 24, 310 7 88, 219, 360 7 24, 357 8 88, 219, 381 8 24, 310, 555 9 219, 515 10 219, 360 11 360, 515 12 219, 381 13 88, 219, 508 14 88, 291 15 88, 219, 291, 381, 515 16 88, 381 17 88, 502 18 88, 508 19 381, 508 20 360, 596 21 88, 219, 360, 381 22 219, 502 23 219, 360, 381 24 88, 381, 508 25 88, 219, 596 26 508 27 515 28 88, 508, 523 29 88, 172, 219 30 381 31 88, 135, 219 32 88, 219, 360, 515 33 88, 219, 515 34 291, 360 35 219, 523 36 88, 219, 360, 596 37 219, 508 38 219, 502, 523 39 502 40 88, 219, 291 41 88, 502, 515 42 94, 219 43 88, 219, 360, 523 44 88, 219, 558 45 88, 219, 381, 596 46 88, 360, 508 47 219, 596 48 88, 135 49 88, 509 50 94,508 51 88, 219, 282 52 172, 360 53 88, 360, 523 54 103, 360 55 88, 219, 360, 508 Year 2010 1-4 1-55 1-8

8. Table 1. PRRS virus Restriction Fragment Length Polymorphism (RFLP) cut sites MluI Digestion = A^CGCGT HincII Digestion = GT(CT)^(AG)AC SacII Digestion = CCGC^GG RFLP # Cut Sites RFLP # Cut Sites RFLP # Cut Sites 1 - 1 - 1 - 2 408 2 88 2 24 3 336 3 219 3 555 4 532 4 88, 219 4 24, 555 5 360 5 24, 582 6 88, 360 6 24, 310 7 88, 219, 360 7 24, 357 8 88, 219, 381 8 24, 310, 555 9 219, 515 10 219, 360 11 360, 515 12 219, 381 13 88, 219, 508 14 88, 291 15 88, 219, 291, 381, 515 16 88, 381 17 88, 502 18 88, 508 19 381, 508 20 360, 596 21 88, 219, 360, 381 22 219, 502 23 219, 360, 381 24 88, 381, 508 25 88, 219, 596 26 508 27 515 28 88, 508, 523 29 88, 172, 219 30 381 31 88, 135, 219 32 88, 219, 360, 515 33 88, 219, 515 34 291, 360 35 219, 523 36 88, 219, 360, 596 37 219, 508 38 219, 502, 523 39 502 40 88, 219, 291 41 88, 502, 515 42 94, 219 43 88, 219, 360, 523 44 88, 219, 558 45 88, 219, 381, 596 46 88, 360, 508 47 219, 596 48 88, 135 49 88, 509 50 94,508 51 88, 219, 282 52 172, 360 53 88, 360, 523 54 103, 360 55 88, 219, 360, 508 March 30 2015 1-4 1-114 1-12 November 17 2015 1-5 1-125 1-13

9. RFLP pattern does not identify genetic relationships JZ1 None 142 CleenyWest None 132 JZ2 None 142 JZ8 None 142 E32 None 124 NVSL AF325691 144 Mt.Echo None 132 JA142 AY424271.1 142 NVSL 97 AY545985 142 Juan ATP EF532801.1 142 JZ4 None 142 Juan MN30100 EF536000.1 142 CH1a AY032626 141 P129 AF494042 132 Fostera NONE 132 FlagshipBefore EF532805.1 172 Flagship3(FF3) EF532808.1 172 Flagship4(FF4) EF532809.1 172 Hawkeye4Before EF532813.1 144 Quality2(After) EF536002.1 144 Juan VR2332 EF536003.1 262 Juan ISU EF532816.1 152 16244b AF046869 152 Quality1(Before) EF536001.1 252 1784(IA) None 252 PA8 AF176348 252 MLV AF066183 252 Hawkeye7Sow1 DQ459471 252 VR2332a AY150564.1 252 VR2332b PRU87392 252 AL27 None 144 EP37 None 144 BI-Sample1 None 144 BI-Sample2 None 144 1-2-3Yeske None 123 K10(Kingston2010) None 144 K11(Kingston2011) None 144 K12(B)(Kingston2012) None 144 K9(Kingston2009) None 144 Hawkeye2After EF532810.1 1182 Hawkeye2Before EF532811.1 144 JA1262 None 1262 BonHomme(Spronk) None 1182 Hawkeye4After(H4New) EF532812.1 184 Hawkeye7sow2(After) EF532814.1 184 Hawkeye7Dlab(Before) EF532815.1 184 MFFOLD(After) EF532819.1 184 BissonetteAfter(BA) EF532802.1 184 BissonetteBefore(BB) EF532803.1 184 LewisAfter(WindmillAfter) EF532817.1 184 LewisBefore(WindmillBefore) EF532818.1 184 FlagshipAfter EF532804.1 184 FlagshipFitzsimmons2(FF2) EF532807.1 184 FlagshipFitzsimmons1(FF1) EF532806.1 184 MFFNEW(Before) EF535999.1 184 Hungary2 0.02 1-4-4 RFLP shows up in 3 widely divergent families

10. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 percentageofPRRSvirussequencesfittinganRFLPpattern Figure 1. Distribution of major PRRS virus RFLP cut patterns from University of Minnesota Veterinary Diagnostic Laboratory case submissions sequenced from 2001-2010 2 5 2 ATP 1 4 2 1 8 4 1 4 4 1 2 2 1 18 2 1 26 2 Ecology of PRRSV

11. 0.05 6774 PRRSV isolates 1998-2015 Type 1 N=107 (1.6%) 15 years of PRRSV Diagnostic Sequencing in USA 5 Large US Swine Producers 98.4% are Type 2 Conclusions:  Large outbreaks with little genetic change are frequent  Control programs are effective  Genbank does not show reality

12. PRRSV2/CHN/DC/2010 PRRSV2/CHN/10-10FUJ-1/2010 PRRSV2/CHN/10-10GX-5/2010 PRRSV2/CHN/GX10-48/2006 PRRSV2/LAO/10-LW8-1/2010 PRRSV2/CHN/10-10BJ-1/2010PRRSV2/CHN/10-10SD/2010PRRSV2/CHN/09JS/2009PRRSV2/CHN/BB0907/2009PRRSV2/CHN/JN-HS2008PRRSV2/CHN/09HEN1/2009PRRSV2/CHN/10HD-GD/2010PRRSV2/CHN/GD-2011/2011 PRRSV2/CHN/10-10HEB-3/2010 PRRSV2/CHN/10-10JX/2010 PRRSV2/CHN/JX PRRSV2/CHN/BJ1102/2011 PRRSV2/CHN/09HUB7/2009 PRRSV2/CHN/HLJHL/2009 PRRSV2/CHN/09DB2/2009 PRRSV2/CHN/10-10JL/2010 PRRSV2/CHN/WUH3/2008 PRRSV2/CHN/Henan-1 PRRSV2/CHN/SY0608/2006 PRRSV2/CHN/09HUN1/2009 PRRSV2/CHN/SCwhn09CD/2009 PRRSV2/CHN/09HEB/2009 PRRSV2/CHN/SX-1/2009 PRRSV2/CHN/09SD/2009 PRRSV2/CHN/09BJ/2009 PRRSV2/CHN/ZP-1/2009 PRRSV2/CHN/SD0901 PRRSV2/CHN/09HUB2/2009 PRRSV2/CHN/09SC/2009 PRRSV2/CHN/SX2009/2009 PRRSV2/CHN/Henan-A8/2013 PRRSV2/CHN/XJu-1/2012 PRRSV2/CHN/BJsy06/2006 PRRSV2/CHN/NX06 PRRSV2/CHN/BJ/2007 PRRSV2/CHN/11GZ-GD/2011 PRRSV2/CHN/XH-GD PRRSV2/CHN/JSyx/2006 PRRSV2/CHN/GDBY1/2008 PRRSV2/CHN/SD16/2012 PRRSV2/CHN/07HEN/2007 PRRSV2/CHN/07HEBTJ/2007 PRRSV2/CHN/07NM/2007 PRRSV2/CHN/Jiangxi-3 PRRSV2/CHN/NVDC-GD2-2011/2011 PRRSV2/CHN/HUN2/2006 PRRSV2/CHN/GD/2006 PRRSV2/CHN/JXM80/2008 PRRSV2/CHN/HEB1/2006PRRSV2/CHN/SD-CXA/2009PRRSV2/CHN/NVDC-JS2-2011/2011 PRRSV2/CHN/GX1002/2010 PRRSV2/CHN/JL-0412/2012 PRRSV2/CHN/KPPRRSV2/CHN/YD/2009 PRRSV2/CHN/WUH4/2011 PRRSV2/VIE/10-10QN/2010 PRRSV2/CHN/LN/2006 PRRSV2/CHN/HV PRRSV2/CHN/SHH/2006 PRRSV2/CHN/SY0909/2009 PRRSV2/CHN/AH0701/2007 PRRSV2/CHN/GDQJ/2007 PRRSV2/CHN/TP/2006 PRRSV2/CHN/HPBEDV PRRSV2/CHN/JXA1/2006 PRRSV2/CHN/08SDWF/2008 PRRSV2/VIE/07QN/2007 PRRSV2/CHN/SDA3/2011 PRRSV2/CHN/HUN4 PRRSV2/CHN/HN-HW/2006 PRRSV2/CHN/07BJ/2007 PRRSV2/CHN/GD/2007 PRRSV2/CHN/CWZ-1-F3/2008 PRRSV2/CHN/08HuN/2008 PRRSV2/VIE/SRV07/2007 PRRSV2/CHN/GX09-16/2009 PRRSV2/CHN/CG/2007 PRRSV2/CHN/GDQY/2007 PRRSV2/CHN/SH1211/2012 PRRSV2/CHN/HZ-31/2012 PRRSV2/CHN/NJ-1106/2012 PRRSV2/CHN/NT0801/2008 PRRSV2/CHN/GD3/2005 PRRSV2/CHN/BJ0706/2007 PRRSV2/CHN/HK4/2003 PRRSV2/CHN/SHB/2005 PRRSV2/CHN/HK12/2004 PRRSV2/CHN/HB-1(sh)/2001 PRRSV2/CHN/LN1101 PRRSV2/CHN/Em2007/2007 PRRSV2/CHN/CH-1a/1999 PRRSV2/CHN/CH-1R PRRSV2/CHN/GM2/2011 PRRSV2/CHN/QY2010/2010 PRRSV2/CHN/QYYZ/20011 PRRSV2/USA/MN30100PRRSV2/USA/NC16845/2006 PRRSV2/USA/JA142/2004 PRRSV2/USA/INGELVAC_ATP PRRSV2/USA/MtEchoPRRSV2/USA/NVSL97-7985/1997PRRSV2/USA/SDSU73 PRRSV2/USA/E32 PRRSV2/USA/JZ1 PRRSV2/USA/CleenyWest PRRSV2/USA/JZ8 PRRSV2/USA/JZ2 PRRSV2/USA/Hawkeye4_Before PRRSV2/USA/QUAL2_After PRRSV2/USA/FF4_After PRRSV2/USA/FF3_Before PRRSV2/USA/Flagship_Before PRRSV2/USA/Prime_Pac/1996 PRRSV2/KOR/LMY/2002PRRSV2/USA/ISU-P PRRSV2/DEN/DK-2004-2-1/2004 PRRSV2/DEN/DK-2008-10-1-3/2008 PRRSV2/DEN/DK-2003-2-3/2003 PRRSV2/CHN/HN1 PRRSV2/DEN/DK-2011-88005-A8-Pl/2011 PRRSV2/DK/DK-2010-10-13-1/2010 PRRSV2/DEN/DK-2010-10-4-1/2010 PRRSV2/DEN/DK-2012-01-11-3/2012 PRRSV2/USA/QUAL1_Before PRRSV2/USA/1784(IA) PRRSV2/DEN/DK-1997-19407B/1997 PRRSV2?/KOR/PL97-1/1997 PRRSV2/KOR/PL97-1-LP1/1997 PRRSV2/CHN/PRRSV03 PRRSV2/USA/VR2332/1995 PRRSV2/USA/A2MC2 PRRSV2/USA/VR2332a PRRSV2/USA/SD95-21/1995 PRRSV2/USA/VR2332 PRRSV2/CHN/YN-2011/2011 PRRSV2/CHN/CC-1 PRRSV2/USA/MLV PRRSV2/CHN/GS2004/2004 PRRSV2/CHN/BJ-4/2000 PRRSV2/CHN/SD1-100 PRRSV2/CHN/DY/2007 PRRSV-2_Hungary_102_2012PRRSV2/KOR/CA-2/2013 PRRSV2/USA/Biss_After PRRSV2/USA/Biss_Before PRRSV2/USA/Lewis_After PRRSV2/USA/Lewis_Before PRRSV2/USA/MFF_AfterPRRSV2/USA/MN184BPRRSV2/USA/MN/MN184CPRRSV2/USA/MN184A PRRSV2/USA/MFF_Before PRRSV2/USA/FF1_Before PRRSV2/USA/FF2_After PRRSV2/USA/Flagship_After PRRSV2/USA/Hawkeye4_After PRRSV2/USA/Hawkeye7_After PRRSV2/USA/Hawkeye7_Before PRRSV2/USA/Hawkeye2_After PRRSV2/USA/Hawkeye2_Before PRRSV2/USA/K9/2009 PRRSV2/USA/NADC30/2008 PRRSV2/CHN/HENAN-HEB PRRSV2/CHN/HENAN-XINX/2013 PRRSV2/USA/BonHomme(Spronk) PRRSV2/USA/MN11A/2012 PRRSV2/USA/MN14/2012 PRRSV2/USA/MN15/2012 PRRSV2/USA/JA1262 PRRSV2/USA/MN11B/2012 PRRSV2/USA/MN9A/2012 PRRSV2/USA/MN9B/2012 PRRSV2/USA/IA12/2012 PRRSV2/USA/IL8/2012 PRRSV2/USA/MN2/2012 PRRSV2/USA/MN1/2012 PRRSV2/USA/MN3/2012 PRRSV2/USA/MN6/2012 PRRSV2/USA/MN7/2012 PRRSV2/USA/AL27 PRRSV2/USA/EP37 PRRSV2/USA/BI-Sample1 PRRSV2/USA/BI-Sample2 PRRSV2/USA/MN4/2012 PRRSV2/USA/MN17A/2012 PRRSV2/USA/MN17B/2013 PRRSV2/USA/MN16/2011 PRRSV2/USA/1-2-3Yeske PRRSV2/USA/MN5/2012PRRSV2/USA/K10/2010 PRRSV2/USA/K11/2011 PRRSV2/USA/K12/2012 0.02 Chinese HP-PRRSV 2006-2009 >99% identical 2006-2011 >98% identical

13. Type 2 PRRSV Type 1 PRRSV One System 160 ORF5 sequences + References

14. Type 2 Only

15. Apr 1, 2012–Jun 17, 2013 1-4-4 1-4-4 1-4-4 1-4-4 1-4-4 1-4-4 1-4-4 Outbreaks

16. May 21, 2014–March 31, 2015 1-7-4 1-7-4 1-7-4 1-7-4 1-7-4 Outbreaks

17. May 21, 2014–March 31, 2015 1-7-4 1-7-4 1-7-4 1-7-41-4-41-6-4 1-6-4 1-7-3 1-21-4 1-7-4 Outbreaks Same virus – Multiple RFLP patterns

18. 1-7-4-PRRSV Family Story 241 1-7-4 family Jan 2014 -Mar 2015 0 .0 5 6774 sequences 1998-2015

19. Anatomy of Disaster 1-7-4 Outbreaks Investigation Jun 2014 Jun 2014 May 2014 Apr 2014 Jun 2014 Sep 2014 Dec 2014 Jan 2015 Jan 2015

20. IA-N 20150224 Q IA-N 20150309 W IA-N 20150223 O IA-N 20150128 I IA-N 20150128 H IA-N 20150204 K IA-N 20150306 S SO 20150206 M NC 20140520 174 OH-20140408-A IA-N 20140923 D IA-N 20150105 G IA-N 20141218 E IA-N 20150102 F MN-20140630-C NC-20150223-P NC-20150129-J NC-20150310-U NC-20150309-T NC-20150310-V IA E 20140601 B IA-S-20150303-R IA-S-20150206-L IA-S-20150220-N J (1-18-2) 2008 D13-046045 1-73-2 AS (1-16-3) 2013 PRRSV2/USA/MN184A 2009012092 1-18-4 A13-13598 1-4-4 ISU55 L5.2 PrimePac(2) 02-01676 L9 NADC20 PRRSV2/USA/E32 CH-1a CHN L8 VIE/10-10QN/2010 JXAI CHN L8 IA-N20150224Q IA-N20150309W IA-N20150223O IA-N20150128I IA-N20150128H IA-N20150204K IA-N20150306S SO20150206 M NC 20140520 174 OH-20140408-A IA-N 20140923 D IA-N 20150105 G IA-N 20141218 EIA-N20150102F MN-20140630-C NC-20150223-P NC-20150129-J NC-20150310-U NC-20150309-T NC-20150310-V IAE20140601B IA-S-20150303-R IA-S-20150206-L IA-S-20150220-N J(1-18-2)2008 D13-0460451-73-2 AS(1-16-3)2013PRRSV2/USA/MN184A2009012092 1-18-4 A13-13598 1-4-4 ISU55 L5.2 PrimePac(2) 02-01676 L9 NADC20 PRRSV2/USA/E32 CH-1aCHNL8 VIE/10-10QN/2010 JXAICHNL8 0.02 The Devil’s Spawn Distant Offspring of the 1-8-4 Family

21. nsp2 Deletions are Unremarkable No other distinctive features are apparent

22. Signal Peptide Ectodomain 1 TM Ectodomain 2 Proteins are Essentially the Same Envelope Glycoprotein 5 (GP5) No evidence of directed evolution or selection during outbreak

23. Bayesian Phylodynamics Skyline Plot of Estimated Population Size over Time Bayesian phylogenetic methods incorporate associated epidemiological information (e.g. geographic location, time of isolation)

24. History of Spread Between Systems

25. Outbreaks are Concentrated in Sow Farms

26. Dynamic representation

27. Shields and Mathews (2003). Interstate Livestock Movements. USDA-Economic Research Service Outlook Report www.ers.usda.gov/publicatons/ldp/jun03/ldpm10801/ldpm10801.pdf. A B Swine outflows from North Carolina Swine inflows to Minnesota Interstate pig movements in the U.S.A. in 2001

28. Take Home Messages Large-scale PRRS outbreaks in the history of type 2 PRRSV Genetic change during outbreaks is limited Bayesian phylodynamics helps understand disease spread PRRSV goes where pigs go

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