Characterization of Swine H1N1 from Canada John Pasick

Transcription

1 Characterization of Swine H1N1 from Canada John Pasick National Centre for Foreign Animal Disease 2007 Her ajesty the Queen in right of Canada (Canadian Food Inspection Agency), all rights reserved. Use without permission is prohibited. 2 1

2 anitoba 22% 2,605,000 Saskatchewan 6% 736,000 Alberta 13% 1,495,000 BC 1% 90,000 Ontario 24% 2,7,200 Atlantic Prov 1% 130,400 Quebec 33% 3,925, million 3 Swine Influenza in Canada pre-2009 Swine influenza is not a reportable disease under the federal Health of Animals Act Classical H1N1 predominated until 2005 Identification of other subtypes in pigs have been sporadic Wholly Human H3N2, Quebec 10 Wholly Avian H4N6, Ontario 19 Wholly Human H1N2 and Human-Swine H1N2 and H1N1 reassortants, Ontario Triple reassortant H3N2 viruses became widespread beginning in

3 5 Relevant History Canadian contract worker was hired to work on the ventilation system in the barns of an Alberta pig farm on April 14, 2009 Contract worker had returned from exico April 12 at which time he had exhibited symptoms of ILI Herd had prior problems with swine respiratory disease complex PRRS +, H +, APP 5b + Heightened awareness of the evolving influenza outbreak in humans involving a swine origin H1N1 virus Given the public concern and scientific uncertainty regarding this emerging influenza, CFIA & AARD issued a precautionary quarantine pending results of laboratory tests and full epidemiological investigation 6 3

4 vr (-) 3 UCGUUUUCGUCCNNN UUUUUNNNGGAACAAAGAUGAppp5 C Hoffman et. al Archives of Virology 146: One Shot ach1 -T1 R Chemically Competent E. coli 7 8 4

5 Amino Acid Substitutions in Gene of Alberta Swine ph1n1 Isolates Amino Acid Position GenBank Isolate 1 2 accession no GQ A/X/4487/09 C T G Q Y V V D V T I A T K N GQ Pig no. 1 (33-1) R A GQ Pig no. 2 (33-2) N V GQ Pig no. 3 (33-3) - - E V I A - - GQ Pig no. 7 (33-7) - A T GQ Pig no. 21 (33-21) R A V GQ Pig no. 23 (33-23) E - GQ Pig no. 24 (33-24) H GQ Pig no. 8 (33-8) synonymous + 24 non-synonymous nucleotide substitutions estimated overall substitution frequency of 4 x 10-3 non-synonymous:synonymous nucleotide substitutions overall substitution frequency (1.69 x 10-4 to 8.89 x 10-4 previously documented) Estimated Herd Level Prevalence of Active Viral Shedding and Seroprevalence Prevalence (%) Estimated herd level prevalence of viral shedding by rrt-pcr testing Estimated herd level seroprevalence to Influenza A Week of Investigation 10 5

6 Regulatory Response Animal and public health authorities supported the continuation of movement restrictions while there was still evidence of live virus circulating A controlled marketing approach allowing the movement of test negative animals to slaughter was proposed Despite uneventful clinical recovery of animals no slaughter facility would accept the animals after the quarantine was removed At the owner s request and with the assistance of AARD, approximately 2300 pigs were humanely destroyed between June 4 th and 6th 11 Human-like H1N1, Saskatchewan June 2009 two pig farm workers ill with ILI Nasopharyngeal swab specimens were tested at the Saskatchewan Disease Control Laboratory Test results suggested the occurrence of a novel reassortant virus July 2009, PC announces the identification of a novel influenza A virus and genes derived from human H1N1 closely related to A/Brisbane/59/2007 Remaining genes derived from triple reassortant H3N2 Nasal swab specimens are collected from pigs on the affected hog operation 12 6

7 Hu-H1N1 ph1n1 Origin of gene segments Human seasonal H1N1 Triple reassortant H3N2 Pandemic H1N1 13 olecular and Antigenic Characterization of H1N1 Swine Influenza Viruses Isolated from Canadian Pigs Viruses originated from pigs in Quebec, anitoba, Saskatchewan, Alberta and British Columbia 57 of the viruses were isolated prior to arch of the viruses were isolated after the first reported outbreak of ph1n1 in pigs 14 7

8 ASS SHY SHY SHY SHY SHY SHY SHY SHT B QC QC-7-59 SHY SHY SHY SHY QC-7-26 SHT SHY SHT B 9 0 SHT A 4 4 STF STF QC-7-25 STF STF SHY SHY STF STF STF STF STF STF SHY SHY STF SHY STF SHY QC-7-29 SHY SHY SHY QC-7-31 SHY SHY STF SHY SHY ASS A/SW/ON/53518/2003 A/SW/ON/23866/2004 SHY QC QC AFRI NCFAD AFRI-NCFAD A/SW/SHY/106/11 A/SW/ON/1112/2004 A/SW/IOWA/2/1987 A/SW/ON/57561/03 A/SW/AB/56626/ A/SW/IN/1726/1988 A/WI/4755/ A/SW/IA/24297/11 A/IA/CEID23/2005 A/SW/IA/00239/ A/SW/IA/930/01H1N2 A/SW/NC/36883/2002 H1N A/SW/ N/55551/ A/SW/NC/98225/01(H1N2 A/SW/ N/37866/ A/SW/OH/511445/2007 H1N1 5 9 A/SW/N/00194/2003 H1N2 A/SW/ N/16419/01H1N A/SW/KS/00246/2004 H1N A/SW/OH/891/01H1N2 A/SW/N/23124-T/01 H1N2 9 0 A/SW/IL/100085A/01 H1N2 A/SW/N/1192/2001 H1N2 A/SW/IN/P12439/2000 H1N2 95 NCFAD AFRI NCFAD QC-7-51 NCFAD-SASK A/Russia/165/ QC QC QC QC QC QC QC QC QC QC-7-22 AFRI NCFAD AFRI-46 AFRI NCFAD A/Ontario/9698/ AFRI NCFAD AFRI-NCFAD AFRINCFAD AFRI NCFAD AFRI NCFAD AFRI NCFAD QC QC QC QC QC-7-24 A/SW/AB/OTH-33-23/ A/SW/AB/OTH-33-24/2009 A/Canada-AB/RV1644/ Big Sky 71 Big Sky 48 A/Toronto/3141/ QC-7-21 A/SK/5131/ A/SK/5351/2009 A/SK/5350/2009 Big Sky Big Sky 35 A/SW/N/ /2007 A/SW/IL/00685/2005 A/SW/NC/00573/2005 A/SW/ON/55383/ A/SW/ON/48235/ A/SW/IL/ /2007 H1N2 44 A/SW/ON/52156/ A/NY/294/2003H1N Phylogeny of the SIV H1N1 Canada GENE North American classical swine H1N1 origin ph1n1 of North American classical swine H1N1 origin Seasonal human H1N1 origin ST F QC-7-29 SHY SHY SHY SHY SHY SHY ST F SHY STF STF ST F ST F STF SHY ST F SHY ST F ST F ST F ST F SHT B SHY SHT A SHT QC-7-26 SHY SHY SHY SHY QC QC-7-36 SHY SHY SHY SHT A SHT B SHY SHY SHY SHY SHY SHY STF SHY ASS SHY SHY QC-7-31 A/SW/ON/57561/ QC-7-5 AFRI NCFAD AFRI NCFAD QC QC-7-38 A/SW/ON/11112/04 A/SW/QC/5393/91 A/SW/KS/3228/1987 A/SW/N/37866/17 ASS A/SW/IN/PU542/04(H3N1) A/SW/AB/56626/03 A/SW/KN/77778/2007 A/SW/OH/24366/07 A/SW/WS/1/1968 A/SW/IA/1945 A/SW/IA/15/1930 Big Sky 16 Big Sky 35 A/Sk/5351/2009 A/SW/OH/K1207/06 A/NY/228/2003 A/NY/220/2002 AFRI NCFAD AFRI NCFAD AFRI NCFAD QC QC QC QC QC QC QC QC-7-15 WIN-AH WIN-AH QC QC-7-28 A/SW/AB/OTH-33-24/2009 A/SW/AB/OTH-33-23/2009 Big Sky48 Big Sky 71 AFRI-NCFAD QC QC-7-18 WIN-AH A/ON/35273/2009 AFRI-NCFAD A/T oronto/r8557/2009 NCFAD AFRI NCFAD AFRI NCFAD A/Russia/178/2009 NCFAD-SASK AFRI-46 AFRI QC-7-19 WIN-AH GENE North American classical swine H1N1 origin Seasonal human H1N1 origin ph1n1 of Eurasian avian -like swine H1N1 origin 15 Phylogeny of the SIV H1N1 Canada A/TK/OH/313053/04 H3N2 A/SW/OH/511445/07 H3N2 A/ON/RV1273/05 H3N2 A/SW/OH/C62006/06 ASS STF STF A/SK/5131/09 Big Sky 16 A/SK/5351/09 A/SK/5350/09 STF ASS AFRI NCFAD SHT B SHY SHY SHY STF STF STF STF STF STF STF SHY SHY SHY SHY STF SHY STF SHY SHY SHY SHY SHY SHY SHY SHY SHT A STF B SHY SHT SHY SHY SHY SHY ASS SHY SHY SHY SHY STF A/TK/IA/ /92 AFRI NCFAD A/TAIWAN/126/09 NCFAD-2010-QC-7 A/SW/IA/35573/09 A/SINGAPORE/KK066/2010 A/ON/315637/09 NCFAD-SASK A/SW/T AIWAN/T D-411B2/09 AFRI-46 AFRI-NCFAD AFRI AFRI NCFAD AFRI NCFAD Big Sky 48 Big Sky 71 A/Canada-PQ/RV1758/09 A/SW/AB/OTH-33-21/09 A/SW/AB/OTH-33-14/09 A/SW/AB/OTH-33-25/09 atrix gene North American classical swine H1N1 origin ph1n1 atrix of Eurasian avian-like swine influenza origin 16 8

9 ASS SHY SHY SHY SHY SHY SHY SHY SHT B QC QC-7-59 SHY SHY SHY SHY QC-7-26 SHT SHY SHT B 9 0 SHT A 44 STF STF QC-7-25 STF STF SHY SHY STF STF STF STF STF STF SHY SHY STF SHY STF SHY QC-7-29 SHY SHY SHY QC-7-31 SHY SHY STF SHY SHY ASS A/SW/ON/53518/2003 A/SW/ON/23866/2004 SHY QC QC AFRI NCFAD AFRI-NCFAD A/SW/SHY/106/11 A/SW/ON/1112/2004 A/SW/IOWA/2/1987 A/SW/ON/57561/03 A/SW/AB/56626/ A/SW/IN/1726/1988 A/WI/4755/ A/SW/IA/24297/11 A/IA/CEID23/2005 A/SW/IA/00239/ A/SW/IA/930/01H1N2 A/SW/NC/36883/2002 H1N A/SW/N/55551/ A/SW/NC/98225/01(H1N2 A/SW/N/37866/19 79 A/SW/OH/511445/2007 H1N1 5 9 A/SW/N/00194/2003 H1N2 A/SW/N/16419/01H1N A/SW/KS/00246/2004 H1N A/SW/OH/891/01H1N2 A/SW/N/23124-T/01 H1N2 9 0 A/SW/IL/100085A/01 H1N2 A/SW/N/1192/2001 H1N2 A/SW/IN/P12439/2000 H1N2 9 5 NCFAD AFRI NCFAD QC-7-51 NCFAD-SASK A/Russia/165/ QC QC QC QC QC QC QC QC QC QC-7-22 AFRI NCFAD AFRI-46 AFRI NCFAD A/Ontario/9698/ AFRI NCFAD AFRI-NCFAD AFRINCFAD AFRI NCFAD AFRI NCFAD AFRI NCFAD QC QC QC QC QC-7-24 A/SW/AB/OTH-33-23/ A/SW/AB/OTH-33-24/2009 A/Canada-AB/RV1644/ Big Sky 71 Big Sky 48 A/Toronto/3141/ QC-7-21 A/SK/5131/ A/SK/5351/2009 A/SK/5350/2009 Big Sky Big Sky 35 A/SW/N/ /2007 A/SW/IL/00685/2005 A/SW/NC/00573/2005 A/SW/ON/55383/ A/SW/ON/48235/04 88 A/SW/IL/ /2007 H1N2 4 4 A/SW/ON/52156/03 57 A/NY/294/2003H1N2 Gene combination of 2009/2010 SIV H1N1 in Canada rh1n1 Human-like H1N1 ph1n1 17 Phylogeny of the SIV H1N1 Canada swh1α? swh1α swh1β swh1γ ph1n1 swh1δ 18 9

10 Antigenic characterization of H1N1 Viruses Antibodies from pigs experimentally infected with different types of csiv H1N1 in the USA in 2008 (Amy Vincent, DC, Ames, IA) sh1α sh1β sh1γ sh1δ 19 Pandemic H1N1 Virus Isolates A/Tk/On/ FAV- A/Tk/On/ FAV- B Homologous HI 110/04/20 114/04/20 AFRI 09- QC2010 QC2010 QC2010 QC2010 QC2010 AB OTH AB OTH Serum ID titer #14 #19 #22 #56 #60 33 #2 33 #3 A/SW/N/02053/2008 α H1N A/SW/N/02053/2008 α H1N A/SW/N/02093/2008 α H1N A/SW/N/02093/2008 α H1N A/SW/IA/02096/2008 β H1N A/SW/IA/02096/2008 β H1N A/SW/KY/02086/2008 β H1N A/SW/KY/02086/2008 β H1N A/SW/NE/02013/2008 β H1N A/SW/NE/02013/2008 β H1N A/SW/NC/02084/2008 β H1N A/SW/NC/02084/2008 β H1N A/SW/NC/02023/2008 γ H1N A/SW/NC/02023/2008 γ H1N A/SW/OH/02026/2008 γ H1N A/SW/OH/02026/2008 γ H1N A/SW/O/02060/2008 γ H1N A/SW/O/02060/2008 γ H1N A/SW/TX/01976/2008 δ1h1n A/SW/TX/01976/2008 δ1 H1N A/SW/IA/02039/2008 δ1 H1N A/SW/IA/02039/2008 δ1 H1N A/SW/N/02011/2008 δ H1N A/SW/N/02011/2008 δ H1N

11 Non-Pandemic H1N1 Isolates B QC SHY-09- QC ASS- QC SHY- QC SHY- QC 2010 QC 2010 QC SHY- QC SHY- AFRI 09- Serum ID Homologous HI titer #37 # A/SW/N/02053/2008 α H1N A/SW/N/02053/2008 α H1N A/SW/N/02093/2008 α H1N A/SW/N/02093/2008 α H1N A/SW/IA/02096/2008 β H1N A/SW/IA/02096/2008 β H1N A/SW/KY/02086/2008 β H1N A/SW/KY/02086/2008 β H1N A/SW/NE/02013/2008 β H1N A/SW/NE/02013/2008 β H1N A/SW/NC/02084/2008 β H1N A/SW/NC/02084/2008 β H1N A/SW/NC/02023/2008 γ H1N A/SW/NC/02023/2008 γ H1N A/SW/OH/02026/2008 γ H1N A/SW/OH/02026/2008 γ H1N A/SW/O/02060/2008 γ H1N A/SW/O/02060/2008 γ H1N A/SW/TX/01976/2008 δ1h1n A/SW/TX/01976/2008 δ1 H1N A/SW/IA/02039/2008 δ1 H1N A/SW/IA/02039/2008 δ1 H1N A/SW/N/02011/2008 δ H1N A/SW/N/02011/2008 δ H1N Canadian pandemic H1N1 Canadian non-pandemic H1N1 DC classic-like H1N1 rh1n1 H1N2-like Human-like H1N1 Pandemic H1N

12 Summary ph1n1 likely has infected pig herds in all pig producing areas across Canada rh1n1 appears to have replaced classical H1N1 Non-pandemic H1N1 viruses appear to be phylogenetically most similar to the αh1 cluster but antigenically most similar to the γh1 cluster Significant antigenic drift of Canadian nonpandemic H1N1 viruses relative to 2008 USA αh1 and γh1 cluster viruses Identification of novel reassortants between Hu- H1N1 and ph1n1 highlights the need for strategies to minimize these types of events 23 Acknowledgements Yohannes Berhane Tamiko Hisanaga Helen Kehler William Swiderski Kathleen Hooper-cGrevy arsha Leith John Copps Soren Alexandersen Oliva Labrecque Nicola Lewis David Suarez Jan Bystrom Yan Li Hana Weingartl James Neufeld Egan Brockhoff Tomy Joseph Charles Nfon Shunzhen Zhang Amy Vincent 24 12

13 2007 Her ajesty the Queen in right of Canada (Canadian Food Inspection Agency), all rights reserved. Use without permission is prohibited