Identification of novel influenza A viruses in Australian swine

Transcription

1 Identification of novel influenza A viruses in Australian swine OFFLU SIV Group Annual Meeting, Rome, April 2013 Frank Wong 1, Ian Barr 2, David Smith 3, David Williams 1, Kelly Davies 1, Vicky Stevens 1, Songhua Shan 1, Peter Mohr 1, Kerri Bruce 1, Naomi Komadina 2, Yi-Mo Deng 2, James Watson 1, Sam McCullough 1, Peter Daniels 1 1. CSIRO Australian Animal Health Laboratory, Geelong, VIC. 2. WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, VIC. 3. PathWest QEII Medical Centre, Nedlands, Western Australia.

2 Introduction Influenza A in Australian pigs OIE does not list SI as a notifiable disease; however detection of influenza A in pigs in Australia is nationally notifiable Australia claims freedom from endemic swine influenza A viruses (SIV) in its pig population (but...) The first confirmed detections of influenza infections in Australian pigs occurred in 2009, with the pandemic H1N1 virus Pandemic H1N1 reported in Australian pigs to 2012, however no active surveillance for influenza A viruses in pigs in the country (knowledge gap)

3 Novel influenza A viruses in Australian swine, 2012 Recent investigations of respiratory disease in commercial pigs in Western Australia (July 2012) and Queensland (August 2012) have identified influenza A virus in lung tissue and nasal swabs Virus isolations and molecular analysis have identified novel reassortant influenza A viruses in WA and QLD pigs Clinical samples positive by FluA TQM PCR and virus culture in eggs and MDCK cells Characterisation of clinical samples and virus isolates have confirmed independent H1N2 and H3N2 reassortant viruses (in WA); and H1N2 reassortant viruses (in QLD) with genes derived from old human seasonal influenza A strains and ph1n1 2009

4 Isolation of novel IAV from pigs, 2012 Western Australia and Queensland (AAHL & WHO-CC) SAN Subtype Origin Date Isolation* Eggs MDCK nh1n2 Gingin, WA 7/8/2012 Y N nh1n2 nh3n2 Gingin, WA 10/8/2012 N Y nh1n2 Kingaroy, Qld 23/8/2012 Y N nh1n2 Kingaroy, Qld 31/8/2012 Y Y ph1n1 Kingaroy, Qld 21/9/2012 Y N *All isolates confirmed by FLU-A TQM PCR and WGS

5 Genome constellations of reassortant influenza A viruses detected in Australian pigs, 2012 Virus Subtype H1N2 H3N2 H1N2 H1N2 ph1n1 Source WA pigs WA pigs QLD pigs QLD pigs QLD pigs Gene Segment PB2 PB1 PA HA NP NA MP NS Origin of gene segment: ph1n1/2009 (post.2009) Different human H1N1 (circa.1980 and 1990) Different human H3N2 (circa.1970 and 2000)

6 A/South Carolina/1/18 A/New York/1/18 A/Brevig Mission/1/1918 A/swine/Ontario/52156/03 H1N2 A/New York/209/2003 H1N2 A/swine/Minnesota/239106/2010 H1N2 A/swine/Oklahoma/ /2008 H1N2 A/Minnesota/12/2012 H1N2v A/swine/Texas/008648/2008 H1N2 A/Sydney/12/2003 H1N2 A/Brisbane/116/2002 H1N2 hu-h1n2 A/Wisconsin/12/2001 H1N2 A/New Caledonia/20/1999 H1N1 A/New A/Darwin/5/2001 South Wales/24/1999 A/Western Australia/19/2001 A/South Australia/1/2008 A/Brisbane/59/2007 A/Brisbane/59/2007 H1N1 A/South Australia/11/2009 A/Perth/33/2009 A/Victoria/501/2007 A/Perth/200/2008 A/Brisbane/297/2006 A/Michigan/09/2007 H1N2 swoiv A/swine/Minnesota/ /2007 A/South Australia/58/2005 A/South Australia/44/ Qld H1N2 A/Baylor/11735/1982 A/England/333/1980 A/Finland/5/1984 A/Chile/1/1983 A/Tientsin/78/1977 hu-h1 A/Mongolia/231/85 A/Finland/20/1978 A/Roma/1949 A/Lackland/7/1978 A/Sw/WA/ R/12 H1N2 A/Denver/57 A/Sw/WA/ X/12 H1N2 A/Kojiya/1/1952 A/Malaya/302/1954 A/Albany/12/1951 A/Hickox/1940 A/AA/Marton/1943 A/Iowa/1943 A/Bel/1942 A/Puerto Rico/8/34 A/Henry/1936 A/Melbourne/1/1946 A/Melbourne/35 A/United Kingdom/1/1933 A/Iowa/05/2007 A/swine/Indiana/240218/2010 H1N2 Sw-H1 b A/duck/NC/91347/01 H1N2 A/California/07/2009 H1N1 pdm09 A/swine/Italy/116114/2010 H1N2 A/Wisconsin/10/98 H1N1 A/swine/Kansas/77778/2007 Sw-H1 g A/Ohio/01/2007 A/swine/Iowa/1/1987 A/Indiana/05/1995 A/swine/Wisconsin/1915/1988 A/Philippines/344/2004 H1N2 Sw-H1 a A/swine/Tennessee/19/1976 A/Thailand/271/2005 A/mallard/Ohio/118/1993 A/Switzerland/8808/2002 A/Swine/Spain/50047/2003 hu-h hu-h1 sw-h1 d HA phylogeny of 2012 H1N2 reassortants from WA and QLD Sw-H1 Eurasian pigs: (courtesy WHO-CC Melb) Grouped with human H1 lineage. Matched closest to older human H1 strains. Distinct from viruses in Eurasian swine H1 lineage and North American classical and TRIG swine H1 lineages. Extent of evolutionary distance indicates period of unsampled evolution (in Australian pigs). Similar story for respective H3-HA and N2-NA genes in the H3N2 and H1N2 variants.

7 HI typing of novel IAVs from Australian pigs, 2012 Origin Reference Antisera (subtype) Homol. titre WA pigs nh1n2 WA pigs nh3n2 QLD pigs nh1n2 A/swine/Nakhon Pathom/2002 (Eurasian swh3n2) A/California/7/2009 (pandemic H1N1) A/swine/New Jersey/8/1976 (classical swh1n1) A/NC/20/1999 (huh1n1) A/Sydney/5/1997 (huh3n2) A/Minnesota/11/2010 (H3N2v-USA) A/California/7/2009 (pandemic H1N1) A/NC/20/1999 (huh1n1) A/Sydney/5/1997 (huh3n2) A/Minnesota/11/2010 (H3N2v-USA) A/swine/Nakhon Pathom/2002 (Eurasian swh3n2) A/California/7/2009 (pandemic H1N1) A/swine/New Jersey/8/1976 (classical swh1n1) A/NC/20/1999 (huh1n1) A/Sydney/5/1997 (huh3n2) A/Minnesota/11/2010 (H3N2v-USA) Test samples 20

8 Synopsis Novel H1N2 viruses in WA and QLD pigs appear to be independent triple reassortant viruses with HA and NA genes from older human H1N1 and H3N2 strains respectively, on an ph1n1/2009 genomic backbone (all internal genes from pandemic H1N1 virus). The H1N2 reassortants likely occurred after 2009 when the pandemic H1N1 virus was introduced to Australian swine from the human population. An novel H3N2 reassortant was also present in WA pigs containing a huh1n1 PA gene on an huh3n2 genomic backbone [ strange virus ]. The current H1N2 and H3N2 viruses in WA and QLD represent the first report of non-pandemic influenza A virus in Australian pigs. Molecular evidence supports the probable long-term circulation of humanderived H1 and H3 viruses in Australian swine, previously unsampled due to the absence of influenza A surveillance in pigs. The viruses in Australian pigs are not the H3N2v and H1N2v variant viruses currently circulating in North American domestic pigs and causing concern to public health due to incidences of pig-to-human transmissions.

9 Conclusions There is no evidence of transmission of these viruses to humans, including in sampled in-contact persons (piggery workers). Occurrence of these novel reassortant viruses in Australian pigs are of concern to both human and animal health sectors. As these viruses contain surface genes from older human strains that are no longer present in humans, antigenic relatedness and effectiveness of current seasonal vaccines is an issue. Work is continuing to better characterise these viruses, including transmissibility/infection studies using mammalian animal models. Broader national surveillance for these variant viruses in pigs was debated, but... Field surveillance of pigs in the affected locations and more broadly nationally in Australia is NOT progressing

10 Acknowledgements The AAHL DSR team, particularly the Sequencing, Avian Virology, Molecular Diagnostics, and Duty Vet Groups The WHO and the team at WHO Influenza Collaborating Centre Melbourne State departmental veterinary and public health field and laboratory staff from WA and QLD The OFFLU Animal Influenza Network (communicated to OFFLU)

11 Thank you Australian Animal Health Laboratory Frank Wong t e frank.wong@csiro.au w CSIRO ANIMAL HEALTH AND FOOD SCIENCE