OFFLU Technical Meeting Coordinating world-wide surveillance for influenza in swine OIE Paris, 6-7 April 2011

Transcription

1 OFFLU Technical Meeting Coordinating world-wide surveillance for influenza in swine OIE Paris, 6-7 April 2011 Frank Wong CSIRO Australian Animal Health Laboratory, Geelong, Australia

2 OIE Reference Laboratory functions of AAHL OIE Collaborating Centre for New and Emerging (transboundary & zoonotic) animal diseases OIE Reference Laboratory for: Avian Influenza Newcastle disease Bluetongue viruses Henipah virus diseases Relevant aquatic viral diseases OIE Collaborating Laboratory for Capacity Building National reference laboratory for rabies WHO collaborating centre for SARS

3 AAHL Regional Program AAHL has a ongoing commitment to working in the SE Asian region as an OIE Collaborating Laboratory for Capacity Building. AAHL has many projects in the region to support capacity for tackling the major TADs (eg. AI, FMD & CSF). Projects look at improving disease diagnostics in the region and also at AAHL. Biosafety & Quality Assurance is a important part of AAHL s regional training program Improved harmonization of diagnostic approaches and interpretation criteria is also an important focus area.

4 Representative Regional Projects AusAID Laboratory Partnerships Program - Capacity Building for New & Emerging Diseases ( ): Capacity Building to allow detection of zoonotic agents Focus on relevant TADs/zoonotic agents: CSF, FMD, PRRS & AI Biosafety, cell culture, virus isolation, ELISA, VNT, PCR & sequencing, QA OIE/AusAID Project on Strengthening Veterinary Services (PSVS) in SE Asia ( ): Proficiency Testing (PT) for AI diagnostics (serology and PCR); with some USDA funding Gap analysis of laboratories Establish QA and IQC in each laboratory Biosafety & Biosecurity procedures. Skills & proficiency training for veterinary scientists

5 Representative Regional Projects Vietnam: World Bank projects on Laboratory Gap analysis and Quality Assurance for HPAI ( ). Establishing QA system in 2 national & 6 regional laboratories Support towards ISO accreditation Malaysia: OIE Twinning with Ipoh VRI to be regional OIE reference lab for region (2009-present). VI, serology, PCR, sequencing & molecular characterization QA system Support towards ISO accreditation Classical and 2009p SIVs present in SEA but no systematic surveillance

6 Representative Regional Projects Indonesia: Indonesia Veterinary Laboratory Capacity Building - AusAID ( ): Serological and molecular diagnostics Lab outreach (epidemiology) program OFFLU/FAO HPAI control in Indonesian poultry ( ): HPAI vaccine update for Indonesia Extensive collection and characterisation of poultry HPAI isolates Sequencing & harmonized guidelines for genetic analysis of HPAI Antigenic cartography of H5N1 in poultry Transfer of genetic and antigenic analytical capability to Indonesian veterinary diagnostic reference labs

7 Animal influenza: Strengthening Lab Capacity for Member Countries (ASEAN) in Diagnosis and Molecular Characterization of Animal Influenza FAO PR. No AAHL, Murdoch Univ & FAORAP ( ): Focus on harmonized epidemiology & diagnostic standards for surveillance of HPAI and ph1n1 in poultry and swine in ASEAN region Full participation by 8 ASEAN countries: Cambodia, Indonesia, Laos PDR, Malaysia, Myanmar, Philippines, Thailand, & Vietnam (observing participants included China and South Asian countries) Outputs: Recommendations to harmonized surveillance & lab approaches for animal influenzas with contributions from several international ref institutions (AFFSA, FLI, AAHL) Training in lab diagnostic protocols for virology, serology, PCR and genetic characterization (sequencing), and QA, biosafety & biosecurity Backstopping and training at national vet lab of each country; provision of reference SOPs and reagents Drafted Regional Guiding Principles for Animal Influenza Diagnosis & Characterization in Asia towards sharing a harmonized approach Contribution to FAO global TCP projects in Asia on swine influenza surveillance

8 Harmonized ph1n1 diagnostic algorithm from FAORAP Guidance Document CSIRO. Insert presentation title, do not remove CSIRO from start of footer

9 Regional Constraints/Practicalities Biosafety/Biosecurity Workflow Proper use of BSCII Use of adequate disinfectant Virkon (not UV & 70% EtOH) Waste disposal Disinfection > Autoclaving > Incineration PPE, Bags, Virkon (often hard to source) Need for increased in-lab contact time Restrictions to sample shipments (to ref labs) QA Increased contact time needed Staff training & reagents (including use of controls) Feedback (eg. timely IQC & PT results) Staffing Influenza work takes staff from other areas Need to support all other key disease activities Equipment Maintenance Budget (eg. BSCII s) Standardisation (eg. equip, test kits) Makes testing easier and cheaper Linking Lab & Field Clear goals/joint goals what to do with results? Field activities that allow testing in labs Lab needs to feed results quickly back to field and field to farms

10 Australia was the 3rd country reporting to the OIE of ph1n1 influenza in commercial swine (OIE, 31/07/2009 outbreak in a NSW pig farm) 1st confirmed case of swine influenza in Australia: national notification and EID biosecurity measures taken In-contact humans with ILI a common link suggesting spill-over interspecies transmission CSIRO. Insert presentation title, do not remove CSIRO from start of footer

11 Pandemic H1N1 influenza - First outbreaks in Australian swine Confirmed cases of pandemic (H1N1) 2009 in Australia, to 28 August 2009 by jurisdiction. Australian piggery outbreaks: 24 Jul 09; central-western NSW 18 Aug 09; northern VIC 23 Aug 09; southeast Infections in pigs clinically mild and self limiting (inappetance, coughing, lethargy) Source: AUSTRALIAN INFLUENZA SURVEILLANCE SUMMARY REPORT No.16, Commonwealth of Australia Samples submitted to AAHL for diagnostic confirmation: - FluA rrt-pcr (M) - ph1 and pn1 rrt-pcrs - HI test of sera - Virus isolation - Rapid HA gene sequencing - Whole genome sequencing

12 ph1n Influenza from across the human-animal interface in Australian swine HA protein residue alignment analysis Phylogenetic analysis of HA gene showing relationships between circulating A(H1N1)2009 viruses NSW VIC Classical swine H1N1 Human seasonal H1N1 NSW VIC Classical swine H1N1 Human seasonal H1N1 VIC NSW VIC Classical swine H1N1 Human seasonal H1N1 NSW VIC Classical swine H1N1 Human seasonal H1N1 HA sequence analysis further confirmed identity of pig farm viruses as ph1n Viruses from the separate piggery outbreaks distinguishable, with closest identity to viruses circulating in the human population in the same region at the time; evidence supporting separate spill-over transmissions

13 Outbreak of ph1n influenza in piggery: at the animal-human interface Whole genome sequence similarities with piggery human virus strain: A//2015/2009 (swab from in-contact person) Nucleotide % identity Gene segments PB2 PB1 PA HA MP NA NP NS A/swine// /2009 (swab from positive pig) A/swine// /2009 (ckn egg culture of above) 100% (partial) 100% (partial) 100% (partial) 100% n/a 100% (partial) 100% (partial) 100% 100% 100% 99.9% 100% 100% 99.9% 100% n/a A//2011/ % 99.8% 100% 99.9% 99.9% 99.9% 99.8% 100% A/swine/Alberta/HTH33-8/ % 99.6% 99.7% 99.4% 99.5% 99.4% 99.2% 99.4% A/California/07/ % 99.9% 99.9% 99.5% 99.7% 99.7% 99.6% 99.8% A/Auckland/1/ % 99.9% 96.9% 98.9% 99.7% 99.5% 99.7% 99.8% Two persons reported clinically with ILI after dealing with sick pigs, confirmed for ph1n1. Samples from infected pigs and direct in-contact humans at piggery outbreak subjected to whole genome sequencing (all 8 gene segments) Whole virus genome sequences had 100% concordance between swine and human specimens (in contrast to sequence dissimilarities in ph1n1 viruses from unrelated cases)

14 Evidence of zoonotic transmissions Substitutions in HA protein of ph1n influenza viruses from humans and swine Virus strain Sample date Substitution at indicated amino acid position (H3 numbering) A/California/07/ / A P D T S R I I V A/Auckland/1/ /2009 S A V A//2011/ /2009 S A T V I A/swine// / /2009 T S A T V V I A/swine// / /2009 S N A T V V I A//2014/ /2009 T S A T V V I A//2015/ /2009 S N A T V V I A/VIC/2025/ /2009 S A T K V I A/swine/VIC/02797/ /2009 S A T K V I piggery viruses from pigs and humans share unique I276V substitution Respective viruses from the two subsequently infected persons link to two distinct strains zoonotically transmitted from pigs to humans: - Strain A with unique A10T substitution - Strain B with unique D104N substitution

15 No reassortment with non-pandemic influenza A viruses Phylogenetic ML dendrogram of major swine influenza A lineages with 8 genes concatenated Whole genome analysis of viruses from piggery outbreak confirmed that they belonged to the ph1n lineage, with its evolutionarily distinct constellation of gene segments. Swine influenza lineages: European avian-like H1N1 Triple reassortant H1N2 Classical swine H1N1 H1N1pdm 2009 Viruses associated with piggery outbreak Australian ph1n1 viruses (in both pigs and humans) so far show no evidence of genome reassortment with other influenza A lineages

16 CONCLUSIONS AAHL has strong exiting partnerships with both national and regional veterinary diagnostic labs in many SE Asian countries can contribute at the reagents provision and consultative level Swine influenza surveillance for the region has been on agenda for past several years but problems in getting local prioritization and/or sustained interest The 2009 piggery outbreaks of ph1n1 influenza were the first confirmed cases of swine influenza (of any type) in Australia Molecular epidemiology of Australian ph1n1 outbreaks supported multiple independent human-to-pig transmissions of pandemic virus at affected pig farms Outbreak investigation at one Australian piggery showed for the first time, direct evidence of zoonotic ph1n1 transmission from pigs back to humans Highlights importance of close surveillance of influenza viruses at the animal-human interface, especially where epidemiologic events suggest a link Both public health (WHO ) and animal health (OFFLU) sectors need to be more epidemiologically alert and cooperative to avoid missing timely informative surveillance opportunities during influenza activity at the animal-human interface

17 Australian Animal Health Laboratory Diagnosis Surveillance & Response Frank Wong Phone: frank.wong@csiro.au Web: Thank you CSIRO. A(H1N1) 2009 Influenza in Australian pigs Contact Us Phone: or enquiries@csiro.au Web: