Activities in 2009 Research on Emerging Avian Diseases




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Activities in 2009

Research on Emerging Avian Diseases

David E. Swayne

Southeast Poultry Research Laboratory, Agricultural Research Service, US Department of Agriculture


934 College Station Road, Athens, Georgia 30605, USA
Tel.: (1-706) 546.3433, Fax: (1-706) 546.3161
e-mail address: David.Swayne@ars.usda.gov

Summary of activities specifically related to the mandate of
OIE Collaborating Centres


1. Activities as a centre of research, expertise, standardisation and dissemination of techniques within the remit of the mandate given by the OIE

  • SEPRL is the U.S. Department of Agriculture’s primary facility for research on exotic and emerging viral diseases of avian species including avian influenza (AI), Newcastle disease (ND), avian metapneumovirus (aMPV), enteric viruses of poultry and Marek’s disease herpes virus

  • Major accomplishments for 2009 relative to international issues included:

    • Demonstrated that turkeys, quail, domestic ducks and geese can be susceptible to wild bird influenza viruses and such species can be entry points of such viruses into agricultural systems.

    • 2.3% of samples collected from land-habitat birds in southern China (2004-2007) tested for avian influenza virus (AIV) using real-time reverse transcriptase polymerase chain reaction (RRT-PCR), indicating that species other than waterfowl can serve as hosts for the virus.

    • Triple reassortant H3N2 turkey-origin influenza viruses replicated and transmitted efficiently in turkeys but exhibited poor replication and transmissibility in chickens and ducks.

    • Three H5N1 high pathogencity (HP) AIV from chickens in Nigeria were determined to be genetically related to recent viruses from Europe and the Middle East, and produced systemic and severe disease in chickens typical of this lineage of viruses.

    • House sparrows were found to be highly susceptible to H5N1 HPAI viruses, but rock pigeons were resistant to infection and only shed low titers of virus for short periods of time indicating that house sparrows could play a role in dissemination of the virus among birds including poultry, but rock pigeons are unlikely to be important for the ecology of this HPAIV lineage.

    • The birds vaccinated with Newcastle disease viruses (NDV) vaccines made from isolates that were genetically similar to the challenge virus shed less virus in oral secretions and had fewer birds shedding virus than the birds vaccinated with vaccines made from viruses genetically divergent from the challenge virus suggesting using NDV vaccines genetically closer to field viruses may improve field protection.

    • NDV were obtained from recent outbreaks in the U.S., Mexico, Russia, Egypt, Dominican Republic, Belize, Peru, Vietnam and Pakistan were genetically similar to previously described viruses, but viruses from Dominican Republic were genetically different enough from the other viruses to be considered as new genotypes.

    • Muscovy ducks (Cairina moschata) had less protection after vaccination and longer duration of HPAIV challenge virus shedding than domestic ducks (Anas platyrhynchos) when using the same vaccine and vaccination protocol indicating new vaccine and vaccination protocols need development for Muscovy ducks.

    • By comparing different schedules of domestic duck (Anas platyrhynchos) vaccination, it was determined that vaccinating at 7 days and boosting at 21 days of age protected ducks against disease and mortality after a virulent H5N1 HPAI challenge at a month of age.

    • The functional Mx gene provided only partial protection to chickens against HPAI virus challenge.

    • There was demonstration of the lack of broad H7 vaccine protection between Eurasian, North American, South American and Australian lineages of H7 avian influenza viruses

2. Proposal or development of any procedure that will facilitate harmonisation of international regulations applicable to the surveillance and control of animal diseases, food safety or animal welfare

  • The RRT-PCR test for avian influenza virus H7 hemagglutinin was updated to detect newer strains of H7 viruses

  • The RRT-PCR test for influenza A virus matrix gene reverse primer was updated to improve sensitivity for detecting the pandemic H1N1 virus and works well in a duplex test with the original reverse primer to detect both avian influenza and the pH1N1 viruses

  • A polymerase chain reaction (PCR)-based diagnostic test was developed and validated for the detection of chicken- and turkey-origin enteric parvoviruses

3. Placement of expert consultants at the disposal of the OIE

  • David Swayne provided assistance to OFFLU through the Technical Group on Avian Influenza Vaccination in Indonesia.

  • David Suarez provided technical assistance on H5N1 HPAI virus sequencing and analysis to National Laboratory for Quality Production, Cairo, Egypt

  • David Swayne and David Suarez provided technical assistance to OFFLU on diagnostics and poultry studies on pandemic H1N1 virus.

  • David Suarez and Mary Pantin-Jackwood conducted studies and provided data on molecular changes in H5N1 HPAI viruses and vaccine efficacy and pathogenesis studies in ducks to Ministry of Agriculture, Vietnam

  • David Suarez, Qingzhong Yu, Darrell Kapczynski and Patti Miller provided technical assistance to ARRIAH (Vladimir, Russia) and Ivanovski Institiute (Moscow, Russia) on poultry disease research and on collaborative projects

Other activities related to the mandate
of OIE Collaborating Centres


4. Provision of scientific and technical training, within the remit of the mandate given by the OIE, to personnel from OIE Members

  • One scientist from Pakistan and one scientist from Egypt were trained in sequencing and phylogenetic analysis of avian influenza viruses, real-time RT-PCR and virus isolation through individualized two week training programs.

  • Two scientists from Georgia, one scientist from Afghanistan, two scientists from Azerbaijan, one scientist from Russia, two scientists from Morocco, two scientists from Libya, two scientists from Mongolia, one scientist from Kazakhstan and two scientists from Ukraine were trained in sequencing and phylogenetic analysis of avian influenza viruses, real-time RT-PCR, HI assays and virus isolation through individualized two week training programs.

  • Three scientists from Pakistan were trained in sequencing and phylogenetic analysis, real-time RT-PCR and basic virological techniques for Newcastle disease and avian influenza viruses.

  • A three day short course on RNA extraction, RRT-PCR and troubleshooting was held and attended by 21 scientists from Afghanistan (1), Brazil (2), Kazakhstan (2), Kenya (3), Mexico (1), Nigeria (3), Pakistan (1), Palestine (1), Russia (1), Yemen (1), Turkey (2), Morocco (2) and Egypt (1).

  • As part of an OFFLU research project, five scientist from Egypt have participated in a 9 month project in avian influenza vaccine seed strain selection and included training in RNA extraction and sequencing of NS and M genes for ten 2008 Egyptian H5N1 high pathogenicity avian influenza viruses, and phylogenetic analysis; and vaccine production and vaccination, separation of oil emulsion vaccines, challenge studies, antisera production, HI and AGID antigen production, antigenic cartography, egg inoculation, tissue culture techniques, and molecular diagnostics (sample processing, RNA extraction, RRT-PCR reactions and results interpretation, primer design) and introduction to the reverse genetics systems for avian influenza virus production.

5. Organisation of scientific meetings on behalf of the OIE

  • Organized the 7th International Symposium on Avian Influenza, April 5-8, 2009, University of Georgia, Center for Continuing Education, Athens, Georgia, USA. The symposium had 411 registered participants from 54 countries. The program included 79 oral and 122 poster presentations. A special half-day session dedicated to OFFLU was included. Co-chairs were David E. Swayne, Ian H. Brown and David Stallknecht.

6. Coordination of scientific and technical studies in collaboration with other laboratories or organisations

  • SEPRL has ongoing collaborations with personnel from the University of Alaska and the Wildlife Conservation Society for the collection of swab samples from numerous wild bird species in North America, Asia and South America. These samples are processed for AIV detection by SEPRL and isolates are characterized by gene sequencing

  • SEPRL conducted Indonesia AI vaccine efficacy studies and constructed a reverse genetic low pathogenic H5N1 vaccine seed strain. This project was in collaboration with Ministry of Agriculture in Indonesia, AAHL (Australia), FAO (Indonesia and Rome), OIE (Paris), USDA/APHIS and USAID.

  • SEPRL conducted Egyptian AI vaccine efficacy studies and constructed reverse genetic low pathogenic H5N1 vaccine seed strains. This project was in collaboration with National Laboratory for Quality Production (Cairo, Egypt), Central Laboratory for Evaluation of Veterinary Biologicals (Cairo, Egypt), FAO (Cairo and Rome), and USAID.

7. Publication and dissemination of any information within the remit of the mandate given by the OIE that may be useful to Member Countries of the OIE

  • Presentations at International Conferences

Day, J.M., Determination of the turkey gut RNA virus metagenome, 16th World Veterinary Poultry Association Congress, Marrakesh, Morocco, November 8-12, 2009

Miller, P. J., Improved Newcastle Disease Vaccine Approaches Using Virus Strains Selected on Antigenic Composition, Precongress Cientifico Avicola, Investigacion Aplicada, S.A. (IASA)'s 9th Scientific Forum, Convencion Annual de Especialistas en Ciencias Avicolas de Mexico (ANECA), Acapulco, Mexico, August 13-17, 2009.

Pantin-Jackwood, M., Afonso C.L., Wasilenko J., Sarmento L., Kapczynski, D.R., Differences between Pekin and Muscovy ducks in response to vaccination against HPAI H5N1 virus, 5th Orthomyxovirus Research Conference 2009, Freiburg, Germany, September 9-12, 2009

Pantin-Jackwood, M., Swayne D., Suarez D., Spackman E., and Kapczynski D.R., Research Update on Avian Influenza Viruses and H1N1 Influenza Virus in Poultry, 44th U.S.-Japan Cooperative Program in Natural Resources of Animal and Avian Health Meeting, Tsukuba, Japan, November 30-December 5, 2009

Pantin-Jackwood, M., Afonso C., and Miller P., Newcastle Disease: New Challenges in Diagnostic and Vaccination. 44th U.S.-Japan Cooperative Program in Natural Resources of Animal and Avian Health Meeting, Tsukuba, Japan, November 30-December 5, 2009

Spackman, E., Fouchier, R., Swayne, D., Abbas, M., Smith, D., Sarmento, L., Rehmani, R., Naeem, K., Ahmed, Z. and Hameed, A., Antigenic Cartographic Analysis of H7 Avian Influenza Viruses With Chicken Serum, 7th Avian Influenza Symposium, Athens, GA April 6th, 2009.

Spatz, S.J., Gimeno I. M. and Heidari, M., The Genomes of Marek’s Disease Virus exist as Quasispecies at Defined Intervals during Serial Passage-induced Attenuation, The 2009 International Herpesvirus Workshop, Ithaca, New York, USA, July 24-31, 2009.

Suarez, D.L., Control of Avian Influenza in the United States. Animal Health Workshop, Agriculture, Fisheries, and Conservation Department, Hong Kong November 24, 2009.

Suarez, D.L., Development of Novel Technologies To Improve Avian Influenza Vaccines for Poultry. 7th Avian Influenza Symposium, Athens, GA April 6th, 2009.

Swayne, D.E., Impact of Poultry Vaccines on Control of H5N1 High Pathogenicity Avian Influenza, XI International Symposium on Respiratory Viral Infections, Bangkok, Thailand, February 19 – 22, 2009

Swayne, D.E., Mechanisms of Transmission of H5N1 High Pathogenicity Avian Influenza Virus in Birds and Mammals, Pulawy Branch of Polish Society of Veterinary Sciences, Pulawy, Poland, June 1, 2009.

Swayne, D.E., 2009 Emergent H1N1 Influenza A Virus: Differential Molecular Diagnostic Test Development, and Infectivity and Transmission Studies in Poultry, and New Paramyxovirus from Falkland Island Penguins (APMV-10) or a Variant of APMV-8? 15th European Union Avian Influenza Reference Laboratory meeting, Pulawy, Poland, June 3-4, 2009.

Swayne, D.E., Mechanisms of Transmission of H5N1 High Pathogenicity Avian Influenza Virus in Birds and Mammals, Birdflu2009: Avian Influenza and Human Health Conference, St Hilda's College, Oxford, United Kingdom, 9-10 September, 2009.

Swayne, D.E., Progress in Avian Influenza Control with Special Reference to Vaccine Development, and Avian Influenza Virus, One Problem, Multiple Technological Solutions, 16th World Veterinary Poultry Congress, Marrekesh, Morocco, November 8-12, 2009

Zsak, L., The Genome of Chicken Parvovirus, 8th International Congress of Veterinary Virology, Budapest, Hungary, August 21-27, 2009

Zsak, L., Comparative Sequence Analysis of Chicken and Turkey Parvoviruses, XVIth World Veterinary Poultry Association Congress, Marrakesh, Morocco, November 6-13, 2009

Yu, Q., Generation of recombinant avian metapneumovirus subgroup C (aMPV-C) viruses containing different length of the G gene. The 6th International Symposium on Avian Corona- and Pneumoviruses and Complicating Pathogens, Rauischholzhausen, Germany, June 14-17, 2009


  • Scientific Publications

Adcock, N.J., Rice, E.W., Sivaganesan, M., Brown, J.D., Stallknecht, D.E., Swayne, D.E. 2009. The use of bacteriophages of the family Cystoviridae as surrogates for H5N1 highly pathogenic avian influenza viruses in persistence and inactivation studies. Journal of Environmental Science and Health, Part A, 44(13):1362-1366.

Aiki-Raji, C.O., Aguilar, P.V., Kwon, Y., Goetz, S.K., Suarez, D.L., Jethra, A.I., Nash, O., Adeyefa, C.O., Adu, F.D., Swayne, D.E., Basler, C.F. 2008. Phylogenetics and pathogenesis of early avian influenza viruses (H5N2), Nigeria. Emerging Infectious Diseases. 14(11):1753-1755.

Bogoyavlenskiy, A., Berezin, V.E., Prilipov, A.G., Usachev, E.V., Lyapina, O.V., Korotetskiy, I.S., Zaitceva, I.A., Asanova, S.E., Kydyrmanov, A., Daulbaeva, K., Shakhvorostova, L.M., Sayatov, M.K., King, D.J. 2009. Newcastle disease outbreaks in Kazakhstan and Kyrgystan during 1998, 2000, 2001, 2003, 2004 and 2005 were caused by viruses of the genotypes VIIb and VIId. Virus Genes. 39:94-101.
Brown, J.D., Stallknecht, D.E., Swayne, D.E. 2009. Infectious and lethal doses of H5N1 highly pathogenic avian influenza virus for house sparrows (Passer domesticus) and rock pigeons (Columbia livia). Journal of Veterinary Diagnostic Investigation. 21:437-445.

Brown, J.D., Stallknecht, D.E., Berghaus, R.D., Leathers, V., Kistler, W., Costa, T., Luttrell, P., Yabsley, M., Swayne, D.E. 2009. Evaluation of a commercial blocking ELISA as a serologic assay for avian influenza virus in experimentally infected wild avian species. Clinical and Vaccine Immunology, 16(6):824-829.

Chakrabarti, S., King, D.J., Cardona, C.J., Gerry, A.C. 2008. Persistence of exotic Newcastle disease virus (ENDV) in laboratory infected Musca domestica and Fannia canicularis. Avian Diseases. 52:375-379.

Day, J.M. 2009. The diversity of the orthoreoviruses: molecular taxonomy and phylogentic divides. Infection, Genetics and Evolution. 9:390-400.

Day, J.M., Spackman, E., Pantin Jackwood, M.J. 2008. Turkey-origin reovirus induced immune dysfunction in specific-pathogen free and commercial turkey poults. Avian Diseases. 52:387-391.

Davis, L.M., Spackman, E. 2008. Do crocodilians get the flu? Looking for influenza A in captive crocodilians. Journal of Experimental Zoology. 309A:1-10.

Dong, J., Matsuoka, Y., Maines, T.R., Swayne, D.E., O’Neill, E., Davis, C.T., Van-Hoven, N., Balish, A., Yu, H.J., Katz, J.M., Klimov, A., Cox, N., Li, D.X., Wang, Y., Guo, Y.J., Yang, W.Z., Donis, R.O., Shu, Y.L. 2009. Development of a new candidate H5N1 avian influenza virus for pre-pandemic vaccine production. Influenza and Other Respiratory Viruses 3(6), 287–295.

Faust, C., Stallknecht, D.E., Swayne, D.E., Brown, J. 2009. Filter-Feeding bivalves can remove avian influenza viruses from water and reduce infectivity. Proceedings of the Royal Society B: Biological Sciences 276:3727-3735.

Kapczynski, D.R., Gonder, E., Liljebjelke, K.A., Lippert, R., Petkov, D., Tilley, B. 2009. Vaccine induced protection from egg production losses in commercial turkey breeder hens following experimental challenge with a triple reassortant H3N2 avian influenza virus. Avian Diseases. 53:7-15.

Kim, L.M., King, D.J., Guzman, H., Tesh, R.B., Bueno, R., Dennett, J.A., Afonso, C.L. 2008. Biological and phylogenetic characterization of pigeon paramyxovirus serotype-1 circulating in North American pigeons and doves. Journal of Clinical Microbiology. 46(10):3303-3310.

Kwon, Y.K., Lipatov, A.S., Swayne, D.E. 2009. Bronchointerstitial pneumonia in guinea pigs following inoculation with H5N1 high pathogenicity avian influenza virus. Veterinary Pathology 46:138-141.

Layton, S.L., Kapczynski, D.R., Cox, M.M., Higgins, S., Higgins, J., Wolfenden, A.D., Liljebjelke, K.A., Bottje, W.G., Swayne, D., Berghman, L.R., Kwon, Y.M., Hargis, B.M., Cole. K. 2009. Recombinant salmonella expressing M2e and CD154 increase protection against avian influenza in chickens, Poultry Science 88(11):2244-52.

Lipatov, A.S., Kwon, Y.K., Pantin-Jackwood, M., Swayne, D.E. 2009. Pathogenesis of H5N1 influenza virus infections in mice and ferret models differ between respiratory and digestive system exposure. Journal of Infectious Diseases 199(1 March):717-725.

Matsuoka, Y., Swayne, D.E., Rameix-Welti, M.A., Naffakh, N., Warnes, C., Altholtz, M., Donis, R., Subbarao, K. 2009. Neuraminidase stalk length and additional glycosylation of the hemagglutinin of H5N1 viruses influence the virulence of H5N1 viruses for mice. Journal of Virology 83(9):4704-4708.

Miller, P.J., Estevez, C., Yu, Q., Suarez, D.L., King, D.J. 2009. Comparison of viral shedding following vaccination with inactivated and live Newcastle disease vaccines formulated with wild-type and recombinant viruses. Avian Diseases. 53:39-49.

Miller, P.J., Kim, L.M., Afonso, C.L., Ip, H.S. 2009. Evolutionary dynamics of Newcastle disease virus. Virology. 391:64-72.


Pantin Jackwood, M.J., Rosenberger, S.S. 2008. Antigen detection systems. In: Dufour-Zavala, L., Swayne, D.E., Glisson, J.R., Pearson, J.E., Reed, W.M., Jackwood, M.J., Woolcock, P.R., editors. Isolation, Identification, and Characterization of Avian Pathogens. Fifth edition. Athens, GA: American Association of Avian Pathologists Inc. p. 233-240.

Pantin-Jackwood, M.J., Swayne, D.E. 2009. Pathogenesis and pathobiology of avian influenza virus infection in birds. OIE Scientific and Technical Reviews 28(1):113-136.

Perozo, F., Villegas, P., Afonso, C.L. 2008. Genomic comparison of the complete coding and intergenic regions of the VG/GA Newcastle disease virus and its respirotropic clone 5. Virus Genes. 37(2):161-167.
Perozo, F., Merino, R., Afonso, C.L., Villegas, P., Calderon, N. 2008. Biological and phylogenic characterization of virulent Newcastle disease virus circulating in Mexico. Avian Diseases. 52(3):472-479.

Peterson, A.T., Bush, S.E., Spackman, E., Swayne, D.E. 2008. Influenza A virus infections in landbirds, People’s Republic of China. Emerging Infectious Diseases. 14(10):1644-1646.

Pillai, S.S., Pantin Jackwood, M.J., Jadhao, S.J., Suarez, D.L., Wang, L., Yassine, Y., Saif, Y., Lee, C. 2009. Pathobiology of triple reassortant H3N2 influenza viruses in breeder turkeys and its potential implication for vaccine studies in turkeys. Vaccine. 27:819-824.

Sarmento, L., Afonso, C.L., Estevez, C., Wasilenko, J.L., Pantin Jackwood, M.J. 2008. Differential host gene expression in cells infected with highly pathogenic H5N1 avian influenza viruses. Veterinary Immunology and Immunopathology. 125:291-302.

Spackman, E., Ip, H.S., Suarez, D.L., Slemons, R., Stallknecht, D. 2008. Analytical validation of a real-time reverse transcription polymerase chain reaction test for Pan-American lineage H7 subtype avian influenza viruses. Journal of Veterinary Diagnostic Investigation. 20:612-616.

Spackman, E., Pantin Jackwood, M.J., Swayne, D.E., Suarez, D.L. 2009. An evaluation of avian influenza diagnostic methods with domestic duck specimens. Avian Diseases. 53(2):276-280.

Spackman, E., Swayne, D.E., Suarez, D.L., Das, A., Sodnomdarjaa, R., Sugar, S., Orgil, D., Senne, D., Lubroth, J., Sims. L. Joly, D.O., Gilbert, M., Zahler, P.I., Karesh, W.B., Cardona, C. 2009. Characterization of low pathogenicity avian influenza viruses isolated from wild birds in Mongolia 2005 through 2007. Virology Journal 6:190 doi:10.1186/1743-422X-6-190.

Suguitan, A.L., Marino, M.P., Desai, P.D., Chen, L.M., Matsuoka, Y., Donis, R.O., Jin, H., Swayne, D.E., Kimble, G., Subbarao, K. 2009. The influence of the multi-basic cleavage site of the H5 hemagglutinin on the attenuation, immunogenicity and efficacy of a live attenuated influenza A H5N1 cold-adapted vaccine virus. Virology 395(2):280-288.

Swayne, D.E. 2009. Avian influenza vaccines and therapies for poultry. Comparative Immunology, Microbiology and Infectious Diseases 32:351-363.

Swayne, D.E., Kapczynski, D.R. 2008. Strategies and challenges for eliciting immunity against avian influenza virus in birds. Immunological Reviews. 225:314-331.

Swayne, D.E., Slemons, R.D. 2008. Using mean infectious dose of wild duck-and poultry-origin high and low pathogenicity avian influenza viruses as one measure of infectivity and adaptation to poultry. Avian Diseases. 52:455-460.

Swayne, D.E., Pantin-Jackwood, M., Kapczynski, D., Spackman, E., Suarez, D.L. 2009. Limited susceptibility of Japanese quail (Coturnix japonica) and resistance of other poultry species to the 2009 novel H1N1 influenza A virus. Emerging Infectious Diseases 15(12):2061-2063.

Szretter, K.J., Gangappa1, S., Zeng, H., Chen, H., Matsuoka, Y., Sambhara, S., Tumpey, T.M., Swayne, D.E., Katz, J.M. 2009. Early Control of H5N1 Influenza Virus Replication by the Type I Interferon Response in Mice. Journal of Virology 83(11):5825-5834.

Thomas, C., Manin, T.B., Andriyasov, A.V., Swayne, D.E. 2008. Limited susceptibility and lack of systemic infection by an H3N2 swine influenza virus in intranasally inoculated chickens. Avian Diseases. 52(3):498-501.

Thomas, C, Swayne, D.E. 2009. Thermal inactivation of H5N2 high pathogenicity avian influenza virus in dried egg white with 7.5% moisture. Journal of Food Protection 72(9):1997-2000.

Van Hoeven, N., Belser, J.A., Szretter, K.J., Staeheli, P., Swayne, D.E., Katz, J.M., Tumpey, T.M. 2009. Pathogenesis of the 1918 pandemic and H5N1 influenza virus infection in a guinea pig model: The antiviral potential of exogenous alpha-interferon to reduce virus shedding. Journal of Virology 83(7):2851-2861.

Velayudhan, B. T., Yu, Q., Nagaraja, K. V., Estevez, C. N., Halvorson, D. A. 2008. Glycoprotein gene truncation in avian metapneumovirus subtype C isolates from the United States. Virus Genes. 37(2):266-72.

Volkening, J.D., Spatz, S.J. 2009. Purification of DNA from the cell-associated herpesvirus Marek's disease virus for 454 pyrosequencing using micrococcal nuclease digestion and polyethylene glycol precipitation. Journal of Virological Methods. 157(1):55-61.

Wasilenko, J.L., Sarmento, L., Pantin Jackwood, M.J. 2009. A single substitution in amino acid 184 of the NP protein alters the replication and pathogenicity of H5N1 avian influenza viruses in chickens. Archives of Virology. 154:969-979.

Zsak, L., Strother, K.O., Day, J.M. 2009. Development of a polymerase chain reaction procedure for detection of chicken and turkey parvoviruses. Avian Diseases. 53:83-88.

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Annual reports of OIE Reference Laboratories and Collaborating Centres, 2009


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