Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.

In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans.

Evaluation of three commercially available influenza A type-specific blocking enzyme-linked immunosorbent assays for seroepidemiological studies of influenza A virus infection in pigs.

The reverse zoonotic transmission of the pandemic H1N1 2009 influenza virus to swine necessitates enhanced surveillance of swine for influenza virus infection. Using a well-characterized panel of naturally infected swine sera, we evaluated and optimized the performances of three commercially available competitive enzyme-linked immunosorbent assays (ELISAs), namely, the IDEXX Influenza A Ab test, IDEXX AI MultiS-Screen Ab test, and IDVet ID Screen influenza A antibody competition ELISA, for detecting influenza A virus-reactive antibodies in swine. Receiver operating characteristic (ROC) analysis suggests that adjustment of the manufacturer-recommended cutoff values optimizes the sensitivity and specificity of these assays, making them applicable for seroepidemiology studies of swine influenza. Using such optimized cutoff levels, the sensitivity and specificity of the IDEXX Influenza A Ab test were 86% and 89%, respectively; those for the IDEXX AI MultiS-Screen Ab test were 91% and 87%, respectively; and those for the IDVet ID Screen influenza A test were 95% and 79%, respectively.

Evaluation of a Subunit H5 Vaccine and an Inactivated H5N2 Avian Influenza Marker Vaccine in Ducks Challenged with Vietnamese H5N1 Highly Pathogenic Avian Influenza Virus.

The protective efficacy of a subunit avian influenza virus H5 vaccine based on recombinant baculovirus expressed H5 haemagglutinin antigen and an inactivated H5N2 avian influenza vaccine combined with a marker antigen (tetanus toxoid) was compared with commercially available inactivated H5N2 avian influenza vaccine in young ducks. Antibody responses, morbidity, mortality, and virus shedding were evaluated after challenge with a Vietnamese clade 1 H5N1 HPAI virus [A/VN/1203/04 (H5N1)] that was known to cause a high mortality rate in ducks. All three vaccines, administered with water-in-oil adjuvant, provided significant protection and dramatically reduced the duration and titer of virus shedding in the vaccinated challenged ducks compared with unvaccinated controls. The H5 subunit vaccine was shown to provide equivalent protection to the other two vaccines despite the H5 antibody responses in subunit vaccinated ducks being significantly lower prior to challenge. Ducks vaccinated with the H5N2 marker vaccine consistently produced antitetanus toxoid antibody. The two novel vaccines have attributes that would enhance H5N1 avian influenza surveillance and control by vaccination in small scale and village poultry systems.

Identifying the species-origin of faecal droppings used for avian influenza virus surveillance in wild-birds.

BACKGROUND: Avian influenza virus (AIV) surveillance in birds is important for public health. Faecal droppings from wild-birds are more readily available for such studies, but the inability to identify the species-origin of faecal samples limits their value. OBJECTIVES: To develop, optimise, and field-test a method to simultaneously detect AIV and identify the species-origin from faecal samples. STUDY DESIGN: Analytical sensitivity of the species-identification RT-PCR was assessed on serial dilutions of faecal droppings. Overall sensitivity of the methods for species-identification and AIV detection was assessed on 92 faecal and cloacal samples collected from wildlife, poultry markets, and experimentally H5N1-infected birds. RESULTS: All 92 samples were correctly identified to 24 different species, with a detection limit of 2.8mug of faecal material. All 20 specimens previously shown by virus culture to be positive for influenza virus were correctly identified by RT-PCR for influenza A using the same nucleic-acid extracts used for species-identification. CONCLUSION: We have optimised and evaluated a method for identifying the species of origin and detecting AIV from bird faecal droppings that can be applied to routine surveillance of influenza viruses in wild-birds.