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Preprint: Association of Poultry Vaccination with the Interspecies Transmission and Molecular Evolution of H5 Subtype Avian Influenza Virus

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  • Preprint: Association of Poultry Vaccination with the Interspecies Transmission and Molecular Evolution of H5 Subtype Avian Influenza Virus

    Preprint: Association of Poultry Vaccination with the Interspecies Transmission and Molecular Evolution of H5 Subtype Avian Influenza Virus


    Until a few years ago - with the notable exceptions of China, Indonesia, Egypt, Vietnam and Hong Kong - most of the world's nations avoided the use of poultry avian influenza vaccinations in favor of the long-standing OIE recommendation to `stamp out' HPAI infections by culling infected flocks.

    That policy advised that vaccines should only be used as a temporary measure, stating that: `Any vaccination campaign must include an exit strategy” i.e. a return to classic disease control measures.'

    But as the HPAI H5 threat has spread globally, and the economic losses have continued to mount, some countries have expressed interest in using poultry vaccines to protect their flocks. A few countries, including France and Mexico, have already begun limited field use, while others (including the United States) are still evaluating the benefits and risks.

    Although poultry vaccines can help protect flocks against HPAI H5, they must be properly applied and frequently updated, and even then they don't always offer complete protection.

    Meaning that some birds may still become infected, but due to their vaccination status, they may not show signs of illness. This, many fear, could increase the chances of the virus spreading (to other birds, or potentially, even humans).

    As we've seen many times in the past, the track record of using poultry vaccines to control avian influenza over the years has been mixed.
    • And a 2012 study (see Egypt: A Paltry Poultry Vaccine), examined the effectiveness of six commercially available H5 poultry vaccines used in Egypt and found only one actually appeared to offer protection.

    While there is clear evidence of short-term benefits from using poultry vaccines (fewer birds are lost to the disease and/or culling), there are also potential long-term risks. We've examined some of these concerns over the years, including:
    Today we've got another take, in the form of a preprint from researchers at Oxford, Cambridge, and Beijing's Normal University. While not drawing any hard conclusions, these researchers report that the impact of vaccination on poultry - and the movement of AIV lineages between wild birds and poultry - are complex and not fully understood.

    They also note that regions that have heavily employed poultry vaccines have also seen more rapid evolution of avian flu viruses.

    I've only reproduced the abstract - and a snippet from the conclusion - so follow the link to read the preprint in its entirety. I'll have a brief postscript after the break.

    Association of poultry vaccination with the interspecies transmission and molecular evolution of H5 subtype avian influenza virus

    Bingying Li, Jayna Raghwani, Sarah C Hill, Sarah Francois, Noemie Lefrancq, Yilin Liang, Zengmiao Wang, Lu Dong, View ORCID ProfilePhilippe Lemey, Oliver G. Pybus, Huaiyu Tian

    Preview PDF


    The effectiveness of vaccinating poultry in preventing the transmission of highly pathogenic avian influenza viruses (AIVs) has been questioned for years and its impact on wild birds is uncertain (1-3). Here we reconstruct movements of H5 subtype AIV lineages among vaccinated poultry, unvaccinated poultry, and wild birds, worldwide from 1996 to 2023.
    We find that lineage transitions among host types are lagged and that movements from wild birds to unvaccinated poultry were more frequent than those from wild birds to vaccinated poultry. However, we also find that the HA gene of the AIV lineage that circulated predominately among Chinese poultry with high vaccination coverage underwent faster evolution and greater nonsynonymous divergence than other lineages.

    Further, this Chinese poultry lineage contained more codons inferred to be under positive selection, including at known antigenic sites, and its rates of nonsynonymous divergence and adaptative fixation increased after mass poultry vaccination began.

    Our results indicate that the epidemiological, ecological and evolutionary consequences of widespread AIV vaccination in poultry may be linked in complex ways, and that much work is needed to better understand how such interventions may affect AIV transmission to, within and from wild birds.


    In conclusion, we find that vaccination in Asian poultry likely reduced the inter species transmission of these viruses. H5 AIV in Chinese poultry, which are highly vaccinated, show evidence of greater HA gene molecular evolution and adaptation after the introduction of vaccination.

    Such circumstances may have increased the probability that birds susceptible to AIV belong to wild species at the interface between wild birds and poultry, leading to shifts in selection pressure on the virus. As avian influenza continues to pose significant challenges to wild and domestic animal health, our research can help inform the development of preventive measures against AIV, such as global vaccination policies.

    (Continue . . .)

    Many people understandably see poultry vaccines as the only practical tool to limit the economic losses from the global spread of HPAI, while others look back at the last 20+ years and wonder how much of our current avian flu problem has been exacerbated by suboptimal vaccine campaigns of the past.

    While it is seems reasonable that a properly applied, well-matched, and frequently updated poultry vaccination program can be an effective strategy against avian flu - at least in captive birds - history has shown those standards to be difficult to maintain.

    As more countries decide to embrace AI poultry vaccination (as I suspect many will), the need for a better understanding of its impact - and potential risks - only increases.

    For now, decisions appear to be driven more by events and biases, than a wealth of scientific evidence.

    All medical discussions are for educational purposes. I am not a doctor, just a retired paramedic. Nothing I post should be construed as specific medical advice. If you have a medical problem, see your physician.