Time to put farming in the dock re h5n1 spread

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    Enough already of the wild birds witchhunt! When even experts are reduced to looking for an “avian version of the Stealth Bomber”, it’s clear there should be more focus on another potential culprit for harbouring and spreading H5N1. Farming, for instance.

    Suppose we could interrogate farming, what might we ask. Let me count the questions. (Others may think of more.)

    Six main questions here:

    1) Why does the poultry industry continue to spawn highly pathogenic avian influenzas?
    2) What role might poultry vaccines play in sustaining and spreading H5N1?
    3) What roles might transport of poultry and other captive birds, and poultry equipment, play in spreading H5N1?
    4) Does chicken manure – especially chicken manure used in fishponds – play a role in spreading H5N1 beyond poultry farms?
    5) Do officials tend to play down or not report H5N1 outbreaks resulting from poultry industry, but readily blame wild birds?
    6) Is there an FAO report into the role of farming in the recent spread of H5N1; and if not, why not?

    1) We’ve known for years that poultry farming can spawn highly pathogenic avian influenzas. Strains that are of little or no consequence in wild birds can evolve to become highly lethal to poultry, and to other species – rarely including humans.

    Why, then, do we continue to see such virulent strains evolving in poultry farms; why aren’t we seeing efforts to transform poultry farming techniques? (Seems it’s too late to guard against wild viruses entering poultry)

    2) Until H5N1, eradication of infected flocks has been the main means of eradicating HPAI; but with H5N1, poultry vaccines are being widely used. What roles – if any – are poultry vaccines playing in sustaining and spreading the nasty H5N1 variant (genotype Z and near allies)?

    Even with good vaccines, infected poultry can retain H5N1, but at levels below those needed for transmission (presentation by Robert Webster). With substandard vaccines, poultry may not show symptoms, but may harbour H5N1 at transmissible levels, thus promoting spread in live markets.

    To what extent has the use of vaccines enabled the “Z” H5N1 to survive for nearly a decade – perhaps mostly as a “silent epidemic” (New Scientist)? Does H5N1 survive like a peat fire – mostly almost unseen, but flaring up when into susceptible populations, whether unvaccinated poultry or wild birds?

    Where are vaccines used, both iegally and ilegally [eg poultry vaccines have been smuggled into Thailand]; and to what extent are substandard vaccines used?
    [In China, vaccination reportedly cheaper than using antibiotics, so surely tempting for at least large-scale farmers elsewhere]

    Correct use of poultry vaccines should include deployment of sentinel birds – non-vaccinated poultry, in case H5N1 is indeed present (and even spreading). Are these indeed always used in conjunction with vaccines – or are there “accidental sentinels” – non-vaccinated poultry, wild birds.

    3) Previous studies have shown that avian influenzas can be readily transported within the poultry industry (an FAO document suggested that once bird flu enters poultry, the mode of transportation shifts “from the flyways to the highways and byways”) What movements of poultry (and captive birds that may be directly or indirectly infected by poultry) may be involved in spread of H5N1?

    What is known of legal movements: how extensive, what are the key routes?

    What of illegal poultry/captive bird movements? With Italy recently seizing a consignment of smuggled Chinese poultry including 36,000 duck eggs, these may be extensive. How easy is it to take, say, eggs across international borders?

    What, too, of special cases such as fighting cocks, implicated as partial culprits of h5n1 bird flu spread in Thailand?
    To what extent are vaccinated poultry (including those given substandard vaccines) traded in markets, moved along legal and illegal trade routes?

    As well as eggs and birds, even poultry equipment such as crates contaminanted with droppings can spread avian flu. How extensively are these moved?

    4) Is there a link between use of chicken manure, including in aquaculture, and spread of h5n1 beyond poultry farms?

    How widely used is chicken manure as fertilizer/feed for aquaculture? After recent news report told of chicken manure being dumped by the truckload in a lake in Vietnam (at least 100 tonnes of chicken excrement a day), to increase fish production, cursory enquiries revealed it is also used in Yugoslavia,

    Might H5N1 infected chicken manure be the cause of the deaths of mute swans in Croatia, and perhaps Romania?
    In Croatia, swans that were evidently healthy during a prior stopove in Hungary died after landing on fishponds.
    In Romania, a BBC news report included, “like the fish farm behind Maliuc, where 86 dead swans have been found in the last week alone.”

    5) Is there a strong tendency for local and even national officials to play down or even fail to report outbreaks in and resulting from poultry farms – but a willingness to quickly blame wild birds (with or without any actual evidence)?
    If so, does this significantly distort the picture regarding the true major culprit for sustaining and spreading H5N1 (genotype Z)?

    6) FAO has produced a report into the apparent role of wild birds in the spread of H5N1. Why – to my knowledge – is there no equivalent FAO report on the role of farming?

    Post edited by: martin, at: 2005/11/12 03:09



    Try the following document for answers to a number of your questions.


    This FAO document clearly states that the main risk arises from domestic poultry with special emphasis on poorly managed live bird markets that can act as “reservoirs” of infection, non-biosecure poultry farming (i.e. smallholder and village poultry in much of Aisa) and domestic ducks that can be infecte,d not show signs of disease and excrete virus for a week or two.

    The situation remains that most of the spread of H5N1 HPAI has been associated with the poultry industry especially in places where the virus is endemic.

    Wild birds have almost certainly been involved in some of the long distance spread of virus recently (genetic evidence supports this as well), but that once established in a region, spread via poultry or items used with poultry will occur. Iif the disease is not rapidly controlled this becomes the main route of transmission.

    You are right to point out that vaccination should be accompanied by appropriate surveillance. However it is also important to recognise that vaccination was used as a response to endemic infection – it was not the initial cause. Vaccination was used in China, Viet Nam and Indonesia only after it was apparent that the disease was out of control and widespread – and the methods that work when a disease is identified early and in a small area, such as depopulation, were no longer feasible.

    To eliminate the disease in places such as Viet Nam it is likely that virtually all of the small holder and live poultry marketing sector would have to be shut down for a considerable period of time, which would affect the livelihood of some 13 million poor households and many others involved in this trade. Vaccination is being used to reduce the levels of virus excretion as a prelude to implementation of changes to the way that poultry are raised.

    Put simply, the disease cannot be eradicated from Asia unless or until there are major changes in the way that poultry are reared (or the virus changes to something more benign). The socio-economic implications of this are enormous and vaccination will be required as one of the control measures for some time.

    I can assure you that without vaccination the situation in Asia would be much worse than it is today.

    Les Sims


    Hi Les:

    Thank you for another informed post.

    Haven’t had time yet to read the FAO document (60 plus pages I noticed!).

    I’d thought China was using vaccine against H5N1 before use really sanctioned by FAO – and FAO had been leery re poultry flu vaccines (broadly, emergency use only).
    “The current virulent strain of H5N1 emerged among vaccinated poultry in China.” said New Scientist

    Now, seems emergency is throughout China’s poultry industry.

    China’s Ministry of Agriculture said in Beijing on Monday that the country now produces more than 100 million doses of bird flu vaccine every day, which can meet the demand in major areas for epidemic prevention and control.

    A press release on the ministry’s website says the ministry has enhanced the research, manufacture and quality supervision of bird flu vaccine to guarantee supply.

    The ministry also enhanced crackdown upon counterfeit vaccines and issued 8.2 million fake-proof labels for this purpose.


    Might a virus strain that can thrive in vaccinated poultry also evolve to high virulence, compounding problems with H5N1?

    Not that always need a virus strain that thrives with good vaccine, when there can be problems with counterfeits, and other bad vaccines in China. In 12 November South China Morning Post, a news item started:

    Drugs salesmen who smuggled out an unlicensed
    vaccine still being tested and sold it on the market have been blamed
    for the massive outbreak of bird flu in Liaoning province.

    Says many farmers in Heishan county had used a vaccine produced by
    Inner Mongolia Jinguu Group, and this offered little protection against
    the deadly disease. The vaccine was intended for testing, but not
    supposed to be sold.

    In a Nature commentary, Robert Webster and Diane Hulse argue for use of good poultry vaccines coupled with sentinel birds. But using vaccines isn’t straightforward, partly as also get sub-standard vaccines:

    The few comparative tests that have been done on agricultural vaccines from different suppliers show that some are good and some are bad. Bad vaccines prevent the symptoms of disease but not virus excretion, which can lead to later infection. One of the many arguments against the use of agricultural vaccines is that they promote the selection of mutations in the circulating virus, perpetuating the risk of infection either in the original species or in others.

    Controlling avian flu at the source

    As well as China, Indonesia has adopted poultry vaccines, yet:
    Indonesia says some poultry vaccine below standard

    Vietnam in U-turn over bird flu vaccination is a New Scientist news item from May – about Vietnam about to start large-scale testing of poultry flu vaccines.

    This article notes that Thailand allows vaccination only for fighting cocks, and free range ducks and chickens. Yet, I’ve seen reports of poultry vaccines smuggled into Thailand:
    Thailand finds 2 million doses of bird flu vaccine smuggled in (26 Feb 2004 report)

    So, it now seems you’re damned if you vaccinate, damned if you don’t.

    With today’s poultry farms evidently serving as “disease factories” (as termed by science writer Wendy Orent) – where Paul Ewald’s theory re evolutionary biology predicts virulent strains of flu will evolve [and can persist while very sick birds can readily transmit disease], it seems the nasty H5N1 variant will remain with us.
    Halting vaccination, coupled with fully effective culling (yes, this failed in Vietnam, so hardly hopeful) just might prove a short, extremely sharp shock that could eradicate it – like Hong Kong in 97, but on a massive scale.

    Otherwise, need radical transformation of poultry farming – so very sick birds can no longer readily transmit H5N1 and other virulent flus. Something more like wild situation, where dead ducks don’t fly.

    A shocking notion, now people hooked on apparently cheap chicken.
    Yet Prof Peter Singer notes that we’re seeing something of the true costs of our chicken farms, in
    `Factory farming’ is unnatural, unsustainable and dangerous

    Post edited by: martin, at: 2005/12/11 00:55



    I should have added in my previous post that the use of substandard vaccine is to be deplored and that one of the reasons for doing post-vaccination surveillance is to ensure that the vaccine being used is stimulating the immune system of vaccinated poultry.

    However, if a chicken with poor immunity (i.e. one vaccinated with a sub-standard vaccine) is exposed to a current Asian H5N1 virus it is extremely unlikely to become a carrier – instead it will almost certainly die (as occurred with the poultry given poor quality vaccine in Liaoning Province). Poor quality vaccines may give farmers a false sense of security but these poorly protected flocks shouldn’t spread any more virus than fully susceptible non-vaccinated flocks exposed to a similar virus.

    There has been a major shift in thinking on use of vaccines for AI recently. Until the Hong Kong experience in 2002-03 (when it was apparent that the virus was endemic in the region and repeated culling was not sustainable) no one had really tried systematic vaccination against highly pathogenic avian influenza. It worked.

    The earlier policy on vaccination from international authorities were based on previous situations where the disease was newly diagnosed and recently introduced, not a situation where the virus was endemic.

    On Peter Singer’s article, it is worth noting that the vast majority of cases of HPAI now are in the backyard and scavenging/free range sector not the large “industrial” farms. In fact well managed large farms pose a much lower risk than the non-biosecure backyard farms because they can practice good biosecurity.

    Groups and indviduals who oppose industrial farming are using the current outbreaks of avian influenza to discredit this type of farming. I will not go into the merits or otherwise of their case re intensive farming but using avian influenza to attack this practice is lousy science and opportunisitic.

    Les Sims


    Thanks again, Les

    As noted in a post above, Webster says that with substandard vaccines, poultry may not show symptoms, but may harbour H5N1 at transmissible levels, thus promoting spread in live markets – ie not necessarily dying as you suggest.

    Report in today’s S China Morning Post on a woman who died of H5N1 in China says bird flu wasn’t noticed in her village; Guan Yi suggests fake vaccines – widely used in China – maybe to blame, with chickens apparently ok but having H5N1 at levels high enough to lead to transmission.

    So, I still wonder about substandard vaccines.
    Find it hard to see how else this h5n1 strain persists, like peat fire: nothing happens much of the time, then it flares up, maybe in widely separated locales.
    If there were only properly vaccinated flocks, and non-vaccinated ones, shouldn’t we see none in vaccinated flocks and no transmission from them; and non-stop succession of outbreaks/epidemic where it persists elsewhere?

    Interesting re large farms having less HPAI. Sick chickens noticed and removed before any transmission possible – both from existing, and potentially evolving HPAI?


    Post edited by: martin, at: 2005/11/18 07:15


    Dear Martin,

    The disease has persisted in Viet Nam since mid 2003 without the use of vaccination (only just being implemented) indicating that vaccination is not a prerequisite for persistence.

    In China and Indonesia vaccination coverage has not been 100% but in places where coverage is good, such as the flocks supplying Hong Kong (which also practice good biosecurity) the virus does not occur.

    Part of the ebb and flow in disease levels results from culling/control activities(which dampens down infection) and also from the fact that flocks with this disease may experience close to 100% mortality rates. This reduces the number of susceptible poultry in an area. However these gains are short lived if the virus is circulating elsewhere and then returns once new susceptible birds are being reared.

    Domestic ducks almost certainly play a role in persistence of H5N1 viruses as do poorly run live bird markets where virus can persist.

    Weather conditions help in that the virus survives longer in the colder months and there is also increased movement of poultry for the major Chinese/Asian festivals in the winter.

    Definite seasonal patterns occur with other diseases, including influenza in humans in which there is low level infection that flares up periodically.

    I will follow up on the comments you cite from GuanY i and RobWebster – I will try to locate the data they have to back up their claims.


    Les Sims


    Dear Les:

    Thank you again.

    I forgot about domestic ducks when making the post; even here, some H5N1 can be lethal, but also know of sometimes infecting without symptoms.

    The comment on bad vaccines by Robert Webster was in a presentation/document, titled Research Issues in Animal Surveillance and Pandemic Planning.

    I’d thought of temperature for autumn, in China (read of cooler rainy seasons in more tropical places leading to H5N1 outbreaks perhaps increasing); not re the movements for festivals etc.


    A critical phase in the evolution of a bird flu pandemic could play out in China in the coming weeks, world bird flu expert Robert Webster said in Dunedin yesterday. … He said a campaign in China to vaccinate its 14 billion poultry flock could precipitate a worst case scenario. The doomsday scenario was that the Chinese would use a poor-quality vaccine that did nothing more than force the virus to mutate into something more lethal. "The international community has no way of knowing whether China will use a good one," Professor Webster said. "There is a big argument that they will simply help the virus to evolve to become a human pathogen."

    he also mentions h5n1 in flamingos in Kuwait, without noting that in one bird, and that may have been a captive bird. Nor with any apparent thought about how a flamingo could have been infected by H5N1 (if not in trade). Nor that migration is essentially over for this autumn – this isnn’t a step towards Africa as he suggests; nor that no wild waterbirds in Asia ex-Russia known to have the virus this autumn. Seems to me that Webster has made grand contributions to flu, but he’s currently a bit of a doomsayer, and quick to blame wild birds for spread with nary a shred of evidence. Though I don’t suppose that harms potential for obtaining research grants.

    Bird flu expert says virus entering critical phase


    Re virus persisting in Vietnam, even without vaccines:

    Would this have been case without China as northern neighbour? China seems key place of origin and reservoir for H5N1 (with vaccination used before thumbs-up from FAO).
    – H5N1(Z) in Vietnam surely came from China in first place; was it introduced only once, or continually?

    Do domestic ducks really make a suitable “trojan horse” reservoir, especially given research showing H5N1 can evolve to less virulent forms even in domestic ducks? That is, if they were the key reservoir for Vietnam, shouldn’t H5N1 in the country have shifted more strongly away from the genotype Z?

    What research has been done or is planned into movements of poultry and other captive birds between China and Vietnam; and indeed between these and other countries?


    Dear Martin,

    The origin of the Vietnamese strain of H5N1 remains unknown. The viruses in Thailand and Viet Nam form a separate “clade” within the Z genoytype. This clade persisted in Vietnam throughout 2003 to 2005. Genetically it remained remarkably homogenous through 2004 although some changes are now being seen in 2005 – some through mutation and others probably through newly introduced virus.

    Yes there is illegal movement of traffic of poultry from China into Viet Nam but this depends entirely on market conditiosn. With depressed markets in Viet Nam at present it is unlikely to be very lucrative. Nevertheless it is a potential source of new strains of virus.

    Z genotype H5N1 viruses first appeared in domestic ducks in 2001 and seem to have survived and thrived in domestic ducks since then. There is still much we don’t understand about why certain ducks die when exposed to these viruses and others don’t. However these viruses retain their high virulence when they are introduced to chickens.




    Hi Les:

    Thank you again for expert comment.

    I’d thought all the H5N1 forms causing trouble were broadly Z, and traced to Guangdong goose 1996 (then HK in 97).
    Clearly too simplistic – and maybe I should again read the genotype Z paper and some more, inc one I’ve some memories you co-authored.

    Google search, and about 88,700 results for “sims h5n1”; include (for others who read this thread):
    Origin and evolution of highly pathogenic H5N1 avian influenza in Asia (summary available to all)
    Reassortants of H5N1 Influenza Viruses Recently Isolated from Aquatic Poultry in Hong Kong SAR (summary)
    Avian Influenza in Hong Kong 1997–2002 (summary)
    An Update on Avian Influenza in Hong Kong 2002 (summary)


    Post edited by: martin, at: 2005/11/24 09:49


    You are right about all of these viruses being linked genetically to a goose virus from Guangdong in 1996 but there have been a number of jumps in the evolution of some strains for which the immediate precursor is not known and so we can only specualte on where they came from.

    The paper at the following website from Emerging Infectious Diseases provides more on the various ‘clades’



    Reuters has item on research, showing: Chicken vaccination can halt bird flu spread -study – protection best from two weeks after vaccine giving

    ProMed just cited news item, re poultry vaccine use in China

    ProMed, 26 Nov 05

    News item included:

    In a circular issued on Wednesday, the State Council, China’s cabinet, asked local governments to support and supervise designated vaccine producers, and strike hard at those manufacturing fakes.

    – suggesting there are significant problems with fakes. There’s list of main manufacturers, including one producing live vaccine – which apparently could lead to problems, as potential for the virus to replicate, become virulent.

    ProMed, 8 Mar 05

    ProMed also published lengthy review of use of poultry vaccines by David Swayne (poultry disease expert in US):

    ProMed, 7 Mar 05 – this seems based on experience in US, rather than in China where vaccines used for thousands of millions of poultry (surely leading to even greater difficulties in ensuring vaccines stored and administered properly – should be given individually), and there are problems with fakes. Even so, notes vaccination is not perfect, and need other measures at same time. Very difficult for China, I think – partly because of scale. Also, shortcuts often taken, to cut costs etc (eg spate of coal mine disasters: to too many officials, safety isn’t a major issue).


    Dear Martin,

    The comment in Promed about live virus vaccines was misplaced given the only live virus vaccine being produced is a fowl pox vaccine which acts as a vector for a small part of the influenza virus.

    This type of vaccine has been used widely elsewhere in the world and cannot revert to a virulent influenza strain.



    Item in yesterday’s South China Morning Post on vaccination of poultry in Guangdong province, quoting Yu Yedong, provincial animal inspection and quarantine inspection head.

    – 94% of Guangdong’s chicken population vaccinated; but shortage of vaccines meant some birds only given one shot, so may still be vulnerable to H5N1. (Best protection after booster shots given, 3-4 weeks after first ones given to 14-day old chicks.) Big farms all give two shots.
    A veterinary expert said two shots ok for chickens maturing in summer; three better for winter maturing birds.
    – Guangdong allocated several million doses of H5N1 and H5N2 vaccines a day.
    – Flocks for export to other than Hong Kong are not vaccinated, as some countries say that if detect antibodies they can’t tell if due to vaccines or they’re sick birds.
    “But Mr Yu said the administration’s own tests found that the virus was so potent that no chickens survived infection.”
    (Much as seems typical with infected wild birds; maybe

    Today’s SCMP has item with Guan Yi quoted as saying vaccinating China’s billions of poultry is impossible. Notes re no of months needed even if great many people (soldiers) vaccinating birds each day; and once done, have to start again as more chickens reared.

    Echoes concerns in recent news item quoting US poultry disease experts:
    China bird vaccination crews could spread virus
    Teams might carry germ farm to farm

    In this:

    China’s plans to vaccinate billions of chickens against avian flu could backfire and end up spreading the disease, poultry and vaccine experts warn.

    Vaccination teams can easily carry the virus from farm to farm on their shoes, clothes and equipment unless they change or sterilize them each time, the experts said. That could be particularly difficult in China, where the veterinary care system is underfinanced and millions of birds are kept in small flocks by families.

    Also, experts said, the task is likely to be overwhelming because the Chinese eat about 14 billion chickens a year, so mass vaccinations would have to be repeated again and again, while the risk of the disease being reintroduced by migratory birds, in which it is now endemic, would be constant. [Note: seems there’s no real evidence for this assertion; I’ve emailed Carol Cardona about it, but nothing solid in reply – chiefly based on work with domestic ducks; ignoring, say, 74,000 apparently healthy wild birds tested, only one positive result – faecal sample from Mongolia]

    Bird vaccination campaigns involve a huge amount of labor because the animals must be injected one by one. China’s Agriculture Ministry said Tuesday that it would inject all of the nation’s 5.2 billion chickens, geese and ducks with a vaccine.

    Dr. Leon Russell, president of the World Veterinary Association, said that an official from Vietnam told him recently that Vietnam had despaired of ever vaccinating all its birds because it would need 100,000 more trained vaccinators.

    “So, for the life of me, I can’t figure out how China will vaccinate billions of chickens,” he said.

    Post edited by: martin, at: 2005/12/03 10:04

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