Saturday, August 20, 2016

Genetic Characterization of Avian Influenza Viruses In Vietnamese LBMs


In addition to their slow and steady evolution via antigenic drift, influenza viruses are able to swap out large chunks of their genetic material with other flu viruses - a process called reassortment or Antigenic Shift - that can abruptly create new, hybrid viruses.

Most products of reassortment are evolutionary failures, unable to compete with the existing strains.  They die out quickly - often never spreading beyond the original host.

But successful reassortments do occur, are a major driver of influenza's evolution, and have even produced pandemic strains in the past (see NIAID Video: How Influenza Pandemics Occur).

This ability to swap out interchangeable genetic parts is what makes LBMs (Live Bird Markets) so dangerous.  They bring into prolonged confined contact many different types of birds (chickens, ducks, geese, quail, etc.) - often from distant farms - frequently carrying diverse influenza subtypes.

Not only does this provide enhanced opportunities for avian flu viruses infect to humans, it is also a low tech way to generate new reassortant viruses.

While attempts have been made to shut down live bird markets  (see The Lancet: Poultry Market Closure Effect On H7N9 Transmission), these live markets remain ubiquitous and operational across much of Asia.

Some recent blogs on the risks include:
J. Infection: Aerosolized H5N6 At A Chinese LBM (Live Bird Market)

Emerg. Microbes & Infect.: LBM Surveillance As Early Warning For H5N6 Infection

Sci Rpts: Intense Circulation Of A/H5N1 In Cambodian LBMs & Evidence Of Subclinical Human Infection

Study: Co-Circulating H5, H9, H10 Avian Flu Subtypes In Nanchang, China LBMs

It is probably fair to say the greater the number of flu strains circulating at these LBMs, the more `interchangeable parts' that are available, and the greater the risk of seeing a novel virus emerge. 

Short of closing live markets entirely, some interventions (i.e. keeping poultry and aquatic birds separate, rest days, and banning live poultry in markets overnight) have been suggested (see The Lancet: Interventions To Reduce Zoonotic & Pandemic Risks From Avian Flu In Asia) to reduce the risks. 
We've a report today from the journal Veterinary Microbiology, which not only details the constellation of avian viruses detected in Vietnamese live markets, it compares those findings between markets that have taken (unspecified) interventions to reduce avian flu risks, and those that have not. 

In addition to finding the rates of infection comparable in these two groups, suggesting that the intervention methods being used were inadequate, they also found the recently emerged HPAI H5N6 virus in healthy appearing ducks.

Genetic and antigenic characterization of H5, H6 and H9 avian influenza viruses circulating in live bird markets with intervention in the center part of Vietnam

Duc-Huy Chua, b, Masatoshi Okamatsua, Keita Matsunoa, c, Takahiro Hionoa, Kohei Ogasawaraa, Lam Thanh Nguyena, Long Van Nguyenb, Tien Ngoc Nguyenb, Thuy Thu Nguyenb, Dong Van Phamb, Dang Hoang Nguyenb, Tho Dang Nguyenb, Thanh Long Tob, Hung Van Nguyene, Hiroshi Kidac, d, Yoshihiro Sakodaa, c, ,


  • The efficacy of the intervention LBMs in Vietnam was evaluated.
  • Various subtypes of AI viruses were identified at both types of LBMs.
  • H5N6 viruses (clade are genetically related to those isolated in China.
  • H6 and H9 viruses at both types of LBMs were genetically identical.
  • Hygiene practices in LBMs should be improved.


A total of 3,045 environmental samples and oropharyngeal and cloacal swabs from apparently healthy poultry have been collected at three live bird markets (LBMs) at which practices were applied to reduce avian influenza (AI) virus transmission (intervention LBMs) and six conventional LBMs (non-intervention LBMs) in Thua Thien Hue province in 2014 to evaluate the efficacy of the intervention LBMs. 

The 178 AI viruses, including H3 (19 viruses), H4 (2), H5 (8), H6 (30), H9 (114), and H11 (5), were isolated from domestic ducks, muscovy ducks, chickens, and the environment. 

The prevalence of AI viruses in intervention LBMs (6.1%; 95% CI: 5.0–7.5) was similar to that in non-intervention LBMs (5.6%; 95% CI: 4.5–6.8; χ2 = 0.532; df = 1; P = 0.53) in the study area. 

Eight H5N6 highly pathogenic avian influenza (HPAI) viruses were isolated from apparently healthy ducks, muscovy ducks, and an environmental sample in an intervention LBM. The hemagglutinin genes of the H5N6 HPAI viruses belonged to the genetic clade, and the antigenicity of the H5N6 HPAI viruses differed from the H5N1 HPAI viruses previously circulating in Vietnam. 

Phylogenetic and antigenic analyses of the H6 and H9 viruses isolated in both types of LBMs revealed that they were closely related to the viruses isolated from domestic birds in China, Group II of H6 viruses and Y280 lineage of H9 viruses. 

These results indicate that the interventions currently applied in LBMs are insufficient to control AI. A risk analysis should be conducted to identify the key factors contributing to AI virus prevalence in intervention LBMs.

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