Challenges and control of Avian Influenza

April 17, 2013

Dr. Khalid Naeem & Dr. Muhammad Akram Muneer

Animal Science Institute, NARC, Pak Road, Islamabad


Avian Influenza
Avian Influenza

Avian Influenza (AI) is a highly contagious disease of poultry having significant impact on the survival and economy of livestock farmers. In Pakistan, AI caused by many types of an H7N3 type virus (AIV) was first diagnosed in 1994 in the poultry flocks housed in the hilly areas of Islamabad, Abbtabad, Murree and Mansehra. Later on this disease spread to many poulty producing areas of country and infected broiler- breeder, commercial broiler and layer flocks. However, this outbreak costing billions of Pakistan rupees to poultry flock owners was controlled by the efforts of local Scientists who developed homologous inactivated vaccination and advocated its mass scale use in the poultry flocks throughout Pakistan. Again in 1998, a relatively lower virulent AIV type H9N2 was isolated from flocks in Karachi and its control in poultry flocks was also tried through vaccination. However, the problem of H9N2 virus infection in poultry flocks continues till to-date.

In February 2006, a dead AIV strain (H5N1) infection was diagnosed at farms in Peshawar and Charsada. This strain caused huge mortality in chicks and lead to culling of around 0.5 million birds including broiler breeders, commercial broiler, layer flocks etc. throughout country the intensity of infection being more in KPK and Sindh flocks.

National Reference Laboratory for the Poultry Diseases (NRLPD) at NARC, Islamabad is engaged in the diagnosis of AI/bird flu in poultry in commercial flocks and backyard poultry since early 1990’s. The scientists in this laboratory developed and got approved a Government of Pakistan funded project entitled, “National Program for the control and Prevention  of AI in Poultry in Pakistan” worth Rs. 1180.343 millions. This project was implemented during the period from 2007 to 2011. Through this project a national net work of diagnostic laboratories on AI at national (n=2), provincial (n=10) and regional (n=40) levels was established or strengthened. The HPAI infected flocks were culled by the government officers as to deal with the outbreaks in poultry, a total of 66 rapid response units were established. This project staff, cooperated, coordinated and collaborated with the poultry industry and through its efforts and cooperation of poultry farmers, the flocks in Pakistan have been free from AI/bird flu since June 2008. The Provincial laboratories on Avian Influenza collected and analyzed over 0.6 million samples consisting of infected tissues, tracheal and cloacal swabs and blood sera, for the presence of AIVs or their HI antibodies during the period from July 2007 through June, 2011. The NRLPD staff worked on confirmation of findings in 10 per cent of total samples by the provincial and special area (FATA, Gilgit Baltistan , AJK, ICT) labs. The NRLPD reported 26, laboratory confirmed outbreaks of HPAI in 2006, 59 outbreaks in 2007, and 08 outbreaks in poultry in 2008. Although, since, June 2008, no HPAI outbreak has been reported from any of the provincial labs or by NRLPD; the NRLPD is continuing AI surveillance work to-date through its own resources offered by PARC, and some financial and technical support from FAO. The data reported by NRLPD on AI through period from June 2011 to date indicates that there presently no outbreaks of HPAI (H or H5) anywhere in country. During the period from March 2012 to February, 2013, NRLPD analyzed samples as per following details

Tracheal and Cloacal Swab samples  :    2715

Morbid tissue samples                       :   2325

Blood sera                                          :   4446

The laboratory analysis on above samples indicates that none of the poultry flocks in the country was positive for serum antibody to H5 or H7 virus.

However, the H9N2 virus is being repeatedly isolated from flocks throughout country as indicated by the following data.

  • March 12:   H9N2 (22)
  • April 12:     H9N2 (17)
  • May 12:      H9N2 (06)
  • June 12:      H9N2 (09)
  • July 12:       H9N2 (03)
  • August 12:  H9N2 (02)
  • Sept. 12:     H9N2 (03)
  • Oct. 12:      H9N2 (02)
  • Nov. 12:     H9N2(02)
  • Dec. 12:     H9N2 (03)
  • Jan. 13:      H9N2 (04)
  • Feb. 13:     H9N2 (02)

The isolation of H9N2 virus from the flocks  is of serious concern as this virus has potential for under-going mutation and emerging into novel virus strain; its role as immunosuppressve agent in poultry is known, and it can also cause human infections.


The strategy implemented to control this disease in chickens was as under.

  •  Awareness of public, veterinarians and medical professional on HPAI virus, the AI disease, and virus potential to cause the human illness.
  •   Bio – security implementation at the poultry farms & practice of bio-safety in the labs dealing with infected materials so as to prevent the contamination of lab premises,, environment and farms with this deadly virus of poultry.
  • Diagnostics; strengthening of diagnostic facilities the national and provincial labs and at the regional surveillance units.
  • Collection of tissue, cloacal and trachea swabs, and blood samples from the commercial and backyard poultry flocks and also those from the live bird markets for test of those samples at the laboratory for the presence of HPAI virus
  •  Strategic vaccination against HPAI H5N1 virus of all poultry flocks in 5 KM radius areas of outbreak confirmed flock (s).
  •  Containment and culling of each infection confirmed flock, and its burial under aseptic cover deep in the soil. More the infected farm premises were cleaned, washed and disinfected; and kept closed for 03 months period before housing the new flocks.
  •   Rehabilitation of Farmers through payment of compensation. About 25 million rupees were paid to the HPAI affected farmers as compensation.
  • Constant monitoring of efficacy of HPAI virus imported and locally manufactured vaccines.
  • Arrangement of trainings for the professional staff and laboratories and those working in the field as regional surveillance officers and those in the rapid response teams.

Present status of HPAI in the SAARC countries.


Poultry in many SAARC member countries is suffering from HPAI H5N1 virus infection outbreaks. Reports from Bangladesh, Nepal, Bhutan and India indicate the occurrence of many out breaks of H5N1 deadly virus in poultry flocks. As per an information the number of HPAI H5N1 outbreaks in Bangladesh, Bhutan, India, and Nepal recorded during 2012 through April, 2013 were 23, 09, 11 and 33. These outbreaks were recorded in back yard poultry, commercial broilers, commercial layers, parent flocks and wild birds. Since this HPAI virus infection is being constantly reported from our neighboring and regional countries, we need to keep on monitoring the situation and be alive to handle any emergent situation on HPAI in Pakistan.

Although, poultry flocks in Pakistan are free from HPAI virus outbreaks since June, 2008, a lot needs to be done to keep this freedom from avian influenza. The some of the suggested measures include enhanced regular surveillance at country level of poultry flocks, wild birds and live bird markets for HPAI; use of strict biosecuirty at farms, all measures to disinfect the contamination, improved sanitation and use of vaccination from a reliable source. Efforts and resources be used to revive the early AI warning system that was established under the National Program for the Control and Prevention of Avian Influenza. Revival of Regional surveillance units and laboratories; reactivation of Rapid Response Teams; continuous reporting and sample analysis from the poultry flocks are key factors in keeping a control on AI in poultry.

Although our scientists, veterinarians, farmers, and other stakeholders of poultry industry are well aware of HPAI influenza and the losses caused by mild type AIV H9; the authors would like to reinforce following important information on AI.

Avian influenza (AI) is caused by an ortho-myxovirus; influenza A type viruses. It can affect a variety of domestic and wild bird species. The infection with these viruses may range from asymptomatic to severe disease, depending on the virulence of the virus and the susceptibility of the avian host. The AI in the chickens and turkeys is classified according to disease severity, with two recognized forms: highly pathogenic avian influenza (HPAI), also known as fowl plague; and low-pathogenic avian influenza (LPAI). The AI viruses (AIVs) that cause HPAI in various avian species are very virulent and may cause up to 100% mortality in the infected flocks. The LPAI viruses are generally less virulent. However, the LPAI infection in the poultry flocks must be kept under control as this type of viruses may serve as progenitors to HPAI viruses. Besides infecting poultry, many types of AIV strains have been to infect he human beings. Some of those AIVs include the H5 subtype (H5N1), the H7 subtype (H7N2, H7N3, H7N7), the H9 subtype (H9N2), and the H10 subtype (H10N7). Very recently, human infections with a novel A/H7N9 virus in china have been reported. This virus has caused 11 human deaths.

Survival of Avian Influenza Viruses

  • Influenza viruses remain infectious after 24 to 48 hours on nonporous environmental surfaces and less than 12 hours on porous surfaces.
  • Influenza A viruses can persist for extended periods of time in water A review of latest available evidence on risks to human health through potential transmission of avian influenza [H5N1] through water and sewage. One study of subtype H3N6 found that virus resuspended in Mississippi River water was detected for up to 32 days at 4°C and was undetectable after 4 days at 22°C. Theauthors while working at the University of Minnesota were able to report AI viruses in lake water samples. Another study found that several avian influenza viruses persisted in distilled water for 207 days at 17°C and 102 days at 28°C.
  • A report indicates that the pH, temperature, and salinity in natural aquatic habitats can influence the ability of avian influenza viruses to remain infective within such environments.
  • Inactivation of the virus occurs under the following conditions:
  1. Temperatures of 56°C for 3 hours or 60°C or more for 30 minutes
  2.  Acidic conditions

3.   Presence of oxidizing agents such as sodium dodecyl sulfate, lipid solvents, and B-propiolactone

4.   Exposure to disinfectants: formalin, iodine compounds

Avian Influenza Hosts

  • AI viruses can infect a variety of domestic and wild avian species (including chickens, turkeys, ducks, domestic geese, quail, pheasants, partridge, parrots, gulls, shorebirds, seabirds, emu, eagles, and others).  Ducks, shore birds, and gulls are considered the natural reservoirs for avian influenza viruses. The waterfowl generally do not develop disease when infected with AIVs. The H5N1 appears to be virulent for a variety of wild bird species. The presence of H5N1 influenza virus in asymptomatic eagles has been reported.
  • HPAI H5N1 viruses were isolated from asymptomatic tree sparrows in the Henan province of China in 2005.

The clinical manifestation of AI virus infection in birds ranges from asymptomatic infection to rapid high mortality.

Influenza A viruses have been known to cause disease in horses, pigs, whales, and seals. H5N1 influenza A has now been shown to infect cats, leopards, tigers, civets, and dogs.


Disease Virus Transmission

  • Routes of bird-to-bird transmission include:
    • Airborne transmission if birds are in close proximity
    • Direct contact with contaminated respiratory secretions or fecal material
  • Vertical transmission is not known to occur
  • Other factors that contribute to spread within and between flocks include the following:
    • Broken contaminated eggs in incubators infecting healthy chicks
    • Movement of infected birds between flocks
    • Movement of fomites such as contaminated equipment, egg flats, feed trucks, and clothing and shoes of employees and service crews
    • Contact with infected wild birds and waterfowl
    • Fecal contamination of drinking water
    • Garbage flies (suspected of transmitting the virus during the 1983-1984 epidemic in Pennsylvania)

The disease is highly contagious. One gram of contaminated manure can contain enough HPAI virus particles to infect 1 million birds.

Major outbreaks of avian influenza are highlighted in the table below.


Sr. No



Estimated Deaths

Sub – type of A virus Strain



“Spanish Flu”

Up to 50 million




“Asian Flu”

1-4 million




“Hong Kong Flu”

1-4 million



2006 -08

“Current outbreaks)

246 deaths






History of Avian Influenza Outbreaks in Pakistan

H7N3 virus Infection

The AI outbreak of 1994-1995 caused by a highly pathogenic strain of AIV H7N3 resulted in high economic losses primarily in breeding stocks in the northern region of Pakistan.

It caused exceptionally high mortality (about 0.6 million) in breeders, layers and broilers in hilly areas of Murree. The outbreaks due to H7N3 AIV subtype overall caused the death of over 3.2 million birds in 1995. A vaccination campaign with the isolated virus vaccine, coupled with increased biosecurity measures, was practiced which ultimately led to the control of HPAI outbreaks.

In March 2001, AI viruses were identified in chickens and at farms 200 km southwest of Islamabad. The affected population was layers, broilers and broilers breeder chickens. Approximately 75% of the population at those farms indicated mortality between 20 and 85%. The isolates obtained through flock sampling were H9N2 and H7N3 AI and Newcastle disease viruses alone and in combinations.

H9N2 virus Infection

Muneer and co-workers in 2001 reported a severe syndrome due to H9N2 virus and associated pathogens involving the respiratory and gastro-intestinal tract causing a severe clinical illness with 30-80% mortality in commercial broiler and layer flocks in Karachi during 1999.

AI H5N1 virus outbreaks in poultry

            During February 2006, two poultry flocks having a total of 26,450 chickens and indicating mortality in NWFP (Charsada and Abbotabad areas) were suspected for AIV.

The clinical signs indicated by the birds at both the farms (a layer flock, n= 10,450 birds; broiler breeder flock, n= 16000 birds) consisted of laboured breathing, whistling sounds, cyanosis of combs and wattles, and drop in egg production. Laboratory investigations conducted at the National Reference Laboratory for Avian Influenza, Animal Science Institute, National Agricultural Research Centre (NARC), Islamabad using diagnostic procedures like virus isolation, agar gel precipitation, hemagglutination (HA) and hemagglutination inhibition (HI) and polymerase chain reaction (PCR) indicated presence of an H5 virus infection. The morbid material was also sent to Veterinary Laboratory Agency (VLA), Weybridge, UK (OIE/FAO Reference Laboratory for Avian Influenza) where the samples were subjected to further testing using RT-PCR, and Sequence Analysis (Naeem et al., 2006). Those samples were tested as positive for HPAI H5N1 virus. Subsequently, poultry flocks at Sehala and Taralai in Islamabad area and some others in Punjab province were also tested positive for H5N1 virus infection.



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