The Khan et al. 7:1444-1448, (2011) article is featured on the cover page of the July issue of the journal "Ophthalmology".

About me

After obtaining an M.Sc. in Biochemistry from the University of Peshawar, I worked as a Scientific Officer at the National Institute of Health, Islamabad, Pakistan. I then proceeded to USA to work towards my Ph.D in the Department of Biochemistry & Molecular Biology, University of North Texas, Denton, Texas, USA.

During my stay in the US I worked as a Research Assistant at the Department of Biochemistry, University of North Texas and as a Research Associate at the Department of Microbiology & Immunology, Texas College of Osteopathic Medicine, Fort Worth, Texas, USA. After completing my Ph.D. I came back to Pakistan and joined Dr. A. Q. Khan Research Laboratories as a Senior Scientific Officer and was subsequently promoted to the position of Principal Scientific Officer. From 1998 to 2001 I worked for a while, with Dr. Chris Tyler-Smith at the Department of Biochemistry, University of Oxford, Oxford, UK in the lab of Prof. E.M. Southern. In 2002 I joined Shifa College of Medicine as Assistant Professor of Biochemistry and in 2003 was promoted to the post of Associate Professor & also appointed as the Director of PCR Labs. .....Read more

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Bird Flu

Prof. Dr. Raheel Qamar

Origin and spread among birds.

The Bird Flu virus was first identified in Italy in the 1900s and has subsequently been shown to be endemic worldwide in the bird populations.  The birds carry the virus in their intestines and these infected birds then shed the virus in their saliva, nasal secretions and feces.  Unaffected birds become infected when they come in contact with secretions or excretions from the affected birds or come in contact with surfaces that have been contaminated with the secretions and excretions of the infected birds.  The mode of transmission from one region to another is via wild migratory water fowl like ducks, geese and swans.  These water fowl transmit the virus to the poultry of an unaffected country by their droppings which contaminate either the water and food sources or surfaces with which the unaffected poultry comes in contact.  Pakistan is on the migratory flight path of these water fowl — these birds spend summers in Siberia and they winter in Afghanistan, Pakistan, Iran and India.  Since these other countries have demonstrated clearly the presence of the H5N1 viral subtypes so it is inconceivable that Pakistan does not have the virus in its poultry populations.

Virus classification.

The bird flu virus belongs to the Orthomyxoviridae family which infects different vertebrates — this family includes the influenza viruses A, B & C.  Influenza A virus is known to infect humans, other vertebrates and birds.  In the latter it causes the Avian Influenza or bird flu.  Influenza B virus which is the other major type of this family is known to infect humans and seals; this virus along with a couple of the variants of Influenza A virus causes human flu worldwide which in United States alone results in 36,000 deaths annually.  Influenza C virus infects humans and pigs; this is the rarest but most severe form of the viruses that cause flu in humans.  The other types of this family include Isavirus which causes severe anemia in Atlantic salmon and Thogotovirus which is found in ticks and some vertebrates.

The bird flu virus (Influenza A virus) is further labeled into subtypes depending upon which types of proteins are present on their surface.  There are two major surface proteins found on the viral surface i.e. Hemagglutinin (HA), and Neuraminidase (NA).  There are a total of 16 known HA protein variants (H1 to H16) and 9 known NA variants (N1 to N9).  The combination of these 16 HA variants with the 9NA variants can theoretically generate 144 different viral subtypes, luckily not all these potential combinations result in highly pathogenic forms of the virus.

Low risk to high risk.

Usually the bird populations worldwide only carry the low pathogenic forms of any bird flu virus; however, these low pathogenic forms sometimes develop into a high pathogenic form due to certain mutations, i.e. changes in the genetic material (genome) of the virus.  This then results in the deadly form of the disease, the recent example of which is the H5N1 type seen in poultry in Asia and Europe.  This type of virus is easily transmitted between the birds and also to humans coming in contact with these diseased birds, but luckily the H5N1 virus has not mutated (changed its genome) enough for it to be transmitted from one human to another.  Only a few such cases have been reported and this transmission has not been observed to continue beyond one person.  However, the potential is there that H5N1 can mutate to such an extent that human to human transmission can occur easily resulting in a global pandemic, an example of which has been seen previously in the case of the 1918 Spanish Flu, when the H1N1 subtype of the bird flu virus changed to a variant that resulted in a worldwide pandemic which killed 50 to 100 million people over the course of one year.  This deadlier variant was only different from the parent H1N1 at 25 to 30 of the virus’s 4,400 amino acids i.e. the two viruses were different from each other by less than 1%.  This was a clear demonstration that only a slight change in the genome of a virus can turn it into a deadlier form.  The recent outbreak of the deadly bird flu virus subtype H5N1 currently has the potential of only being transmitted from birds to birds or birds to humans, however it has the potential of mutating so that human to human transmission can occur easily which will then cause a worldwide pandemic.  This type of mutational changes are a slower process, a more rapid process is that of the H5N1 virus exchanging some of its genome with one of the current human flu viruses and thus acquiring the potential of human to human transmission.  This can occur either in a human who acquires both the viruses simultaneously with a subsequent exchange occurring between the two viruses or it can also occur in pigs which are a reservoir of the human flu virus and also have a high potential of acquiring the H5N1 infection from birds.  In the latter case, a genomic swap will also occur in the creation of a deadly variant of the H5N1 virus which will then have the potential of human to human transmission and will thus result in a worldwide pandemic resulting in a massive number of deaths.  WHO was initially estimating this number to be more than 50 million deaths worldwide, but they have now scaled this number down to 5 million deaths.  This massive number of deaths would be because humans have not previously been exposed to this deadlier form of the virus, thus they will not have acquired any immune protection to this subtype.

Vaccination, but can it really protect?

One way of acquiring an immune protection against the bird flu would be to vaccinate the human populations with a vaccine developed against bird flu.  The problem with such a vaccine is that first of all it is an arduous process to develop a vaccine and requires significant time and effort as well as capital and after vaccine development it requires time to scale it up to production levels.  Secondly even if a vaccine to the current H5N1 subtype is developed it might not necessarily provide protection against the more virulent form of the virus that can emerge as a result of the genetic swap mentioned above.  Thus by the time that the deadlier form of the disease emerges and is identified it will take at least a year for an effective vaccine to be developed against it and by that time the virus would have taken a significant toll on the human populations worldwide.  Even after the first year all the combined production capabilities of the world will not be enough to produce enough vaccine to immunize the whole world population, thus only the Industrialized countries will be able to produce enough vaccine for their own population, which will still leave the underdeveloped parts of the world vulnerable to a second attack of the virus the following year.  Thus, the majority of the casualties will be concentrated in the underdeveloped countries that will have no way of combating this deadly disease.  In human history there have been a number of occasions when the human populations have gone through bottlenecks when the worldwide population has been reduced drastically due to a calamity.  In fact at a few points certain diseases had taken such a heavy toll on the human population that it almost became extinct, however sufficient number of humans were able to survive for the human race to continue.  It is feared that if a deadly form of bird flu hits the human population it will probably see another of these bottlenecks in the human race where the population will reduce to such a drastic level that humans will be on the verge of extinction.

How can it become a pandemic?

In order for a flu pandemic to start, three conditions must be met: first a new influenza virus must emerge in the existing pool of viruses, second this virus must infect humans and cause serious illness in them and lastly in order for this to be a sustainable pandemic this virus must have the ability to spread from human to human.  The recent outbreak of the H5N1 virus satisfies the first two conditions, i.e. it is a new viral subtype which can infect humans with a high morbidity rate — over 50% of the humans infected die after an incubation period of 3 to 4 days.  However, this virus still does not meet the last criteria of human to human spread, thus the bird flu pandemic in humans has not started yet.  Though in birds this pandemic is already underway with 140 million birds dying or having been destroyed in the Asian countries in 2004, causing more than $10 billion financial losses.


The traditional flu that humans suffer from each year cause only mild respiratory symptoms in most people.  As opposed to this, H5N1 infection may follow a more aggressive path with symptoms including fever, cough, sore throat, muscle aches, eye infections, pneumonia, acute respiratory distress syndrome and other severe life-threatening complications.  Such patients are usually immediately quarantined and a battery of tests is performed in order to ascertain the causative agent.  These tests can include molecular as well as viral surface tests to determine the nature of the virus.  For these tests, usually an oral or a nasal swab is taken and submitted for testing.

How it is spread to Humans.

The virus can be transmitted from birds to humans by their coming in contact with the feathers of the infected birds as well as any nasal secretions or the gut of the bird.  Most of the recent human transmissions of the virus have been linked to direct exposure to dead or diseased poultry, notably during home slaughtering, de-feathering, disemboweling and preparation of raw poultry for cooking.  Raw poultry meat can carry the live virus, so anyone cleaning or cooking the chicken can easily generate droplets of the virus due to which large amounts of the virus can easily spread and contaminate the environment and be hazardous to anyone inhaling the virus.  House wives or cooks who come in contact with the meat before it is cooked can also easily contract the disease; this is true for fresh as well as frozen or thawed raw poultry meat.  In order to avoid being contaminated by the virus, good hygienic practices should be followed including separating the raw meat from cooked or ready to eat food.  The same chopping board should not be used for raw and cooked meat.  When handling both raw and cooked food at the same time, hands should be thoroughly washed with soap in between.  In addition the meat should be cooked thoroughly to inactivate the virus.  To date, well cooked meat has not been shown to contain live virus.  However, in order for the virus to die, the internal temperature of the cooked meat has to be at least 70oC, which can be achieved at normal cooking heats.  Pink flesh visible when meat is cut to the bone can harbor the virus.  So make sure that in addition to achieving 70oC internal temperature, the meat is cooked long enough for the virus to perish.  Though cooking is enough to kill the virus, WHO and FAO still recommend that no meat from infected flocks should enter the food chain.

In addition to poultry meat, eggs can also harbor a significant amount of the virus.  In areas where the virus is present, runny, half boiled and half fried eggs should not be eaten.  In addition, food items which are prepared with raw eggs like mayonnaise should not be consumed.  Though baking and cooking will kill the virus, all egg products should still be avoided, e.g. soufflé, quiche, egg salad, custards such as crème brulee, flan and lemon custard and meat dishes such as sausages and pate.  In addition, all bakery items containing egg should be avoided, like cakes, biscuits, cake rusk and breaded items in which egg is used as the binding agent.

 Precautions if there is another out break.

During the unfortunate event of an outbreak, restrict movement as unnecessary human contact will result in the transmission of the disease.  Wearing a tight fitting face mask may prevent contracting the disease.  Loose fitting surgical mask will not prevent the virus from entering the lungs of the unaffected person, a mask or a respirator with a minimum rating of N95 is required for adequate protection.  Food and water will need to be stored because farmers will not be able to cultivate their lands and produce will not be processed and transmitted to the cities for distribution and sale.  This unfortunately will result in further deaths due to malnutrition and starvation where secondary cause of casualties can be a weakening of the immune system and further susceptibility to viral attacks.  Hopefully this is the worst case scenario that humans will never have to face.  The survival of the virus is in keeping the human race alive so that it can have a host to occupy.  Any extremely deadly form of the virus will perish itself and this will be viral evolutionary suicide.

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