Colorized transmission electron micrograph of Avian influenza A H5N1 viruses (seen in gold). Image provided by CDC/C. Goldsmith, J. Katz, and S. Zaki.
Influenza Virus Evolution and Adaptation
By Grattan Woodson, MD, FACP
The influenza pandemics of 1957 and 1968 were mild compared with the devastating 1918 flu. Studies show that genetic reassortment between avian and human flu strains led to the creation of the viruses that caused both these minor pandemics. In contrast, the 1918 pandemic virus adapted to humans by way of mutation and recombination. This alternative method of adaptation to humankind may contribute to the lethality of the virus because our immune system is less ready to deal with it. Another unique feature of the 1918 Spanish flu was the presence of killer gene segments (lethal polymorphisms). These gene segments are associated with widespread organ failure and damage not seen during the seasonal flu or the minor pandemics. Disturbingly it was discovered recently that not only was H5N1 bird flu was following the same evolutionary path taken by the 1918 virus it had also accumulated many of the same lethal polymorphisms found in Spanish Flu. These observations are among some of the reasons to think that if bird flu achieves pandemic status it will be a man killer on par with the 1918 strain.
Influenza virus mutation, reassortment, and recombination
The three influenza viruses that caused pandemics in the 20th century and the H5N1 bird flu have been genetically sequenced and their origins determined. The behavior and character of the influenza virus is dependent on instructions found in its eight genes. These eight genes make up the flu’s genome, or complete collection of genes. Flu genes are inherently unstable and mutate regularly. A genetic mutation occurs through the imperfect recopying of genes during viral reproduction. Mutation is a very important source of variability for the flu. It helps it adapt quickly to a new environment or host.
Genes are structured like a string of pearls with each pearl representing a specific molecule called a nucleotide. Most organisms make their genes from just 4 or 5 nucleotides. These molecules are reserved by biology for the exclusive purpose of making genes and carrying genetic instructions. An organism’s characteristics are determined by the arrangement of the nucleotides in its genes.
Influenza genes are composed of single strand or nucleotides called RNA (Ribonucleic Acid). Human genes use a double strand of nucleotides called DNA (Deoxyribonucleic Acid). All human cells make and use single stranded RNA and rely on this molecule to transfer messages from the DNA in the nucleus to the cell cytoplasm. Once in the cytoplasm, RNA serves as a message that directs the cell to make molecules needed for health. The influenza virus takes advantage of this by hijacking the process substituting its own RNA, which tells the cell to make many thousands of copies of the virus. It is during this process of viral reproduction that mutations, reassortment, and recombination occur.
Influenza has two natural hosts; the members of the avian and mammalian species. In addition to mutation there are at least two other ways the flu virus can come up with new combinations of genetic material. When two flu strains infect the same host cell at the same time they can exchange genetic material with each other. If the exchange is of one or more whole genes the process is called reassortment. If two strains exchange a short segment of a gene the process is called recombination.
For the flu, successful and rapid adaptation to a new host animal is entirely dependent on frequently throwing the genetic dice. Adaptation means making it easer for the virus to enter and infect the target host’s cells. Its survival depends upon its ability to adapt.
Influenza epidemics and pandemics are caused antigenic drift and shift
Antigenic drift occurs when a small genetic change occurs in the flu. This usually happens by mutation or the process of recombination. These small genetic changes give the viral offspring a slightly new appearance to the human immune system and set the stage for a flu epidemic during the following flu season. A flu epidemic occurs when our immune system can’t recognize or see the “drifted” flu virus as well as the progenitor virus it had been sensitized to. The seasonal flu makes slight changes all the time and this is why flu shots have to be taken every year to maintain immunity.
When a human seasonal flu strain exchanges a genes with a new avian flu strain, the offspring can be so different that our immune system has much greater difficulty managing it initially than when it has to deal with a simple mutation. The reason for this is that there is no or at best imperfect immune memory of the newly formed composite strain within the blood cells that form our immune system. This process is called antigenic shift and was the cause of the last two minor pandemics.
The Spanish Flu’s surprising origin unveiled
The origin of the influenza virus that caused the 1918 Spanish Influenza Pandemic had been a mystery until a team lead by Dr. Jeffery Taubenberger¹ published the most recent in a long series of scientific articles on this virus in the Journal Nature in October 2005.²Over the past decade, his team has engaged in the painstaking task of piecing the H1N1 Spanish Flu’s eight genes together one bit at a time. Dr. Taubenberger’s team were able to isolate the virus in fragments of lung tissue taken 90-years ago at the autopsy of a solder dying of flu at Fort Jackson, SC. Other specimens were obtained from the frozen remains of an Inuit woman who died of the 1918 Spanish Flu in her Alaskan village.³ Her body was preserved by virtue of its being buried in permafrost. They also obtained specimens from various other repositories maintained at universities in the US and in Paris, France. From these sources, they isolated enough genetic material to reconstruct the complete sequence of all eight genes using modern methods only recently available including reverse transcription-polymerize chain reaction. The team compared the structure of the H1N1 Spanish Flu with other influenza virus sequences that were circulating in the human, bird, and swine population before, during, and after the Great Influenza Pandemic of 1918.
The 1918 Spanish Flu contained no genes of human flu origin
Many important discoveries and insights have emerged from this team’s many years of work. One that I thought was particularly interesting was announced several years ago. The team found that the Spanish Flu just didn’t look like any of the other prevailing strains of the day. This made little sense to investigators since prevailing influenza dogma predicted that the 1918 flu should have originated by reassortment between a human seasonal flu strain and a new avian flu strain. This idea stemmed from the knowledge that this was the evolutionary path followed by the 1957 and 1968 pandemic viruses and it was assumed, incorrectly, that all pandemics must begin the same way. During reassortment, a whole gene was exchanged between an avian and previously adapted human flu strain resulting in a new strain of influenza. The resulting antigenic shift in the appearance of the virus to the human immune system produced the 1957 and 1968 influenza pandemics. If the Spanish Flu had been created as a result of reassortment then its genes would have to share a close resemblance with other strains circulating in humans, swine, or birds at the time, which it did not.
The Great Influenza virus’s unique evolutionary path exposed
In October 2005 the team shocked the virology and medical world with their second major finding. The Spanish Flu evolved from the avian world to humans on the strength of mutation and recombination alone without recourse to reassortment. It is speculated that one of the reasons for the high mortality associated with the Spanish flu is due to this alternative adaptation pathway followed by the H1N1 virus. This path resulted in the absence of any human flu genes in its genome. The lack of human genes meant the proteins present on the surface of the virus were entirely foreign to our immune systems leaving us highly vulnerable. Our immune system’s naïveté gave the virus a significant advantage. This provided it with extra time to reproducing itself in our lungs before we could mount an immune defense. By the time we were able to respond, the extent of viral damage and quantity of virus within the body was much greater than during seasonal flu or minor pandemics.
Lethal polymorphisms help explain the Spanish Flu’s virulence
Another finding by Dr. Taubenberger’s team was that the 1918 flu genome contained several small genetic sequences or polymorphisms that caused it to have lethal characteristics. Polymorphisms are simply different combinations of nucleotides that compose one or more RNA genes of the virus. For instance, differences in hair color are due to polymorphisms in the human hair pigment gene. All these human genes do the same thing, determine hair pigment but the result of their work is a little different. The differences are due to polymorphisms within the gene structure. Lethal polymorphisms are nucleotide combinations within a flu gene that code for a particularly nasty behavior. For instance, one of these directs the virus to attack the brain; others cause the virus to disrupt the blood clotting system, while some result in attack of the heart and liver. These behaviors are often fatal and this is why these polymorphisms are called lethal. The lethal polymorphisms were absent from the genes of the 1957 and 1968 pandemic strains. Many of these same lethal polymorphisms have been identified in the genome of the H5N1 bird flu. Not every strain has all of these lethal polymorphisms. Their presence in bird flu is unsettling and is likely to be an important determinate of that virus’s case fatality rate should it achieve pandemic status.
Putting it all in context
The combination of Spanish Flu having a new antigenic appearance to most people in 1918 and the presence of lethal polymorphisms in its genome may explain why this pandemic killed so many people. Do these similarities between the H1N1 Spanish flu and the H5N1 bird flu have ominous implications for the severity of the next pandemic? At the present time, this is unknown but the parallels in both the developmental pathway and acquisition of the same lethal polymorphisms is at the very least cause for concern.
Dr. Taubenberger’s finding’s also increases the significance of the outbreak of an increasing number and size of bird-to-human, human-to-human, and possibly swine-to-human bird flu clusters in Indonesia, China, and the Middle East. They highlight the fact that the H5N1 virus is adapting quickly to humans without the need for reassortment with genes from a human flu strain. This fact is manifest by the ease with which bird flu was passed from birds to people visiting the Jakarta Zoo in the summer of 2005 and the limited but growing number and size of human-to-human clusters reported since then. These features were not observed with the sporadic cases of bird-to-human transmission seen in Vietnam, Cambodia, Thailand, and Laos in 2003-2004 and in early 2005.
The force of natural selection is favoring viral offspring with qualities that adapt it better to all its hosts including birds, mammals, and man. Adaptation to humans is occurring simultaneously in every geographic location the H5N1 virus is reproducing and even when doing so in hosts other than humans like birds, swine, cats, and dogs. At some point the process will end as far as we are concerned. The result will be a new pandemic virus, possibly H5N1 bird flu that is highly adapted to infect and reproduce within human cells. The sign that the adaptation is complete will be when it displays efficient human-to-human transmission. When this event occurs, a development that influenza experts say could happen soon, it would signal the beginning of the pandemic.
While it is not possible to predict now how lethal the next pandemic will be, all pandemics are a lot worse than routine seasonal flu. No matter what avian influenza virus causes the next pandemic including H5N1, it is very unlikely to be as lethal as native H5N1 bird flu has been to the people who have caught it from birds. The history of pandemics is strongly supportive of this view since if the pandemic strains of the past had case fatality rates in the 50% rage, they would have wiped humankind out centuries ago. Since this has not happened despite many hundreds of pandemics, it is not likely to happen. In the opinion of Dr. Michael Osterholm, PhD,4 writing in the New England Journal of Medicine, the most likely scenario for a major pandemic, is for an event that approximates the death rate seen during 1918 Spanish Flu.5 On the other hand, we can hope that if bird flu becomes pandemic it will emerge as a mild or moderate disease that would not represent a dire threat to humanity or lead to a significant disruption in our way of life.
1 Department of Molecular Pathology, Armed Forces Institute of Pathology, Rockville, Maryland, USA
2 Elodie Ghedin1, Naomi A. Sengamalay1, Martin Shumway1, Jennifer Zaborsky1, Tamara Feldblyum1, Vik Subbu1, David J. Spiro1, Jeff Sitz1, Hean Koo1, Pavel Bolotov2, Dmitry Dernovoy2, Tatiana Tatusova2, Yiming Bao2, Kirsten St George3, Jill Taylor3, David J. Lipman2, Claire M. Fraser1, Jeffery K. Taubenberger4 & Steven L. Salzberg1 Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution Nature 2005;437; 1162-6
3 In 1918, a remote Inuit village in Alaska was virtually wiped out by the Great Influenza. The residents were buried in a mass grave. Permission for the exhumation of this person’s remains was obtained from the tribal elders before her body was recovered.
4 Director of the Center for Infectious Disease Research and Policy, the associate director of the National Center for Food Protection and Defense, and a professor of public health at the University of Minnesota, Minneapolis
5 M Osterholm, Preparing for the next pandemic., N Engl J Med 2005;352:1839-1842