November 9, 2009 Bioe 109 Fall 2009 Lecture 19 Evolution and human health. The evolution of flu viruses

Transcription

1 November 9, 2009 Bioe 109 Fall 2009 Lecture 19 Evolution and human health The evolution of flu viruses - the potential harm of disease epidemics in human populations has received considerable attention lately. - it is clear that diseases can be spread throughout the world at a rapid rate and this certainly sets the stage for a global pandemic to spread well before we can contain it. - a growing number of evolutionary biologists have recently begun to study the evolution of viruses. - we ve already discussed the rapid evolution of the HIV-1 virus. - today, we ll consider the evolution of the influenza A virus. - the influenza A virus is responsible for the annual flu epidemics we experience each year. - it also has been responsible for the occasional global pandemics that in the past century have occurred in 1918, 1957 and flu is not recognized as a deadly disease but it is. - in the US, it now kills about 30,000 35,000 people each year. - especially virulent strains have been responsible for large numbers of deaths. - the most deadly pandemic in the past 100 years occurred in this was called the Spanish flu. - estimates of the number of deaths caused by the Spanish flu range from 50 million to 100 million people. - the Spanish flu certainly didn t originate in Spain. - by May 1918, it was spreading on both sides of the European frontline during WWI. - then it seemed to subside. - by late summer it reappeared and spread with deadly speed. - within a period of months it had sickened some 20% of the world s population. - the complete sequence of the 1918 virus was published in fall it was isolated from two sources from slices of lung tissues isolated by pathologists from flu victims in a military hospital in Fort Jackson, South Carolina. - the second source was from a mass grave in a remote village in Alaska where a female body was found that had intact lung tissue. - the virus has been reconstructed by reverse genetics and tested in mice and chickens. - the origin of the 1918 H1N1 virus remains unknown, but many flu researchers think it may have originated from a bird species (that has yet to be identified). - the complete sequence of the 1918 virus might provide new insights into battling the next pandemic. - the influenza A virus is a retrovirus that encodes a total of 11 proteins (coding for coat proteins, structural proteins and polymerases).

2 - its genome is composed of 8 RNA molecules. - the predominant coat protein is called hemagglutinin this is the key protein through which our immune system primary identifies and attacks the virus. - in order to be transmitted from host to host the flu virus needs to find a steady supply of hosts that have never been exposed to its version of hemagglutinin. - the specific sites that the immune system recognizes and remembers (through memory cells) are called antigenic sites. - sites that are not recognizable by the immune system are called non-antigenic sites. - flu strains with novel antigenic mutations should enjoy a selective advantage over other strains because they represent a novel challenge to the immune system. - one can study the evolution of viruses very easily for two reasons. - first, they evolve extremely rapidly - the influenza A virus evolves a million times faster than humans. - second, they can be preserved in the freezer and then rethawed at a future date for genetic analysis. - one recent study examined the phylogenetic relationships among flu viruses sampled over the period of 1968 to this 20-year period is equivalent to 20 million years of human evolution (and we have diverged from the lineage leading to chimpanzees only 5 million years ago). - a study by Walter Fitch et al. (1991) studied the hemagglutinin gene in this temporal sample. - two interesting patterns were apparent. 1. a constant rate of divergence with time. - the strains accumulated changes in their hemagglutinin proteins at a constant rate of about 6.7 x 10-3 substitutions per site per year. - although this is consistent with a clock-rate substitution of neutral alleles, it is more likely caused by strong (and consistent) natural selection. 2. most strains represented extinct side branches on the phylogeny - interestingly, all strains studied were closely related and derived from a single ancestral strain present in the late 1960 s. - other stains present at this time left no descendants. - what allowed this one lineage to survive while the others dies out? - the answer appears to be antigenic mutations. - a total of 109 amino acid replacement mutations were present. surviving lineage extinct lineage in antigenic sites in non-antigenic sites

3 - over 3/4 of the mutations found in the surviving lineages occurred at antigenic sites. - this suggests that antigenic mutations have played an important role in the long-term survival of flu strains. - a follow up study examined 357 flu strains collected over the period of 1985 and a total of 331 substitutions were identified. - of these, 191 (58%) were silent mutations and 140 (42%) were replacement mutations. - this is not too different than expected under a neutral model of evolution. - however, non-neutral changes were observed at 18 amino acid sites. - one powerful way to test for the action of natural selection at a protein is to compare the rate of non-synonymous substitutions (ka) to the rate of synonymous substitutions (ks). ka = rate of non-synonymous substitution ks = rate of synonymous substitution - since most non- synonymous changes are deleterious, the ratio of ka/ks should be less than unity. - this demonstrates the action of purifying selection. - when the ratio of ka/ks exceeds one it indicates that more non- synonymous changes are occurring than synonymous changes. - this is called positive selection. ka/ks < 1 ka/ks > 1 purifying selection positive selection - within the hemagglutinin gene there were 18 sites experiencing elevated rates of replacement substitutions, i.e., ka/ks ratios greater than 1. - all 18 involved antigenic sites. - this strongly implies the action of selection favoring mutations at the these sites - why is the information useful? - because it allows the manufacturers of flu vaccines to make a more reasonable guess about which circulating flu strains will be the next season s epidemic. - these would be the strains that have the most number of replacement changes at these 18 antigenic sites. - this allowed the researchers to correctly predict the epidemic strain in 9 out of 11 recent flu seasons. The origin of pandemic flu strains - the phylogeny of human flu strains suggests that viruses with radically different hemagglutinin genes could attain a major fitness advantage and cause a pandemic. - how can this occur?

4 - by the process of recombination that may occur when two flu strains simultaneously infect the same host cell. - when this happens, some of the RNA strands can mix between strains. - phylogenies based on different flu genes shows convincing evidence that this process does occur. - figure 14-7 is a phylogeny based on the flu s nucleoprotein gene. - distinct clades are present that are found in different groups - there are equine strains, human strains, etc. - within the clade of human strains are some interesting exceptions. - the H3N2 strain has a nucleoprotein gene similar to other human strains but hemagglutinins that are distantly related. - how did this occur? - apparently by lateral gene transfer. - before 1968, no H3 gene had ever been found in viruses infecting humans. - so where did this H3 gene come from? - figure 14-8 shows that it likely came from birds. - how did a human flu strain acquire a H3 gene from birds? - the most reasonable hypothesis is that it occurs within a different host - pigs. - a human strain and a bird strain simultaneously infect a pig, swap genes, then it later jumps back to humans. - alternatively, an avian strain and human strain infecting the same cell can recombine and produce a highly novel and virulent pathogen. - both the 1957 and 1968 viruses were avian/human reassortants in which 2-3 RNA avian segments were added to the then-circulating human-adapted virus. The avian flu threat - we are currently experiencing the first flu pandemic of the 21 st century. - in many ways, we are fortunate that the H1N1 (swine) flu is not more virulent it is killing about the same percentage as the normal seasonal flu. - a much greater danger is the avian flu (H5N1). - this virus is frighteningly lethal in chickens, which can die within hours of exposure. - it also is highly dangerous to humans and other mammals roughly half of people infected with H5N1 die. - in May 1997, an outbreak of the H5N1 virus occurred among chickens in Hong Kong. - this wasn t unusual in any way and did not cause much concern avian flus do not jump to humans. - however, this one broke the rules. - that same month a 3 year old boy was admitted to a Hong Kong hospital with a cough and a fever. - his symptoms worsened quickly even though he was put on a ventilator and given numerous antibiotics. - within 6 days he was dead.

5 - pathologists were astonished when swabs from the boy s windpipe yielded a H5N1 virus. - it turned out to be the same virus that had infected the local chickens. - this death looked like a fluke until another 17 people checked into hospitals around Hong Kong with similar symptoms that were also confirmed as H5N1. - many of these victims had either visited or worked in Hong Kong s live-poultry markets. - public health experts descended on the city and persuaded the government to kill every last bird on the island all 1.5 million of them. - the mass slaughter apparently worked the H5N1 virus disappeared from sight. - in 2001 another deadly H5N1 strain appeared in Hong Kong again, apparently coming into the territory from Southern China. - for the past 5 years, it has swapped genes with other avian-flu viruses to generate a large group of new H5N1 strains. - radiating from southern China, the virus spread to Japan, Indonesia and southern Asia by migrating waterfowl. - in summer 2006, the virus killed thousands of wild geese and gulls in western China. - it is spreading throughout the world having been found in western Europe (Turkey) and into Britain by an infected parrot. - it hasn t yet been identified in North America. - it may have already arrived from migratory waterfowl arriving from NE Asia. - however, the virus kills birds so quickly that it may not allow them to fly long distances. - according to the WHO, the H5N1 virus has killed 262 people since 2003, the majority being in Indonesia. - H5N1 spreads to all tissues in birds but in humans, like the 1918 flu, it attacks the lungs first. - estimates of the mortality caused by H5N1, if it successfully evolves human-to-human transmission, is 20 million (at the low end) to roughly 1 billion people. - the recently obtained complete sequence of the 1918 virus reveals that it did not result from reassortment, as did the 1957 and 1968 epidemics. - this adds to the concern that the H5N1 strain could adapt to humans in toto. The evolution of virulence - virulence is a measure of the harm done to a host by a pathogen during the course of infection. - a highly virulent pathogen has a major effect on its host (e.g., Ebola) whereas a pathogen with low virulence has a negligible effect on host fitness (e.g., some herpes viruses). - a classic example of the evolution of parasitic virulence involves the myxoma virus in populations of Australian rabbits. - rabbits have been an important pest species in Australia for well over a hundred years. - they were introduced to Australia in 1859 by a Mr. Thomas Austin who bought 12 rabbits from a company in England. - knowing what rabbits are known for, it is not surprising to hear how quickly they multiplied on Mr. Austin s farm.

6 - 6 years after they were introduced, it was estimated that 30,000 rabbits were present on his farm. - they escaped and exploded in abundance all over the country. - in an attempt to eradicate the epidemic, the Australian authorities introduced the myxoma virus into the country in the 1950 s in an attempt to bring down the rabbit population. - this virus causes the disease known as myxomatosis. - the virus was transmitted from rabbit to rabbit by means of mosquitoes. - because of the large population of biting insects down under, the disease spread quickly. - myxomatosis initially decimated the standing populations - reducing them by 99% in some regions. - the virus was extremely virulent when introduced into Australia. - in fact, it killed 100% of its hosts. - it wasn t too long, however, before its level of virulence began declining. - there were two factors involved in this response. - first, the virulence of the virus itself declined - this was demonstrated by infecting lab strains of rabbits with the virus sampled from natural populations over a number of years. - interestingly, the same virus was introduced into France in 1952 and surreptitiously into Britain in in both of these countries, the virus also declined quickly in virulence Virulence grade high low I II IIIa IIIb IV V Australia France Britain this example shows that reduced virulence can rapidly evolve. - myxoma virus that killed their hosts too quickly were not spread to new hosts as effectively (because mosquitoes do not bite dead rabbits). - therefore, viruses that allowed their hosts to survive longer enjoyed a higher fitness. - over time, no highly virulent forms of myxoma persisted in the wild. - why have pathogens evolved to be so variable in their level of virulence? - three models have been proposed to account for the evolution of virulence.

7 1. The coincidental evolution hypothesis - this proposes that the virulence of many pathogens in humans is not a direct target of selection. - rather, it is a result of selection acting on the pathogen in a different environment. - for example, tetanus is caused by a soil bacteria Clostridium tetani. - when this bacteria finds itself in a human wound it can rapidly grow in number. - the bacterium also produces a deadly toxin which makes such infections extremely dangerous. - since this bacterium does not normally live nor reproduce in humans the secretion of this toxin cannot be directed at humans but at something they encounter in their typical soil environment. 2. The short-sighted evolution hypothesis - pathogens commonly undergo many generations in a host before being able to infect a new host. - as a result, traits that increase the within-host fitness of the pathogen may actually be detrimental to the transmission of the pathogen to a new host. - hence, the virulence is short-sighted. - an example here is the poliovirus. - this virus normally infects cells that line the digestive tract and cause few symptoms. - occasionally, the virus infects cells of the nervous system. - this may increase the fitness of this lineage (because they face fewer competing strains) but are an evolutionary dead-end. 3. The trade-off hypothesis - the basis of this hypothesis is that a pathogen should evolve to a point in which its costs to the host are balanced by its capacity to propagate itself to other hosts. - therefore, pathogens may evolve to a point where they harm their hosts considerably. - the detriment caused to the host represents an optimal balance between harm to the host and benefit to the pathogen. - higher reproductive rates should benefit pathogens but if this reproductive rate is too fast, the harm done to the host could reduce pathogen fitness. - this idea was tested in a recent study by Messenger et al. (1999) involving the bacterium E. coli and a virus, the bacteriophage f1. - this phage can propagate both vertically and horizontally. - vertical transmission occurs when the host bacterium divides and the two daughter cells contain the phage. - horizontal transmission occurs when the phage moves to a new host. - Messenger et al. (1999) performed an experiment in which they restricted the transmission to being only vertical or only horizontal. - for the vertical transmission treatment, they simply prevented secreted virions from infecting new bacterial cells. - the only way the phage could propagate was through the reproduction of their hosts.

8 - for the horizontal transmission treatment, the researchers harvested secreted virions and introduced them to cultures of uninfected bacteria. - the only way virions could now spread was through secretion. - two sets of cultures were established: 1. 8 day long vertical transmission period followed by a brief horizontal phase day vertical phase with a brief horizontal phase. - the researchers made two predictions. 1. reduced virulence should evolve in the 8 day treatment. 2. phage reproductive rates should correlate negatively with host growth rates. - both predictions were met - phage strains that reduced their hosts growth rate most were those that reproduced more quickly in their hosts. - these findings are consistent with the trade-off hypothesis. - further support exists for the trade-off hypothesis in human pathogens. - first, vectorborne diseases tend to much virulent than diseases transmitted by direct contact. - this pattern is also found for bacteria that can be transmitted by infected water (like cholera) versus those that are transmitted by direct contact. Factors leading to increased virulence: 1. Live host not needed for transmission. - examples here include the ebola virus and some parasitic fungi (see fig !) 2. Multiple infections in a single host. - this leads to competition among pathogens within a host. - those that reproduce more rapidly (harming the host) would be favored. 3. Transmission is horizontal (i.e., from individual to individual) instead of vertical (i.e., from parent to offspring).