January 8th, 2010
BIOE 109
Winter 2010
Lecture 2
Evolution in action: the HIV virus
- when Darwin first developed his theory of natural selection he believed that the process occurred too slowly to be directly observed and/or measured.
- although Darwin was correct much more often than he was wrong, this is clearly one of those rare cases.
- in fact, today Darwin would be shocked at our ability to measure natural selection over short time periods (i.e., over several generations) and how strong selection commonly is in nature.
An Example - the HIV virus versus AZT
- the WHO estimated in December of 2006 that about 40 million people are presently infected with the HIV virus.
- there are really three separate epidemics occurring around the world.
- the one that we’re most familiar with is the epidemic among homosexual men and intravenous drug users in Europe and N. America (1.9 million infected).
-the second far larger epidemic is among heterosexual men and women in sub-Saharan Africa where upwards of 25-30 million people are now believed infected with HIV-1.
- the third and most recent epidemic is occurring in SE Asia (mainly Thailand) and parts of the Indian subcontinent, again mainly among heterosexuals (7.5 million infected).
What is HIV?
- the HIV virus is a retrovirus responsible for indirectly producing a disease known as AIDS.
- retroviruses contain RNA, rather than DNA, as their genetic material.
- when a retrovirus infects a cell, the first thing it does is copy its RNA into DNA.
- it does this by means of a special enzyme known as reverse transcriptase.
- the viral genome is then inserted into a transcriptionally active region of the host cell where it uses the cells transcriptional and translational apparatus to manufacture new virions that burst from the cell to begin a new infective cycle.
- the HIV virus is unusual for retroviruses in having 9 genes (most have 3 or 4) and in being diploid.
How does HIV produce AIDS?
- basically, the HIV virus accomplishes this by infecting a key player in the vertebrate immune system called “helper T cells”.
- they infect a class of T cells that have a protein called CD4 on their cell surface.
- it is through this protein receptor that the HIV virus is capable of entering a cell.
- helper T cells are the critical link in our immune system and it is through their destruction of CD4 helper T cells that the HIV virus slowly weakens the immune system.
- once the immune system is debilitated, the body can no longer ward off bacterial and fungal pathogens.
- it is the manifestation of these secondary infections that we call “AIDS”.
- why are CD4 helper T cells so important for out immune system function?
- they are responsible for the so-called “cell-mediated response” by stimulating killer T cells that recognize and kill infected T cells.
- they also mediate the so-called “humoral response” by stimulating B cells to secrete antibodies that bind free virus particles allowing them to be destroyed by macrophages.
- by infecting helper T cells, our body’s own immune system responds and ends up destroying our T cell population over time.
- the destruction of CD4 cells occurs slowly - typically over a period of 10-15 years.
- AIDS develops usually develops when the CD4 count drops below 200 cells/ml.
Natural selection and the HIV virus
- considerable excitement was generated about 20 years ago by an AIDS drug called AZT (short for azidothymidine).
- AZT is a “base analog”.
- it is incorporated by the HIV virus’ reverse transcriptase into growing DNA strands in the place of T (thymidine).
- if AZT is incorporated into a growing strand, DNA replication is halted - new bases cannot be added past this point.
- thus, AZT works by poisoning the replication of the virus.
- AZT is effective against the HIV virus for a period of 1-2 years and then has little or no effect.
Why? Because of the rapid evolutionary response of the HIV virus to a very strong selective agent - AZT.
- the HIV virus evolves a reverse transcriptase (RT) that has a dramatically lower affinity for the base analog AZT.
- the location of these mutations can be mapped right onto the active site of the enzyme where the growing strand of DNA is made from the RNA template.
- how do we know this?
- because we can isolate and sequence the reverse transcriptase (pol) gene in newly-infected patients and later in the course of infection (once AZT has ceased to be effective) and find mutations in the active site of the enzyme.
- functional studies on the mutant RT show that they indeed have a significantly reduced affinity of AZT.
- therefore, they are able to replicate much more effectively in an AZT environment and will displace viruses that do not have this mutation.
- this represents the process of adaptation by natural selection.
- the population of viruses present in an infected individual evolve over time to become predominated by AZT-resistant genotypes.
- natural selection favoring AZT-resistant reverse transcriptases has occurred repeatedly in virtually every patient treated with AZT.
- this is a striking case of what is called “parallel evolution”.
- parallel evolution refers to the evolution of similar traits in closely-related species in response to the same selective agent.
How does the HIV virus achieve such a dramatic evolutionary response?
- there are two factors responsible for the rapid evolutionary response of the HIV virus to AZT.
- the first factor is its incredibly high mutation rate - some 106 times higher than humans.
- the viral reverse transcriptase does not have a “proofreading” function (i.e., its capacity to correct mistakes in converting RNA to DNA).
- this results in a mutation rate of 1 x 10-3 to 10-4 (per site per generation) compared with human DNA polymerase, which has a mutation rate of about 5 x 10-9.
- this means that the virus can “throw out” an incredibly large number of mutations each replicative cycle.
- most of these will decrease, rather the increase, viral fitness but a small proportion will be advantageous.
- the second factor that is responsible for the rapid evolution of the HIV virus is its short generation time.
- a viral generation can be accomplished in just over a day.
- in a year, it may undergo about 300 generations.
- over the course of a 10 year infection period, when the virus is waging war with the host immune system, it may undergo 3,000 generations.
- in combination with the high mutation rate, HIV virus can evolve over a ten year period what would take human populations 2-3 million years.
The origin of HIV-1 and HIV-2
- a fascinating story is emerging about the origin of the HIV-1 and HIV-2 viruses.
- tracing the evolutionary history of organisms is a branch of evolutionary biology called systematics.
- the main objective behind this field is to reconstruct the evolutionary histories of “taxa” to produce a phylogenetic tree.
- we will study the rules for making phylogenetic trees in lecture 6.
- today we will just present some trees to infer how and where HIV evolved.
- the phylogeny based on DNA sequences of the pol gene illustrates shows two facts about HIV-1 and HIV-2.
- first, they are both closely related simian immunodeficiency viruses (SIV’s) and only distantly related to infectious viruses isolated from other mammals.
- this indicates that the HIV viruses evolved from primate ancestors.
- second, the pattern of viral evolution does not closely mimic the pattern of primate evolution.
- the three HIV strains on the tree do not show any close affinity to each other.
- one of the HIV-2 strains clusters with a virus from the stump-tailed macaque, the other is off on its own showing no affinity with any of the species included in the tree.
- this clearly doesn’t mean that this strain did not have a simian ancestor; just that it isn’t included in the analysis.
- the one HIV-1 strain included in the tree is very similar to an SIV from the common chimpanzee, Pan troglodytes.
- at present the minimum number of times this has occurred is 6 but this is likely to be an underestimate since we have only examined a limited number of HIV sequences.
- the inter-species transfer of infectious diseases like HIV are known as zoonoses.
- a paper came out in February 1999 in Nature, which traced the origin of the HIV-1 virus to one subspecies of chimpanzee, Pan troglodytes troglodytes.
- a subspecies may be thought of as an incipient species - a species in the process of becoming evolutionarily independent of its most closely related species.
- one can construct the phylogenetic relationships of SIV’s in the four subspecies.
- all four subspecies have distinct clades of SIV’s showing that these viruses have been co-evolving with these chimps for a reasonable period of time.
- the subspecies are thought to have been formed about 150,000 to 200,000 years ago and the SIV’s found in each group have been persisting with for at least this period (otherwise the clades would no be so distinct).
- one can then map onto this tree of SIV’s the various HIV-1 strains sequenced to date.
- there are 3 principal groups of HIV-1 viruses.
- M, is the main group that comprises the majority of subtypes spread throughout the world.
- O, is an “outlier” group found in Cameroon, Gabon and Equatorial Guinea.
- N, is a “new” group found in 1998 in two people from Cameroon.
- all three subgroups cluster within the P. t. troglodytes clade.
- furthermore, the origin of HIV-1 in west-central Africa coincides perfectly with the geographic distribution of P. t. troglodytes but not any other subspecies.
- this tells us that P. t. troglodytes was the source of the HIV-1 currently spreading through human populations.
- how did these zoonoses occur?
- it is thought that the recent slaughtering and eating of chimpanzee meat that is responsible for the “jump” of HIV from chimps to humans.
- ape-hunting has become big business in west-central Africa.
- hunters are paid by timber companies to provision logging camps.
- the kills of freelance hunters are traded as far as the cities where ape-meat can fetch premium prices in high class restaurants.
- the numbers of wild chimpanzees are plummeting and all subspecies are endangered.
- this is unfortunate and may prevent us from learning more about virus in its previous host and using this information to halt the epidemic.