How does a virus like HIV mutate into so many strains, and yet all of them are harmful to our immune system? What gives this virus the ability to mutate so efficiently?
Others have already touched the important points. Consider this as a summary.
What gives HIV the ability to mutate?
All organisms mutate by two mechanisms:
- Replication errors
- Mutagenesis by physical/chemical agents that cause a chemical change (lesion) on DNA
The main enzyme responsible for HIV replication is reverse transcriptase which makes a DNA copy of its RNA genome. All RNA and DNA polymerases make some amount of error but the error rate of reverse transcriptase is much higher than usual DNA-dependent DNA polymerases because it does not have a proofreading mechanism.
How does a virus like HIV mutate into so many strains, and yet all of them are harmful to our immune system?
As indicated in previous answers, the mutations will produce a virions with a spectrum of infectivity/pathogenicity (some can even be non-infective). However, the immune system acts as a selective barrier which selects only those mutants that can survive (similar to what happens in evolutionary process of natural selection). The selected strains expand their population and that is how these strains get established.
What gives HIV the ability to mutate?
HIV is a single standed RNA virus. DNA is much more stable than RNA as it has a stronger backbone and it is typically double stranded. But HIV mutates at a rate far higher than just being a RNA virus. That's because it uses an enzyme called reverse transcriptase (RT) to build it's RNA genome from RNA bases.
RT is meant to copy the old HIV and make a new one but it does a rubbish job. Most the time it copies it well but every now and then (3 x 10−5 per nucleotide base) it puts in a random base. That might seem like a small rate but that's HUGE if that was coding our genome we would die (if we ever even lived). And since HIV's replication rate is enormously high, there's always going to be a range of good and junk HIV (but it's mostly just junk - next answer for why that's not a bad thing).
But that's not all, RT doesn't just use one old HIV to make a new one. It can use several different old HIVs to make a new one that's not only a combination of all the other ones but then add in the mutations from above, completely different.
So I get that there's lots of mutated strains all over the place. Surely that'd make them useless because the mutations are random?
Yeah they are random and yes that does mean some virus particles are useless. But it's very variable. There's ones which are greatly infectious, partly infectious, slightly infectious and basically junk. The body doesn't really know which ones are which and that's the beauty of it all. The body tries to fight all of them and has no clue which one to get. If it happens to target the greatly infectious one, the numbers of this go down but then the partly infectious one will become the most infectious one and the cycle continues. The junk HIV is basically just a sticky pool of most of the HIV particles that just gets the immune system going crazy and diverts it from the real threat.
Viral recombination produces genetic variation that contributes mostly to the evolution of the HIV-1 virus.
HIV being an RNA Virus utilizes an enzyme called reverse transcriptase, which produces DNA from RNA. HIV also has two RNA genomes. After infection and then replication, which is catalyzed by reverse transcriptase, recombination between the two genomes can occur. specifically the single-strand (+)RNA genomes are reverse transcribed to form DNA. Then during this reverse transcription the nascent DNA can switch multiple times between the two copies of the viral RNA and multiple recombination occur throughout the genome. Furthermore, multiple events per genome may occur during each replication cycle, thus compounding the mutation.
Simple answer is that those mutations that create inactive virus, will never show up on screen, since it will be asymptomatic. In same fashion if virus loses its ability to infect new target (via sexual contact or blood directly) it will show up only in first victim, so that effectively be a non-problem for society.
Addendum: I think I answered portion, starting with "and yet...", which seems to be most important in the question. I think that exact mechanism of mutagenesis must be covered in literature, if known. Also, it seems that since there are no vaccine for HIV, it's mutagenesis cannot be really "efficient", since it is not actively fighting anything.
First, you have to keep in mind that patients are not infected with a single strain. Because HIV is a chronic disease, and given its rapid mutation rate, it has enough time to evolve into a pool of enormous strains called "quasi species". So the virulence manifested is not virulence of individual strain, but the overall virulence of the quasi species.
Actually, because of its high mutation rate, HIV produces many failure strains. These strains are even unable to replicate and account for around half of its progenies! So they're certainly avirulent. But these progenies will die out very soon. However, HIV makes billions of copies per day. So there will always be fully replication competent and fully virulent strains. That's how its virulence sustains. So patients will always develop AIDS if left untreated.
Also, HIV may produce progenies with varying virulence. But the overall virulence is not determined by a single strain. And our immune system may serve as a natural selection. Only strains with good replication efficiency and immune evasion ability can survive. This may also explain how the virulence sustains.
Actually, there're a few people infected with Nef deficient HIV mutants. Nef is an accessory gene. HIV without it can still replicate but cause much milder disease. However, Nef is crucial to the immune evasion mechanism of HIV. So HIV strains without it are more likely be out competed by fully virulent ones.
I think influenza is another example. Influenza is also rapidly mutating, but its virulence varies greatly. From highly pathogenic avian flu to mild seasonal flu. I think the reason is that influenza don't cause chronic infection, so they don't generate quasi species, and there's no natural selection process. That's why the virulence of influenza fluctuates greater. Warning, this is just my guess.