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Why do retroviruses (e.g.HIV) convert their RNA genome to DNA (using reverse transcriptase) and then transcribe it back into viral RNA (and translate that into viral proteins). Surely to replicate their genome it would be simpler to use RNA-dependent RNA polymerases as RNA viruses like Measles Virus do.

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    $\begingroup$ Biology isn't as stringent as quantum physics, but still, "everything which is not forbidden is allowed." Retroviruses use reverse transcriptase because a) they can and b) it works. You can get into complex evolutionary arguments about comparative benefits, but ultimately retroviruses stick around because reverse transcriptase works well enough for them to continue to survive. Evolution isn't goal oriented - it doesn't seek simplicity just for simplicity's sake. What works, works, and what doesn't, doesn't. $\endgroup$ – R.M. Sep 8 '17 at 20:51
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    $\begingroup$ I now feel my previous comments were based on a misunderstanding of the question. On this basis I have withdrawn them, answered the question, and reversed my close vote. The question is still very basic, but I can see how you might have become confused if the subject was not introduced to you properly. $\endgroup$ – David Sep 10 '17 at 21:13
  • $\begingroup$ I have changed your title and question to clarify it as several people have been confused by it. If this is not what you meant could you please elaborate. $\endgroup$ – David Sep 11 '17 at 15:34
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I am going to focus the answer on mainly "why HIV virus has evolved such mechanisms to go from RNA to DNA and back to RNA when it could simply use the first RNA to make its copies". While others have already discussed the broad point, I will discuss more about the details. There are a few points which might support this, all of which basically come down to evolution.

  • Increased Mutations: the process of conversion of viral RNA to DNA is carried out by the viral enzyme reverse transcriptase. The point here is that this process of reverse transcription is extremely error prone (Zheng et al, 2005), which increase its chances of evolving drug resistance and other abilities.

  • Recombination: again, the enzyme reverse transcriptase possesses ability to cause recombination of viral DNA. During recombination, the nascent DNA can switch multiple times between the two copies of the viral RNA (Charpentier et al, 2006), known as copy-choice recombination, and can rapidly shuffle the genetic information between the parental and progeny genomes.

  • Post-transcriptional modifications: after the viral DNA is completely transcribed, it undergoes splicing to form mature mRNA. These mRNAs lead to production of viral proteins Tat and Rev. Accumulationof Rev inside nucleus allowes the full mRNAs to leave the nucleus and form viral genomes or structural proteins Gag and Env (Pollard et al, 1998). Thus, reverse transcription is vital for the virus.

References:

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Interpreting the question

Initially I interpreted the question as little more than “Why one type of virus rather than another?” (dsDNA. ssDNA, ssRNA [+ve v. –ve] etc.), and this (which would be unanswerable) was the way @Taimur seems to have understood it. And I also felt that the poster’s reference to ‘complexity’ reflected more his familiarity with other viruses than any real appreciation of what is complex in a molecular manner.

However I now think I misunderstood the question because of not appreciating the erroneous assumption on which I believe it is based. If I am correct, it could be rephrased in the following manner to make that assumption clear:

If the only purpose of integrating a DNA copy of the retroviral RNA into the host genome is to replicate the RNA in the virion, why is an RNA-dependent RNA polymerase not used as in other RNA viruses?"

Answer

This stage of the retroviral life cycle in which a DNA copy is integrated into the host genome is not an incidental stage in a mechanism to replicate the virion RNA — it is the key element of the modus operandi or strategy of existence of the virus.

Explanation

As explained in the first paragraph of the Wikipedia article on retroviruses, once integrated into the host genome it can persist there:

“The host cell then treats the viral DNA as part of its own genome, translating and transcribing the viral genes along with the cell's own genes…”

One way of thinking of this is as a strategy the virus adopts for ‘hiding’ until circumstances are suitable for it to produce more infectious progeny. One might even regard the form that is integrated into the host DNA as the viral genome — rather than the form that is encapsulated by lipid and protein into virus particles.

This sort of lifestyle is similar in some ways to that of certain DNA bacteriophages that can produce either lytic or lysogenic infections. Such persistence of viral genomes in the host is also seen in some eukaryotic DNA viruses like herpes simplex virus, in which an individual may have what is called a latent infection, which produces occurrences of cold sores (in the case of HSV1) throughout the lifetime of the individual as the virus is activated from time to time by various stimuli.

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Viruses are one of the particles whose evolutionary origin is still a mystery to scientists. Various hypotheses have been presented but none of them have been proven so far.

However, as one of our commenters has said, "What works, works and what doesn't, doesn't." This is the basic concept of the evolutionary theory. All organisms which can survive in an environment using a certain adaptation, whether it takes more time or less time, will survive and continue using the same adaptation.

One more point to consider is that individual organisms never evolve, only populations (organisms of the same species living in the same area at the same time) evolve. This means that a retro virus will not change to adapt to a simpler method just because it takes less time. If conditions arise that do not favour retroviral method of using reverse transcriptase but favours the method of other RNA viruses, then retroviruses will simply then decrease in number until they are zero and RNA viruses will survive.

I hope to have satisfactorily answered your inquiry.

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    $\begingroup$ Well, dude! You are not writing a letter. While we do expect formal language in questions and answers here, please don't post "overformal" answers. $\endgroup$ – another 'Homo sapien' Sep 9 '17 at 16:08
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    $\begingroup$ @another'Homosapien' I will make sure to avoid that next time. Thank you. $\endgroup$ – Taimur Sep 9 '17 at 16:46
  • $\begingroup$ @another'Homosapien' I have made the edits. $\endgroup$ – Taimur Sep 9 '17 at 16:47

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