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There are two copies of the RNA in the HIV virion. These are retroviruses. So, they can make cDNA from even just one copy using reverse transcriptase.

What is the use of the other? Are both integrated into host chromosomes?

My guesses are:

  1. To ensure increased chance of getting integrated. But, if one gets in, the other also should be able to.

  2. To increase the amount of protein translated (if both get integrated).

  3. Two for two sets of chromosomes. (Seems juvenile but still a possibility. although, I do not think there are specific sites of preference for the viral DNA. Are there?)

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You are not totally correct because these two strands don't have to be the same, they can be genotypically different, which occurs when a cell is infected by two distinct HIV strains. Also HIV uses reverse transcriptase which can "jump" from one strand to the other so sometimes pieces get repeated, skipped etc. So you will get a recombinant --> more genetic diversity(see this article) I won't go into to much detail but if you want to know more I would highly recommend to read the article I linked after genetic diversity. So to summarize:

  • genetic diversity, because of switching between the two strands (this makes it so hard to cure AIDS e.g.)
  • If one RNA strand gets damaged it can use parts of the other RNA strand as template, so to synthesize DNA
  • apparently the dimeric form of RNA in HIV is essential for successive replication of the virus

Source: previous mentioned article(HIV-1 RNA dimerization: It takes two to tango.)

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  • $\begingroup$ This indeed is the best article on the matter and is worth the time to read. $\endgroup$ – Dart Feld Oct 17 '16 at 19:06

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