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The HIV-1 virus is about 120-150 nm in size and has a genome only about 10,000 base pairs long.

Other viruses are far more efficient, for example lambda phage has something like a tenth the volume and a genome five times longer. In other words, while half the volume of a lambda phage is taken up with DNA, in HIV it's more like 1%. Why is HIV so space inefficient?

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    $\begingroup$ One point is that lamba infects bacteria, which are more simple than eukaryotic cells. $\endgroup$ – Chris Feb 29 '16 at 15:31
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There are many other things inside the HIV capsid besides RNA. The ssRNA is bound to the p7 nucleocapsid protein, the p6 late assembly protein, as well as integrase and reverse transcriptase, both of which are vital for infectivity. Also enclosed within the virion are Vif (Viral Infectivity Factor), protease, Nef (Negative Regulatory Factor), Tat (HIV Transactivator), and Vpr (Viral Protein R). Surrounding the capsid is a matrix formed by the p17 viral protein, and finally the lipid membrane envelope (taken from the host cell upon budding), which contains host cell proteins as well as the vital trimer of gp120/gp41 heterodimers, which bind to the target cell.

HIV Structure

From Wikimedia

HIV (and many other viruses) depend on binding to certain cell surface receptors, and a larger total size increases the chances of binding to multiple receptors and potentially triggering receptor-mediated endocytosis, if that is part of the virus's entry strategy.

The naked λ phage binds to the lamB porin of single-celled prokaryotic E. coli by way of the phage's J protein and injects its DNA load into the bacterium, where host factors circularize and supercoil it, allowing for transcription to begin. While the phage's genomic material can be integrated into the host's chromosome, it is not required. Additionally, there is no nuclear barrier to cross.

lambda phage

From Wikimedia, numbers in parentheses are copies per virion.

On the other hand, HIV is a highly complex enveloped lentivirus that targets very specific cells in its multicellular eukaryotic host HIV requires reverse transcription and the assembly of a large pre-integration complex to transport the viral DNA into the nucleus and integrate it into the host's genome, all before it can even start producing new viral proteins.

Trying to compare the "packing efficiency" of HIV to the λ phage isn't just comparing apples to oranges, it's comparing apples to goats. The two viruses are completely different, with the only essential similarities being that they are viruses that infect cells.

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First, your idea that "efficiency" has some relation to "genome size" divided by "diameter" is odd. You end up with arbitrary numbers that are not any kind of measure of "efficiency".

Second, HIV is an enveloped virus, while lambda phage is not; the internal viral core, less than half the size, is a better comparison. Other enveloped viruses like influenza (100 nm, 14000 bp) are in the same ballpark. Even many non-enveloped viruses, like Tobacco mosaic virus (40x300 nm, 6400 bp) have similar or "worse" ratios than HIV.

But the most important point is that it doesn't much matter. It's not a measure of any kind of "efficiency" in the biological sense.

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    $\begingroup$ First, that's not my idea. My idea is that "efficiency" could be related to cell volume dividing by genome volume. That's called "packing efficiency". If you think DNA packaging is weird and biologically meaningless, you're simply wrong. See any number of references that immediately come up when searching for DNA packaging $\endgroup$ – Mark Eichenlaub Feb 29 '16 at 17:10
  • $\begingroup$ @MarkE can you clarify what you mean? Everything that comes up for me when searching for "DNA packaging" has to do with chromosomes and how that interacts with protein production - but viruses by themselves don't produce any proteins in that state. $\endgroup$ – YviDe Mar 1 '16 at 7:06
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    $\begingroup$ Obviously DNA packaging is important. But obviously your measure of "efficiency" is meaningless. Why? Because so many viruses violate it. You've created a hypothesis ("DNA:Volume ratio is important"), facts don't match it (phage to HIV have a huge range), so your hypothesis is wrong. Facts always beat hypotheses. $\endgroup$ – iayork Mar 1 '16 at 10:54
  • $\begingroup$ I created no such hypothesis. You read the word "efficiency" and put meaning into it yourself that I did not imply. Regardless, see "Cell Biology By the Numbers", pp 9 "the viruses show strong economy of size, minimizing the required volume to carry their genetic material". If some viruses do show this economy of size and some do not, there must be reasons for that based on what the viruses do. Figuring out what those reasons are would be an excellent answer to the question. $\endgroup$ – Mark Eichenlaub Aug 24 '16 at 15:54

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