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What are the odds that the variants are the way the body is supposed to be and the "non" variants are actually the result of bad genetics 100s or 1000s of years ago.

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At the protein level the body has backup systems in case of the failure of one. In the case of CCR5 it has a number of other CCR receptors that bind the same ligands. I have no idea of what order the CCR receptors developed. What is known is that the deletion of the CCR5 alleles came about anywhere from a few thousand years ago to possibly 10,000 years ago. The CCR5 genes must have been first since they exist in animals that predate the human species.