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Creating an Emerging 3-DCR HIV NYC Recombinant

Recombinomics Commentary
February 15, 2005

>> In a slightly different scenario, Klotman says it's possible two different strains of the virus were contracted almost simultaneously from two different sources, and they landed in a single cell.
"It has been well documented in the past that when two strains infect a single cell they can recombine their genetic material and create a new and seemingly more powerful virus," says Klotman. <<

There are several reasons why recombination is the more likely mechanism for acquisition of CXCR4 tropism, wild type RC, and 3-DRC.  Since the same profile has been seen in two others, it is unlikely that they were all dually infected with the same two viruses.  It is much easier to generate a match if the same virus is involved, but the virus is a recombinant.  As a recombinant, the same three properties are encoded by the same genome and then transmit faithfully together.  A single virus would also generate a cleaner signal in the sequencing, and if all three patients had two viruses, there would be mixed signals in all three sequences.

In addition, the timing of the other two infections predates the NYC case that progressed rapidly,  Thus, although multiple encounters involving unprotected sex could generate a recombinant, it was probably generated earlier, and the earlier patient may have engaged in the same type of dangerous encounters.

Full sequences from all three patients can resolve these issues, but at this time it sounds like a recombinant that was generated at an earlier date and appeared on both coasts of the United States at about the same time last fall.

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