Analysis of HIV type 1 reverse transcriptase: comparing sequences of viral isolates with mutational data.

A result of the high level of mutagenesis during HIV-1 viral replication is that many, if not most, HIV-1 virions and proviruses are defective and are not infectious. There is a vast amount of HIV-1 sequence data available. Unless any particular sequence is shown to be from a stable DNA clone (e.g., lambda) that can transfect cells and produce virions, then it is not known if that sequence was from an infectious HIV-1. Most sequences have not been shown to be from infectious clones. We have reported a saturation mutagenesis of a 109-amino acid region of the HIV-1 reverse transcriptase, in which we assayed the effects of 366 single-amino acid substitutions. We examined a set of sequences in the Los Alamos HIV-1 sequence database. We found that none of the sequences derived from stable infectious clones had substitutions that produce an inactive reverse transcriptase. However, we found that other sequences in this database had substitutions that inactivate the reverse transcriptase. We predict that these sequences are not from infectious clones. This method may also be useful for evaluating the sequences of other viruses.