Analysis of HIV type 1 reverse transcriptase: Comparing sequences of viralisolates 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. U nless 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 bee n shown to be from infectious clones. We have reported a saturation mutagen esis of a 109-amino acid region of the HIV-1 reverse transcriptase, in whic h we assayed the effects of 366 single-amino acid substitutions. We examine d a set of sequences in the Los Alamos HIV-1 sequence database. We found th at none of the sequences derived from stable infectious clones had substitu tions that produce an inactive reverse transcriptase. However, we found tha t other sequences in this database had substitutions that inactivate the re verse transcriptase. We predict that these sequences are not from infectiou s clones. This method may also be useful for evaluating the sequences of ot her viruses.