The use of primers from highly conserved pol regions to identify uncharacterized retroviruses by the polymerase chain reaction

Abstract

Two degenerate oligonucleotide primers derived from regions of pol conserved among retroviruses have been synthesized. Polymerase chain reactions utilizing these primers amplify a 135-bp pol fragment in every retrovirus DNA tested to date. The polymerase chain reaction has been linked to a reverse transcriptase step so that a pol-specific DNA fragment can be obtained from a moderate amount of a purified retrovirus or viral RNA. The identity of an unknown retrovirus can be determined by sequencing of the amplified fragment following molecular cloning. This procedure was tested on an unidentified (non-HIV) retrovirus expressed by a B-cell lymphoma line obtained from an AIDS patient. Our PCR assay identified the retrovirus as being highly similar to Mason-Pfizer monkey virus (MPMV) and simian retrovirus 1, which are closely related immunosuppressive type D viruses that cause simian AIDS.