Rapid and simple characterization of in vivo HIV-1 sequences using solid-phase direct sequencing

Abstract

Solid-phase direct sequencing was used to obtain in vivo sequence data of polymerase chain reaction (PCR)-amplified HIV-1 p25/p7 gene segments. The solid-phase sequencing method was compared to double-strand sequencing of preparative gel electrophoresis-purified amplification products and found to give more consistent results. Lysates of cells were compared to purified DNA as PCR template. HIV-1 sequences were as well amplified from lysates as from purified DNA and 7,780 bp of sequence from 41 samples were produced by direct sequencing. Sequence analysis revealed common sequence motifs relating the sequence to the Euroamerican and African groups of sequences previously described. The results indicate that many viruses of diverse origin circulate in Finland, although the majority seems to be of Euroamerican type. Solid-phase direct sequencing may provide a valuable tool for both epidemiological and pathogenic studies of in vivo HIV-1 infections.