Novel methods for HIV sequencing and genotyping

Abstract

Methods are provided for amplifying regions of the HIV pol gene amplifying double-stranded nucleic acid template derived from HIV tube RT-PCR with novel PCR primers to produce amplified target sequences. Methods are also provided for analyzing the nucleotide sequence of these amplified targets using novel sequencing primers and the data is analyzed. The determined nucleotide sequence can be compared to the sequence of known drug resistance mutations in the HIV pot gene to determine the viral genotype.

1 - 42 . (Canceled)  
     
     
         43 . A method of identifying mutations associated with drug resistance in an HIV quasi-species comprising: 
 a) preparing nucleic acid from a human body fluid sample;    b) preparing double stranded nucleic acid template from HIV RNA in the nucleic acid;    c) amplifying a region of HIV pol from the double stranded nucleic acid template to obtain an amplification product;    d) sequencing the amplification product using one or more specific sequencing primers; and    e) identifying mutations associated with drug resistance in an HIV quasi-species.