Comparative analysis and generation of a robust HIV-1 DNA quantification assay.
Details
Serval ID
serval:BIB_62022265AD93
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Comparative analysis and generation of a robust HIV-1 DNA quantification assay.
Journal
Journal of virological methods
ISSN
1879-0984 (Electronic)
ISSN-L
0166-0934
Publication state
Published
Issued date
01/2019
Peer-reviewed
Oui
Volume
263
Pages
24-31
Language
english
Notes
Publication types: Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Publication Status: ppublish
Abstract
HIV-1 infection cannot be cured due to the presence of the latent reservoir (LR). Novel cure or treatment strategies, such as "shock and kill" or therapeutic vaccination, aim to reduce or eradicate the LR. Cure strategies utilise robust DNA quantification assays to measure the change in the LR in low copy scenarios. No standard assay exists, which impedes the reliable comparison of results from different therapy and vaccine trials and HIV-1 total DNA quantification methods have not been previously compared. The HIV-1 long terminal repeat (LTR) has been shown to be the best target for DNA quantification. We have analysed two HIV-1 quantification assays, both able to differentiate between the variant HIV-1 DNA forms via the use of pre-amplification and primers targeting LTR. We identify a strong correlation (r=0.9759, P<0.0001) between assays which is conserved in low copy samples (r=0.8220, P<0.0001) indicating that these assays may be used interchangeably. The RvS assay performed significantly (P=0.0021) better than the CV assay when quantifying HIV-1 total DNA in patient CD4+ T lymphocytes. Sequence analysis demonstrated that viral diversity can limit DNA quantification, however in silico analysis of the primers indicated that within the target region nucleotide miss-matches appear infrequently. Further in silico analysis using up to-date sequence information led to the improvement of primers and enabled us to establish a more broadly specific assay with significantly higher HIV-1 DNA quantification capacity in patient samples (p=0.0057, n=17).
Keywords
CD4-Positive T-Lymphocytes/virology, Cell Line, DNA, Viral/analysis, DNA, Viral/genetics, Genetic Variation, HIV Infections/virology, HIV Long Terminal Repeat/genetics, HIV-1/genetics, HIV-1/isolation & purification, Humans, Polymerase Chain Reaction, Viral Load/methods, Cure, DNA quantification, HIV-1, Reservoir, Therapeutic vaccines
Pubmed
Web of science
Create date
29/10/2018 16:42
Last modification date
20/08/2019 15:18