Comparative analysis of cell culture and prediction algorithms for phenotyping of genetically diverse HIV-1 strains from Cameroon.

AIDS Research and Therapy
Viswanath RagupathyIndira Hewlett

Abstract

With the advent of entry inhibitors, monitoring of viral tropism in the clinical setting is important. Conventional methods are cell-based and lengthy, therefore V3 sequence based prediction algorithms are becoming increasingly attractive as monitoring tools. Here we report a comparative analysis of viral tropism of strains circulating in Cameroon where diverse and emerging variant strains are prevalent. Viruses were isolated from 17 HIV positive individuals from three cities in Cameroon. Ghost cell lines expressing either CCR5 or CXCR4 with CD4 or CD4 alone (NIH AIDS Reagent Program) were used to determine co-receptor usage. HIV replication was determined by measuring p24 antigen levels. Plasma viral load (VL) was determined using the Versant bDNA assay. Nucleotide sequencing was performed on the V3 region and sequences were edited, aligned and translated into amino acids as described in the algorithm. Bio-informatics tools based on the 11/25 and charge rule were used to predict co-receptor usage. The majority of patient isolates in our study were CRF02_AG or CRF02_AG containing recombinants. Tropism of these complex viruses based on the cell culture assay was determined to be R5 in 15/17 (88.2%) patients. However, two patient...Continue Reading

References

Feb 6, 1997·Nature·M T DittmarP Simmonds
Mar 15, 2005·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Pierre DelobelJacques Izopet
Dec 11, 2007·Nature Biotechnology·Thomas LengauerRolf Kaiser
Jun 12, 2008·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Carmen de MendozaUNKNOWN Spanish HIV Seroconverter Study Group
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Dec 14, 2011·Journal of Visualized Experiments : JoVE·Saleta SierraThomas Lengauer

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Citations

Jan 14, 2011·AIDS Research and Human Retroviruses·Ana RevillaMichael M Thomson
Oct 20, 2011·The Journal of Antimicrobial Chemotherapy·Elena DelgadoLucía Pérez-Álvarez
Nov 8, 2014·PloS One·Christelle Mbondji-WonjeIndira K Hewlett

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Methods Mentioned

BETA
PCR
sequence based prediction

Software Mentioned

Performa
Clustal
geno2pheno

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