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Displaying record number 58425

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HXB2 Location	Gag(180-188) p24(48-56) DNA(1327..1353)	Gag Epitope Map
Author Location	Gag(180-188)
Epitope	TPQDLNTNL	Epitope Alignment
Subtype	A1
Species (MHC/HLA)	human(B*42:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	ML1111: A*30:01, A*36:01, B*42:01, B*57:03, C*17:01, C*18:01
Country	Kenya
Experimental methods	Other
Keywords	assay or method development

Notes

• Ultra-deep parallel pyrosequencing using nested PCR was compared to and found to be vastly superior to Sanger clone-based sequencing. 96 ART-naive HIV-1 (clade A1, B, C or D) -infected subjects' HIV-Gag protein when sequenced by both methods, revealed 14,034 variations by pyrosequencing technology versus 3,632 variations by Sanger's method. These variations were located in previously experimentally determined CTL epitopes of Gag. The sequencing method chosen for a study affects genetic variations found, host-virus interactions detected and evolutionary conclusions drawn.
• Parallel 454 pyrosequencing method detected sequence that generated a cosensus epitope read of TPQDLNTNL from patient ML1111. When Sanger clone-based sequencing was used however, the same functional, immunogenic site output a different consensus epitope of T(T/I)PQDLNTNL.

References

Liang2011 Binhua Liang, Ma Luo, Joel Scott-Herridge, Christina Semeniuk, Mark Mendoza, Rupert Capina, Brent Sheardown, Hezhao Ji, Joshua Kimani, Blake T. Ball, Gary Van Domselaar, Morag Graham, Shane Tyler, Steven J. M. Jones, and Francis A. Plummer. A Comparison of Parallel Pyrosequencing and Sanger Clone-Based Sequencing and Its Impact on the Characterization of the Genetic Diversity of HIV-1. PLoS One, 6(10):e26745, 2011. PubMed ID: 22039546. Show all entries for this paper.