Evaluation of pre-screening methods for the identification of HIV-1 superinfection.
The aim of this study was to compare sensitivity thresholds of two pre-screening methods - the heteroduplex mobility assay (HMA) and the presence of ambiguity codes in population-based sequences - applied for detection of HIV-1 superinfection. HIV-1 env C2-C4 PCR products generated from 48 serum samples isolated from 24 HIV-1 positive and therapy-naïve homosexual men at seroconversion and at approximately 1 year thereafter were subjected to HMA and population sequencing. Clonal sequence analysis was used to determine the sensitivity of each method to detect sequence variability. Results from HMA were compared to pairwise genetic distance of clonal sequences; heteroduplexes resulted from as little as 1.4% pairwise distance between two sequences and were detected even when only 1.5% of the pairwise distance comparisons exceeded this distance threshold. By contrast, the ambiguity code approach using population-based sequencing detected only 20.1% of existing sequence variation and was less sensitive to minority populations <or=20%, resulting in an underestimation of HIV-1 diversity. Thus, HMA was found to be more sensitive for detection of sequence variations than the ambiguity code approach, suggesting that HMA would be a more appropriate method to pre-screen for HIV-1 superinfection.
Rachinger
Andrea
A
Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands.
van de Ven
Tom Derks
TD
Burger
Judith A
JA
Schuitemaker
Hanneke
H
van 't Wout
Angélique B
AB
D024202:Electrophoretic Mobility Shift Assay / Q000379:methods*; D015658:HIV Infections / Q000175:diagnosis* / Q000821:virology; D015497:HIV-1 / Q000235:genetics / Q000302:isolation & purification*; D020180:Heteroduplex Analysis / Q000379:methods*; D018451:Homosexuality, Male; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D015163:Superinfection / Q000175:diagnosis* / Q000821:virology; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics
D054299:env Gene Products, Human Immunodeficiency Virus