Rapid identification of human immunodeficiency virus type 1 CRF01_AE and BC recombinants by subtype-specific PCR.
A subtype-specific PCR approach is described for the identification of HIV-1 intersubtype CRF01_AE and BC recombinants, the two predominant subtypes in Southern China. Primers were designed based on the env and gag regions of the HIV-1 genome. Nested PCRs with primers targeting the env region were performed to amplify subtype C, CRF01_AE, or BC recombinants. To differentiate BC recombinants from subtype C virus, a BC recombinant specific gag PCR was then performed. In order to identify the CRF07_BC and CRF08_BC recombinant forms, an additional PCR step was included. Four HIV-1 samples of known subtype, 77 samples with unknown-subtype, and 30 HIV-negative control samples were tested by the new assay. The results of this PCR-based subtyping approach were compared with that of a sequence-based phylogenetic analysis. In total, 73 (94.8%) samples were amplified by the subtype-specific PCR reactions, of which 39 were identified as CRF01_AE, 14 as CRF07_BC, and 20 as CRF08_BC. The sensitivity of this assay was 90.7% for the CRF01_AE recombinant and 100% for BC recombinants. The specificity was 100% when used to identify 30 HIV-negative samples. The reproducibility was 93.8% for CRF01_AE, and 100% for BC recombinants. This subtype-specific PCR technique represents a simple, rapid, and low-cost assay for the identification of HIV-1 CRF01_AE and BC recombinants in Southern China.
Center for AIDS Research & Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning 530021, China.
Hao
H
Luo
Qi-Jian
QJ
Su
Yi-Ming
YM
Shao
Hui
H
Xing
Jie
J
Chen
Wei
W
Liu
Zhi-Yong
ZY
Zhang
Ning
N
Zang
Xin
X
Xiao
Hao
H
Liang
D002681:China; D017931:DNA Primers / Q000235:genetics; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D011995:Recombination, Genetic; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014773:Virology / Q000379:methods*; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics
D017931:DNA Primers; D054299:env Gene Products, Human Immunodeficiency Virus; D054301:gag Gene Products, Human Immunodeficiency Virus