title: Differentiation of subtypes B and E of human immunodeficiency virus type 1 by polymerase chain reaction using novel env gene primers.
abstract: Novel sets of env gene PCR primers for distinguishing human immunodeficiency virus type 1 (HIV-1) subtypes B and E were designed. These primers anneal to different regions of the env gene and amplify DNA fragments of distinct sizes in a subtype-specific manner. Blood samples from 11 HIV-1 carriers in Thailand and 46 carriers in Japan were examined by PCR. The new env primers detected HIV-1 proviral DNA in 100% (11/11) and 88% (37/42) of the subtype B and E infection cases, respectively. The env primers also detected proviral DNA in saliva and breast milk samples in seven of 11 cases and two of three cases, respectively. The PCR subtyping results matched completely with those obtained by nucleotide sequencing of the env V3 region. The results suggest that the PCR using the env primers designed in this study may be an accurate and cost-effective method for differentiating subtypes B and E of HIV-1 in a large number of clinical samples. However, subtype E specific primer cross-react with subtype A, C, G, the new primer in this study is useful for regions in South East Asia where subtype E is predominant.
authors.affiliation: Department of Developmental Medical Sciences, Institute of International Health, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-0033, Tokyo, Japan.
authors.forename: Fumihiro
authors.initials: F
authors.lastname: Yagyu
authors.forename: Yusei
authors.initials: Y
authors.lastname: Ikeda
authors.forename: Koya
authors.initials: K
authors.lastname: Ariyoshi
authors.forename: Wataru
authors.initials: W
authors.lastname: Sugiura
authors.forename: Som Arch
authors.initials: SA
authors.lastname: Wongkhomthong
authors.forename: Michiaki
authors.initials: M
authors.lastname: Masuda
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ushijima
mesh_terms: D000328:Adult; D001483:Base Sequence; D015331:Cohort Studies; D016384:Consensus Sequence; D017931:DNA Primers; D004279:DNA, Viral / Q000032:analysis* / Q000097:blood; D005260:Female; D005312:Fetal Blood / Q000821:virology; D015752:Genes, env; D015750:Genes, gag; D015658:HIV Infections / Q000175:diagnosis*; D015497:HIV-1 / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D007231:Infant, Newborn; D007564:Japan; D008297:Male; D008895:Milk, Human / Q000821:virology; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012463:Saliva / Q000821:virology; D013785:Thailand
chemical_list: D017931:DNA Primers; D004279:DNA, Viral