title: Molecular epidemiology of HIV Type 1 in preparation for a Phase III prime-boost vaccine trial in Thailand and a new approach to HIV Type 1 genotyping.
abstract: To characterize HIV-1 genotypes in candidate populations for a prime-boost phase III vaccine trial in Thailand, specimens from prevalent and incident HIV-1 infections from a family planning clinic population in Rayong Province and a community cohort in Chon Buri Province, collected from 1998 to 2001, were genotyped. A new multiregion hybridization assay, MHAbce, capable of distinguishing HIV-1 CRF01_AE, subtype B, and subtype C and their recombinants, was developed and applied to prevalent infections. Most incident and selected prevalent infections were studied by complete genome sequencing. By MHAbce, 168 of 194 prevalent infections were genotyped. Of these, 90.5% were CRF01_AE, 2.4% were subtype B, and 7.2% showed discordant or dual probe reactivity, indicative of recombination or dual infection, respectively. Among 23 incident infections, 20 were sequenced. Eighteen CRF01_AE, one subtype B, and one CRF01/B recombinant strains were seen. Two CRF01/B and one CRF01/C recombinant were identified among selected prevalent infections. These results indicate that incident and prevalent HIV-1 infections in Rayong and Chon Buri during 1998-2001 were 90% CRF01_AE, 3% subtype B, and 7% either recombinant or dual. This study frames the genetic diversity of HIV-1 in these cohorts in their preparatory phase for the ongoing ALVACHIV (vCP1521) prime, AIDSVAX B/E boost, phase III vaccine trial and will provide a benchmark for interpretation and analysis.
authors.affiliation: Department of Pediatrics, Phramongkutklao Hospital School of Medicine, Bangkok, Thailand.
authors.forename: Veerachai
authors.initials: V
authors.lastname: Watanaveeradej
authors.forename: Michael W
authors.initials: MW
authors.lastname: Benenson
authors.forename: Mark De
authors.initials: MD
authors.lastname: Souza
authors.forename: Narongrid
authors.initials: N
authors.lastname: Sirisopana
authors.forename: Sorachai
authors.initials: S
authors.lastname: Nitayaphan
authors.forename: Chalermsri
authors.initials: C
authors.lastname: Tontichaivanich
authors.forename: Ramase
authors.initials: R
authors.lastname: Amphaipit
authors.forename: Philip O
authors.initials: PO
authors.lastname: Renzullo
authors.forename: Arthur E
authors.initials: AE
authors.lastname: Brown
authors.forename: John G
authors.initials: JG
authors.lastname: McNeil
authors.forename: Merlin L
authors.initials: ML
authors.lastname: Robb
authors.forename: Deborah L
authors.initials: DL
authors.lastname: Birx
authors.forename: Sodsai
authors.initials: S
authors.lastname: Tovanabutra
authors.forename: Jean K
authors.initials: JK
authors.lastname: Carr
authors.forename: Francine E
authors.initials: FE
authors.lastname: McCutchan
mesh_terms: D016915:AIDS Vaccines / Q000627:therapeutic use*; D000328:Adult; D005260:Female; D014644:Genetic Variation / Q000235:genetics; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000235:genetics / Q000379:methods*; D010802:Phylogeny; D012313:RNA / Q000235:genetics; D016865:Reassortant Viruses / Q000235:genetics*; D013785:Thailand / Q000453:epidemiology
chemical_list: D016915:AIDS Vaccines; C039919:RNA, recombinant; D012313:RNA