title: Identification and characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx recombinant subtypes in Mali, West Africa.
abstract: Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subtypes in this area have not been systematically assessed. Herein, we undertook genetic analyses on full-length env sequences derived from HIV-1-infected individuals living in the capital city of Mali, Bamako. Of 23 samples we examined, 16 were classified as CRF02_AG and three had a subsubtype A3. Among the remaining HIV-1 strains, CRF06_cpx and CRF09_cpx were each found in two patients. Comparison of phylogenies for six matched pol and full-length env sequences revealed that two strains had discordant subtype/CRF designations between the pol and env regions: one had A3(pol)CRF02_AG(env) and the other had CRF02_AG(pol)A3(env). Taken together, our study demonstrated the high prevalence of CRF02_AG and complexity of circulating HIV-1 strains in Mali. It also provided evidence of ongoing virus evolution of CRF02_AG, as illustrated by the emergence of more complex CRF02_AG/A3 intersubtype recombinants in this area.
authors.affiliation: Clinical Services Program, SAIC-Frederick, Inc. , NCI-Frederick, Frederick, Maryland 21702, USA. himamichi@nih.gov
authors.forename: Hiromi
authors.initials: H
authors.lastname: Imamichi
authors.forename: Ousmane
authors.initials: O
authors.lastname: Koita
authors.forename: Djeneba
authors.initials: D
authors.lastname: Dabitao
authors.forename: Sounkalo
authors.initials: S
authors.lastname: Dao
authors.forename: Mahamadou
authors.initials: M
authors.lastname: Ibrah
authors.forename: Dramane
authors.initials: D
authors.lastname: Sogoba
authors.forename: Robin L
authors.initials: RL
authors.lastname: Dewar
authors.forename: Steve C
authors.initials: SC
authors.lastname: Berg
authors.forename: Min-Kang
authors.initials: MK
authors.lastname: Jiang
authors.forename: Mark
authors.initials: M
authors.lastname: Parta
authors.forename: Janice A
authors.initials: JA
authors.lastname: Washington
authors.forename: Michael A
authors.initials: MA
authors.lastname: Polis
authors.forename: H Clifford
authors.initials: HC
authors.lastname: Lane
authors.forename: Anatole
authors.initials: A
authors.lastname: Tounkara
mesh_terms: D000293:Adolescent; D000328:Adult; D016000:Cluster Analysis; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D008297:Male; D008302:Mali / Q000453:epidemiology; D008875:Middle Aged; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D015995:Prevalence; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D054299:env Gene Products, Human Immunodeficiency Virus