Frequent intra-subtype recombination among HIV-1 circulating in Tanzania.
The study estimated the prevalence of HIV-1 intra-subtype recombinant variants among female bar and hotel workers in Tanzania. While intra-subtype recombination occurs in HIV-1, it is generally underestimated. HIV-1 env gp120 V1-C5 quasispecies from 45 subjects were generated by single-genome amplification and sequencing (median (IQR) of 38 (28-50) sequences per subject). Recombination analysis was performed using seven methods implemented within the recombination detection program version 3, RDP3. HIV-1 sequences were considered recombinant if recombination signals were detected by at least three methods with p-values of ≤0.05 after Bonferroni correction for multiple comparisons. HIV-1 in 38 (84%) subjects showed evidence for intra-subtype recombination including 22 with HIV-1 subtype A1, 13 with HIV-1 subtype C, and 3 with HIV-1 subtype D. The distribution of intra-patient recombination breakpoints suggested ongoing recombination and showed selective enrichment of recombinant variants in 23 (60%) subjects. The number of subjects with evidence of intra-subtype recombination increased from 29 (69%) to 36 (82%) over one year of follow-up, although the increase did not reach statistical significance. Adjustment for intra-subtype recombination is important for the analysis of multiplicity of HIV infection. This is the first report of high prevalence of intra-subtype recombination in the HIV/AIDS epidemic in Tanzania, a region where multiple HIV-1 subtypes co-circulate. HIV-1 intra-subtype recombination increases viral diversity and presents additional challenges for HIV-1 vaccine design.
Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania.
Ireen E
IE
Kiwelu
Vladimir
V
Novitsky
Lauren
L
Margolin
Jeannie
J
Baca
Rachel
R
Manongi
Noel
N
Sam
John
J
Shao
Mary F
MF
McLane
Saidi H
SH
Kapiga
M
M
Essex
D000328:Adult; D015331:Cohort Studies; D005260:Female; D005787:Gene Frequency; D015752:Genes, env; D014644:Genetic Variation / Q000502:physiology; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D011995:Recombination, Genetic; D013636:Tanzania / Q000453:epidemiology; D019562:Viral Load
D015699:HIV Envelope Protein gp120