Dataset Information

Deciphering the complex distribution of human immunodeficiency virus type 1 subtypes among different cohorts in Northern Tanzania.

ABSTRACT:

Background

Increased understanding of the genetic diversity of HIV-1 is challenging but important in the development of an effective vaccine. We aimed to describe the distribution of HIV-1 subtypes in northern Tanzania among women enrolled in studies preparing for HIV-1 prevention trials (hospitality facility-worker cohorts), and among men and women in an open cohort demographic surveillance system (Kisesa cohort).

Methods

The polymerase encompassing partial reverse transcriptase was sequenced and phylogenetic analysis performed and subtype determined. Questionnaires documented demographic data. We examined factors associated with subtype using multinomial logistic regression, adjusted for study, age, and sex.

Results

Among 140 individuals (125 women and 15 men), subtype A1 predominated (54, 39%), followed by C (46, 33%), D (25, 18%) and unique recombinant forms (URFs) (15, 11%). There was weak evidence to suggest different subtype frequencies by study (for example, 18% URFs in the Kisesa cohort versus 5-9% in the hospitality facility-worker cohorts; adjusted relative-risk ratio (aRR)?=?2.35 [95% CI 0.59,9.32]; global p?=?0.09). Compared to men, women were less likely to have subtype D versus A (aRR?=?0.12 [95% CI 0.02,0.76]; global p?=?0.05). There was a trend to suggest lower relative risk of subtype D compared to A with older age (aRR?=?0.44 [95% CI 0.23,0.85] per 10 years; global p?=?0.05).

Conclusions

We observed multiple subtypes, confirming the complex genetic diversity of HIV-1 strains circulating in northern Tanzania, and found some differences between cohorts and by age and sex. This has important implications for vaccine design and development, providing opportunity to determine vaccine efficacy in diverse HIV-1 strains.

SUBMITTER: Njai HF

PROVIDER: S-EPMC3859540 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Deciphering the complex distribution of human immunodeficiency virus type 1 subtypes among different cohorts in Northern Tanzania.

Njai Harr F HF Ewings Fiona M FM Lyimo Eric E Foulongne Vincent V Ngerageza Dhamira D Mongi Aika A Ssemwanga Deogratius D Andreasen Aura A Nyombi Balthazar B Ao Tony T Michael Denna D Urassa Mark M Todd Jim J Zaba Basia B Changalucha John J Hayes Richard R Kapiga Saidi H SH

PloS one 20131211 12

<h4>Background</h4>Increased understanding of the genetic diversity of HIV-1 is challenging but important in the development of an effective vaccine. We aimed to describe the distribution of HIV-1 subtypes in northern Tanzania among women enrolled in studies preparing for HIV-1 prevention trials (hospitality facility-worker cohorts), and among men and women in an open cohort demographic surveillance system (Kisesa cohort).<h4>Methods</h4>The polymerase encompassing partial reverse transcriptase ...[more]

PMID: 24349139

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Project description:Full-length reference clones and sequences are currently available for eight human immunodeficiency virus type 1 (HIV-1) group M subtypes (A through H), but none have been reported for subtypes I and J, which have only been identified in a few individuals. Phylogenetic information for subtype I, in particular, is limited since only about 400 bp of env gene sequences have been determined for just two epidemiologically linked viruses infecting a couple who were heterosexual intravenous drug users from Cyprus. To characterize subtype I in greater detail, we employed long-range PCR to clone a full-length provirus (94CY032.3) from an isolate obtained from one of the individuals originally reported to be infected with this subtype. Phylogenetic analysis of C2-V3 env gene sequences confirmed that 94CY032.3 was closely related to sequences previously classified as subtype I. However, analysis of the remainder of its genome revealed various regions in which 94CY032.3 was significantly clustered with either subtype A or subtype G. Only sequences located in vpr and nef, as well as the middle portions of pol and env, formed independent lineages roughly equidistant from all other known subtypes. Since these latter regions most likely have a common origin, we classify them all as subtype I. These results thus indicate that the originally reported prototypic subtype I isolate 94CY032 represents a triple recombinant (A/G/I) with at least 11 points of recombination crossover. We also screened HIV-1 recombinants with regions of uncertain subtype assignment for the presence of subtype I sequences. This analysis revealed that two of the earliest mosaics from Africa, Z321B (A/G/?) and MAL (A/D/?), contain short segments of sequence which clustered closely with the subtype I domains of 94CY032.3. Since Z321 was isolated in 1976, subtype I as well as subtypes A and G must have existed in Central Africa prior to that date. The discovery of subtype I in HIV-1 hybrids from widely distant geographic locations also suggests a more widespread distribution of this virus subtype, or at least segments of it, than previously recognized.

Dataset Information

Deciphering the complex distribution of human immunodeficiency virus type 1 subtypes among different cohorts in Northern Tanzania.

Background

Methods

Results

Conclusions

Publications

Deciphering the complex distribution of human immunodeficiency virus type 1 subtypes among different cohorts in Northern Tanzania.

Similar Datasets

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