Limits...
Genetic analysis of HIV-1 subtypes in Nairobi, Kenya.

Khoja S, Ojwang P, Khan S, Okinda N, Harania R, Ali S - PLoS ONE (2008)

Bottom Line: Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG.Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C.Our analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan.

ABSTRACT

Background: Genetic analysis of a viral infection helps in following its spread in a given population, in tracking the routes of infection and, where applicable, in vaccine design. Additionally, sequence analysis of the viral genome provides information about patterns of genetic divergence that may have occurred during viral evolution.

Objective: In this study we have analyzed the subtypes of Human Immunodeficiency Virus -1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya.

Methodology: 69 blood samples were collected from a diverse subject population attending the Aga Khan University Hospital in Nairobi, Kenya. Total DNA was extracted from peripheral blood mononuclear cells (PBMCs), and used in a Polymerase Chain Reaction (PCR) to amplify the HIV gag gene. The PCR amplimers were partially sequenced, and alignment and phylogenetic analysis of these sequences was performed using the Los Alamos HIV Database.

Results: Blood samples from 69 HIV-1 infected subjects from varying ethnic backgrounds were analyzed. Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG. Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C.

Conclusion: Our analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A. Additionally, the prevalence of highly divergent, complex subtypes, intersubtypes, and the recombinant forms indicates viral mixing in Kenyan population, possibly as a result of dual infections.

Show MeSH

Related in: MedlinePlus

Neighbor-Joining Phylogenetic trees of the three most represented subtypes, A (Fig. 2A), D (Fig. 2B) and C (Fig. 2C), depicting geographical associations of the studied sample group with other global regions.Reference Sequences from Los Alamaos Database have been indicated in bold. Out groups selected for Fig. 2A, B, and C were, respectively, A.EE.02.EST2002 394, NL.x.M12020, and IL.98.98IS002.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2527130&req=5

pone-0003191-g002: Neighbor-Joining Phylogenetic trees of the three most represented subtypes, A (Fig. 2A), D (Fig. 2B) and C (Fig. 2C), depicting geographical associations of the studied sample group with other global regions.Reference Sequences from Los Alamaos Database have been indicated in bold. Out groups selected for Fig. 2A, B, and C were, respectively, A.EE.02.EST2002 394, NL.x.M12020, and IL.98.98IS002.

Mentions: For the three most represented subtypes in our study, namely, A, D and C, deeper phylogenetic analysis was performed to explore their geographic origin (Fig. 2A, B, C). Our sample subtype A sequences clustered with sequences from varied geographical regions represented by Uganda, Kenya, Sweden, Rwanda, South Africa, Australia, India, China and Democratic Republic of the Congo (Fig. 2A). These results indicate a significant diversity among our subtype A sequences, possibly indicating an older HIV-1 infection in the Nairobi population. Conversely, Phylogenetic analysis of subtype D sequences revealed a relatively lesser degree of diversity (Fig. 2B). Sequences of 10 out of 12 strains for subtype D clustered together, and with a reference sequence from Uganda indicating a strong phylogenetic relationship and lesser genetic divergence compared to subtype A sequences. Two out of twelve subtype D sequences clustered independently with reference sequences from Kenya. Lastly, subtype C sequences, in a manner similar to our subtype D sequences, clutered closely together, and with African countries (Fig. 2C). Four out of seven subtype C sequences clustered closely with reference sequence from Ethiopia while three sequences clustered with references from South Africa and Botswana. One of the sequence, 26KE, representing subtype A, was found to be hypermutated by the Hypermut Program at Los Alamos Database (http://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermut.html).


Genetic analysis of HIV-1 subtypes in Nairobi, Kenya.

Khoja S, Ojwang P, Khan S, Okinda N, Harania R, Ali S - PLoS ONE (2008)

Neighbor-Joining Phylogenetic trees of the three most represented subtypes, A (Fig. 2A), D (Fig. 2B) and C (Fig. 2C), depicting geographical associations of the studied sample group with other global regions.Reference Sequences from Los Alamaos Database have been indicated in bold. Out groups selected for Fig. 2A, B, and C were, respectively, A.EE.02.EST2002 394, NL.x.M12020, and IL.98.98IS002.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2527130&req=5

pone-0003191-g002: Neighbor-Joining Phylogenetic trees of the three most represented subtypes, A (Fig. 2A), D (Fig. 2B) and C (Fig. 2C), depicting geographical associations of the studied sample group with other global regions.Reference Sequences from Los Alamaos Database have been indicated in bold. Out groups selected for Fig. 2A, B, and C were, respectively, A.EE.02.EST2002 394, NL.x.M12020, and IL.98.98IS002.
Mentions: For the three most represented subtypes in our study, namely, A, D and C, deeper phylogenetic analysis was performed to explore their geographic origin (Fig. 2A, B, C). Our sample subtype A sequences clustered with sequences from varied geographical regions represented by Uganda, Kenya, Sweden, Rwanda, South Africa, Australia, India, China and Democratic Republic of the Congo (Fig. 2A). These results indicate a significant diversity among our subtype A sequences, possibly indicating an older HIV-1 infection in the Nairobi population. Conversely, Phylogenetic analysis of subtype D sequences revealed a relatively lesser degree of diversity (Fig. 2B). Sequences of 10 out of 12 strains for subtype D clustered together, and with a reference sequence from Uganda indicating a strong phylogenetic relationship and lesser genetic divergence compared to subtype A sequences. Two out of twelve subtype D sequences clustered independently with reference sequences from Kenya. Lastly, subtype C sequences, in a manner similar to our subtype D sequences, clutered closely together, and with African countries (Fig. 2C). Four out of seven subtype C sequences clustered closely with reference sequence from Ethiopia while three sequences clustered with references from South Africa and Botswana. One of the sequence, 26KE, representing subtype A, was found to be hypermutated by the Hypermut Program at Los Alamos Database (http://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermut.html).

Bottom Line: Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG.Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C.Our analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan.

ABSTRACT

Background: Genetic analysis of a viral infection helps in following its spread in a given population, in tracking the routes of infection and, where applicable, in vaccine design. Additionally, sequence analysis of the viral genome provides information about patterns of genetic divergence that may have occurred during viral evolution.

Objective: In this study we have analyzed the subtypes of Human Immunodeficiency Virus -1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya.

Methodology: 69 blood samples were collected from a diverse subject population attending the Aga Khan University Hospital in Nairobi, Kenya. Total DNA was extracted from peripheral blood mononuclear cells (PBMCs), and used in a Polymerase Chain Reaction (PCR) to amplify the HIV gag gene. The PCR amplimers were partially sequenced, and alignment and phylogenetic analysis of these sequences was performed using the Los Alamos HIV Database.

Results: Blood samples from 69 HIV-1 infected subjects from varying ethnic backgrounds were analyzed. Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG. Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C.

Conclusion: Our analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A. Additionally, the prevalence of highly divergent, complex subtypes, intersubtypes, and the recombinant forms indicates viral mixing in Kenyan population, possibly as a result of dual infections.

Show MeSH
Related in: MedlinePlus