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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.

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Phylogenetic analysis of HIV gag gene (p24-p7) sequences (nt 1577–2040, HXB2) from HIV infected Nairobi residents.This tree (neighbor-joining) was created by aligning the selected sequences with reference sequences from Los Alamos database shown in bold). The sequence F1.FR.96.MP411 was selected as the out group.
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pone-0003191-g001: Phylogenetic analysis of HIV gag gene (p24-p7) sequences (nt 1577–2040, HXB2) from HIV infected Nairobi residents.This tree (neighbor-joining) was created by aligning the selected sequences with reference sequences from Los Alamos database shown in bold). The sequence F1.FR.96.MP411 was selected as the out group.

Mentions: 69 samples were successfully amplified for the gag gene in a nested PCR, followed by sequencing. Generated sequences (approximately covering 460–470 bp of p24 and p7 region of gag gene, nt 1577–2040, HXB2) were then used for sequence alignment using Clustal X and to construct the phylogenetic trees using neighbor-joining method with PAUP*. Alignment of sequences with reference sequences from Los Alamos database and Phylogenetic analysis revealed that 39 (56.52%) of the 69 HIV-1 subtypes were A, 13 (18.84%) were subtype D, 7 (10.14%) were subtype C and 2 (2.89%) were subtype G. Simplot analysis revealed a few recombinant types in our study samples: 3 (4.34%) being AD, 1 (1.44%) AC, 1 (1.44%) AG and 3 (4.34%) CRF01_AE (Table 2, Fig. 1).


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

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

Phylogenetic analysis of HIV gag gene (p24-p7) sequences (nt 1577–2040, HXB2) from HIV infected Nairobi residents.This tree (neighbor-joining) was created by aligning the selected sequences with reference sequences from Los Alamos database shown in bold). The sequence F1.FR.96.MP411 was selected as the out group.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0003191-g001: Phylogenetic analysis of HIV gag gene (p24-p7) sequences (nt 1577–2040, HXB2) from HIV infected Nairobi residents.This tree (neighbor-joining) was created by aligning the selected sequences with reference sequences from Los Alamos database shown in bold). The sequence F1.FR.96.MP411 was selected as the out group.
Mentions: 69 samples were successfully amplified for the gag gene in a nested PCR, followed by sequencing. Generated sequences (approximately covering 460–470 bp of p24 and p7 region of gag gene, nt 1577–2040, HXB2) were then used for sequence alignment using Clustal X and to construct the phylogenetic trees using neighbor-joining method with PAUP*. Alignment of sequences with reference sequences from Los Alamos database and Phylogenetic analysis revealed that 39 (56.52%) of the 69 HIV-1 subtypes were A, 13 (18.84%) were subtype D, 7 (10.14%) were subtype C and 2 (2.89%) were subtype G. Simplot analysis revealed a few recombinant types in our study samples: 3 (4.34%) being AD, 1 (1.44%) AC, 1 (1.44%) AG and 3 (4.34%) CRF01_AE (Table 2, Fig. 1).

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