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HIV-1 CRF 02 AG polymerase genes in Southern Ghana are mosaics of different 02 AG strains and the protease gene cannot infer subtypes.

Sagoe KW, Dwidar M, Adiku TK, Arens MQ - Virol. J. (2009)

Bottom Line: The use of the protease gene of HIV-1 for subtyping has shown conflicting results.The polymerase genes of HIV-1 strains from Ghana are made up of recombinants of several CRF 02_AG strains from Ghana, Senegal and Cameroon, but the clinical implications are unknown.Using the HIV-1 protease gene for subtyping will not infer subtypes correctly.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology, University of Ghana Medical School, Accra, Ghana. kwcsagoe@chs.edu.gh

ABSTRACT

Background: Little is known about the detailed phylogeny relationships of CRF 02_AG HIV-1 polymerase genes in Ghana. The use of the protease gene of HIV-1 for subtyping has shown conflicting results.

Methods: The partial polymerase gene sequences of 25 HIV-1 strains obtained with Viroseq reagents were aligned with reference subtypes and alignments trimmed to a 300 bp protease, 661 bp and 1005 reverse transcriptase sequence alignments. Phylogenetic relationships of these alignments were determined with the Neighbour-Joining method using 1000 replicates and recombination patterns determined for the sequences with RIP 3.0 in the HIV sequence database.

Results: Unlike the other alignments, the protease gene had nodes with bootstrap values < 100% for repeat control sequences. Majority of the CRF 02_AG sequences from Ghana were made up of fragments of several strains of CRF 02_AG/AG strains. The protease gene alone is not suitable for phylogenetic analysis.

Conclusion: The polymerase genes of HIV-1 strains from Ghana are made up of recombinants of several CRF 02_AG strains from Ghana, Senegal and Cameroon, but the clinical implications are unknown. Using the HIV-1 protease gene for subtyping will not infer subtypes correctly.

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Phylogenetic trees of sequences from 25 HIV-1 infected patients from Ghana showing relationships of the (a) 300 bp protease (left) and (b) 1305 bp partial polymerase genes (right). Reference subtypes have been prefixed; sequences with accession numbers are sequences obtained by HIV Blast Search. CRF 02_AG sequence with accession number AM279387_R and subtype G with accession number U88826_R are repeat sequences used as internal controls for phylogeny. The CRFs begin with 02 (CRF 02_AG), 01 (CRF 01_AE) and 06 (CRF 06_cpx). The sequences used in this study have been indicated by a filled square.
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Figure 1: Phylogenetic trees of sequences from 25 HIV-1 infected patients from Ghana showing relationships of the (a) 300 bp protease (left) and (b) 1305 bp partial polymerase genes (right). Reference subtypes have been prefixed; sequences with accession numbers are sequences obtained by HIV Blast Search. CRF 02_AG sequence with accession number AM279387_R and subtype G with accession number U88826_R are repeat sequences used as internal controls for phylogeny. The CRFs begin with 02 (CRF 02_AG), 01 (CRF 01_AE) and 06 (CRF 06_cpx). The sequences used in this study have been indicated by a filled square.

Mentions: For the pol. and RT, GHN CRF 02_AG sequences were inferred with sufficient confidence (≥ 70%), but the RTs and prot. had bootstrap values of 57% and 22% respectively. Sequences which were repeated had 100% bootstrap values at their nodes for the pol., RT, and RTs, but not the prot. Although the CRF 02_AG from Cameroon [GenBank: AM279387] and one of the reference subtypes [GenBank: AJ286937] were shown to have the same nucleotide sequences, the node for the two sequences had bootstrap value of 59% for the prot. alignment (Figure 1a). The subtype G from Nigeria [GenBank: U88826] that was repeated in the sequence alignment as U88826_R had bootstrap value of 67% for the prot. alignment (Figure 1a). The bootstrap values for the CRF 02_AG strains were 70% for RT and 57% for RTs, but their tree topologies were similar.


HIV-1 CRF 02 AG polymerase genes in Southern Ghana are mosaics of different 02 AG strains and the protease gene cannot infer subtypes.

Sagoe KW, Dwidar M, Adiku TK, Arens MQ - Virol. J. (2009)

Phylogenetic trees of sequences from 25 HIV-1 infected patients from Ghana showing relationships of the (a) 300 bp protease (left) and (b) 1305 bp partial polymerase genes (right). Reference subtypes have been prefixed; sequences with accession numbers are sequences obtained by HIV Blast Search. CRF 02_AG sequence with accession number AM279387_R and subtype G with accession number U88826_R are repeat sequences used as internal controls for phylogeny. The CRFs begin with 02 (CRF 02_AG), 01 (CRF 01_AE) and 06 (CRF 06_cpx). The sequences used in this study have been indicated by a filled square.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2655287&req=5

Figure 1: Phylogenetic trees of sequences from 25 HIV-1 infected patients from Ghana showing relationships of the (a) 300 bp protease (left) and (b) 1305 bp partial polymerase genes (right). Reference subtypes have been prefixed; sequences with accession numbers are sequences obtained by HIV Blast Search. CRF 02_AG sequence with accession number AM279387_R and subtype G with accession number U88826_R are repeat sequences used as internal controls for phylogeny. The CRFs begin with 02 (CRF 02_AG), 01 (CRF 01_AE) and 06 (CRF 06_cpx). The sequences used in this study have been indicated by a filled square.
Mentions: For the pol. and RT, GHN CRF 02_AG sequences were inferred with sufficient confidence (≥ 70%), but the RTs and prot. had bootstrap values of 57% and 22% respectively. Sequences which were repeated had 100% bootstrap values at their nodes for the pol., RT, and RTs, but not the prot. Although the CRF 02_AG from Cameroon [GenBank: AM279387] and one of the reference subtypes [GenBank: AJ286937] were shown to have the same nucleotide sequences, the node for the two sequences had bootstrap value of 59% for the prot. alignment (Figure 1a). The subtype G from Nigeria [GenBank: U88826] that was repeated in the sequence alignment as U88826_R had bootstrap value of 67% for the prot. alignment (Figure 1a). The bootstrap values for the CRF 02_AG strains were 70% for RT and 57% for RTs, but their tree topologies were similar.

Bottom Line: The use of the protease gene of HIV-1 for subtyping has shown conflicting results.The polymerase genes of HIV-1 strains from Ghana are made up of recombinants of several CRF 02_AG strains from Ghana, Senegal and Cameroon, but the clinical implications are unknown.Using the HIV-1 protease gene for subtyping will not infer subtypes correctly.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology, University of Ghana Medical School, Accra, Ghana. kwcsagoe@chs.edu.gh

ABSTRACT

Background: Little is known about the detailed phylogeny relationships of CRF 02_AG HIV-1 polymerase genes in Ghana. The use of the protease gene of HIV-1 for subtyping has shown conflicting results.

Methods: The partial polymerase gene sequences of 25 HIV-1 strains obtained with Viroseq reagents were aligned with reference subtypes and alignments trimmed to a 300 bp protease, 661 bp and 1005 reverse transcriptase sequence alignments. Phylogenetic relationships of these alignments were determined with the Neighbour-Joining method using 1000 replicates and recombination patterns determined for the sequences with RIP 3.0 in the HIV sequence database.

Results: Unlike the other alignments, the protease gene had nodes with bootstrap values < 100% for repeat control sequences. Majority of the CRF 02_AG sequences from Ghana were made up of fragments of several strains of CRF 02_AG/AG strains. The protease gene alone is not suitable for phylogenetic analysis.

Conclusion: The polymerase genes of HIV-1 strains from Ghana are made up of recombinants of several CRF 02_AG strains from Ghana, Senegal and Cameroon, but the clinical implications are unknown. Using the HIV-1 protease gene for subtyping will not infer subtypes correctly.

Show MeSH