Browsing by Author "Dwidar, M."

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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
(2009-02-26) Sagoe, K.W.; Dwidar, M.; Adiku, T.K.; Arens, M.Q.
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.
HIV-1 CRF 02 AG polymerase genes in southern Ghana are mosaics of different 02 AG strains and the protease gene cannot infer subtypes.
(2009) Sagoe, K.W.; Dwidar, M.; Adiku, T.K.; Arens, M.Q.
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.
Variability of the human immunodeficiency virus type 1 polymerase gene from treatment naïve patients in Accra, Ghana
(Journal of Clinical Virology, 2007-10) Sagoe, K.W.C.; Dwidar, M.; Lartey, M.; Boamah, I.; Agyei, A.A.; Hayford, A.A.; Mingle, J.A.A.; Arens, M.Q.
Background: Little is known about the HIV-1 drug resistance mutations in Ghana. Objectives: To determine the background protease (PR) and reverse transcriptase (RT) mutations of HIV-1 from treatment naïve patients in Ghana. Study design: Twenty-five plasma samples randomly selected were analyzed for drug resistance mutations. The molecular phylogeny and recombinant patterns of the polymerase gene of HIV-1 were also analysed. Results: No major drug-resistance mutations were seen in protease or reverse transcriptase genes. The L10I, L10V, V11I and E35G minor mutations were seen in four patients, while the V179E was observed in a patient with subtype G. An insertion of lysine was found at codon 36 of the protease gene of one patient. The predominant subtype was the CRF02_AG strain (n = 22), but 3 (13.6%) of these were recombinants with HIV-1 subtype K and/or A1. Two patients harboured unclassified/complex strains with D/CRF01_AE and G/CRFAG_02 subtypes for the PR and RT, respectively, using the Stanford Database. Viral loads (VL) ranged from 2290 to >1,500,000 c/ml (mean = 339,065 c/ml). Conclusions: Treatment naïve patients in Ghana before scale-up may have minor but not major PR mutations and high viral loads. The clinical effects of minor mutations/polymorphisms in the PR and RT genes and recombinants need to be investigated. © 2007 Elsevier B.V. All rights reserved.