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Hose residing on isolated branches outside of subtrees containing previously defined HIV-1 subtype or CRF lineages. Outlier sequences on the other hand were defined as those residing on basal branches of subtrees containing previously defined HIV-1 subtype or CRF lineages. Nucleotide sequences were deposited in GenBank [JX244899-JX244948 for gag and JX244949JX245003 for nef]. Clinical and demograp
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Two samples for which only gag or nef was typed, these were classified as belonging to CRF11_cpx. Notably, despite subtypes B and C collectively accounting for approximately 75 infections worldwide [16], none of our sequences were classified as belonging to either of these clades. In 10/46 samples from which both nef and gag sequences were analysed, they were classified as belonging to different
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Replicates following removal of recombinant sequence fragments by a blinded fully exploratory screen for recombination using RDP3. Black squares at the end of the branches represent the gag and nef sequences sampled from Cameroon in this study, while red squares represent intragene recombinant fragments in our samples. The gag tree was rooted using HIV-1 group N, O, P and SIV CPZ isolates, while t
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Replicates following removal of recombinant sequence fragments by a blinded fully exploratory screen for recombination using RDP3. Black squares at the end of the branches represent the gag and nef sequences sampled from Cameroon in this study, while red squares represent intragene recombinant fragments in our samples. The gag tree was rooted using HIV-1 group N, O, P and SIV CPZ isolates, while t
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Ibution of HIV-1 in CameroonSample ID BS01 BS02 BS03 BS04 BS05 BS06 BS09 BS10 BS11 BS12 BS13 BS14 BS16 BS18 BS19 BS20 BS21 BS22 BS23 BS24 BS25 BS26 BS27 BS29 BS30 BS31 BS32 BS35 BS38 BS39 BS40 BS42 BS43 BS44 BS45 BS46 BS47 BS48 BS49 BS50 BS51 BS53 BS54 BS55 gag gene CRF02_AG A-like G G CRF02_AG CRF02_AG CRF02_AG A1 CRF02_AG G CRF02_AG CRF02_AG CRF02_AG NDc CRF02_AG NDc CRF02_AG CRF02_AG CRF02_AG C
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One of the newly sequenced gag genes (BS72) was apparently derived through recombination between F2 and CRF36_cpx parental viruses, one of the nef genes was apparently derived through recombination between F and CRF22_01A1 parental viruses. The phylogenetic analysis of gag sequences derived from the Cameroonian samples further revealed four sequences (BS09, BS25, BS16 and BS42) situated on diverge
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Orrespondence: Darrin.Martin@uct.ac.za; Wendy.Burgers@uct.ac.za 3 Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa 1 Division of Medical Virology, University of Cape Town, Cape Town, South Africain west central Africa, at 5.3 [8]. This, together with the co-circulation of divergent variants of multiple clades, h
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Cias Zembe1, Eitel Mpoudi-Ngole2, Carolyn Williamson1,4 and Wendy A Burgers1*AbstractBackground: Cameroon, in west central Africa, has an extraordinary degree of HIV diversity, presenting a major challenge for the development of an effective HIV vaccine. Given the continuing need to closely monitor the emergence of new HIV variants in the country, we analyzed HIV-1 genetic diversity in 59 plasma s

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