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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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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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S clustered within the CRF02_AG clade, reinforcing the notion that this viral clade is a major contributor of genetic material to new recombinants [20]; an alternative explanation, however, could be that the gag and nef genes were amplified from different viruses co-infecting the same patients. Ongoing molecular and clinical surveillance will reveal whether new recombinants will begin to circulate
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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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F known clades. Although the majority of the outlier viruses found in our study were also URFs, they remained outliers after the removal of recombinant segments. It thus appears that these sequences represent viruses that are genuinely highly divergent and are possibly extant descendants of previously unknown early divergingTable 3 Inter and intraclade recombinantsSample ID BS02 BS09 BS11 BS13 BS2
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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