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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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Harp PM, Hahn BH: Origins of HIV and the AIDS Pandemic. Cold Spring Harb Perspect Med 2011, 1:a006841. 3. Brennan CA, Bodelle P, Coffey R, Devare SG, Golden A, Harris B, Holzmayer V, Luk KC, Schochetman G, Swanson P, Yamaguchi J, Vallari A, Ndembi N, Ngansop C, Makamche F, Mbanya D, Gurtler LG, Zekeng L, Kaptue L, Hackett J Jr: The prevalence of diverse HIV-1 strains was stable in Cameroonian bloo
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Ck squares at the end of the branches represent the nef sequences sampled from Cameroon in this study, while red squares represent intragene recombinant fragments in our samples. Abbreviations HIV: Human Immunodeficiency Virus; CRF: Circulating recombinant form; URF: Unique recombinant form; RNA: Ribonucleic acid; PCR: Polymerase Chain Reaction. Competing interests The authors declare that they ha
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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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Cpx (4 each), and clades A, F, CRF01_AE and CRF36_cpx (2 each). In addition, 22 of the studied viruses apparently had nef and gag genes from viruses belonging to different clades, with the majority (8/10) having either a nef or gag gene derived from CRF02_AG. Interestingly, five gag sequences (10 ) and three (5 ) nef sequences were neither obviously recombinant nor easily classifiable into any
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Kh R, Awazi B, Hewlett I: Increased genetic diversity and intersubtype recombinants of HIV-1 in blood donors from urban Cameroon. J Acquir Immune Defic Syndr 2007, 45:361?63. 6. Ndembi N, Abraha A, Pilch H, Ichimura H, Mbanya D, Kaptue L, Salata R, Arts EJ: Molecular characterization of human immunodeficiency virus type 1 (HIV-1) and HIV-2 in Yaounde, Cameroon: evidence of major drug resistance mu
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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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Es represent the gag sequences sampled from Cameroon in this study, while red squares represent intragene recombinant fragments in our samples. The blue squares show the new divergent branches formed by viruses sampled in this study. Sequence C.ZM.2006.ZM1464F appears to have been mis-labelled in the LANL database, and consistently groups with subtype A1. Additional file 2: Detailed phylogenetic a

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