1
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
1
Combine to form a C5 convertase. Runaway complement activation is prevented by binding of Complement Receptor 1 (CR1) and a constitutively active membrane bound Decay Accelerating Factor (DAF, or CD55) which can prevent the complement cascade[51]. In patients with severe dengue, large amounts of C3a have been detected revealing a role for complement in dengue pathogenesis. This finding might be an
1
Ormation were obtained. RNA was extracted from plasma samples, reverse transcribed and PCR amplified as described previously [12] using subtype non-specific HIV-1 primers for HIV-1 full length gag [12] and nef [13] genes, and sequenced. Sequenced fragments were assembled using ChromasPro. Full length gag and nef sequences were generated and aligned using MUSCLE with manual editing in MEGA5, togeth
1
Trees were constructed from these sequences with 100 full maximum likelihood bootstrap replicates (implemented in PHYML [14]), following either complete removal of recombinant sequence fragments or the division of recombinant sequences into their constituent fragments by a blinded fully exploratory screen for recombination using RDP3 [15]. The recombination screen was fully exploratory in that eve
1
Sion Partial Remission 11 (25) Stable Disease 12 (27) Progressive Disease 21 (48) Not assessable 0 (0) Survival (Months) Time to Progression 3.6 Overall Survival 10.0 (0) 9 (60) 5 (33) 1 (7) 0 (0)0 (0) 2 (9) 8 (32) 13 (59) 0 (0)0 (0) 0.002 10 (36) 10 (36) 0.001 8 (30) 0 (0)0 (0) 1 (6) 2 (13) 13 (81) 0 (0) 0.03 0.7.72.9 9.0.6.4 10.3.1 10.0.Only statistically significant p values have been included.
1
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
1
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
1
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