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. 2012 Aug 27;7(8):e42801. doi: 10.1371/journal.pone.0042801

Figure 2. Sequence analysis of wild-type (WT) and variant LTRs detected in the spleen and brain.

Figure 2

(A) Consensus sequence of variant LTR genotype groups were aligned to reference, wild-type (SIV/17E-Fr mLTR: −236 to −154 bp) sequence. Dashes (-) indicate conserved nucleotides; insertions and deletions are denoted by (:), horizontal rectangles highlight the JC1 and DS1 C/EBP sites. Vertical rectangles highlight +123 bp A/G and +146C/A substitutions within the DS1 C/EBP site. (*) 22nt variant found in 1 of 180 cloned sequences from the SIV/DeltaB670 swarm virus stock. (B) Frequency of LTR genotypes in spleen RNA from the indicated animals euthanized at 10, 21, 42, 48 and 84 days p.i. is depicted. Bars with gray/black background indicate the presence of DS1C/A in the LTRs sequenced. Bars with white background indicate absence of DS1C/A substitutions. (C) Genotype frequency of LTRs sequenced from brain RNA/DNA homogenates from each individual animal, as indicated. (¥) RNA derived LTR sequencing results for one 21 days p.i. animal, PBc2, are shown next to DNA derived LTR sequencing results from the same animal. (†) Indicates variant genotypes that are non-wild-type but lack the DS1C/A substitution.