LLV mutations and their abundance in the pre-suppression profilea

aMutations are numbered beginning with the first nucleotide/amino acid of RT. The region encoding RT amino acids 65-210 was sequenced from LLV samples. Mutation abundance in the pre-suppression profile is expressed as the percentage of 454 sequence reads encoding the given mutation. Dashes (-) indicate that the specified mutation was not observed in sequence reads at a pre-determined 0.5% read threshold. LLV mutations that were not observed in the pre-suppression profile are underlined. LLV mutations associated with RT drug resistance are indicated by bold italics. ND, not determined: samples were either unavailable or not tested because viral loads were below the amplification sensitivity of the 454 sequencing assay. Nucleotide: (nt)bNumber of LLV sequences containing a specific mutation (shown at left).cSample was processed; however, sequence data was not generated at this position.dSample analyzed by single-genome amplification (SGA) and not 454 sequencing. Five sequences were generated by SGA at week 10 PI for RM Mmu 37969.eThe LLV predominant plasma clone (PPC) mutation in RM Mmu 37969 was characterized by the following ten linked RT nucleotide substitutions: C258T, C291T, A304C,T336C, G364A, A378G, A483G, A484T, T537C, and G612A. Nine of these mutations were linked on two individual sequences obtained at week 10 PI. G612A was only present in one of the week 10 PI sequences and is listed separately.