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.a 突变编号以逆转录酶（RT, Reverse Transcriptase）的首个核苷酸/氨基酸为起始。针对LLV样本中编码RT氨基酸65-210的区域完成了测序。预抑制谱中的突变丰度以携带指定突变的454测序读段占比表示。破折号（-）表示在预设的0.5%读段阈值下，该突变未在测序读段中被检测到。未在预抑制谱中观测到的LLV突变以下划线标注。与RT耐药相关的LLV突变以斜体加粗字体标示。ND表示未确定：样本不可获取，或因病毒载量低于454测序检测的扩增灵敏度而未进行检测。核苷酸：(nt)b 携带特定突变的LLV序列数量（左侧所示）。c 样本已完成处理，但未在该位点生成测序数据。d 样本通过单基因组扩增（Single-genome Amplification, SGA）而非454测序进行分析。对于RM Mmu 37969，在感染后（Post Infection, PI）第10周通过SGA生成了5条序列。e RM Mmu 37969的LLV优势血浆克隆（Predominant Plasma Clone, PPC）突变通过以下10个连锁RT核苷酸替换进行表征：C258T、C291T、A304C、T336C、G364A、A378G、A483G、A484T、T537C及G612A。其中9个突变在感染后第10周获得的两条独立序列上发生连锁。G612A仅在1条感染后第10周的序列中存在，故单独列出。