This phase as the SIVmac239Opt infected animals (p = 0.0015 ANOVA).SIVmac
This phase as the SIVmac239Opt infected animals (p = 0.0015 ANOVA).SIVmac239OptXWe recently reported on a pool of molecularly tagged but TAPI-2 site otherwise isogenic variants of SIVmac239 wherein 2? synonymous changes were introduced into the integrase gene to generate genetically distinct but biologically equivalent versions of SIVmac239 [21]. These variants were designed to be combined into a “synthetic swarm” of sequence discriminable but biologically equivalent viruses that can be used to track independent infection events in viral transmission and dissemination; detailed analysis suggested that despite the introduction of only 2? synonymous mutations, two of the variants showed decreased replicative capacity relative to the others (21). We transferred these same molecular tags from the wild type SIVmac239 into the optimized SIVmac239Opt clone and compared replication capacities of each tagged clone. After sequence confirming PubMed ID: that each individual clone had23 9w tabttFennessey et al. Retrovirology (2015) 12:Page 5 ofap27(pg/mL)10 6 10 5 10 4 10Opt WTvRNA copies/mL109 108 107 106 105 104 103time (days)101 100 0 20 40 60 80 100bp27(pg/mL)10 6 10 5 10 4 10Opt WTDays post infectionFigure 4 In vivo replication curves of SIVmac239Opt and wild type SIVmac239. Rhesus macaques were intrarectally infected with either SIVmac239Opt (green), or SIVmac239WT (pink). The average viral load of the macaques infected with SIVmac239WT is shown in red. One macaque infected with SIVmac239Opt rapidly progressed to AIDS and was euthanized at 87 days post infection.time (days)cp27(pg/mL)106 105 104Opt WTreduced replicative capacity of variants D and I, which were reported previously [21] was recapitulated in the optimized versions, confirming our previous report that these two genotypes, despite only three synonymous mutations, restrict viral replication.Primer binding site correctiontime (days)Figure 3 In vitro replication curves of SIVmac239Opt and SIVmac239WT. In vitro replication dynamics of SIVmac239Opt were determined by measuring p27 capsid content six times over 14 days post-infection in CD4+ T-cell enriched PBMCs from three SIVna e, Indian-origin rhesus macaques (a ). Wild type SIVmac239 is displayed in a solid line, and the SIVmac239Opt is displayed with a dashed line.only the reported mutations, each optimized clone was compared to the corresponding wild type clone for in vitro replication in SupT1-R5 cells (Figure 5). Similar to our in vitro replication curves in primary macaque cells, there were some cultures where the optimized virus significantly out performed wild type (clones A, B, H, I, and untagged with p values <0.05 for each clone), but overall, optimized clones were not statistically different from wild type clones (p = 0.377 ANOVA). Interestingly, theIn order to assess the relative fitness costs of each suboptimal nucleotide, wild type virus was grown in vitro on SupT1-R5 cells for 2 months and sampled at least weekly for sequence analysis of vRNA to identify mutants and selection of optimal nucleotides. By day 21, the PBS had completely changed to the optimal version but the Env and Pol mutations had not yet arisen. PubMed ID: While the Env mutation occurred at approximately week 10, the Pol mutations were not seen within the 2 months of this experiment. Although it is clear from published research that all four are suboptimal clones that will mutate to optimal nucleotides given sufficient time and viral replication [1, 6], the mutation with the great.

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