Extended Data Table 3 Phenotypic viral coreceptor tropism analysis for selected variants yielded from deep sequencing

From: In-depth virological and immunological characterization of HIV-1 cure after CCR5Δ32/Δ32 allogeneic hematopoietic stem cell transplantation

  1. Genotypic coreceptor usage was predicted before HSCT using the geno2pheno[454] tool after deep sequencing of the HIV-1 envelope V3 loop (nucleotide 7110–7217 based on the HxB2 reference sequence). In a total of n = 17,701 reads, 0.14% were predicted to be X4-tropic viral sequences. Results are expressed as the probability of classifying an R5-tropic virus falsely as a X4-tropic virus (cutoff 3.5%; FPR ≤ 3.5%, X4-tropic; FPR > 3.5%, R5-tropic). For the phenotypic coreceptor analyses, the nine representative amino acid sequences of the V3 loop shown in the table were cloned into a pHXB2-Δgp120-V3 vector and tested in T cell culture with MT2 cells and the U373-MAGI-CCR5E (CD4+CCR5+CXCR4−) and U373-MAGI-CXCR4CEM (CD4+CCR5−CXCR4+) cell lines. FPR, false positive rate; R5, CCR5-tropic virus; X4, CXCR4-tropic virus.
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