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Fig. 6 | Retrovirology

Fig. 6

From: Replication-competent HIV-1 in human alveolar macrophages and monocytes despite nucleotide pools with elevated dUTP

Fig. 6

Sequence analyses of virus produced in MC, AM, and CD4+ T cell QVOA. A The HIV-1 genome structure and the region targeted for sequencing is shown. The first PCR (6953-7530) and second PCR (7015-7374) regions were targeted by nested PCR primers using cDNA obtained from AM, MC, and T cell QVOA’s from P2 to P5. The purified amplicons (359 bp) were then sequenced using Illumina MiSeq. B Outline of the stepwise procedure used in targeted amplicon sequencing. C Major env amino acid sequences derived from sequencing extracellular viral RNAs produced in QVOAs. The consensus reference sequence is derived from 2635 HIV-1 clinical isolates. Boxed regions at the protein sequence level show the mutation spectrum within the CD4-associated and co-receptor binding sites. The positions are relative to the HXB3 strain. Sequences derived from myeloid cell infections are indicated in blue [either monocyte (M) or alveolar macrophage (AM)] and sequences obtained from T cell infections are in red with the numerical patient identification shown in Tables 1 and 2. The major variant percentages are indicated

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