Viral RNA-sequencing for the detection of the viruses replicating in humanized mice

The analysis of RNA-sequencing data reveals the proportion of the three viruses simultaneously inoculated into humanized mice. Overall design: Three different HIV-1, CH185 wild-type, the CH185 delta PTAP1 mutant (i.e., CH185_dPATAP1), and the CH185 delta PTAP2 mutant (i.e., CH185_dPATAP2) were co-inoculated into nine humanized mice. At two weeks post-infection, the mice were sacrificed after anesthesia and plasma and spleen were collected. To analyze the proportion of the three different viruses in plasma and spleen samples prepared above, the RT-PCR amplicon sequencing that targets the p6 gag region in HIV-1 was performed. As RT-PCR primers, the CH269-PTAP-F “TAGGGAAAATTTGGCCTTCC” and the CH269-PTAP-R “CCTCCAATTCCCCCTATCAT” were used.