Richa's paper from when she was in the lab has been published. She had a lot of help from Youya as well as Chris and Doug. The aim of the study was to determine why a specific polymorphic amino acid substitution in HIV-1 reverse transcriptase (RT), V179I, arises in people living with HIV and treated with antiretroviral therapy containing newer non-nucleoside RT inhibitors (NNRTIs) like etravirine or rilpivirine. Richa showed that V179I increases NNRTI resistance in combination with the mutations Y181C or Y181V but not E138K.
She and Youya also showed that V179I also slightly improved replication of Y181C or Y181V HIV-1 in the presence of rilpivirine. These results suggest that V179I provides a selective advantage for the virus in the presence of etravirine and rilpivirine.
Like in humans, we previously detected low frequencies of V179I in HIV-1 from 4/10 humanized mice that became infected despite rilpivirine pre-exposure prophylaxis. The V179I substitution involves a G to A point mutation, which is characteristic of mutations induced by the host proteins APOBEC3F and APOBEC3G. We analyzed single-genome sequences from our mouse study and found that the mice with no detectable V179I HIV-1 had a significantly lower frequency of HIV-1 genomes that contained G to A mutations in the RT coding region than the group of mice with V179I HIV-1 (left). In contrast, the frequency of other mutations (not G to A) in RT was similar in both groups of animals (right).
To show whether APOBEC3 could induce V179I, Richa and Youya grew Y181C HIV-1 in cells with low APOBEC3F/G (CEM-SS) and cells with high APOBEC3F/G (CEM) with or without increasing concentrations of rilpivirine over 4 rounds of selection.
After the first round of selection in the first experiment, 0.12 - 0.14% of HIV-1 genomes from CEM cells, with or without RPV selection, encoded V179I. In the presence of RPV, V179I rose to nearly 0.5% frequency in CEM cells. In contrast, 0.05 - 0.08% of HIV-1 genomes isolated in CEM-SS cells after round 1 encoded V179I. V179I was not detected after four rounds of selection in CEM-SS cells. In the second experiment, the frequency of V179I was below 0.9% in the cultures after rounds 1 and 2 with the exception of virus grown in CEM cells in the presence of RPV, in which the mutation was detected at 1.2 - 1.3%. After rounds 3 and 4, the frequency of V179I rose to 7.3% and 5.4% in CEM cells + RPV but remained < 0.8% in the other cultures. Surprisingly, genomes containing V179I rose to 11.2% frequency in CEM-SS cells after 4 rounds of selection. These results suggest that APOBEC3F/G accelerates selection of V179I in HIV-1 RT in the presence of RPV and that V179I provides a selective advantage for the virus.
The results from this study provide insight in how and why the enigmatic V179I substitution is selected in HIV-1 RT during NNRTI treatment. While this residue change does not directly affect HIV-1 susceptibility to NNRTIs, and also likely NNRTI binding to RT, it appears to provide better replication in the presence of diarylpyrimidine NNRTIs by either enhancement of resistance or replication. This information could be useful in designing better RT inhibitors that can still inhibit prevalent NNRTI-resistant HIV-1 variants. Read more here!
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