Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus

The use of methamphetamine and infection of HIV are both considered public health issues by the Centers of Disease Control and Prevention (CDC). Many studies have shown the effect of methamphetamine, HIV, and both to the central nervous system. The use of methamphetamine not only increases the tendency of HIV transmission, but also the severity of the infection, which may lead to neurodegeneration and neurocognitive disorders. Several studies have examined the gene expression changes in the host due to viral infection, antiretroviral treatment, and the use of methamphetamine, but there is a lack of understanding of their impact on the virus. We investigated their effect on the HIV-1 virus by analyzing the amount of reads obtained from RNA sequencing. We showed that the use of antiretroviral drugs reduced viral read levels, whereas methamphetamine increased them. The expression level of some of the HIV-1 genes such as gag, pol, and nef, inferred from the count of reads mapped to their genomic locations, showed different temporal states among our biological samples.