Decoding HIV-1 Next Move Through Matrix Protein p17 Quasi-Species

Since the introduction of combined antiretroviral therapy, acquired immune deficiency syndrome (AIDS)-related lymphomas account for a growing proportion of deaths among people living with human immunodeficiency virus (PLWHIV). In addition to the immune deficiency caused by AIDS and other cofactors, it has been shown that circulating HIV-1 proteins play a critical role in lymphoma development. The HIV-1 matrix protein p17 (refp17) is released from infected cells and accumulates in lymph nodes of PLWHIV, even during effective pharmacological control of viral replication. Circulating refp17 deregulates the biological activity of different immune cells. Moreover, p17 variants (vp17s) characterized by peculiar amino acid insertions occurring in the C-terminal region of the protein, differently from the refp17, also induce B-cell growth and clonogenicity. Notably, vp17s were found at a significantly higher prevalence in PLWHIV with than without lymphoma. HIV-1 mutants expressing clonogenic vp17s are actively spreading, and their prevalence is globally increasing worldwide. RNA viruses exist as a population of quasi-species, transmitted from one host to another, which ultimately leads to viral evolution by generating new master sequences. Here, we developed a next-generation sequence approach to evaluate the frequency of vp17 quasi-species in PLWHIV upon time and demonstrated that the incidence of vp17s also increases at quasi-species levels. Additionally, we established a regression model capable of predicting the insertions with higher probability to be fixed, further highlighting the evolutionary relevance of the C-terminal region in the adaptation of p17 to the human host.