Molecular Evolution Methods to Study HIV-1 Epidemics

Abstract

Nucleotide sequences of HIV isolates are obtained routinely to evaluate the presence of resistance mutations to antiretroviral drugs. But, beyond their clinical use, these and other viral sequences include a wealth of information that can be used to better understand and characterize the epidemiology of HIV in relevant populations. In this review, we provide a brief overview of the main methods used to analyze HIV sequences, the data bases where reference sequences can be obtained, and some caveats about the possible applications for public health of these analyses, along with some considerations about their limitations and correct usage to derive robust and reliable conclusions.

Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning

“…These prediction methods are not capable of adequately identifying the multiple genetic sources of CRF sequences. Detailed comparative studies of these methods for the classification of infectious diseases, especially for the HIV viruses can be found in (Patiño-Galindo and González-Candelas, 2018;Fabeni et al, 2017). More recently, a recombination analysis tool was developed to understand the status of viral recombination in the early stages of HIV infection (Song et al, 2018).…”