Role of genomic regions encoding non-structural proteins of human immunodeficiency virus type 1 in determining its genetic variant

Introduction. HIV infection remains a global public health problem. One of the key elements in the system of measures aimed at controlling HIV-infection is molecular genetic surveillance. The data obtained make it possible to solve a number of problems in the field of practical epidemiology, and are also of fundamental importance, expanding the understanding of the mechanisms underlying the variability of HIV-1. Most often, the HIV-1 genetic variant is determined by analysing the pol gene region. However, a number of studies are currently underway to investigate other fragments of the HIV-1 genome, such as genes coding its non-structural proteins. The aim of the study is to assess the role of regions of the genome encoding non-structural proteins of HIV-1 in determining its genetic variant, in particular, for viruses circulating in Russia. Materials and methods. Genomic maps of reference sequences of HIV-1 circulating recombinant forms and the HIV-1 nucleotide sequences obtained from HIV-infected patients were analyzed. The study design included stages collection of biosamples, proviral DNA extraction, amplification, sequencing, identification of HIV-1 genetic variants and analysis of the obtained data. Recombination breakpoints frequencies in different regions of the genome were compared using the Mann–Whitney criterion with Bonferroni multiplicity correction and chi-square with Benjamin–Hochberg multiplicity correction. Results. It was found that among the regions of the HIV-1 genome encoding its structural proteins, the most frequent recombination breakpoints occurred in pol (RT) (p 0.001/0.002); among the regions encoding non-structural proteins — in nef (p 0.001/0.007/0.018). At the same time, the genotyping of the nef gene region more often (in 38% of cases) influenced the final HIV-1 genetic variant determination when assessed on a random sample of patients. Conclusion. The regions of the HIV-1 genome with a high frequency of recombination breakpoints were determined.