Abstract
Previous molecular characterization of Human immunodeficiency virus (HIV-1) samples from Cabo Verde pointed out a vast HIV-1 pol diversity, with several subtypes and recombinant forms, being 5.2% classified as AU-pol. Thus, the aim of the present study was to improve the characterization of these AU sequences. The genomic DNA of seven HIV-1 AU pol-infected individuals were submitted to four overlapping nested-PCR fragments aiming to compose the full-length HIV-1 genome. The final classification was based on phylogenetic trees that were generated using the maximum likelihood and bootscan analysis. The genetic distances were calculated using Mega 7.0 software. Complete genome amplification was possible for two samples, and partial genomes were obtained for the other five. These two samples grouped together with a high support value, in a separate branch from the other sub-subtypes A and CRF26_A5U. No recombination was verified at bootscan, leading to the classification of a new sub-subtype A. The intragroup genetic distance from the new sub-subtype A at a complete genome was 5.2%, and the intergroup genetic varied from 8.1% to 19.0% in the analyzed fragments. Our study describes a new HIV-1 sub-subtype A and highlights the importance of continued molecular surveillance studies, mainly in countries with high HIV molecular diversity.
Highlights
Human immunodeficiency virus (HIV) originated from multiple zoonotic transmission events of the simian immunodeficiency virus (SIV) from non-human primates to humans in Central and West Africa, resulting in two types of HIV-1 that encompassed groups M, N, O, and P [1,2,3], in addition to HIV-2 [4]
The HIV-1 M group is responsible for the HIV/AIDS pandemic and, currently, phylogenetic analyses based on complete genomes revealed that this group is composed of 10 subtypes (A, B, C, D, F, G, H, J, K, L), as well as circulating (CRFs) or unique (URFs) recombinant forms [5,6]
In a previous study of HIV samples from Cabo Verde, molecular epidemiological data of the pol region revealed a high prevalence of HIV-1 subtypes G (36.6%) and CRF02_AG (30.6%), URFs (10.4%), sub-subtype F1 (9.7%), B (5.2%), CRF05_DF (3.0%), C (2.2%), CRF06_cpx (0.7%), CRF25_cpx (0.7%), and CRF49_cpx (0.7%), while all HIV-2 infections belonged to group A
Summary
Human immunodeficiency virus (HIV) originated from multiple zoonotic transmission events of the simian immunodeficiency virus (SIV) from non-human primates to humans in Central and West Africa, resulting in two types of HIV-1 that encompassed groups M, N, O, and P [1,2,3], in addition to HIV-2 (groups A–H) [4]. The HIV-1 M group is responsible for the HIV/AIDS pandemic and, currently, phylogenetic analyses based on complete genomes revealed that this group is composed of 10 subtypes (A, B, C, D, F, G, H, J, K, L), as well as circulating (CRFs) or unique (URFs) recombinant forms [5,6]. In 2018, a reclassification of HIV-1 A sub-subtypes was proposed based on phylogenetic analyses carried out with full-genome sequences obtained from public sequence databases. In a previous study of HIV samples from Cabo Verde, molecular epidemiological data of the pol region revealed a high prevalence of HIV-1 subtypes G (36.6%) and CRF02_AG (30.6%), URFs (10.4%), sub-subtype F1 (9.7%), B (5.2%), CRF05_DF (3.0%), C (2.2%), CRF06_cpx (0.7%), CRF25_cpx (0.7%), and CRF49_cpx (0.7%), while all HIV-2 infections belonged to group A. The aim of the present work was to obtain and characterize the HIV-1 full-length genome sequences, which allowed the description of a new HIV-1 sub-subtype A, here denominated as A8
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