Abstract
Surveillance of HIV circulating recombinant forms (CRFs) is important because HIV diversity can affect various aspects of HIV infection from prevention to diagnosis and patient management. A comprehensive collection of pol sequences obtained from individuals diagnosed with HIV-1 from 2000 to 2016 in Slovenia was subtyped to identify possible unique recombinant forms (URFs). Selected samples were subjected to near full-length genome (NFLG) sequencing and detailed recombination analyses. Discordant subtyping results were observed for 68/387 (17.6%) sequences and 20 sequences were identified as the most probable URFs and selected for NFLG characterization. Further, 11 NFLGs and two sequences of >7000 base pairs were obtained. Seven sequences were identified as “pure” subtypes or already characterized CRFs: subtype B (n = 5), sub-subtype A6 (n = 1), and CRF01_AE (n = 1). The remaining six sequences were determined to be URFs; four displayed a single recombination event and two exhibited a complex recombination pattern involving several subtypes or CRFs. Finally, three HIV strains were recognized as having epidemic potential and could be further characterized as new CRFs. Our study shows that the identification of new CRFs is possible, even in countries where HIV diversity is considered limited, emphasizing the importance of the surveillance of HIV recombinant forms.
Highlights
Even though a successful antiretroviral treatment (ART) has been available for over two decades, human immunodeficiency virus (HIV) remains one of the major global disease burdens, causing770,000 deaths in 2018 [1]
These sequences were aligned together with the Compendium alignment which was obtained from the Los Alamos database and a set of the most similar sequences to serve as controls [18]
The subtyping tools yielded at least one discordant result in 68/387 (17.6%) partial pol sequences obtained from individuals with an HIV-1 diagnosis from 2000 to 2016 in Slovenia (Table 1)
Summary
Even though a successful antiretroviral treatment (ART) has been available for over two decades, human immunodeficiency virus (HIV) remains one of the major global disease burdens, causing770,000 deaths in 2018 [1]. Even though a successful antiretroviral treatment (ART) has been available for over two decades, human immunodeficiency virus (HIV) remains one of the major global disease burdens, causing. Two major hurdles are the viruses ability to integrate into the human genome and its high genetic diversity, hampering the extensive efforts to design a drug to eradicate HIV from its reservoirs and to design an effective prophylactic vaccine. Even if a vaccine becomes available and adopted, continuous surveillance of HIV subtypes and recombinant forms will remain crucial [2]. The major pandemic HIV-1 group M is represented by 10 subtypes (A–D, F–H, J, K, and the recently established subtype L) and 98 characterized circulating recombinant forms (CRFs), found in at least three epidemiologically unlinked individuals [3,4,5].
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