HIV-1 unique recombinant forms identified in Slovenia and their characterization by near full-length genome sequencing

Lunar, Maja M. (author), Mlakar, Jana (author), Zorec, Tomaž Mark (author), Poljak, Mario (author)

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.

• Language: English
• Keywords: molecular epidemiology, HIV-1, subtype, unique recombinant form, near full-length genome, next-generation sequencing, surveillance
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2020
• Number of pages: 22 str.
• Numbering: Vol. 12, iss. 1, art. 63
• PID: 20.500.12556/RUL-133285
• UDC: 616.9
• ISSN on article: 1999-4915
• DOI: 10.3390/v12010063
• COBISS.SI-ID: 34697433
• Publication date in RUL: 19.11.2021

Record is a part of a journal

• Title: Viruses
• Shortened title: Viruses
• Publisher: MDPI
• ISSN: 1999-4915
• COBISS.SI-ID: 517597977

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 03.01.2020

Secondary language

• Language: Slovenian
• Keywords: molekularna epidemiologija, HIV-1, podtip