Molekularna in filogenetska opredelitev slovenskih izolatov človeškega virusa imunske pomanjkljivosti

Lunar, Maja (author), Poljak, Mario (mentor)

Človeški virus imunske pomanjkljivosti (angl. human immunodeficiency virus, HIV) sodi med genetsko najbolj raznolike viruse. V doktorski disertaciji smo želeli določiti značilnosti epidemije HIV v Sloveniji in opredeliti slovenske izolate. V raziskavo smo vključili več kot polovico vseh novo odkritih HIV-pozitivnih oseb v Sloveniji v različnih časovnih obdobjih. Potrdili smo, da podtip B ostaja najbolje zastopan podtip v Sloveniji, določili smo ga v več kot 80 % izolatov. Odkrili smo, da je epidemija podtipa B v Sloveniji predvsem na račun lokalnega širjenja, saj je večina posameznikov (66 %) pripadala večjim filogenetskim skupinam. Pri osebah, ki so pripadale velikim filogenetskim skupinam smo našli statistično značilno povezavo z naslednjimi dejavniki: osebe so navedle Slovenijo kot državo, kjer so se najverjetneje okužile s HIV; diagnoza okužbe s HIV je bila postavljena po letu 2004; in pri osebah nismo odkrili mutacij povezanih z odpornostjo HIV. Statistično značilne povezave pripadnosti velikim filogenetskim skupinam s homo/biseksualnim načinom okužbe in nedavno okužbo nismo zaznali. Kljub temu je več kot polovica velikih filogenetskih skupin vključevala le posameznike moškega spola in dve filogenetski skupini le posameznike iz skupine moških, ki ima spolne odnose z moškimi (MSM). Izvor najstarejše velike filogenetske skupine smo določili v letu 1986 in s tem ocenili začetek epidemije podtipa B v koncu 80-ih let. Podtipi ne-B so bili redkeje zastopani, najpogostejši je bil podtip A. Dve tretjini oseb okuženih s podtipom ne-B je poročalo heteroseksualni način prenosa, za razliko od le 11 % oseb okuženih s podtipom B. Poleg tega smo okužbo s podtipom ne-B zasledili statistično značilno pogosteje med ženskami in imigranti in med osebami, ki so navajale okužbo znotraj partnerskega razmerja. Izbranim izolatom z neopredeljivim podtipom smo določili skoraj-celotno zaporedje genoma HIV in ga opredelili. Pridobili smo 11 skoraj-celotnih genomov HIV in dve zaporedji z dolžino > 7.000 baznih parov. Sedem zaporedij smo opredelili kot znane podtipe HIV ali krožeče rekombinantne oblike (angl. Circulating Recombinant Forms, CRF). Preostalih šest zaporedij smo opredelili kot enkratne rekombinantne oblike (angl. Unique Recombinant Forms, URF); pri štirih smo opazili le en dogodek rekombinacije, dve zaporedji sta imeli kompleksno sestavo in je njun genom vključeval več različnih podtipov, CRF in regij neznanega izvora. Tri zaporedja smo prepoznali kot epidemiološko pomembna in bi jih lahko v nadaljnjih raziskavah opredelili kot nove CRF.

• Language: Slovenian
• Keywords: HIV, molekularna epidemiologija, filogenetska analiza, rekombinantne oblike
• Work type: Doctoral dissertation
• Organization: MF - Faculty of Medicine
• Year: 2020
• PID: 20.500.12556/RUL-117531
• COBISS.SI-ID: 24491523
• Publication date in RUL: 15.07.2020

Secondary language

• Language: English
• Title: Molecular and phylogenetic characterization of Slovenian isolates of human immunodeficiency virus

Abstract

Human immunodeficiency virus (HIV) is one of the most genetically divergent viruses. In this doctoral thesis, we wished to describe the HIV epidemic in Slovenia and to characterize Slovenian samples. We included samples obtained from more than half of HIV-positive individuals diagnosed with HIV in Slovenia in diverse time frames. We confirmed subtype B as the most prevalent HIV subtype, identified in over 80% of samples. We observed that subtype B epidemic was mainly due to local transmission, because the majority of individuals (66%) belonged to large transmission clusters. Persons belonging to large clusters had statistically significant association with the following: Slovenia reported as most likely country of HIV acquisition, HIV diagnosis after the year 2004, and no surveillance drug resistance mutations detected. On the contrary, we did not find an association with homo/bisexual HIV mode of transmission and recent HIV infections. However, more than half of large transmission clusters were exclusively male clusters and two clusters encompassed only individuals declaring themselves as men who have sex with men (MSM). We estimated the origin of the oldest phylogenetic cluster in the year 1986 and with this the start of Slovenian subtype B epidemic in the late 1980s. Non-B subtypes were detected less often, the most prevalent was subtype A. Two thirds of persons infected with non-B subtype reported heterosexual mode of HIV transmission vs. 11% of persons infected with subtype B. In addition, non-B subtype was seen more often among women and immigrants, and persons who reported to have acquired HIV in a stable relationship with the source. Near full-length genome sequence was obtained for a selected set of samples with unassigned HIV subtype. We obtained 11 near full-length genomes and two sequences of > 7.000 base pairs. Seven sequences were identified as “pure” subtypes or already characterized circulating recombinant forms (CRFs). The remaining six sequences were determined to be unique recombinant forms (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.

• Keywords: HIV, molecular epidemiology, phylogenetic analysis, recombinant forms