Introduction International guidelines endorse the screening of patients for human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV) and Chlamydia trachomatis before assisted reproductive techniques (ART). At present no such guidelines exists in South Africa. At the Reproductive and Endocrine Unit (referred to as “the Unit”) of Steve Biko Academic Hospital, all patients with unknown HIV status are counselled and a blood sample is collected during the initial visit for automated laboratory based HIV screening. These HIV results are not available before semen samples are processed. Furthermore, patients are not screened for HBV, HCV and Chlamydia trachomatis. Couples attending the Unit are of a low to middle socio-economic status and experience financial constraints. Moreover, automated laboratory based assays are expensive to perform. Rapid testing is a cost effective and practical method from screening patients, with a 20–30 minute result turnover time. Until screening at the Unit is improved, the possible identification of semen characteristics that could indicate HIV infection would be a useful tool. Materials and Methods The following rapid point-of-care assays were evaluated: Determine® HIV-1/2 combo test (n=100), Determine® HBsAg test (n=100), DIAQUICK HCV kit (n=74), and the DIAQUICK Chlamydia trachomatis kit (n=30). For profiling, parameters from a basic semen analysis of HIV-positive males (n=60) were compared with HIV-negative males (n=60). Information pertaining to CD4 count, antiretroviral treatment and plasma viral load of HIV-positive males were analysed. Results From all patients included in the study, 8% tested positive for HIV. The risk of a female being HIV-positive was 3.73 times higher than for males. In the pilot study to explore rapid testing for HBV and HCV, 1% and 1.4% of patients tested positive respectively. When testing for Chlamydia trachomatis 31.3% of females, but no males tested positive. Comparing semen profiles, no significant differences were found between samples from HIV positive and negative males or between HIV positive males categorised by CD4 cell count (p>0.05). For the HIV-positive group with a detectable plasma HIV viral load (>40 copies/ml), a significant difference was observed in the semen viscosity (p=0.0460). Significant differences were noted in the sperm motility (immotile sperm p=0.0456, progressive sperm p=0.0192) of patients receiving antiretroviral (ARV) therapy. Discussion and Conclusion The use of rapid testing is an acceptable and feasible option for improving current screening protocols at the Unit. The absence of definite alterations in the semen characteristics of HIV-positive men further motivates the need for a simpler, point-of-care screening protocol. The prevalence of HBV was lower than that reported in the general population of South Africa and further investigation is needed. Although the sample size was small, HCV prevalence was similar to that of the general population. One third of females tested positive for Chlamydia trachomatis. The methodology used was possibly not appropriate for males. This study highlighted the need for guidelines that address the specialised needs of ART clinics in resource-limited and developing countries with a high HIV prevalence. / Dissertation (MSc)--University of Pretoria, 2013. / gm2014 / Obstetrics and Gynaecology / unrestricted

MSc (Microbiology) / Department of Microbiology / Background: Prostate cancer (PCA) is a major health concern in males, particularly those above 40 years old. It is the most common form of cancer in males worldwide, including South Africa. In South Africa, the rate of histologically diagnosed prostate cancer is 40 per 100 000 in whites and 14 per 100 000 in blacks, and 1 in 8 men will develop PCA in their lifetime. Several reports have suggested the association of viruses in the pathogenesis of prostate cancer. Objectives: This study was aimed at identifying Hepatitis B virus (HBV), human papilloma virus (HPV) and human herpes virus type 8 (HHV-8), implicated in other forms of cancer, in a cohort of South African patients with either PCA or benign prostatic hyperplasia (BPH); and to seek possible associations thereof. Methods: The study group comprised 187 male patients recruited from Polokwane Hospital presenting with either PCA (staged by Gleason scores) or BPH. Enzyme-linked immunosorbent assay was used to detect antibodies to HHV-8 and HPV; and to detect hepatitis B surface antigen (HBsAg) in the plasma of the study subjects. Total DNA was extracted from plasma and targeted for the identification of HBV and HHV-8 DNA by nested PCR protocols. The HBV nested PCR protocol amplifies a 336bp fragment of the overlapping surface polymerase gene of HBV. The HHV-8 nested protocol amplifies a 233bp fragment of the ORF 26 gene of HHV-8. Amplified DNA products were purified, sequenced by the Sanger protocol and phylogenetically analysed for viral genotypes. The Chi-square test was used to infer statistically significant differences in the level of detection of viruses and the stage of prostate cancer development. Results: Of the 187 participants, a seroprevalence of 4.8% (9/187, HBsAg), 5.3% (10/187, HPV IgG antibody) and 27% (33/124, HHV-8 IgG antibody) were observed. HBsAg was detected more in individuals with BPH than those without and this was statistically significant at ( 2=6.0, p< 0.05). HHV-8 DNA was detected more in individuals in the 60-79 years age range and this was statistically significant at ( 2=61.1, p< 0.05). Occult HBV infection (that is the presence of HBV DNA in the absence of HBsAg) was detected in 23/178 (12.9%) of patients. Taking into account occult HBV infection, the overall prevalence of HBV was 17.7%. HBV genotype E was more prevalent (86.7%) followed by genotype A (13.3%). HHV-8 genotypes K and R were inferred. Apparently, this is the first report on the identification of HHV-8 genotypes K and R from South Africa. Conclusion: The current study has demonstrated for the first time, the presence of genotypes K and R of HHV-8 in South Africa. This study also suggests that there is a high level of occult genotype E HBV infection. Future studies will explore the virome in prostate cancer biopsies.

Eine Monotherapie mit Tenofovir disoproxil fumarate (TDF) stellt eine hoch effiziente Therapie-option für multipel vorbehandelte Patienten mit chronischer Hepatitis-B-Virusinfektion (HBV) dar. Eine Resistenz gegen TDF wurde bislang nicht beschrieben, jedoch wird ein möglicher negativer Einfluss von Adefovir dipivoxil (ADV)-Resistenzvarianten auf die TDF-Ansprechrate diskutiert. Diese retrospektive Kohortenstudie untersucht die Dynamik von Nukleos(t)id-Analoga (NA)-Resistenzvarianten im HBV-Polymerasegen mit Fokus auf ADV-Resistenzvarianten bei 18 chronisch HBV-infizierten Patienten mit Therapieversagen auf eine vorangegangene Lamivudin (LAM)- und ADV-Therapie, sowie nur partiellem Therapieansprechen auf eine TDF-Monotherapie. Zur Detektion von NA-Resistenzvarianten wird eine HBV-Genomsequenzierung mit Tiefenpyrosequenzierung (Genome Sequencer FLX, Roche Diagnostics, Germany) (UDPS), direkte Sequenzierung (TRUGENETM HBV Genotyping Kit, OpenGeneTM DNA Sequencing Sys-tem, Siemens Healthcare Diagnostic, USA) (TG) und Line Probe Assay (INNO-LiPa DRv2 und v3, Innogenetics, Belgium) (INNO-LiPA) durchgeführt. Unter TDF kommt es zu einer quantitati-ven Shift zugunsten der ADV-Resistenzvarianten mit konstant bleibendem Anteil und deutlich höher persistierender Virämie zu Monat 12 im Vergleich zu Patienten ohne ADV-Resistenzvarianten. Vor allem werden die Varianten rtA181V und rtN236T selektiert, jedoch nicht die Variante rtA181T. Die absolute Anzahl der LAM-Resistenzvarianten hingegen halbiert sich. Varianten mit einem initial per UDPS detektierten Anteil von >20% der patientenspezifi-schen HBV-Population werden meist selektiert und nehmen im Verlauf den Hauptanteil der Quasispezies ein. UDPS stellte ein potentes Medium der Detektion, Identifikation und Quantifi-zierung von HBV-Varianten dar und ist INNO-LiPa und TG überlegen. Es ergibt sich kein Hin-weis auf TDF-Resistenzvarianten, jedoch zeigt das Vorliegen von ADV-Resistenzvarianten ei-nen tendentiell negativen Einfluss auf die virale Kinetik. Weitere größere Langzeitstudien sind zur Bestätigung dieser Beobachtung notwendig.:INHALTSVERZEICHNIS 2 ABBILDUNGSVERZEICHNIS 5 TABELLENVERZEICHNIS 6 1 BIBLIOGRAPHISCHE ZUSAMMENFASSUNG 8 ABKÜRZUNGSVERZEICHNIS 9 2 EINFÜHRUNG 10 2.1 Epidemiologie der chronischen Hepatitis-B-Virusinfektion 10 2.2 Aufbau, Replikation und Resistenzentwicklung des Hepatitis-B-Virusgenoms 10 2.3 Antivirale Therapie 13 2.4 Sequenziermethoden 14 3 AUFGABENSTELLUNG 15 4 MATERIAL UND METHODE 16 4.1 Studiendesign und Beschreibung der Kohorte 16 4.2 Evaluation der TDF-Monotherapie und Resistenzanalyse 17 4.3 Statistische Auswertung 18 4.4 Verbrauchsmaterialien und Reagenzien 18 4.5 Puffer 22 4.6 Geräte 22 4.7 Durchführung der Laborarbeiten 24 4.8 HBV-DNA Quantifizierung und Bestimmung biochemischer Parameter 24 4.9 Extraktion von Nukleinsäuren aus Serumproben 24 4.10 Tiefenpyrosequenzierung mittels Genome Sequencer FLX System (454 Life Science, Roche Diagnostic, Branford, CT) 25 4.10.1 GS FLX HBV-DNA-Library 25 4.10.2 GS FLX Emulsions-PCR 31 4.10.3 GS FLX Sequenzierung 37 4.10.4 GS FLX Datenauswertung 41 4.11 Direkte Sequenzierung mittels TRUGENETM HBV Genotyping Kit (OpenGeneTM DNA Sequencing System, Siemens Healthcare Diagnostic, USA) 42 4.11.1 PCR-Amplifikation 42 4.11.2 CLIP-Amplifikations-Reaktion 42 4.11.3 Genotyp-und Variantenanalyse 44 4.12 Sequenzierung mittels Line Probe Assay INNO-LiPa HBV DRv2 und v3 (Innogenetics, Belgium) 44 4.12.1 HBV-DNA Amplifikation 45 4.12.2 Denaturierung und Hybridisierung 46 4.12.3 Farbentwicklung 46 5 ERGEBNISSE 47 5.1 Patientencharakteristika zur Baseline 47 5.2 Virologisches Ansprechen 48 5.3 Biochemisches Ansprechen 49 5.4 Serologisches Ansprechen 50 5.5 Therapie-Adhärenz und medikamentöse Verträglichkeit 50 5.6 Ergebnisse der Tiefenpyrosequenzierung mit Genome Sequencer FLX System (454 Life Science, Roche Diagnostic, Branford, CT) 50 5.6.1 Verschiedene Einzelverläufe der NA-Resistenzvarianten 55 5.6.2 Kombiniert oder isoliert auftretenden NA-Resistenzvarianten 57 5.6.3 Entwicklung der ADV-Resistenzvarianten 61 5.6.4 Entwicklung der LAM-Resistenzvarianten 66 5.6.5 Entwicklung der ETV-Resistenzvarianten 68 5.6.6 Shift der NA-Resistenzvarianten und Auswirkung auf die Dynamik der HBV-DNA 70 5.6.7 Entwicklung der potentiellen NA-Resistenzvarianten 72 5.6.8 Entwicklung der HBsAg-Varianten 75 5.6.9 Entwicklung der HBV-Quasispezies 77 5.7 Ergebnisse der direkten Sequenzierung mit TRUGENETM HBV Genotyping Kit (OpenGeneTM DNA Sequencing System, Siemens Healthcare Diagnostic, USA) 80 5.8 Ergebnisse des Line Probe Assays mit INNO-LiPa HBV DRv2 und v3 (Innogenetics, Belgium) 81 5.9 Vergleich der Sequenziermethoden 81 6 DISKUSSION 83 6.1 Patientenkohorte und Ansprechen auf die TDF-Monotherapie 83 6.2 Entwicklung und Einfluss der ADV-Resistenzvarianten unter TDF-Monotherapie 84 6.3 Entwicklung und Einfluss der LAM-Resistenzvarianten unter TDF-Monotherapie 90 6.4 Entwicklung und Einfluss der ETV-Resistenzvarianten unter TDF-Monotherapie 92 6.5 Entwicklung und Einfluss der HBV-Wildtyp-Varianten unter TDF-Monotherapie 93 6.6 Entwicklung und Einfluss der potentiellen NA-Resistenzvarianten 94 6.7 Entwicklung und Einfluss der HBsAg-Varianten 96 6.8 Einfluss von multiplen Vortherapien unter TDF-Monotherapie 98 6.9 Entwicklung und Einfluss der HBV-DNA-Serumkonzentration 98 6.10 Entwicklung und Einfluss von HBV-Quasispezies unter TDF-Monotherapie 100 6.11 Vergleich der Sequenziermethoden 101 7 ZUSAMMENFASSUNG DER ARBEIT 106 8 LITERATURVERZEICHNIS 109 9 EIDESSTATTLICHE VERSICHERUNG 114 10 CURRICULUM VITAE 115 11 ANTEILSERKLÄRUNG AN ERFOLGTEN PUBLIKATIONEN 116 12 DANKSAGUNG 117 / Tenofovir disoproxil fumarate (TDF) is a highly efficient treatment option for nucleos(t)ide analogue (NA) pre-treated patients with chronic hepatitis B virus (HBV) infection. Little is known about the reasons for persistent virus replication in some rare cases. As of today, no TDF resistance variants have been identified, but a possible linkage to Adefovir dipivoxil (ADV) resistance associated variants negatively influencing HBV-DNA suppression by TDF has been suspected, based on the similarity of the chemical structure. In this retrospective cohort study the dynamics of NA resistance variants in the HBV polymerase gene with focus on ADV resistance variants were assessed. For this, we have chosen a cohort including patients with multiple failures to treatment with different NAs. Thus, data of 18 patients with previous treatment failure to LAM and ADV was analysed, showing a persistent viremia (HBV-DNA >35 copies/mL) despite switch to TDF monotherapy (median HBV-DNA at month 12 3,5±0,8 (2,1-4,9) log10 copies/mL). Sequencing analysis was performed with ultra-deep pyrosequencing (UDPS) (Genome Sequencer FLX, 454 Life Science, Roche Diagnostic, Branford, CT), direct sequencing (TG) (TRUGENETM HBV Genotyping Kit, OpenGeneTM DNA Sequencing System, Siemens Healthcare Diagnostic, USA) and line probe assay (INNO-LiPA) (INNO-LiPa DRv2/v3, Innogenetics, Belgium). Using TDF monotherapy, a quantitative shift in favour to ADV resistance variants was observed in this cohort. The percentage of substitutions conferring resistance to ADV at baseline (BL) and at the time of the last sequencing endpoint (EP) of the HBV genome remained constant (BL 35%, 13/37, EP 36%, 9/25). The variants rtA181V and rtN236T were mostly selected, whereas rtA181T was not selected. The total amount of substitutions conferring resistance to Lamivudin (LAM) showed a strong decline, however remained the majority part of all NA resistance variants (BL 51% (19/37), EP 40% (10/25)). The percentage of ETV resistance variants increased slightly (BL 14% (5/37), EP 24% (6/25)). Known ADV, Lam and ETV resistance variants emerged in variable abundance (1,0-99,6%) of quasispecies during TDF therapy. A homogenization of HBV quasispecies took place. Especially mutations occurring in higher abundance (>20% of viral population) were mostly selected (BL 51% (19/37), EP 80% (20/25)). No new HBV variants with possible association to resistance against TDF were identified, but patients with ADV resistance variants showed the highest HBV-DNA level at month 12 of TDF therapy (median HBV-DNA 3,57±0,72 (2,14-3,96) log10 copies/mL, not significant). A negative influence of ADV resistance variants on viral suppression with TDF monotherapy may be assumed, however more long-term studies are needed to confirm the role of ADV resistance variants in TDF therapy. UDPS is a potent medium for detection, identification and quantification of dominant to low level variants in HBV-DNA. It is superior to direct sequencing and line probe assay in the detection of variants.:INHALTSVERZEICHNIS 2 ABBILDUNGSVERZEICHNIS 5 TABELLENVERZEICHNIS 6 1 BIBLIOGRAPHISCHE ZUSAMMENFASSUNG 8 ABKÜRZUNGSVERZEICHNIS 9 2 EINFÜHRUNG 10 2.1 Epidemiologie der chronischen Hepatitis-B-Virusinfektion 10 2.2 Aufbau, Replikation und Resistenzentwicklung des Hepatitis-B-Virusgenoms 10 2.3 Antivirale Therapie 13 2.4 Sequenziermethoden 14 3 AUFGABENSTELLUNG 15 4 MATERIAL UND METHODE 16 4.1 Studiendesign und Beschreibung der Kohorte 16 4.2 Evaluation der TDF-Monotherapie und Resistenzanalyse 17 4.3 Statistische Auswertung 18 4.4 Verbrauchsmaterialien und Reagenzien 18 4.5 Puffer 22 4.6 Geräte 22 4.7 Durchführung der Laborarbeiten 24 4.8 HBV-DNA Quantifizierung und Bestimmung biochemischer Parameter 24 4.9 Extraktion von Nukleinsäuren aus Serumproben 24 4.10 Tiefenpyrosequenzierung mittels Genome Sequencer FLX System (454 Life Science, Roche Diagnostic, Branford, CT) 25 4.10.1 GS FLX HBV-DNA-Library 25 4.10.2 GS FLX Emulsions-PCR 31 4.10.3 GS FLX Sequenzierung 37 4.10.4 GS FLX Datenauswertung 41 4.11 Direkte Sequenzierung mittels TRUGENETM HBV Genotyping Kit (OpenGeneTM DNA Sequencing System, Siemens Healthcare Diagnostic, USA) 42 4.11.1 PCR-Amplifikation 42 4.11.2 CLIP-Amplifikations-Reaktion 42 4.11.3 Genotyp-und Variantenanalyse 44 4.12 Sequenzierung mittels Line Probe Assay INNO-LiPa HBV DRv2 und v3 (Innogenetics, Belgium) 44 4.12.1 HBV-DNA Amplifikation 45 4.12.2 Denaturierung und Hybridisierung 46 4.12.3 Farbentwicklung 46 5 ERGEBNISSE 47 5.1 Patientencharakteristika zur Baseline 47 5.2 Virologisches Ansprechen 48 5.3 Biochemisches Ansprechen 49 5.4 Serologisches Ansprechen 50 5.5 Therapie-Adhärenz und medikamentöse Verträglichkeit 50 5.6 Ergebnisse der Tiefenpyrosequenzierung mit Genome Sequencer FLX System (454 Life Science, Roche Diagnostic, Branford, CT) 50 5.6.1 Verschiedene Einzelverläufe der NA-Resistenzvarianten 55 5.6.2 Kombiniert oder isoliert auftretenden NA-Resistenzvarianten 57 5.6.3 Entwicklung der ADV-Resistenzvarianten 61 5.6.4 Entwicklung der LAM-Resistenzvarianten 66 5.6.5 Entwicklung der ETV-Resistenzvarianten 68 5.6.6 Shift der NA-Resistenzvarianten und Auswirkung auf die Dynamik der HBV-DNA 70 5.6.7 Entwicklung der potentiellen NA-Resistenzvarianten 72 5.6.8 Entwicklung der HBsAg-Varianten 75 5.6.9 Entwicklung der HBV-Quasispezies 77 5.7 Ergebnisse der direkten Sequenzierung mit TRUGENETM HBV Genotyping Kit (OpenGeneTM DNA Sequencing System, Siemens Healthcare Diagnostic, USA) 80 5.8 Ergebnisse des Line Probe Assays mit INNO-LiPa HBV DRv2 und v3 (Innogenetics, Belgium) 81 5.9 Vergleich der Sequenziermethoden 81 6 DISKUSSION 83 6.1 Patientenkohorte und Ansprechen auf die TDF-Monotherapie 83 6.2 Entwicklung und Einfluss der ADV-Resistenzvarianten unter TDF-Monotherapie 84 6.3 Entwicklung und Einfluss der LAM-Resistenzvarianten unter TDF-Monotherapie 90 6.4 Entwicklung und Einfluss der ETV-Resistenzvarianten unter TDF-Monotherapie 92 6.5 Entwicklung und Einfluss der HBV-Wildtyp-Varianten unter TDF-Monotherapie 93 6.6 Entwicklung und Einfluss der potentiellen NA-Resistenzvarianten 94 6.7 Entwicklung und Einfluss der HBsAg-Varianten 96 6.8 Einfluss von multiplen Vortherapien unter TDF-Monotherapie 98 6.9 Entwicklung und Einfluss der HBV-DNA-Serumkonzentration 98 6.10 Entwicklung und Einfluss von HBV-Quasispezies unter TDF-Monotherapie 100 6.11 Vergleich der Sequenziermethoden 101 7 ZUSAMMENFASSUNG DER ARBEIT 106 8 LITERATURVERZEICHNIS 109 9 EIDESSTATTLICHE VERSICHERUNG 114 10 CURRICULUM VITAE 115 11 ANTEILSERKLÄRUNG AN ERFOLGTEN PUBLIKATIONEN 116 12 DANKSAGUNG 117

<p>Vi&scaron;e od 100 vrsta virusa ljudi i životinja se izlučuje u spolja&scaron;nju sredinu. Prisustvo ovih virusa u povr&scaron;inskim vodama reflektuje fekalnu kontaminaciju i ukazuje na<br />opasnost za zdravlje ljudi i životinja. Na području Srbije se ne prati prisustvo patogenih virusa u povr&scaron;inskim vodama, pa&nbsp; čak ni u vodama za piće, a nije uspostavljena&nbsp; ni&nbsp; metodologija ovih ispitivanja. Shodno tome, cilj disertacije je da se utvrdi i analizira prisustvo animalnih i humanih virusa u povr&scaron;inskim vodama primenom najsavremenijih metoda koncentrovanja i detekcije virusa. U okviru disertacije ispitano je prisustvo sledećih virusa u povr&scaron;inskim vodama na teritoriji Vojvodine: humanih adenovirusa (HAdV); norovirusa (NoV) i hepatitis A virusa (HAV), adenovirusa svinja (PAdV),&nbsp; poliomavirusa goveda (BPyV) i hepatitis E virus (HEV).</p><p>Ispitano je ukupno 108 uzoraka povr&scaron;inskih i otpadnih voda koji su prikupljani od oktobra 2012. godine do juna 2014. godine. U radu su primenjene najsavremenije metode koncentrovanja i detekcije virusa u vodi, koje se u Srbiji nisu koristile za ovu namenu. Sprovedenim ispitivanjima dokazano je da su animalni i humani virusi prisutni u povr&scaron;inskim vodama na području Vojvodine. Najče&scaron;će detektovan&nbsp; virus u povr&scaron;inskim vodama je humani adenovirus (42,4%), a potom norovirusi GII i GI (40,4% i 15,2%), adenovirus svinja (11,1%), poliomavirus goveda (7,1%) i hepatitis E virus (3,0%). U ukupno 9 testiranih uzoraka gradske kanalizacione vode najče&scaron;će je detektovan HAdV (44,4%), NoV GII i GI&nbsp; (66,7% i 22,2%), BPyV je detektovan u samo jednom od 9 uzoraka, a niti u jednom nisu detektovani PAdV i HEV. Hepatitis A virus nije detektovan u uzorcima, a eksperimentalno je potvrđeno da su metode primenljive i za detekciju ovog virusa. Na osnovu rezultata prinosa procesne kontrole i utvrđenog prisustva virusa u uzorcima,&nbsp; zaključeno&nbsp; je da se ove metode mogu veoma uspe&scaron;no koristiti za detekciju virusne kontaminacije&nbsp; povr&scaron;inskih voda. Izvr&scaron;ena je igenotipizacija virusa iz odabranih uzoraka metodom sekvenciranja dela virusnog genoma. Indirektno je potvrđeno da su infekcije&nbsp;&nbsp; detektovanim virusima prisutne u populaciji životinja i ljudi. Prisustvo virusa u&nbsp;&nbsp; povr&scaron;inskim vodama i uzorcima gradske kanalizacije odražava infektivni status stanovni&scaron;tva, ali predstavlja i značajan rizik za zdravlje životinja i ljudi na području koje gravitira ispitanim vodama.&nbsp;</p> / <p>Over 100 types of pathogenic viruses are excreted in human and animal wastes. The presence of human and animal pathogenic enteric viruses in water environments reflects fecal contamination and indicates a risk to public health.&nbsp; Republic of Serbia does not implement surveillance for the presence of pathogenic human and animal viruses in surface waters and even in drinking water, neither is the established methodology of these studies in any institution in Serbia.&nbsp; Accordingly, the aim of the study was to determine and analyze the presence of human and animal viruses in surface water,&nbsp; using the latest methods&nbsp; of&nbsp; concentration and detection of the viruses.&nbsp; Within the dissertation examined the presence of the following viruses in surface waters in Vojvodina:&nbsp; Human adenoviruses&nbsp; (HAdV), noroviruses (NoV)&nbsp; and hepatitis A virus), Porcine adenovirus (PAdV) and Bovine polyomavirus (BPyV)&nbsp; and&nbsp; Hepatitis E virus (HEV).<br />A total of 108 samples of surface water and waste water were collected from October 2012 to June 2014. The paper are applied the most advanced methods and the concentration of virus detection in water, which in Serbia are not used for this purpose. The conducted tests have proven that the animal and human viruses present in surface waters in Vojvodina. The most commonly detected virus in surface water was human adenovirus (42.4%), followed by Norovirus GI&nbsp; and GII (40.4% and 15.2%),&nbsp; Porcine adenovirus&nbsp; (11,1%),&nbsp; Bovine polyomavirus&nbsp; (7.07%) and hepatitis E virus (3,0%).<br />In total of&nbsp; nine analysed sewage samples human adenovirus was detected in 44,4%&nbsp; of&nbsp; samples. The prevalence of norovirus GII and GI in sewage&nbsp; samples was&nbsp; 66,7%&nbsp; and 22,2%. Bovine&nbsp; polyomavirus was detected in one of nine samples while porcine adenovirus and hepatitis E virus were not detected in any of analyzed samples.&nbsp; Hepatitis A virus was not detected in samples, but&nbsp; it has been experimentally confirmed that the methods applicable for detection of the virus. Based on the results of process control and yield determined the presence of virus insamples, it was found that these methods can be successfully used to detect viral contamination of surface waters. Also, in these study was performed genotyping of viruses from selected samples by sequencing a part of the viral genome. Indirectly it is confirmed that the infection detected viruses present in a population of animals and humans. The presence of virus in samples of surface water and urban sewage reflects the infectious status of the population, but also constitutes a significant risk to the health of animals and people in the area that gravitates with tested waters.</p><p>&nbsp;</p>

L’infection par le virus de l’hépatite C (VHC) est l’un des principaux problèmes de santé publique chez les utilisateurs de drogues injectables (UDI). Actuellement, plusieurs outils sont disponibles pour réduire le fardeau du VHC dans cette population. Ceux-ci incluent des programmes de réduction des méfaits, tels que le traitement par un opioïde agoniste (TAO), pouvant réduire le risque d'infection par le VHC, ainsi que des traitements antiviraux extrêmement efficaces pour éradiquer le virus parmi les infectés. Plus récemment, il y a eu un intérêt national et international à éliminer le VHC en tant que menace pour la santé publique d'ici 2030, tout en priorisant les UDI dans les efforts de prévention et traitement. Parallèlement à ce mouvement, plus globalement, le fardeau des méfaits liés aux pratiques d’injection chez les UDI, tels que la surdose, soulignent la nécessité d’adopter une vision plus large sur leur santé. Dans l’ensemble, cette thèse vise à combler certaines lacunes dans les connaissances vis-à-vis de l’élimination du VHC chez les UDI. Premièrement, puisque le lien entre l’adéquation du dosage des TAO et le risque d’infection au VHC est peu connu, j’examine cette relation dans un échantillon d’UDI suivis dans la cohorte HEPCO à Montréal. Les résultats indiquent que le risque d'infection par le VHC ne serait pas systématiquement réduit chez toutes les personnes recevant des TAO, mais plutôt que ce risque varie en fonction de la dose prescrite et de l’adéquation du dosage telle que perçue par le patient. Ces résultats soulignent qu’un élargissement de l'accès aux TAO ne serait pas suffisant pour atteindre les objectifs de prévention et d'élimination du VHC, et que l’adéquation du dosage devrait être prise en compte dans le cadre de nos efforts de prévention. Deuxièmement, l’accès aux traitements antiviraux est faible chez les UDI, en partie à cause des préoccupations des prestataires et des décideurs politiques qui craignent une augmentation de la consommation de drogues et des comportements à risque après le traitement. En capitalisant sur deux études différentes - la cohorte IMPACT à Montréal et les essais SIMPLIFY / D3FEAT menés dans plusieurs pays - je montre que les comportements liés à la drogue diminuent ou restent stables après le traitement du VHC. Ensemble, ces deux études suggèrent que les préoccupations liées à une consommation élevée de drogue ou à une hausse des comportements à risque après le traitement ne seraient pas fondées. Ainsi, ces résultats appuient davantage une augmentation de l’accès au traitement chez les UDI. Troisièmement, allant au-delà du VHC en tant que problématique principale, en capitalisant une fois de plus sur les données collectées dans HEPCO, j’examine les associations entre trois facteurs - le TAO, le logement et le revenu - et la fréquence d’injection chez les UDI. Puisque la consommation de drogues est dynamique dans le temps, j'examine dans quelle mesure ces trois facteurs sont liés à la fréquence d’injection chez des UDI ayant des trajectoires d’injection variées. Nos résultats indiquent que la stabilité socioéconomique et le TAO seraient systématiquement liés à une fréquence d'injection inférieure chez les UDI, quelles que soit leurs trajectoires d’injection sous-jacentes. Globalement, ces résultats suggèrent qu’il y aurait des moyens de soutenir tous les UDI à atteindre de petits changements comportementaux qui pourraient réduire les risques liés aux pratiques d’injection, qu’ils soient ou non en mesure d’arrêter l’injection de drogues. En conclusion, alors que presque tous les pays ont lancé un effort mondial pour éliminer le VHC, des efforts sont nécessaires pour optimiser les programmes de réduction des méfaits bien établis afin de réduire la transmission du VHC, et d’accroître l’accès au traitement chez ceux qui sont infectés, tout en considérant les besoins et les préoccupations des communautés touchées. Cette thèse a fourni des données permettant d’éclairer (i) l’optimisation des TAO dans la prévention de la transmission du VHC, (ii) l’élargissement de l’accès au traitement du VHC et (iii) l’accès à des logements et revenus stables afin de réduire plus globalement les risques liés aux pratiques d’injection chez les UDI. Ainsi, ces résultats pourraient aider à réduire le fardeau du VHC chez les UDI et à soutenir le progrès vers l'élimination du VHC. / Infection with hepatitis C virus (HCV) is one of the main public health concerns affecting people who inject drugs (PWID). Although no effective prophylactic vaccine currently exists to prevent acquisition of HCV, a number of other tools are available to curb the HCV burden among PWID. These include harm-reduction programs, such as opioid agonist treatment (OAT), which can reduce the risk of HCV infection among those susceptible, and highly effective antiviral therapies to eradicate the virus among those who are infected. In recent years, there has been national and international interest in eliminating HCV as a public health threat by 2030, prioritising PWID in prevention and treatment efforts given that they are the population most affected. In parallel to this global effort, the high prevalence of injection-related harms among PWID that are unrelated to HCV, such as overdose, highlight a need to adopt a broader view on drug user health. Overall, this thesis is concerned with addressing some of the knowledge gaps and barriers that remain to achieving HCV elimination in PWID. First, because little is known about the importance of OAT dosage in influencing the risk of HCV acquisition, I examine this relationship in a sample of PWID followed in the Hepatitis Cohort (HEPCO) in Montreal. Findings indicate that the risk of HCV infection may not be systematically reduced for everyone receiving OAT and rather, that the risk of infection varies considerably according to the level of the prescribed OAT dosage and patient-perceived dosage adequacy. These findings suggest that simply scaling-up OAT access may not be sufficient to achieving the HCV elimination goals, and that the dosage of treatment should be considered as part of prevention efforts. Second, uptake of HCV treatment is low among PWID, partly due to concerns among providers and policymakers that drug use and injection risk behaviours may increase following treatment, thereby negating the benefits of therapy. Capitalising on two different studies - the IMPACT Cohort in Montreal and the SIMPLIFY/D3FEAT trials conducted in several countries - I illustrate that drug-related behaviours decrease or remain stable following HCV treatment. Together, these two studies suggest that concerns of escalating drug use or risk behaviours following HCV treatment are unfounded, further supporting the importance of expanding access to therapy among PWID. Third, moving beyond HCV as the primary focus of research, and capitalising once more on data collected in HEPCO, I examine the associations between three factors- OAT, housing and income, and patterns of injection frequency among PWID. Recognizing that injection patterns are dynamic over time, I examine the extent to which these three factors relate to injection frequencies among PWID with diverse trajectories of injection drug use, followed over a period of 7.5 years. Our findings indicate that socioeconomic stability and OAT are consistently associated with a lower injection frequency among all PWID, irrespective of their underlying injection trajectory and whether or not they are on a path to cessation. These findings suggest that there may be ways to support PWID in making small behavioral changes that could reduce their risks of injection-related harms, irrespective of whether or not they are in a position to stop injecting. In conclusion, at a time when many countries have embarked onto a global effort to eliminate HCV, efforts are needed to ensure that well-evidenced harm-reduction programs are optimised to reduce transmission of HCV, treatment for HCV infection is scaled-up among those who are infected ,and efforts do not overlook the basic needs and concerns of affected communities. This thesis provided data to help inform (i) optimisation of OAT provision for the prevention of HCV transmission, (ii) expanded access to HCV treatment, and (iii) access to stable housing and income to reduce the risk of injection-related harms among PWID. Ultimately, findings could contribute to reducing the HCV burden among PWID, helping move towards HCV elimination and, more broadly, improving the overall health of this marginalised group.

No description available.

alpha-Interferon (alpha IFN) ist derzeit die Grundlage jeder Behandlung der chronischen Hepatitis C. Zu den unerwünschten Effekten von alpha-IFN gehört die Entwicklung psychiatrischer Nebenwirkungen, die sich häufig als Depressivität äussern. Deren Häufigkeit, Schweregrad und Behandlungsbedarf wurden jedoch bisher nur unzureichend erforscht. 66 Patienten mit chronischer Hepatitis C wurden in einer Pilotstudie mit alpha-IFN als Monotherapie (3x3 MU/ Woche) oder in Kombination mit Ribavirin (1000-1200 mg/ Woche) behandelt. Sämtliche Patienten wurden vor, während und nach der Therapie hinsichtlich ihrer Depressivität beurteilt. Dies geschah sowohl im persönlichen Gespräch als auch mit Hilfe der Selbstbeurteilungsinstrumente ADS (Allgemeine Depressions Skala) und BDI (Beck Depressions Inventar). Die Ausgangsdepressivität der Hepatitispatienten entsprach dem gesunden Eichkollektiv. Im Gesamtdurchschnitt stieg die Depressivität innerhalb der ersten drei Behandlungsmonate um 5,15 (+/-8,94) Punkte auf der ADS und um 3,85 (+/-6,94) Punkte im BDI an. Weniger als ein Drittel der Patienten erlebte keine Zunahme der Depressivität. Patienten, die vor Therapiebeginn eine geringe Depressivität aufwiesen, beschrieben eine stärkere Zunahme depressiver Symptome als Patienten, die initial als depressiv beurteilt wurden. Letztere blieben während des Therapieverlaufs jedoch weiterhin depressiver als die anfangs nicht-depressiven Patienten. Vier Patienten wurden wegen schwerster depressiver Nebenwirkungen stationär psychiatrisch behandelt. Es wurde kein signifikanter Zusammenhang zwischen Ausgangsdepressivität und Behandlungserfolg festgestellt. Um stark gefährdete Patienten frühzeitig zu erkennen, wird vorgeschlagen, sowohl ADS als auch BDI vor und während der Therapie zu verwenden. Anhand eines ADS-Grenzwertes von > 17 vor und >= 30 während der Behandlung konnten 75% derjenigen Patienten, die im Verlauf der Therapie mit alpha-IFN schwerste depressive Symptome entwickelten, identifiziert werden. / Interferon-alpha (alpha-IFN) is presently the mainstay of the treatment of chronic hepatitis C. Side effects include a range of psychiatric symptoms, most frequently the development of depressive symptoms. Their incidence, severity and necessity for therapeutic intervention has not yet been sufficiently studied. 66 patients with chronic hepatitis C were enrolled in a pilot study and treated with either alpha-IFN alone (3x3 MU/ week) or in combination with Ribavirin (1000-1200 mg/ week). All patients went through repeated evaluations concerning their depressive symptoms before, during, and after treatment. Apart from individual interviews with the psychosomatic staff, the psychometric instruments used were the ADS (Allgemeine Depressions Skala, the German version of the Center for Epidemiological Studies Depression Scale, CES-D) and the BDI (Beck Depression Inventory). The initial depression score of the hepatitis C patients was comparable to that of a healthy population. On average, depression scores increased by 5,15 points (+/-8,94) on the ADS and 3,85 points (+/-6,94) on the BDI during the first 3 months of treatment. Less than a third of all patients did not show an increase of depressive symptoms. Patients with an initially low depression score experienced a greater increase of depressive symptoms than patients initially diagnosed as depressive. Nevertheless, the latter patients remained more depressive throughout the study period. Four patients developed severe depressions that necessitated admission to a psychiatric clinic. There was no significant correlation between the initial depression score and the treatment response. In order to recognize those patients at high risk for the development of severe depressions at an early stage, the author proposes the use of ADS and BDI both before and during treatment with alpha-IFN. Using a cut-off score of more than 17 points on the ADS before, and >=30 points during treatment, 75% of all patients developing severe depressions during treatment with alpha-IFN could be identified.

Background: Hepatocellular Carcinoma (HCC) is the third most common cause of cancer related death worldwide and is often diagnosed by measuring serum Alpha-fetoprotein (AFP); a stand-alone biomarker with limited diagnostic proficiency. To compensate for this, AFP is commonly used in conjunction with high performance imaging and radiological methods. However, as the burden of HCC is predominantly in the developing world where such technologies are not readily available, it is imperative that efforts are made to pursue the discovery of novel, high performance, easy to measure and robust biomarkers. With the aim of improving on the diagnostic ability of AFP, our project focuses on the study of plasma proteins as identified by Mass Spectrometry (MS) in order to investigate differences seen in the respective proteomes of controls and subjects with liver cirrhosis (LC) and HCC. Methods: Matrix Assisted Laser Desorption Ionization Time-of-Flight MS (MALDI-TOF MS) was first attempted on weak cation exchange (WCX) fractionated plasma in a pilot selection of forty subjects. On the main case-control group, quantitative MS analysis using liquid chromatography electro spray ionization quadrupole time-of-flight (LC-ESI Q-TOF) was conducted on 339 subjects using a pooled expression profiling approach. Enzyme-linked immunosorbent assays (ELISA) and 1 and 2Dimentional electrophoresis methods were performed to validate and detail candidate protein levels and modification patters in individual and pooled subjects. The human plasma used for the MS based protein discovery experiments was collected as part of a five year Liver Cancer Case-control Study (Gambia, West Africa). A smaller set of samples from subjects who formed a spectrum of non-liver disease controls, LC and HCC were obtained from the Jos University Teaching Hospital (JUTH) in Nigeria and ELISA and gel electrophoresis assays conducted on them to confirm the trends and differences seen in the Gambian subject set. Results: Bioinformatic evaluation of MALDI-TOF data highlighted peak masses 2444m/z, 2583m/z and 2559m/z to have high diagnostic abilities based on area under curve (AUC) statistics of >0.75. Of these polypeptide fragments, one was identified as the plasma glycoprotein, alpha chain fibrinogen. Results from the large-scale label free discovery experiments indicated twenty-six proteins to be differentially expressed between the three subject groups. These prospective markers include proteins previously linked to HCC as well as novel candidates, namely glutathione peroxidase 3, serum amyloid p, carboxypeptidase N and complement factors I and H which have not been implicated in the context of HCC diagnostics. Direct measurement of Hemopexin (HPX), alpha-1-antitrypsin (α1AT), apolipoprotein A1 (Apo A1) and complement component 3 (CC3) levels confirmed their change in abundance in LC and HCC versus control patients. Further biochemical characterization of glycosylated HPX isolated from glycoprotein enriched plasma sample pools showed evidence of isoelectric point shifts, indicating differential glycosylation patterns in high mannose structures of HPX which may be disease stage linked. The direct measurements of HPX, α1AT, Apo A1 & CC3 conducted on the independent Nigerian subject group also confirmed much of the trends reported from the Gambia Liver Cancer Study (GLCS) plasma. Conclusions: The independently validated, significant changes in the quantitative expression of ApoA1, α1AT, CC3 and HPX could be exploited for development into high-performance affordable assays, usable in the diagnosis and monitoring of HCC and LC patients. The unique signatures observed for most of these proteins, from liver disease free controls to LC and HCC suggest their involvement in independent pathways. As such, combining some or all of these four markers within a diagnostic panel could offer a much-needed boost in robustness and accuracy for AFP. The differences in the processing and molecular weight separation of these proteins also offers a novel inroad into biomarker identification. These suggested disease specific signatures could with further study offer highly specific biomarkers able to discern the key stages that predispose individuals to hepatocarcinogenesis. Impact: This is the first MS based discovery and extensive validation study on West African subjects whose primary cause of HCC are the Hepatitis B Virus (HBV) and fungal toxins.

published_or_final_version / Psychology / Doctoral / Doctor of Philosophy

Bakgrund: Den vanligaste smittvägen för hepatit C är genom intravenöst drogmissbruk. Smittöverföring kan även ske via blodtransfusioner eller stickskador i vården. Det finns många fördomar förknippade med sjukdomen och risken är stor att dessa färgar mötet med patienter. Det är viktigt att som vårdpersonal vara medveten om hur den egna synen på sjukdomen kan påverka bemötandet. Syfte: Syftet var att belysa vilka erfarenheter patienter med hepatit C har av bemötandet i vården. Metod: Studien utformades som en allmän litteraturöversikt av tolv kvalitativa artiklar. Manifest innehållsanalys användes. Resultat: Patienter med HCV hade blandade erfarenheter av mottagandet: välkomnande, avvisande eller otryggt. Vidare ledde detta till erfarenheter av stöd eller diskriminering. Patienter kunde ha erfarenheter av professionellt stöd eller brist på professionellt stöd. Diskriminering kunde orsakas av antingen vårdpersonal eller organisation. Slutsats: På grund av stigmatisering kring sjukdomen är patienter med hepatit C en utsatt grupp i samhället. Vårdpersonalens kunskap är en viktig del i bemötandet. Det krävs utbildning för att kunna erbjuda en mer holistisk vård vid hepatit C än i dagsläget. Genom ökad kunskap kring både sjukdom och bemötande kan bemötandet påverkas positivt, det vill säga: mottagandet blir bättre, stödet ökar och diskrimineringen minskar. / Background: The most common route of transmission of hepatitis C is through intravenous drug abuse. Transmission can also occur through blood transfusion. There are many prejudices associated with hepatitis C. Chances are that this colors interactions with patients. It is important that healthcare professionals are aware of how their own perception of the disease may affect the encounter.  The Objective was to highlight the experiences patients with hepatitis C have of the encounter in the healthcare. Method: The study was designed as a general literature review of twelve qualitative articles. Manifest content analysis was used. Results: Patients with hepatitis C had mixed experiences of receipt: welcoming, rejecting or unsafe. This led to experiences of support or discrimination. Patients experienced professional support or lack of professional support. Discrimination could be caused either by healthcare professionals or the organization. Conclusion: Because of stigma surrounding the disease patients with hepatitis C are a vulnerable group in society. The knowledge of healthcare professionals is an important part of the encounter. It requires training to provide holistic care for hepatitis C. Increased knowledge about both the disease and patient-professional relation can positively affect the encounter: the reception gets better, support increases and discrimination is reduced.