Thesis (MScMedSc))--Stellenbosch University, 2012. / Includes bibliography / ENGLISH ABSTRACT: Despite the availability of Hepatitis B virus (HBV) vaccination for over three decades, this infection remains a major public health problem. Whilst the WHO recommends giving a birth dose of the vaccine, in South Africa, routine infant HBV vaccination commences at six weeks of age. This schedule is based on data from the pre-HIV era which showed transmission occurred via the horizontal, rather than the vertical route. In the era of HIV however, maternal HIV co-infection may release HBV from immune control, resulting in higher HBV loads and increasing the risk of vertical transmission. The aim of this study was to determine the prevalence and character of HBV infection in HIV-exposed infected and uninfected infants. Residual plasma samples from routine HIV nucleic acid testing of 1000 HIV-exposed infants aged between 0 and 18 months from the Western Cape were tested. Samples were tested for HBsAg by ELISA (Murex HBsAg Version 3) and confirmed by neutralisation. HBV DNA was quantified using an in-house real-time PCR assay. Infants with HBsAg positive samples were followed up and a blood sample was collected from mother and child. Those HBsAg positive samples were tested for HBeAg/antiHBe (Diasorin) and HBsAg negative samples were tested for antiHBs. HBV DNA was quantified. The surface gene was sequenced and the HBV genotype determined by phylogenetic analysis using HepSEQ (www.hepseq.org.uk). Whole genome sequencing was also performed. Of 1000 samples tested, four samples were positive for HBsAg and/or HBV DNA, indicating a prevalence of HBV transmission of 0.4%. At follow-up, two of three infected infants were positive for HBsAg, with HBV viral loads of greater than 108 IU/ml. The third infant was found to have cleared his infection and the fourth child was lost to follow up. These infected infants had all received HBV vaccination. All four mothers were HBeAg positive. Sequencing analysis showed the HBV strains from the two infants and four mothers belonged to subgenotype A1. The two mother-child paired sequences were identical. The data from this study shows that vertical transmission of HBV infection in HIV-exposed infants from the Western Cape is occurring, despite vaccination. Data from the Western Cape, showing an HBV prevalence of 3.4% in HIV-infected pregnant women, and those presented here suggest a vertical transmission rate of HBV of 12%. This is despite the widespread use of tenofovir and lamivudine in HIV-infected women with low CD4 counts. This study provides data supporting calls to bring HBV vaccination closer to the time of birth. Further work is urgently needed to confirm these findings and to determine the rates of transmission in HIV-unexposed infants. / AFRIKAANSE OPSOMMING: Ten spyte van die beskikbaarheid van die Hepatitis B virus (HBV) inenting vir meer as drie dekades, hierdie infeksie bly 'n groot openbare gesondheid probleem. Terwyl die WGO aan beveel dat'n geboorte dosis van die entstof, in Suid-Afrika, roetine baba HBV inenting op die ouderdom van ses weke gegee word. Hierdie skedule is gebaseer op data van die pre-MIV era wat getoon het dat die oordrag plaasgevind het via die horisontale, eerder as die vertikale roete. In die era van MIV egter, moeder MIV ko-infeksie kan HBV vrylaat van immuun beheer, wat lei in hoër HBV vlakke en die verhoging van die risiko van vertikale oordrag. Die doel van hierdie studie was om die voorkoms en karakter van die HBV infeksie in MIV-besmette en onbesmette babas te bepaal. Residuele plasma monsters van roetine-MIV-nukleïensuur toetse van 'n 1000 MIV-blootgestelde babas tussen die ouderdomme van 0 en 18 maande van die Wes-Kaap was getoets. Monsters was getoets vir HBsAg deur ELISA (Murex HBsAg Version 3) en bevestig deur neutralisering. HBV DNA is gekwantifiseer deur gebruik te maak van 'n in-huis real-time PCR assay. Babas met HBsAg positiewe monsters was opgevolg en 'n bloedmonster is versamel van moeder en kind. Die HBsAg positiewe monsters was getoets vir HBeAg/antiHBe (Diasorin) en HBsAg negatiewe monsters was getoets vir antiHBs. HBV DNA was gekwantifiseer. Die oppervlak gene volgorde en genotipes was bepaal deur filogenetiese analise met behulp van HepSEQ (www.hepseq.org.uk). Die hele genoom-volgordebepaling was ook uitgevoer. Van die 1000 monsters wat getoets was, was vier monsters positief vir HBsAg en of HBV DNA, dit dui op 'n voorkoms van HBV oordrag van 0.4%. By op volg, twee van die drie besmette babas was positief vir HBsAg, met HBV virale vlakke van groter as 108 IE/ml. Die derde baba was gevind dat sy infeksie opgeklaar het en die vierde kind was verlore as gevolg van op volg. Hierdie besmette babas het almal HBV inenting ontvang. Al vier moeders was HBeAg positief. Volgordebepaling analise het getoon die HBV stamme van die twee babas en vier moeders behoort aan subgenotype A1. Die twee moeder-kind gepaarde rye was homoloë. Die data van hierdie studie toon dat die vertikale oordrag van HBV infeksie in MIV-blootgestelde babas van die Wes-Kaap vind plaas, ten spyte van inenting. Data van die Wes-Kaap, wat 'n HBV voorkoms van 3.4% in MIV-besmette swanger vroue, en dié wat hier aangebied is dui op 'n vertikale oordrag koers van 12% van die HBV. Dit is ten spyte van die wydverspreide gebruik van tenofovir en lamivudine in MIV-geïnfekteerde vroue met 'n lae CD4-telling. Hierdie studie bied data wat ondersteunende oproepe van HBV inenting nader aan die tyd van die geboorte bring. Verdere werk is dringend nodig om die bevindinge te bevestig en die pryse van die oordrag in MIV-blootgestelde babas te bepaal. / National Health Laboratory Service Research Trust / Poliomyelitis Research Foundation (PRF) / Harry Crossley Foundation / Stellenbosch University

Thesis (MScMedSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Background: Sudden infant death syndrome (SIDS) is considered the second most frequent cause of infant mortality worldwide. Research specifically pertaining to SIDS is limited in the South African setting. Identifiable causes for sudden infant death remain challenging despite full medico-legal investigations inclusive of autopsy, scene visit and ancillary studies. Viral infections could contribute to some sudden unexpected death in infancy (SUDI) cases, especially since a multitude of respiratory viruses have been detected from autopsy specimens. The specific contribution of viruses in the events preceding death, including the subsequent involvement of the immature immune response in infants, still warrants deciphering. Infancy is characterised by marked vulnerability to infections due to immaturities of their immune systems that may only resolve as infants grow older when these sudden deaths rarely still occur. In South Africa there is a lack of a standard protocol for investigations into the causes of SIDS, including the lack of standard guidelines as to which specimens should be taken, which viruses should be investigated and which laboratory assays should be utilised. Objectives: In this prospective descriptive study we aimed to investigate the prevalence of viruses in SUDI and SIDS cases at Tygerberg Forensic Pathology Service (FPS) Mortuary over a one year period. The primary aim was to explore possible respiratory viral infections in SUDI and SIDS cases and to determine the usefulness of molecular techniques to detect viruses from SUDI cases. To determine the significance of viruses, we assessed signs of infection from lung histology. The secondary objectives included collecting demographic data to investigate possible risk factors for SUDI and to look for possible similarities between viruses confirmed in living hospitalised infants at Tygerberg, during the study period compared to viruses detected from SUDI cases. Methods: Between May 2012 and May 2013 samples were collected from 148 SUDI cases presenting at Tygerberg FPS Mortuary. As part of the mandatory routine investigations into SUDI, shell vial culture (SVC) results were collected from lung and liver tissue specimens and bacterial culture results were collected from left and right lung and heart swabs at autopsy. To investigate the possibility of viruses implicated in some of the infant deaths we used the Seeplex® RV15 Ace detection multiplex polymerase chain reaction (PCR) assay to establish the frequency of 13 ribonucleic acid (RNA) respiratory viruses (influenza A and B, human parainfluenza 1-4, human coronavirus [OC43, 229E/NL63], human rhinovirus A, B and C, respiratory syncytial virus A and B, human enterovirus and human metapneumovirus) from RNA extracted from tracheal and lower left and right lung lobe swabs. Tissue from the lower left and right lung lobes were also assessed for histology signs of infection. Results: During our study we confirmed multiple known demographic risk factors for SIDS, such as the age peak around 1-3 months, the male predominance, bed-sharing, sleeping in the prone position, heavy wrapping in warm blankets, prenatal smoke exposure, and socio-economic factors. With the Seeplex® RV15 Ace detection assay between one and three viruses were detected in 59.5% (88/148) of cases. Of the 88 cases that had viruses detected, 75% (66/88) had one virus and 25% (22/88) had co-detections of two to three viruses. The most common viruses detected were HRV in 77% (68/88) of cases, RSV in 18% (16/88) of cases and HCoV in 14% (12/88) of cases. Many of the viruses we detected from our cases are included in the SVC test that forms part of the medico-legal laboratory investigation for all SUDI cases at Tygerberg FPS Mortuary. SVCs were positive in 9.5% (14/148) of all cases only. We showed that the SVC method is potentially missing most of the 13 respiratory viruses we investigated that could contribute to death in some of the SUDI cases. Conclusion: In some cases that had a Cause of Death Classification - SIDS, the PCR viruses detected cannot be ignored, especially when it is supported by histological evidence of infection. We thus propose that the use of PCR could alter a Cause of Death Classification from SIDS to Infection in some of these cases. Further research is needed to determine the significance of detecting viruses from SUDI cases wherein no significant histological evidence of infection was observed. This questions whether PCR may be too sensitive and is detecting past and latent viral infections that do not play any role in the cause of death. The histological picture also requires further characterisation to determine if it accurately predicts infections or lethal events and can truly support virology findings, especially in young infants whose immune systems are still maturing. Without determining the true prevalence of viruses in SUDI cases and the viral-specific immune response, the contribution of virus-specific infections to this syndrome will remain largely undetermined. / AFRIKAANSE OPSOMMING: Agtergrond: Wiegiedood (“SIDS/SUDI”) word beskou as die tweede mees algemene oorsaak van sterftes in kinders jonger as een jaar wêreldwyd. Toegewyde SIDS-spesifieke navorsing in die Suid-Afrikaanse samelewing is beperk. Dit bly steeds „n uitdaging om oorsake te probeer identifiseer vir hierdie onverwagte sterftes in kinders (SUDI) ten spyte van volledige medies-geregtelike ondersoeke, insluitende die lykskouing, ondersoek van die doodstoneel en aanvullende ondersoeke. Virusinfeksies kan aansienlik bydra tot sommige onverwagte sterftes in kinders, aangesien verskeie respiratoriese virusse alreeds aangetoon is in monsters verkry tydens outopsies. Die spesifieke rol wat virusse speel in die prosesse wat die dood voorafgaan, asook die bydraende rol van „n onder-ontwikkelde immuunrespons in babas, regverdig verdere ondersoek. Die eerste jaar van lewe word gekenmerk deur verhoogde vatbaarheid vir infeksies weens die ontwikkelende immuunstelsels soos wat babas ouer word, en die voorkoms van SUDI neem stelselmatig af met „n toename in ouderdom. In Suid-Afrika bestaan daar tans geen standaard protokol vir die ondersoek van wiegiedood nie en daar is ook nie standaard riglyne oor die tipe monsters wat geneem moet word, watter virusse ondersoek moet word en watter laboratorium toetse uitgevoer moet word nie. Doelstellings: In hierdie prospektiewe beskrywende studie is gepoog om die virusse wat in gevalle van wiegiedood of SUDI voorkom te ondersoek. Die studie is uitgevoer by die Tygerberg Geregtelike Patologie Dienste lykshuis oor 'n tydperk van een jaar. Molekulêre tegnieke om virusse aan te toon in hierdie gevalle is gebruik om spesifieke virusinfeksies te ondersoek. Die resultate is met histologiese tekens van infeksie in longweefsel gekorreleer. Demografiese data is verder versamel om moontlike risikofaktore vir wiegiedood te ondersoek. Dit is verder vergelyk met virusse wat met dieselfde diagnostiese tegnieke in babas geïdentifiseer is wat tydens die studieperiode in Tygerberg Hospitaal opgeneem was met lugweginfeksies. Metodes: Monsters van 148 SUDI gevalle wat by die Tygerberg lykshuis opgeneem is, is versamel tussen Mei 2012 en Mei 2013. As deel van die roetine ondersoeke in SUDI gevalle, was selkultuur resultate verkry van long en lewer weefsel, asook bakteriële kulture van deppers wat van beide longe en hart geneem was tydens die lykskouings. „n Seeplex® RV15 Ace polimerase kettingreaksie (PKR) toets is gebruik om die teenwoordigheid van virusse te ondersoek wat moontlik by die babasterftes betrokke kon wees. Trageale- en longdeppers wat tydens die lykskouings versamel was, was getoets vir 13 ribonukleïensure (RNS) respiratoriese virusse (influenza A and B, human parainfluenza 1-4, human coronavirus [OC43, 229E/NL63], human rhinovirus A, B and C, respiratory syncytial virus A and B, human enterovirus and human metapneumovirus). Resultate: Ons studie het verskeie bekende demografiese risikofaktore vir SUDI bevestig, byvoorbeeld „n ouderdomspiek tussen een en drie maande ouderdom, manlike predominansie, deel van „n bed met ander persone, slaap posisie op die maag, styf toedraai in warm komberse, blootstelling aan sigaretrook voor geboorte en sosio-ekonomiese faktore. Die Seeplex® RV15 Ace toets het tussen een en drie virusse geïdentifiseer in 59.5% (88/148) van die gevalle. Uit die 88 gevalle waarin virusse opgespoor was, was selgs een virus in 75% (66/88) van gevalle gevind en twee en drie virusse in 25% (22/88). Die mees algemene virusse was HRV in 77% (68/88) van gevalle, RSV in 18% (16/88) van gevalle en HCoV in 14% (12/88) van gevalle. Baie van die virusse wat tydens hierdie studie ondersoek was, was ingesluit in die roetine selkultuur toets wat deel vorm van die standaard medies-geregtelike laboratoriumondersoeke in alle SUDI gevalle by die Tygerberg lykshuis, alhoewel die selkulture positief was in slegs 9.5% (14/148) van gevalle. Ons het gevind dat baie respiratoriese virusse potensieel gemisdiagnoseer word wat „n rol kon speel in of bydra tot die dood van sommige SUDI gevalle. Gevolgtrekking: In sommige gevalle waarin SIDS geklassifiseer is as die oorsaak van dood, kan die virusse wat met PKR toetse opgespoor is nie geïgnoreer word nie, veral waar die bevinding ondersteun word deur histologiese bewyse van infeksie. Ons stel dus voor dat die gebruik van PKR toetse die oorsaak van dood klassifikasie kan verander van SIDS na Infeksie in sommige van hierdie gevalle. Verdere navorsing is nodig om die waarde van gelyktydige opsporing van virusse in SUDI gevalle te bepaal wanneer daar geen noemenswaardige histologiese bewyse van infeksie gevind word nie. Dit bevraagteken of die PKR toets dalk te sensitief is en gevolglik vorige en latente virusinfeksies identifiseer wat nie noodwendig 'n rol in die oorsaak van dood speel nie. Die diagnostiese en kliniese waarde van die histologiese beeld in terme van die rol van virusinfeksies as bydraende oorsaak van dood moet verder ondersoek word, veral in jong kinders wie se immuunstelsels nog nie volledig ontwikkel is nie. Indien die werklike voorkoms van virusse in SUDI gevalle en die virus-spesifieke immuunrespons nie bepaal word nie, sal die rol van virus-spesifieke infeksies in hierdie sindroom grootliks onbekend bly. / Harry Crossley Foundation / Poliomyelitis Research Foundation (PRF) / National Health Laboratory Services Research Trust