O Epstein-Barr vírus (EBV) é a única espécie humana pertencente ao gênero Lymphocryptovirus. A transmissão ocorre através da saliva contaminada e geralmente ainda na infância. Nosso estudo analisou 165 amostras clínicas de pacientes, portadores de HIV, em tratamento com antiretrovirais, atendidos no Sistema Hospitalar do Sistema Penitenciário do Estado de São Paulo. Nosso enfoque foi pesquisar o EBV nas células mononucleares do sangue periférico, através das técnicas de PCR, Nested-PCR e seqüenciamento de nucleotídeos. Os resultados obtidos, indicaram que 11,51% (19) das amostras analisadas, apresentaram-se positivas para o EBV. Essas 19 amostras, foram seqüenciadas com primers específicos para a região da EBNA-1 (Epstein Barr Nuclear Antigen 1). As amostras foram alinhadas com o auxílio do DNASTAR. Ao alinharmos as amostras, encontramos uma troca de base (de G para A) em 7 amostras e essa troca não alterou a conformação da proteína EBNA-1. Na análise filogenética de nossas sequências com as depositadas no GenBank, foi possível observar dois grupos, que representam tipo 1 e o tipo 2 do EBV. 100% das amostras estudadas por nós foram identificadas como pertencentes ao grupo que caracteriza o tipo 2. Sendo assim, as 7 amostras que apresentaram a troca sugerem a origem um novo subtipo. / The Epstein-Barr Virus (EBV) is the only species to the genus Lymphocriptovirus that infects humans. One of the possible route for its transmission thought by contamined saliva and usually occurs in the childhood. This study analysed 165 clinical samples from HIV infected patients, treated by HARRT, attended in the Hospitalar System in the Penitentiary System from Sao Paulo State. The aim of this study was to search EBV in peripheral blood mononuclear cells by PCR, Nested-PCR and sequencing analysis. The results showed 11,51% of the analysed samples, positive for EBV. This samples, was sequenced with specifics primers from the EBNA-1 (Epstein Barr Nuclear Antigen 1) region. The samples were aligned by DNASTAR program. The aligned sequences showed the base conversion G to A in seven samples. This conversion caused no alteration in the EBNA-1 protein conformation. In the phylogenetic analysis the studied sequences with the sequences from GenBank was possible to observe two groups represented with type 1 and type 2 from EBV. 100% the samples studied was identified with the group characterized by the type 2 to EBV. So the seven samples showed the conversion, suggesting the origin of the one new subtype.

The purpose of this study was to assess the impact of virologic monitoring frequencies on treatment failure, adherence to therapy, and the emergence of drug resistance in HIV-1 infected patients. A quantitative, meta-analysis was conducted to investigate the virologic outcomes of infrequent and frequent Viral Load (VL) testing among patient on combination antiretroviral therapy (cART). Data was collected through a self-designed data collection form. Two comparison groups emerged being guided by the VL monitoring frequency. In group I, the health outcomes were compared for (≥3 VLs per year) versus (≤2 VLs per year) and (2 VLs per year) versus (≤1 VLs per year) for group II. Data were analysed using the Cochrane's statistical software, RevMan v5.3. The findings support (2 VLs per year) as the optimal VL monitoring strategy for stable and virologically suppressed patients and there is nothing to be gained by (≥3 VLs per year). / Health Studies / M.P.H.

O Epstein-Barr vírus (EBV) é a única espécie humana pertencente ao gênero Lymphocryptovirus. A transmissão ocorre através da saliva contaminada e geralmente ainda na infância. Nosso estudo analisou 165 amostras clínicas de pacientes, portadores de HIV, em tratamento com antiretrovirais, atendidos no Sistema Hospitalar do Sistema Penitenciário do Estado de São Paulo. Nosso enfoque foi pesquisar o EBV nas células mononucleares do sangue periférico, através das técnicas de PCR, Nested-PCR e seqüenciamento de nucleotídeos. Os resultados obtidos, indicaram que 11,51% (19) das amostras analisadas, apresentaram-se positivas para o EBV. Essas 19 amostras, foram seqüenciadas com primers específicos para a região da EBNA-1 (Epstein Barr Nuclear Antigen 1). As amostras foram alinhadas com o auxílio do DNASTAR. Ao alinharmos as amostras, encontramos uma troca de base (de G para A) em 7 amostras e essa troca não alterou a conformação da proteína EBNA-1. Na análise filogenética de nossas sequências com as depositadas no GenBank, foi possível observar dois grupos, que representam tipo 1 e o tipo 2 do EBV. 100% das amostras estudadas por nós foram identificadas como pertencentes ao grupo que caracteriza o tipo 2. Sendo assim, as 7 amostras que apresentaram a troca sugerem a origem um novo subtipo. / The Epstein-Barr Virus (EBV) is the only species to the genus Lymphocriptovirus that infects humans. One of the possible route for its transmission thought by contamined saliva and usually occurs in the childhood. This study analysed 165 clinical samples from HIV infected patients, treated by HARRT, attended in the Hospitalar System in the Penitentiary System from Sao Paulo State. The aim of this study was to search EBV in peripheral blood mononuclear cells by PCR, Nested-PCR and sequencing analysis. The results showed 11,51% of the analysed samples, positive for EBV. This samples, was sequenced with specifics primers from the EBNA-1 (Epstein Barr Nuclear Antigen 1) region. The samples were aligned by DNASTAR program. The aligned sequences showed the base conversion G to A in seven samples. This conversion caused no alteration in the EBNA-1 protein conformation. In the phylogenetic analysis the studied sequences with the sequences from GenBank was possible to observe two groups represented with type 1 and type 2 from EBV. 100% the samples studied was identified with the group characterized by the type 2 to EBV. So the seven samples showed the conversion, suggesting the origin of the one new subtype.

Thesis (MScMedSc (Pathology. Medical Virology))--University of Stellenbosch, 2005. / There are currently an estimated 5.3 million people infected with human immunodeficiency virus / acquired immunodeficiency syndrome (HIV/AIDS) in South Africa. HIV-1 group M Subtype C is currently responsible for the majority of HIV infections in sub-Saharan Africa (56% worldwide). The Khayelitsha informal settlement, located 30 km outside Cape Town, has one of the highest HIV prevalence rates in the Western Cape. The objective of this study was to investigate the molecular epidemiology of HIV-1 in Khayelitsha using serotyping and genotyping techniques. Patient samples were received from the Matthew Goniwe general health clinic located at site C in Khayelitsha. Serotyping was performed through a competitive enzymelinked immunosorbent assay (cPEIA). RNA was isolated from patient plasma and a two step RT-PCR amplification of the gag p24, env gp41 IDR, env gp120 V3 and pol genome regions performed. Sequences obtained were used for detailed sequence and phylogenetic analysis. Neighbour-joining and maximum likelihood phylogenetic trees were drawn to assess the relationship between the Khayelitsha sequences obtained and a set of reference sequences obtained from the Los Alamos National Library (LANL) HIV database (http://www.hiv.lanl.gov/). Through serotyping and genotyping the majority of HIV strains were characterised as HIV-1 group M subtype C. One sample (1154) was characterised as a possible C / D recombinant strain. In 9 other samples HIV-1 recombination cannot be excluded, as only one of the gene regions investigated could be amplified and characterised in these samples. The gag p24 genome region was found to be more conserved than the env gp41 IDR, with the env gp41 IDR more conserved than the env gp120 V3. The variability of the env gp120 V3 region indicates that patients might be dually infected with variant HIV-1 subtype C strains or quasispecies. Conserved regions identified in the Khayelitsha sequences can induce CD4+ T-cell responses and are important antibody recognition target sites. These conserved regions can play a key role in the development of an effective HIV-1 immunogen reactive against all HIV-1 subtypes. The majority of subtype C viruses were predicted to use CCR5 as their major chemokine co-receptor. The pol sequences analysed indicate that mutations associated with minor resistance to Protease Inhibitors (PIs) might be present in the Khayelitsha community. The identification of resistant mutations is vital for people receiving antiretroviral treatment (ART). It can influence the success of their treatment and delay the onset of AIDS. Serotyping is a quick characterisation method, but not always accurate. With genotyping detailed molecular analysis can be performed. However, with genotyping the success of amplification often depends on viral load. In Southern Africa a subtype C candidate vaccine appears to be the best option for future vaccine considerations. The sporadic detection of non-subtype C and recombinant subtype C viruses remains a concern and will thus have to be closely monitored. Phylogenetic analysis can help to classify and monitor the spread and evolution of these viruses.

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

O vírus sincicial respiratório humano (VSRH) é o agente viral mais freqüentemente relacionado a doenças do trato respiratório inferior em crianças abaixo de um ano de idade. Analíse da varibilidade antigênica e gênica mostraram que o VSRH pode ser divido em dois grupos: A e B. O vírus é um membro do gênero Pneumovirus pertencente a família Paramyxoviridea, e possui três principais proteínas que são: glicoproteina F (fusão), glicoproteina G (adesão), glicoproteina SH (pequena proteína hidrofóbica). A proteína F é responsável pela fusão da célula ao vírus, enquanto a proteína G tem papel fundamental na replicação do vírus, porém a função da proteína SH, ainda não está bem definida, estudos recentes mostram-na como responsável por inibir a sinalização do fator de necrose tumoral alfa (TNF-a). Neste estudo foram colhidas amostras de 965 crianças, entre os anos de 2004 e 2005, dentre as quais 424 foram positivas. 117 amostras foram seqüenciadas a proteína SH e G e comparadas com amostras que circularam mundialmente. A analíse filogenética mostrou uma baixa variabilidade entre os genótipos estudados tanto do grupo A quanto do B. / The human respiratory syncytial virus (HRSV) is the major cause of lawer respiratory tract infections in infantis, young children and elderly. Analysis of the antigenic and genetic variability has shown that there are two groups of the virus HRSV, A and B. The virus (HRSV) is a member of the genus pneumovirus in the paramyxoviridae family. The virus encodes three membrane-bound glicoproteins, namely the fusion (F) attachment (G) and small hydrophobic (SH) proteins. The F mediates fusion of the virus and cell membranes and the G proteins is involved in virus attachment. The biological properties of the F and G glicoproteins and role that they play during virus replication relatively well understood, however the functional significance of the SH protein during replication remains unclear, although recent study shown that it can inhibit TNF-alpha. In this study, HRSV strains were isolated from nasopharyngeal aspirates collected from 965 children between 2004 and 2005, yielding 424 positive samples. We sequenced the small hydrophobic protein (SH) gene and protein (G) of 117 samples and compared them with other viruses identified worldwide. The phylogenetic analysis showed a low genetic variably among the isolates but allowed us to classify the viruses into different genotypes for the A and B HRSV strains.

O vírus sincicial respiratório humano (VSRH) é o agente viral mais freqüentemente relacionado a doenças do trato respiratório inferior em crianças abaixo de um ano de idade. Analíse da varibilidade antigênica e gênica mostraram que o VSRH pode ser divido em dois grupos: A e B. O vírus é um membro do gênero Pneumovirus pertencente a família Paramyxoviridea, e possui três principais proteínas que são: glicoproteina F (fusão), glicoproteina G (adesão), glicoproteina SH (pequena proteína hidrofóbica). A proteína F é responsável pela fusão da célula ao vírus, enquanto a proteína G tem papel fundamental na replicação do vírus, porém a função da proteína SH, ainda não está bem definida, estudos recentes mostram-na como responsável por inibir a sinalização do fator de necrose tumoral alfa (TNF-a). Neste estudo foram colhidas amostras de 965 crianças, entre os anos de 2004 e 2005, dentre as quais 424 foram positivas. 117 amostras foram seqüenciadas a proteína SH e G e comparadas com amostras que circularam mundialmente. A analíse filogenética mostrou uma baixa variabilidade entre os genótipos estudados tanto do grupo A quanto do B. / The human respiratory syncytial virus (HRSV) is the major cause of lawer respiratory tract infections in infantis, young children and elderly. Analysis of the antigenic and genetic variability has shown that there are two groups of the virus HRSV, A and B. The virus (HRSV) is a member of the genus pneumovirus in the paramyxoviridae family. The virus encodes three membrane-bound glicoproteins, namely the fusion (F) attachment (G) and small hydrophobic (SH) proteins. The F mediates fusion of the virus and cell membranes and the G proteins is involved in virus attachment. The biological properties of the F and G glicoproteins and role that they play during virus replication relatively well understood, however the functional significance of the SH protein during replication remains unclear, although recent study shown that it can inhibit TNF-alpha. In this study, HRSV strains were isolated from nasopharyngeal aspirates collected from 965 children between 2004 and 2005, yielding 424 positive samples. We sequenced the small hydrophobic protein (SH) gene and protein (G) of 117 samples and compared them with other viruses identified worldwide. The phylogenetic analysis showed a low genetic variably among the isolates but allowed us to classify the viruses into different genotypes for the A and B HRSV strains.

<p dir="ltr">The recent global pandemic, COVID-19, has revealed to all the importance of understanding the complex relationship between viruses and hosts. Before COVID-19, I started my study of viral protein-host lipid interactions in the hemorrhagic fevers Ebola and Marburg viruses. These viruses contain a matrix protein that interacts with the plasma membrane to facilitate the formation of both authentic viruses and virus-like particles. My goal was to understand the limitations of their specific host lipid interactions. However, when the COVID-19 pandemic began, so to be our swift response in the development of a biosafety level 2 compatible model. This model can be used for studying severe acute respiratory distress syndrome 2 (SARS-CoV-2) assembly, egress, and entry. This model enabled exponentially greater access to more facilities to study the intricacies of SARS-CoV-2 assembly. With more access to studying the virus in a safe model, our goal is to push the understanding of viral assembly faster. I then began to take apart the individual pieces of the model and started to look at understanding the roles that they play independently. The membrane protein is the most abundant structural protein and I studied the specific lipid interactions of the soluble fraction of the protein. Physicians observed nucleocapsid protein mutations in the clinic with the increasing number of SARS-CoV-2 variants that are on the rise. The microscopy data collected can give us more insight into perhaps how the nucleocapsid protein induces the formation of filopodia structures at the plasma membrane. The envelope protein proved to be a challenge, but I determined a specific envelope and ceramide interaction in cells. The envelope protein was also causing the formation of microvesicles for an undefined function. I was able to determine the subcellular localization of the protein to the mitochondria. The localization to the mitochondria appears to induce depolarization of the mitochondria membrane action potential and induces the increase in mitochondria dysfunction signal, cytochrome c. Although the mitochondria were dysfunctional, there was no increase in apoptosis signal in the presence of the protein alone.</p>