O vírus respiratório sincicial humano (HRSV) é principal agente causador de infecções do trato respiratório inferior em crianças e lactentes. Um diagnóstico rápido e preciso evitaria o uso desnecessário de antibióticos, nos casos em que a infecção é viral. A reação em cadeia da polimerase após transcrição reversa (RT-PCR) e o ensaio de imunofluorescência indireta (IFI) são considerados ferramentas importantes na detecção do HRSV, pela alta sensibilidade e especificidade. Visando simplificar e minimizar os riscos de contaminação freqüentes, em duas etapas, foi padronizada uma reação em tubo único para detecção do HRSV em amostras clínicas. Aspirados de nasofaringe de 226 crianças de 0-5 anos de idade, com doença respiratória, atendidas no Hospital Universitário da Universidade de São Paulo (HU-USP), foram testados por imunofluorescência indireta, RT semi Nested PCR e RT-PCR em tubo único. Cento e duas amostras (45,1%) foram positivas em pelo menos uma das técnicas e 75 (33,2%) em todas. Três (1,3%) amostras foram positivas por IFI e RT semi Nested PCR, 1 (0,4%) foi positiva por IFI e RT-PCR em tubo único, 5 (2,2%) amostras foram positivas somente por IFI, 2 (0,9%) somente por RT semi Nested PCR e 16 (7,1%) amostras foram positivas pela RT semi Nested PCR e RT-PCR em tubo único. A RT-PCR em tubo único mostrou ser uma técnica rápida, sensível e específica, e o uso combinado de dois métodos aumenta a detecção do HRSV. / Respiratory Syncytial Virus is the main cause of acute lower respiratory tract infection (ALTRs) in infants, elderly and immunodepressed patients. Rapid diagnosis of Respiratory Syncytial Virus (RSV) infection is necessary to efficient treatment, avoiding the unnecessary use of antibiotics and determining patient isolation requirements. The reverse trancriptase polymerase chain reaction (RT-PCR) and indirect immunofluorescence assay (IFA) methods have been referred as important tools for virus detection considering the high sensitivity and specificity, respectively of such methods. In order to maximize the simplicity and minimize the risk of sample cross-contamination by two steps RT-PCR, we developed a RT-PCR using a single-tube to detect HRSV in clinical samples. Nasopharyngeal aspirates (Nas) of 226 patients with acute respiratory illness, ranging 0-5 years old, were collected at the University of São Paulo Hospital (HU-USP) in São Paulo city. Samples were tested by indirect immunofluorescence assay, RT semi Nested PCR and single-tube RT-PCR. One hundred two (45,1%) of the 226 samples were positive at least by one of the three methods tested and 75 (33,2%) were positive by all methods. Three (1,3%) samples were positive only by IFI and RT semi Nested PCR, 1 (0,4%) sample were positive only by IFI and RT-PCR single-tube, 5 (2,2%) were positive only by IFI, 2 (0,9%) were positive only by RT semi Nested PCR and 16 (7,1) were positive only RT semi Nested PCR and RT-PCR single-tube. RT-PCR single-tube, showed to be fast, sensitive and specific for diagnosis of RSV and the combined use of both methods enhanced HRSV detection.

Le virus Zika (ZIKV) est un phénomène épidémiologique sans précédent qui surprit le monde entier. Pendant de nombreuses années, il fut considéré comme un virus anodin responsable d’une poignée d’infections humaines, auto-limitées et bénignes, en Afrique et en Asie du Sud-est. Mais, après des décennies de propagation silencieuse, une première épidémie éclata en Micronésie en 2007 - tel un signal d'alarme. Quelques années plus tard, une soudaine épidémie de ZIKV de plus grande ampleur se déclara dans les îles du Pacifique avant d'atteindre le Brésil en 2015. Au cours de cette période, Zika fut associé à de graves complications neurologiques, mettant en évidence son fort potentiel pathogène pour l'homme. Depuis son émergence, plus de 80 pays et territoires ont été touchés par la pandémie de ZIKV, désormais reconnu comme un virus neurotrope et tératogène. L'association des souches contemporaines de ZIKV à des formes graves de maladie chez l'homme, qui n'ont jamais été signalées auparavant, a soulevé l'hypothèse d'une pathogénicité nouvellement acquise. Ainsi, mes travaux de doctorat visaient à déterminer si l'ampleur de l'épidémie actuelle pouvait en partie avoir été facilitée par des facteurs viraux qui auraient renforcé la fitness du ZIKV. À cette fin, mon projet de recherche s'est concentré sur l'identification des facteurs moléculaires viraux impliqués dans la pathogénicité du virus Zika chez l’homme à partir du développement de clones moléculaires. / Zika virus (ZIKV) is an unprecedented epidemiological phenomenon which surprised the world. For many years, it was considered a trivial virus responsible for only a handful of human infections, self-limited and benign, in Africa and Southeast Asia. But then, after decades of silent spread, a first epidemic broke out in Micronesia in 2007 – like a warning signal. A few years later, a sudden Zika outbreak of larger scale occurred in the Pacific islands before reaching Brazil in 2015. During this period, Zika was associated with severe neurological complications, highlighting its serious pathogenic potential for humans. Since its emergence, more than 80 countries and territories have been affected by the ZIKV pandemic, which is now recognized as a neurotropic and teratogenic virus. The association of contemporary ZIKV strains with severe forms of disease in humans, that have never been reported before, has raised the hypothesis of newly acquired pathogenicity. In this regard, my doctoral research aimed to determine whether the scope of the current epidemic was partly facilitated by viral factors that improved ZIKV fitness. To this end, my research project focused on the identification of the viral molecular factors involved in Zika virus pathogenicity in humans based on the development of molecular clones.

The very virulent (vv) pathotype of infectious bursal disease virus (IBDV) has spread rapidly throughout Europe, Asia, and the Middle East. Although Australia is currently unaffected, there remains the potential for incursion of an exotic isolate. The aim of this study was to identify putative virulence determinants of IBDV to facilitate the development of improved diagnostic assays for detection and characterisation of vvIBDV isolates. Sequencing of Indonesian vvIBDV Tasik94 revealed a unique substitution [ A¨S222] in the hypervariable region (HVR) of viral protein (VP) VP2, which did not appear to impinge on virulence or antigenicity. Phylogenetic analyses indicated that Tasik94 was closely related to Asian and European vvIBDV strains. Extensive alignment of deduced protein sequences across the HVR of VP2 identified residuesI242 I256 and I294 as putative markers of the vv phcnotype. Comparison of the pathology induced by mildly-virulent Australian IBDV 002/73 and Indonesian vvIBDV Tasik94, revealed that histological lesions in the spleen, thymus and bone marrow were restricted to Tasik94-infected birds, suggesting the enhanced pathogenicity of vvIBDV might be attributed to replication in non-bursal lymphoid organs. The biological significance of the VP2 HVR in virulence was assessed using recombinant viruses generated by reverse genetics. Both genomic segments of Australian IBDV 002/73, and recombinant segment A constructs in which the HVR of 002/73 was replaced with the corresponding region of either tissue culture-adapted virus or vvIBDV (Tasik94), were cloned behind T7 RNA polymerase promoter sequences. In vitro transcription/translation of each construct resulted in expression of viral proteins. Co-transfection of synthetic RNA transcripts initiated replication of both tissue culture-adapted parental and recombinant viruses, however attempts to rescue non-adapted viruses in specific-pathogen-free (SPF) chickens were unsuccessful. Nucleotide sequence variation in the HVR of VP2 was exploited for the development of a new diagnostic assay to rapidly detect exotic IBDV isolates, including vvIBDV, using reverse transcription polymerase chain reaction (RT-PCR) amplification and Bmrl restriction enzyme digestion. The assay was capable of differentiating between endemic and exotic IBDV in 96% of 105 isolates sequenced to date.

Bacteriophages are viruses that infect bacteria and they are the most numerous biological entities on Earth. Temperate phage can adopt two different lifestyles. In the lytic lifestyle, a phage injects its genome into the host and a controlled developmental program ensues. The phage DNA is replicated, phage genes are expressed and new viral particles are assembled. Ultimately, the host cell lyses and the phage particles are released into the environment. In the lysogenic lifestyle, a phage integrates its genome into the host chromosome, creating a prophage. The cell containing the prophage is known as a lysogen. Most prophage genes are not expressed. However, those that are encode a wide variety of functions. One function is exclusion, or the prevention of a different phage type from successfully infecting the lysogenic cell. Most exclusion systems are limited to a specific phage. Bacteriophage HK239 is unique in that it has a wide range of exclusion including Lambda, P1vir, P2, HK022, and T4rII. To learn more about HK239, the genome was sequenced and annotated. The genome is 41,538 bp in length and there are 71 open reading frames. It has a genomic organization similar to other lambda phage and is most closely related to bacteriophage HK022. No additional genes that share homology with known exclusion functions were identified through the sequence analysis of the HK239 genome. It is possible that an open reading frame for which no database matches were found may indeed encode an exclusion function.

There is an increasing number of patients failing second line highly active antiretroviral therapy (AZT, DDI and LPV/r) in South Africa, where HIV-1 subtype C predominates. Mutations at gag cleavage sites (CS) have been found to correlate with resistance mutations in protease (PR). Therefore, it is important to collect data on subtype C protease and gag sequences from patients as these mutations may affect the efficacy of protease inhibitor (PI) containing drug regimens. In this study, 30 subtype-C infected second-line failures were genotyped using the ViroSeqTM resistance genotyping kit and the gag region from these isolates were then characterised. These sequences were then compared to 30 HIV-1 subtype C infected first-line failures (PI-naïve) and subtype B, C and group M naïve sequences that were downloaded from the Los Alamos Sequence Database. Amino acid diversity at the CS was measured using Mega version 4.0. To investigate the effect of CS mutations on replication capacity, a mutation was introduced by site-directed mutagenesis (Stratagene’s QuikChange Site-Directed Mutagenesis kit). Of the 30 second-line failures that we genotyped, only 16 had resistance mutations in PR and 23 in gag. The most frequent major PI mutations were: I54V/L, M46I, V82A, and I84V and in gag CS were V390L/I and A431V. Interestingly the A431V mutation significantly correlated with protease mutations M46I/L, I54V and V82A. The virus carrying the A431V mutation in vitro was found to have a lower replication capacity compared to the wild type. These findings emphasize the need for further investigation of gag mutations and their contribution to the evolution of HIV resistance to PIs. / Thesis (M.Med.Sc.)-University of KwaZulu-Natal, Durban, 2010.

O vírus respiratório sincicial humano (HRSV) é principal agente causador de infecções do trato respiratório inferior em crianças e lactentes. Um diagnóstico rápido e preciso evitaria o uso desnecessário de antibióticos, nos casos em que a infecção é viral. A reação em cadeia da polimerase após transcrição reversa (RT-PCR) e o ensaio de imunofluorescência indireta (IFI) são considerados ferramentas importantes na detecção do HRSV, pela alta sensibilidade e especificidade. Visando simplificar e minimizar os riscos de contaminação freqüentes, em duas etapas, foi padronizada uma reação em tubo único para detecção do HRSV em amostras clínicas. Aspirados de nasofaringe de 226 crianças de 0-5 anos de idade, com doença respiratória, atendidas no Hospital Universitário da Universidade de São Paulo (HU-USP), foram testados por imunofluorescência indireta, RT semi Nested PCR e RT-PCR em tubo único. Cento e duas amostras (45,1%) foram positivas em pelo menos uma das técnicas e 75 (33,2%) em todas. Três (1,3%) amostras foram positivas por IFI e RT semi Nested PCR, 1 (0,4%) foi positiva por IFI e RT-PCR em tubo único, 5 (2,2%) amostras foram positivas somente por IFI, 2 (0,9%) somente por RT semi Nested PCR e 16 (7,1%) amostras foram positivas pela RT semi Nested PCR e RT-PCR em tubo único. A RT-PCR em tubo único mostrou ser uma técnica rápida, sensível e específica, e o uso combinado de dois métodos aumenta a detecção do HRSV. / Respiratory Syncytial Virus is the main cause of acute lower respiratory tract infection (ALTRs) in infants, elderly and immunodepressed patients. Rapid diagnosis of Respiratory Syncytial Virus (RSV) infection is necessary to efficient treatment, avoiding the unnecessary use of antibiotics and determining patient isolation requirements. The reverse trancriptase polymerase chain reaction (RT-PCR) and indirect immunofluorescence assay (IFA) methods have been referred as important tools for virus detection considering the high sensitivity and specificity, respectively of such methods. In order to maximize the simplicity and minimize the risk of sample cross-contamination by two steps RT-PCR, we developed a RT-PCR using a single-tube to detect HRSV in clinical samples. Nasopharyngeal aspirates (Nas) of 226 patients with acute respiratory illness, ranging 0-5 years old, were collected at the University of São Paulo Hospital (HU-USP) in São Paulo city. Samples were tested by indirect immunofluorescence assay, RT semi Nested PCR and single-tube RT-PCR. One hundred two (45,1%) of the 226 samples were positive at least by one of the three methods tested and 75 (33,2%) were positive by all methods. Three (1,3%) samples were positive only by IFI and RT semi Nested PCR, 1 (0,4%) sample were positive only by IFI and RT-PCR single-tube, 5 (2,2%) were positive only by IFI, 2 (0,9%) were positive only by RT semi Nested PCR and 16 (7,1) were positive only RT semi Nested PCR and RT-PCR single-tube. RT-PCR single-tube, showed to be fast, sensitive and specific for diagnosis of RSV and the combined use of both methods enhanced HRSV detection.

Hepatitis C virus (HCV) is one of the leading causes of hepatocellular carcinoma worldwide. HCV-neutralizing antibody AP33 recognizes a linear, highly conserved epitope on the viral entry protein E2, disrupting the interaction with the cellular receptor CD81 that leads to viral entry. AP33-related anti-idiotypes (Ab₂s) have the potential to carry the internal image of the antigen E2, eliciting the production of AP33-like antibodies in humans. This study reports the mid-resolution structure of the Fab fragment of anti-idiotype A164.3 and the high-resolution structure of the Fab fragment of AP33 in complex with the Fv fragment of anti-idiotype B2.1A. Analysis of the structures and comparison with the previously published structure of AP33 in complex with a peptide corresponding to the E2 epitope, suggests that while A164.3 does not mimic the antigen E2, B2.1A is characterized by high surface complementarity with AP33 and functional antigen mimicry. Thus, B2.1A can be classified as an Ab₂-β, a subgroup of anti-idiotypes carrying the internal image of the antigen. Preliminary binding studies show that AP33 binds B2.1A with nanomolar affinity, supporting the role of B2.1A as an idiotypic vaccine candidate. Zaire ebola virus causes severe, often lethal hemorrhagic fever in humans. Ebola virus polymerase cofactor VP35 is a multifunctional protein involved in, among other functions, dsRNA binding and inhibition of the host's interferon pathways. VP35 contains an N-terminal oligomerization domain and a C-terminal dsRNA-binding domain (RBD). Preliminary results on the oligomerization domain of VP35 suggest that this region contains a coiled-coil motif, as previously reported. In order to validate a recently-discovered dsRNA end-capping pocket as a drug target, the structure of VP35 RBD I278A mutant was solved at high resolution, showing that even a small perturbation in the binding pocket can cause dramatic binding impairment due to loss of contacts with dsRNA.

Thesis (MSc)--Stellenbosch University, 2003. / ENGLISH ABSTRACT: The aim of this study was to combine two common diagnostic tools: serological kits and genetic fingerprinting to identify cherry leaf-roll nepovirus (CLRV), and to establish a marker system to characterize walnut germplasm. The detection of plant viruses is difficult. Restrictions are imposed for quarantine purposes on the importation of plant material from foreign countries. Modern techniques such as a PCR based screening method for CLRV are required to ensure material do not harbour viruses. A primer pair was designed to amplify a 430 bp non-coding homologous region. For the choice of primers, consensus sequences were considered and areas where the sequence data shared 98.5% homology, were chosen. The sensitivity of this detection method was 100-fold higher when compared to the ELISA. The PCR fragment was verified by nucleotide sequencing. AFLP technology was used to identify polymorphic fragments for 6 walnut cultivars and a rootstock, and SCARs were developed from AFLP specific bands. The AFLP technique distinguished all the walnut cultivars and the rootstock. However, conversion of AFLP fragments to SCAR markers for the development of a simple robust technique for cultivar discrimination, was not successful. Using 27 AFLP primer combinations, polymorphic fragments as high as 47.8% were scored. The reason for the lack of efficient conversion was as the result of the AFLP technique. The SCAR primers were generated from sequences internal to the AFLP primers but the specificity of the markers was in the AFLP primers not the internal sequence. In this study using AFLP, walnut cultivars were found to be closely related. The AFLP primer pairs used, provided polymorphic fragments. From these fragments, 7 SCAR markers were developed. It was expected that these SCARs derived from the AFLP markers would detect slight differences between cultivars. The Paradox SCAR marker was the only one that could divide the cultivars into two groups. When Chandler SCAR products were digested with the restriction enzyme Rsal, the same banding pattern as that of Paradox SCAR products was observed. / AFRIKAANSE OPSOMMING: Die doel van hierdie studie was om twee algemene opsporingstegnieke te kombineer: serologiese toetsstelle en genetiese vingerafdrukke om cherry leaf-roll nepovirus (CLRV) te eien en om In merkersisteem te ontwikkel wat okkerneut kiemplasma kan karakteriseer. Die opsporing van plant virusse is baie moeilik. As gevolg van kwarantyn vereistes, word daar beperkinge geplaas word op die invoer van plant materiaal vanuit die buiteland. Moderne tegnieke soos hierdie een wat op PKR berus, word benodig om te verseker dat CLRV nie in plantmateriaal teenwoordig is nie. In Stel inleiers is ontwerp wat In 430 bp nie-koderende homoloë area amplifiseer. Hiervoor is konsensus volgordes bestudeer en slegs die volgordes wat 98,5% homologie getoon het, is gekies. In vergelyking met ELISA was die sensitiwiteit van hierdie deteksie metode 100 maal beter. DNA volgordebepaling is op die resulterende fragment gedoen om die PKR produk te verifieer. AFLP tegnologie is gebruik om polimorfiese fraqmente vir 6 okkerneut kultivars en 'n onderstok te identifiseer en SCARs is uit hierdie fragmente ontwikkel. Die AFLP tegniek kon tussen al die okkerneut kultivars en die onderstok onderskei. Die omskakeling van die AFLP fragmente in SCAR merkers om sodoende In eenvoudige kragtige tegniek vir kultivar onderskeiding te ontwikkel, was egter nie suksesvol nie. Met die gebruik van 27 AFLP inleier kombinasies, kon polimorfiese fragmente van so hoog as 47.8% verkry word. Die rede hoekom omskakeling onsuksesvol was lê by die aard van die AFLP tegniek. Die SCAR inleiers is ontwikkel uit volyordes intern tot die AFLP inleiers, maar die spesifisiteit van die merkers het juis in die AFLP inleiers gelê en nie in die interne volgordes nie. In hierdie studie, met die gebruik van AFLP, is gevind dat okkerneut kultivars baie naby verwant is. Die AFLP inleierstelle wat gebruik is, het polimorfiese fragmente gelewer. Uit hierdie fragmente is 7 SCAR merkers ontwikkel. Daar is verwag dat die SCARs wat uit die AFLP merkers ontwikkel is, klein verskille tussen kultivars sou opspoor. Dit was egter net die Paradox SCAR merker wat die kultivars in twee groepe kon verdeel. Restriksie ensiem vertering met Rsalop die Chandler SCAR produkte het dieselfde bandpatrone as die van die Paradox SCAR produkte gelewer.

Os vírus Influenza A infectam um largo espectro de hospedeiros e causam epidemias anuais. São vírus com alta variabilidade genética e RNA segmentado, que podem sofrer rearranjos entre os genes de diferentes vírus. Em 2006, foram analisadas 521 amostras de crianças menores de 5 anos atendidas no HU-USP e 25 foram positivas para Influenza A, sendo H3N2 o mais prevalente (68%). Cinco genes de 18 amostras foram seqüenciados e obtivemos 13 sequencias de HA, 12 da NP, 12 de NA, 14 da M e 10 da NS. Verificou-se a presença de várias mutações, especialmente na HA e NA, que favoreceram a substituição da cepa vacinal naquele ano. Todas as amostras H3N2 apresentaram sítios de resistências aos inibidores da M2. Diferentes linhagens circularam no mesmo ano, tanto de H1 como de H3, favorecendo rearranjos entre elas. Foram verificados, também rearranjos envolvendo os genes da HA e NP, indicando o complexo mecanismo de evolução desses vírus e enfatizando a necessidade de monitoramento da circulação e caracterização de seus genes. / Influenza A virus infects a wide range of hosts and cause annual outbreaks. RNA segmented virus has high genetic variability and may have rearrangements between the genes of different viruses. In 2006, 521 samples of children younger than 5 years were analyzed and 25 tested positive for Influenza A virus, of which the subtype H3N2 is the most prevalent (68%). Five genes of 18 samples were sequenced and 13 sequences of HA, 12 of NP, 14 of M and 10 of NS obtained were. The presence of this several mutations, especially in the HA and NA genes probably helped the replacement of the vaccine strain in that year. All H3N2 subtype samples showed points of resistance to M2 inhibitors. The phylogenetic analysis revealed the circulation of different lineages in the same year, for both H1 and H3, and the presence of two rearrangements involving the HA and NP genes. These results indicate the influence of rearrangements in the evolution of the virus and emphasize the need for monitoring of circulation and characterization of genes.

Os Influenzavirus podem ser classificados de acordo com suas glicoproteínas externas hemaglutinina (HA) e neuraminidase (NA), ambas apresentando alta variabilidade genética e antigênica. No presente estudo foi realizada análise molecular do gene HA, do vírus influenza A (IA) em amostras colhidas de crianças e lactentes com sintomatologia respiratória atendidas no Hospital Universitário da Universidade de São Paulo (USP), durante os anos de 1995 a 2006. Um total de 3.009 amostras foram analisadas por duplex RT-PCR e 4,38% (n=132) foram positivas, sendo 12,1% (n=16) Influenza B e 87,9% (n=116) IA, das quais 9% (n=9) eram H1N1, 91% (n=91) eram H3N2 e 13,8% (n=16) não foram subtipadas. A região HA1 do gene HA de 39 amostras foi sequenciada e as sequências comparadas com as cepas vacinais e circulantes dos respectivos anos. A região de ligação ao receptor foi conservada em todas as amostras e foram verificadas alterações de aminoácidos principalmente nos sítios antigênicos e arredores. No geral, as cepas vacinais foram compatíveis com as circulantes em São Paulo. / The Influenzavirus can be classified according to their external glycoproteins hemagglutinin (HA) and neuraminidase (NA), both showing high genetic and antigenic variability. In the present study was carried out molecular analysis of the HA gene of influenza A (IA) in samples harvested from children and infants, with respiratory symptoms attended at University Hospital, University of Sao Paulo (USP), during the years 1995 to 2006. A total of 3,009 samples were analyzed by duplex RT-PCR and 4.38% (n = 132) were positive, being 12.1% (n = 16) Influenza B and 87.9% (n = 116) IA, where which 9% (n = 9) were H1N1 and 91% (n = 91) were H3N2 and 13.8% (n = 16) did not subtyped. The HA1 region of HA gene of 39 samples were sequenced and the sequences compared with vaccine strains and circulating strains in those years. The receptor-binding region was conserved in all samples and aminoacid changes were observed mainly in the antigenic sites and surroundings. Overall, the vaccine strains were consistent with those circulating in Sao Paulo.