Human norovirus (HuNoVs) are the most common enteric pathogen around the world that cause ~50% of foodborne illness of disease outbreaks annually. HuNoVs are the member of the Caliciviridae family, which consist of small (38 nm), unenveloped, single stranded RNA (ssRNA) viruses. Norovirus are divided into 5 genogroup (GI, GII, GIII, GIV, GV, GVI and GVII). The GI, GII, and GIV cause human illness, in addition, GII.4 genotype cause the most human disease. Due to HuNoVs are difficult cultured in vitro, the cultivable HuNoVs surrogates have been widely studied. Recently, some studies have been conducted with HuNoVs surrogates, for example bacteriophage MS2. MS2 is conservative surrogate for nonenveloped viruses which there is a close relationship to the behavior of HuNoVs, thus we can examine the infection control measures for HuNoVs. Despite plenty of treatment method been done on testing antiviral effect on bacteriophage MS2, for example UV inactivation, steam ultrasound and antimicrobial etc., plant-based nanoemulsion treatment has yet to be explored. Carvacrol is a major component of oregano essential oil and is responsible for their antimicrobial activity on the growth of various microorganism. In this study, carvacrol nanoemulsions were formed by using the spontaneous emulsification for testing the nanoemulsion stability (14 days shelf life study on its droplet size and particle charge) and antimicrobial activity. In carvacrol nanoemulsion 14 days shelf life test, the droplet size and particle charge stay stable at three different treatment environments (4°C, 20°C and 37°C). The results proved that nanoemulsion (was formed with surfactant agents and medium-chain triglycerides) is stable system that gives consistent droplet size and charge. Although, the low antimicrobial activity was investigated at carvacrol nanoemulsion, the strong antimicrobial effects have been found when carvacrol or carvacrol combined with ionic surfactant of treatment on MS2 and Escherichia coli. Taken together, in the wake of growing consumer demand for different “natural” products in a number of industries, our study broadly informs the development and study of functionalized carvacrol active compound that can not only provide beneficial health for human but can also examine antimicrobial efficacy of control measures for public health.

Comparing the protein compositions of three fishes, grass carp exhibited lower band intensity at 47.9 KDa, β-tropomyosin (36.5 KDa), and missed the band at 15.9 KDa myosin light chain. Bigmouth buffalo had a darker tropomodulin (38.8 KDa) band and smaller α-tropomyosin (33-37 KDa) than silver and grass carp. The breaking force (611.8 g) and deformation (11.7 mm) of silver carp cooked gel were significantly higher than the other two fish products. The addition of starches at 2, 4, and 6% to the grass carp paste lowered the breaking force of the cooked gel in a dose-responsive manner compared to the control (P<0.05), but no differences were found in bigmouth buffalo. The bioumulated Murine Norovirus-1 (MNV-1) was found to maintain infectivity during storage of live oysters at 5°C for 15 days while the inoculated MNV-1 kept infectious for 20 days in cooked surimi and salmon fillet. Treatments with 4.0 kGy X-ray achieved the reductions of 3.7 log PFU mL-1 in pure culture or 2.7, 2.2, and 2.0 log PFU g-1 in half-shell oyster, salmon sushi and tuna salad, respectively. X-ray significantly reduced the population of internalized MNV-1 in live oysters from 4.3 ± 0.4 log PFU g-1 to 3.6 ± 0.5, 3.2 ± 0.2, 2.8 ± 0.2, and 2.5 ± 0.1 log PFU g-1, by 1.0, 2.0, 3.0, and 4.0 kGy X-ray, respectively. The population of MNV-1 was reduced to less than 2.0 log PFU g-1 at 5.0 kGy X-ray. The survivability of live oysters was not significantly affected by treatment with 5.0 kGy X-ray, in comparison with the control, for up to 10 days, respectively, during storage at 5°C. Fish sauce was fermented from the by-products of silver carp. The total nitrogen content of fish sauce made in April, and November were 9.86±0.9 and 9.71±4.5 g/l, respectively, which was significantly (p<0.05) higher than the sample of February (8.45±0.25 g/l ), reflecting seasonal effect. The total nitrogen, amino acid nitrogen, pH, and sodium chloride of fish sauce made from silver carp by-products met the international fish sauce standard code of CODEX STAN 302-2011.

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Les virus d’origine alimentaire, comme le virus de l’hépatite A (VHA) et le norovirus (NoV),sont des causes importantes d’infections virales. Chaque année, celles-ci déduisent de grandes sommes monétaires aux systèmes de santé canadiens ainsi qu’aux producteurs alimentaires, sans compter les pertes alimentaires et économiques dues aux rappels d’aliments contaminés. Les stratégies de contrôle conventionnelles ne sont pas suffisamment efficaces et présentent, dans certains cas, des risques pour les travailleurs et/ou pour les consommateurs. Il est donc essentiel d’offrir de nouvelles méthodes d’inactivation naturelles et plus sécuritaires. Les produits issus de bleuet et de canneberge ont le potentiel de devenir ces nouvelles méthodes, notamment par leur concentration forte en polyphénols. De plus, ils sont naturels et sécuritaires pour les travailleurs et les consommateurs. Sans oublier qu’ils sont abondants au Québec, et, de ce fait, à moindres coûts. Le potentiel antiviral de ces produits de bleuet et de canneberge a été étudié et analysé dans ce mémoire envers des virus nus d’origine alimentaire (VHA et NVM-1) en plus de tester un modèle de virus enveloppé, soit le virus de l’herpès simplex de type 1(HSV-1). NVM-1 et VHS-1 ont été complètement inactivés à l’aide de jus de canneberge et/ou de bleuet (concentrés à 50 %) en 5 minutes de pré-incubation cellulaire ou virale respectivement. VHA a subi une réduction de 3,70 ± 0,54 log ufp/mL à la suite d’une préincubation virale de 90 minutes. / Foodborne viruses like the hepatitis A virus (HAV) and the norovirus (NoV) are known as important cause of viral infections. Each year, they cost massive amount to the Canadian health-care systems and to the producers without counting the important food loss due to recalls. The conventional methods are not sufficient and can represent in some case a threat to the worker or to the consumer, which is why it is essential to uncover new inactivation methods that are safer and natural, like berries. The blueberry and cranberry products have the potential to become these new methods considering their interesting composition. Furthermore, they are natural, do not show signs of threat to the worker nor to the consumer and above all they are abundant in Québec and at low cost. The antiviral potential of these products from blueberries and cranberries have been tested and studied in this memoir against the HAV and the MNV-1, naked foodborne viruses as well as against the herpes simplex virus type 1 (HSV-1), an enveloped model. The infectivity of MNV-1 was neutralized completely in the presence of this host cells at 37 °C in as little as 5 min of contact with cranberry or blueberry juices (50 % concentration). HSV-1 was also completely neutralized in viral pre-incubation with the same juice concentration and incubation. HAV infectious titer fell 3.70 ± 0.54 log pfu/mL after 90 minutes of contact with cranberry juice. These results suggest that cranberry and blueberry processing could be useful for reducing the transmission of foodborne viruses.

À l'échelle mondiale, le norovirus humain (HuNoV) et le virus de l'hépatite A (VHA) sont associés aux maladies d'origine alimentaire, ce qui constitue une préoccupation majeure pour le secteur de la santé et de l'alimentation. Afin de garantir la salubrité des aliments et des produits transformés en industrie agroalimentaire, plusieurs méthodes d'inactivation virale physiques et chimiques sont employées. Cependant, elles ne sont pas nécessairement applicables sur toutes les matrices alimentaires et certaines peuvent même générer des substances nocives. De ce fait, la présente étude porte sur la détermination du potentiel virucide des substances naturelles. Dans cette étude, le potentiel antiviral de deux huiles essentielles et de quatre extraits naturels a été évalué sur deux virus non enveloppés, soit le norovirus murin 1 (MNV-1), le VHA et un virus enveloppé, le virus de l'herpès simplex 1 (VHS-1). Des concentrations de chaque substance allant de 50 à 200 000 ppm ont été appliquées pendant 90 min de contact. L'extrait de pépins de raisin a été le plus efficace quant à la réduction de l'infectivité du VHA et du MNV-1 soit de 1,94 ± 0,17 log₁₀, 2,85 ± 0,44 log₁₀ respectivement. Pour le VHS-1, une inactivation totale a été observée à 1000 ppm. En revanche, les extraits de canneberge et de thé vert n'ont pas réussi à réduire l'infectivité des trois types de virus de plus de 1 log₁₀. Ces résultats enrichissent les connaissances actuelles sur les propriétés virucides des substances naturelles en démontrant leur potentiel antiviral contre ces trois types de virus. Cette étude ouvre de nouvelles perspectives quant à l'utilisation des composés naturelles, offrant ainsi des applications prometteuses dans divers secteurs / Enteric viruses such as hepatitis A (HAV) and human norovirus (HuNoV) are the main cause of foodborne diseases worldwide. They are recognized as a major concern for public health and food sector. To minimise the risk of infection, many physical and chemical viral inactivation methods have been used. However, these approaches are not applicable to all food matrices and may generate harmful substances. Therefore, the aim of this project is to study the antiviral potential of natural compounds. For this purpose, the antiviral potential of two essential oils and four natural extracts was evaluated with two non-enveloped viruses: murine norovirus 1 (MNV-1), HAV and one enveloped virus, herpes simplex virus 1 (HSV-1) at concentrations ranging from 50 to 200,000 ppm for 90 min contact in viral pre-incubation. Grape seed extract was the most effective in reducing HAV and MNV-1 infectivity by 1.94±0.17 log10, 2.85±0.44 log₁₀ respectively. For HSV-1, a total inactivation was observed at 1000 ppm. Cranberry extract and green tea extract failed to reduce the infectivity of all three virus types by more than 1 log₁₀. This study has contributed to a better understanding of the antiviral potential of natural substances against the three types of viruses tested. Eventually, this project ultimately aims to reveal new perspectives on the use of natural compounds, thus offering promising applications in various sectors.

Les virus d'origine alimentaire, comme le virus de l'hépatite A (VHA) et le norovirus (NoV), sont des causes importantes d'infections virales. Chaque année, celles-ci déduisent de grandes sommes monétaires aux systèmes de santé canadiens ainsi qu'aux producteurs alimentaires, sans compter les pertes alimentaires et économiques dues aux rappels d'aliments contaminés. Les stratégies de contrôle conventionnelles ne sont pas suffisamment efficaces et présentent, dans certains cas, des risques pour les travailleurs et/ou pour les consommateurs. Il est donc essentiel d'offrir de nouvelles méthodes d'inactivation naturelles et plus sécuritaires. Les produits issus de bleuet et de canneberge ont le potentiel de devenir ces nouvelles méthodes, notamment par leur concentration forte en polyphénols. De plus, ils sont naturels et sécuritaires pour les travailleurs et les consommateurs. Sans oublier qu'ils sont abondants au Québec, et, de ce fait, à moindres coûts. Le potentiel antiviral de ces produits de bleuet et de canneberge a été étudié et analysé dans ce mémoire envers des virus nus d'origine alimentaire (VHA et NVM-1) en plus de tester un modèle de virus enveloppé, soit le virus de l'herpès simplex de type 1 (HSV-1). NVM-1 et VHS-1 ont été complètement inactivés à l'aide de jus de canneberge et/ou de bleuet (concentrés à 50 %) en 5 minutes de pré-incubation cellulaire ou virale respectivement. VHA a subi une réduction de 3,70 ± 0,54 log ufp/mL à la suite d'une pré-incubation virale de 90 minutes. / Foodborne viruses like the hepatitis A virus (HAV) and the norovirus (NoV) are known as important cause of viral infections. Each year, they cost massive amount to the Canadian health-care systems and to the producers without counting the important food loss due to recalls. The conventional methods are not sufficient and can represent in some case a threat to the worker or to the consumer, which is why it is essential to uncover new inactivation methods that are safer and natural, like berries. The blueberry and cranberry products have the potential to become these new methods considering their interesting composition. Furthermore, they are natural, do not show signs of threat to the worker nor to the consumer and above all they are abundant in Québec and at low cost. The antiviral potential of these products from blueberries and cranberries have been tested and studied in this memoir against the HAV and the MNV-1, naked foodborne viruses as well as against the herpes simplex virus type 1 (HSV-1), an enveloped model. The infectivity of MNV-1 was neutralized completely in the presence of this host cells at 37 °C in as little as 5 min of contact with cranberry or blueberry juices (50 % concentration). HSV-1 was also completely neutralized in viral pre-incubation with the same juice concentration and incubation. HAV infectious titer fell 3.70 ± 0.54 log pfu/mL after 90 minutes of contact with cranberry juice. These results suggest that cranberry and blueberry processing could be useful for reducing the transmission of foodborne viruses.

Understanding the transmission dynamics of infectious diseases is important to well-informed public health policy, responsive infection control and individual patient management. The on-going revolution in whole-genome sequencing provides unprecedented resolution for detecting evidence of recent transmission and characterising population-level transmission dynamics. In this thesis, I develop and apply evolutionary approaches to investigating transmission, focusing on three globally important pathogens. Hepatitis C virus (HCV) is a major cause of liver disease affecting 150 million people and killing 350,000 annually. I conducted a meta-analysis of twentieth-century HCV epidemics, finding that the age of the epidemic can be predicted by genetic diversity. Using the coalescent, I fitted classic susceptible-infected (SI), susceptible-infected-susceptible (SIS) and susceptible-infected-recovered (SIR) epidemiological models. Most epidemics showed signatures of SI dynamics, but three, from Argentina, Hong Kong and Thailand, revealed complex SIR dynamics. Norovirus is the leading viral cause of diarrhoea, estimated to cost the NHS around £115 million annually. I analysed whole norovirus genomes via a stochastic transmission model, finding that up to 86% of hospital infection was attributable to transmission from another patient in the hospital. In contrast, the rate of new introductions to hospital by infected patients was extremely low (<0.0001%), underlining the importance of ward management during outbreaks. Campylobacter is the most commonly identified cause of bacterial gastroenteritis worldwide. I developed a zoonotic transmission model based on phylogeography approaches to test whether three strains previously associated with multiple host species were in fact aggregates of strongly host-restricted sub-strains, or genuine generalists. Members of the same strain isolated from different host species were often more closely related than those isolated from the same host species. I estimated 419, 389 and 31 zoonotic transmissions in ST-21, ST-45 and ST-828 respectively, strongly supporting the hypothesis that these strains are adapted to a generalist lifestyle.

Doctor of Philosophy / Department of Chemistry / Duy H. Hua / Three research projects were carried out and they are described below. The synthesis of substituted phenolic compounds including halogenated di- and trihydroxybenzenes, aminophenols, and substituted di-tert-butylphenols are described. Redox potentials of the synthesized molecules along with various known laccase substrates were measured, and an inverse relationship between the oxidation potential and the efficiency of oxidation by laccase of halogenated hydroxybenzenes and aminophenols is demonstrated. The synthesized substituted phenols were found to be substrates but not inhibitors of laccase. We discovered a new class of di-tert-butylphenols compounds that inhibits the growth of mosquito larvae at low concentrations. Compound 17, 2,4-di-tert-butyl-6-(3-methyl-2-butenyl) phenol caused greater than 98% mortality of third-instar larvae of Anopheles gambiae in the concentration of 0.18 µM. These compounds do not inhibit laccases. It appears that they affect a new target of the mosquito that is different from those of currently existing pesticides. Two anti-Alzheimer molecules, CP2 and TP70, discovered in our laboratory were studied for their pharmacokinetics and distribution. The distribution of CP2 and TP70 in mouse brain region and various tissues of mice were examined. HPLC analysis revealed that CP2 treatment in primary neurons accumulates in mitochondria fraction. Similarly, the amount of CP2 in the brain tissue from wild type and APP/PS1 mice treated with 25 mg/kg/daily for 2 months also have the highest concentration in the mitochondria fractions in the hippocampus. The results show that CP2 and TP70 can penetrate the blood brain barrier and accumulate in the tissue in significant amounts. Pharmacokinetics and bioavailability of compound TP70 were determined. Area under the curve and bioavailability value F were calculated, and data show that TP70 has a good PK profile and bioavailability. For the preparation of a novel tripeptidyl norovirus 3C-like protease (3CL[superscript]pro) inhibitor, the P3 unnatural amino acid, (S)-3-hydroxyphenylalanine was synthesized. The P3 is designed to increase the polarity with the addition of the alcohol group. After combining the P3 unnatural amino acid with the P1 and P2 to form the novel tripeptidyl compound, a study comparing the relations between the structure and its activity (SAR) will confirm whether prediction is correct in our pursuit for an antiviral therapeutic drug in the form of a protease inhibitor.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2014-09-25T17:34:38Z No. of bitstreams: 2 Dissertação_Lucianna G. N. Lemes.pdf: 2661301 bytes, checksum: c0238e41dfbe2adbd10e5ddcff7a139e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2014-09-26T11:31:18Z (GMT) No. of bitstreams: 2 Dissertação_Lucianna G. N. Lemes.pdf: 2661301 bytes, checksum: c0238e41dfbe2adbd10e5ddcff7a139e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-09-26T11:31:18Z (GMT). No. of bitstreams: 2 Dissertação_Lucianna G. N. Lemes.pdf: 2661301 bytes, checksum: c0238e41dfbe2adbd10e5ddcff7a139e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2013-12-20 / The calicivirus (norovirus and sapovirus) are important etiologic agents of acute gastroenteritis. Recent studies show that in immunocompromised patients such as those undergoing allogeneic hematopoietic stem cell transplantation (HSCT), norovirus infection can lead to worsening of symptoms and be confused with clinical symptoms of graft versus host disease (GVHD). However, calicivirus screening is not performed, routinely, as part of the patients’ follow-up laboratory exams. The main objective of this study was to evaluate the occurrence of norovirus (NoV) and sapovirus (SaV) in patients who underwent HSCT, and to conduct the molecular characterization of the samples positive for these viruses. Fecal samples were collected weekly, and serum samples were obtained every two weeks of ten patients who underwent HSCT, for a minimum period of five months and a maximum of one year. The secretor status was determined by an enzyme immunoassay and the detection of calicivirus was performed by RT-PCR using primers specific for a partial region of the gene encoding the NoV genogroup I and II (GI and GII) and SaV capsid protein. The genomic sequencing was performed for positive samples. The results showed that from ten patients participating in the study, eight had diarrhea. Among these, six (60%) had positive samples for NoV, and all of them had a secretor phenotype. The duration of NoV excretion in feces ranged from five to 143 days. Viral RNA was also detected in serum specimens, ranging from 29 to 36 days in the five patients infected with NoV. Three of the six patients had acute intestinal GVHD. Through genomic sequencing and phylogenetic analysis all NoV-positive samples were characterized as genotype GI.3, and because they had a high nucleotide identity, they were all characterized as a single haplotype. The data highlight the urgent need of the inclusion of calicivirus screening in the routine testing performed before transplantation and during follow-up of these patients. This is the first report of the occurrence of NoV in patients undergoing HSCT in Brazil. / Os calicivírus (norovírus e sapovírus) são importantes agentes etiológicos da gastroenterite aguda. Estudos recentes mostram que em pacientes imunocomprometidos, como os submetidos a transplante alogênico de células progenitoras hematopoiéticas (TACPH), a infecção por norovírus pode levar ao agravamento dos sintomas e ser confundida com quadro clínico da doença do enxerto contra o hospedeiro (DECH). Entretanto, a triagem para calicivírus não é realizada, rotineiramente, como parte dos exames laboratoriais de acompanhamento destes pacientes. O principal objetivo deste estudo foi avaliar a ocorrência de norovírus (NoV) e sapovírus (SaV) em pacientes que foram submetidos ao TACPH e proceder à caracterização molecular das amostras positivas para estes vírus. Foram obtidas amostras de fezes, coletadas semanalmente, e de soro, a cada quinze dias, de dez pacientes que realizaram o TACPH, por um período mínimo de cinco meses e máximo de um ano. O fenótipo secretor dos pacientes foi determinado utilizando um teste imunoenzimático e a pesquisa de calicivírus foi realizada pela RT-PCR, utilizando-se iniciadores específicos para uma região parcial do gene codificante para a proteína dos capsídeos dos NoV do genogrupo I e II (GI e GII) e dos SaV. Os amplicons das amostras positivas foram submetidos ao sequenciamento genômico e análise filogenética. Os resultados obtidos revelaram que de dez pacientes participantes do estudo, oito apresentaram diarreia e vômito. Dentre esses, seis (60%) apresentaram amostras positivas para NoV, sendo que todos foram identificados como secretores. O período de excreção de NoV nas fezes variou de cinco a 143 dias. Foi também detectado RNA viral nas amostras de soro, variando de 29 a 36 dias, em cinco pacientes infectados por NoV. Três, dos seis pacientes, apresentaram DECH aguda intestinal. Através do sequenciamento genômico e análise filogenética, todas as amostras positivas para NoV, de todos os pacientes, foram caracterizadas como genótipo GI.3 dos NoV, e como foi comprovada elevada identidade nucleotídica entre elas, foram caracterizadas como um único haplótipo. Os dados obtidos ressaltam a urgente necessidade da inclusão da pesquisa de calicivírus na rotina de exames realizados antes do transplante, bem como durante o acompanhamento destes pacientes. Este é o primeiro relato da ocorrência de NoV em pacientes submetidos ao TACPH no Brasil.