Objetivo: Describir las características demográficas, clínicas, laboratoriales y de tratamiento de pacientes hospitalizados por la COVID-19 y determinar los factores de riesgo de mortalidad hospitalaria. Materiales y métodos: Estudio de cohorte retrospectivo de pacientes adultos hospitalizados por la COVID-19. Se extrajeron datos demográficos, clínicos, laboratoriales y de tratamiento de las historias clínicas de pacientes que ingresaron al Hospital III Daniel Alcides Carrión de Tacna. Para el análisis de supervivencia se empleó el modelo de riesgos proporcionales de Cox y se calcularon los cocientes de riesgo instantáneos (HR) crudos y ajustados con sus respectivos intervalos de confianza al 95% (IC 95%). Resultados: Se evaluó a 351 pacientes, el 74,1% eran hombres; las comorbilidades más comunes fueron obesidad (31,6%), hipertensión (27,1%) y diabetes mellitus (24,5%). La mediana de tiempo de hospitalización fue 8 días (RIC: 4-15). El 32,9% falleció durante el seguimiento. El análisis multivariado mostró un aumento del riesgo de morir asociado a la edad ≥65 años, HR = 3,55 (IC 95%: 1,70-7,40); al incremento de lactato deshidrogenasa >720 U/L, HR = 2,08 (IC 95%: 1,34-3,22); y a la saturación de oxígeno por debajo del 90%, principalmente cuando fue menor al 80%, HR = 4,07 (IC 95%: 2,10-7,88). Además, el uso de colchicina en el tratamiento tuvo un efecto protector, HR = 0,46 (IC 95%: 0,23-0,91). Conclusiones: Los factores de riesgo de muerte por la COVID-19 incluyeron ser mayor de 65 años, tener saturación de oxígeno menor de 90% y elevación del lactato deshidrogenasa >720 U/L; el tratamiento con colchicina podría mejorar el pronóstico de los pacientes.

Yes / Introduction. Coronavirus disease 2019 (COVID-19) was first detected in China in December, 2019, and declared as a pandemic by the World Health Organization (WHO) on March 11, 2020. The current management of COVID-19 is based generally on supportive therapy and treatment to prevent respiratory failure. The effective option of antiviral therapy and vaccination are currently under evaluation and development. Areas covered. A literature search was performed using PubMed between December 1, 2019–June 23, 2020. This review highlights the current state of knowledge on the viral replication and pathogenicity, diagnostic and therapeutic strategies, and management of COVID-19. This review will be of interest to scientists and clinicians and make a significant contribution toward development of vaccines and targeted therapies to contain the pandemic. Expert Opinion. The exit strategy for a path back to normal life is required, which should involve a multi-prong effort toward development of new treatment and a successful vaccine to protect public health worldwide and prevent future COVID-19 outbreaks. Therefore, the bench to bedside translational research as well as reverse translational works focusing bedside to bench is very important and would provide the foundation for the development of targeted drugs and vaccines for COVID-19 infections. / Research carried out at TN laboratories are funded by the GrowMedtech, The Royal Society and University of Bradford. KH is supported by a project grant by the GrowMedtech awarded to TN. CW is funded by a Ph.D studentship.

L’étiologie des bronchopneumonies infectieuses (BPI) des jeunes bovins est multifactorielle, mettant en cause des agents infectieux comme des bactéries, virus ou parasites, et également des facteurs de risques liés à la conduite d’élevage et à l’environnement. Dans cette thèse nous nous sommes intéressés aux virus respiratoires bovins. Nous avons étudié le virome de l’appareil respiratoire superficiel et profond des jeunes veaux atteints de BPI par des approches de séquençage à haut débit pour mieux caractériser les co-infections virales et identifier de nouveaux virus. Par ailleurs nous nous sommes intéressés au contexte dans lequel les virus opèrent en analysant la structure, la diversité, et le dynamisme du bactériote respiratoire chez des veaux sains et atteints de BPI. Les résultats suggèrent que de nombreux virus agissent en interactions et montrent une prédominance du coronavirus bovin (BCoV) dans les cavités nasopharyngées et également dans les poumons des veaux atteints de BPI. L’étude phylogénétique des BCoV isolés indique une ségrégation entre souches européennes d’une part et américaines et asiatiques d’autre part qui semble résulter d’un phénomène de recombinaison dans les années 1960-70. Par ailleurs un astrovirus bovin a été clairement détecté pour la première fois principalement dans les poumons de veaux atteints de BPI. L’analyse du microbiote indique, elle, une disparité écologique entre cavités superficielles et profondes et des interactions possibles entre agents pathogènes connus et différentes communautés bactériennes de la flore résidente. Enfin une partie des travaux a concerné le virus influenza D (IDV), un nouveau virus respiratoire bovin émergent récemment identifié en France. Lors d’une infection expérimentale chez des veaux nous avons démontré que IDV possède un pouvoir pathogène respiratoire modéré et qu’il module la réponse immunitaire innée du veau. Nous avons aussi confirmé le caractère ubiquiste d’IDV en démontrant sa circulation sur le continent africain. En conclusion, grâce à des méthodes de séquençages à haut débit ce travail a permis une meilleure description et caractérisation des virus respiratoires bovins et de leur environnement immédiat. Il ouvre des perspectives pour mieux comprendre le rôle des interactions virales dans la genèse des signes cliniques respiratoires. / Bovine infectious bronchopneumonia (BIP) is a complex syndrome that affects young bovines, with a multifactorial etiology often involving one or several viruses and bacteria favored by altered host immunity and disturbed environmental factors. First, using viral metagenomics sequencing tools, we explored the upper (URT) and lower (LRT) respiratory tract viromes of calves with BPI and identified unexpected viruses. In addition, in the same calves, we characterized the structure, diversities and dynamism of the bacterial communities. Results showed different patterns of interactions between the different components of the microbiomes. Among the many detected viruses, the bovine coronavirus (BCoV), showed the highest prevalence in both nasal and pulmonary cavities. Evolutionary and phylogenic analysis of the isolated BCoV strains indicated a clear segregation between European and American/Asian strains, which seems to have resulted from a recombination event during the 1960-70’s. Furthermore, a bovine astrovirus was detected for the first time in the lungs of BIP affected calves. A disparity was noticed in the bacterial community structures between the upper and lower respiratory cavities. Also, there were associations between the presences of certain bacterial taxa and known respiratory pathogens. Finally, a part of the work focused on the emerging influenza D virus (IDV) recently identified in France. Carrying an experimental infection, we showed that IDV has a moderate respiratory pathogenicity and can modulate the innate immune response of the calf. We also showed that IDV circulates in Africa thus confirming its global distribution. In conclusion, thanks to high throughput sequencing methods, this piece of work allowed for a detailed characterization of the bovine respiratory virome and its interacting environment, and further opened new perspectives for a better understanding of viral interactions in bovine BIP.

Mechanismen, die zur unterschiedlichen Pathogenität niedrig- und hochpathogener aviärer und humanpathogener Influenzaviren im Menschen beitragen, sind bisher nur ansatzweise verstanden. Auch sind Pathomechanismen, die der Middle East Respiratory Syndrome (MERS)-CoV-Infektion zu Grunde liegen, bisher weitgehend unbekannt. In dieser Arbeit wurde ein humanes ex vivo Lungenkulturmodell für die Untersuchung der Influenzavirus- und der MERS-CoV-Infektion etabliert. Dabei wurde die Replikationsfähigkeit und der Zelltropismus der Viren systematisch verglichen. Während hochpathogene aviäre, saisonale und pandemische Influenzaviren effizient in der humanen Lunge replizierten, konnten sich niedrigpathogene aviäre Viren und ein porcines Virus kaum vermehren. Alle Viren zeigten jedoch den gleichen Zelltropismus und infizierten im Alveolarepithel ausschließlich Typ II Zellen. Die unterschiedliche Pathogenität dieser Viren lässt sich daher nicht durch Unterschiede im Zelltropismus erklären. Gleichwohl konnte der humane und der aviäre Influenzavirusrezeptor sowohl auf Typ II als auch auf Typ I Zellen nachgewiesen werden. Niedrigpathogene aviäre Influenzaviren sind in der humanen Lunge durch die Freisetzung von zum größten Teil nicht infektiösen Viruspartikeln restringiert. MERS-CoV replizierte in humanem Lungengewebe mit ähnlicher Kinetik wie ein hochpathogenes H5N1 Virus. MERS-CoV Antigen war sowohl im Bronchialepithel, Alveolarepithel sowie im Endothel nachweisbar. Der funktionelle Rezeptors des MERS-CoV, die Dipeptidylpeptidase 4, wurde in allen infizierten Zelltypen sowie in Alveolarmakrophagen nachgewiesen. Die mikroskopische Analyse infizierter Gewebeproben weist zudem auf einen infektionsbedingten Alveolarschaden hin. Die Studie trägt wesentlich zum pathophysiologischen Verständnis pulmonaler Influenzavirus- und MERS-CoV-Infektionen bei. Das humane ex vivo Lungenkulturmodell stellt ein klinisch relevantes Modell zur Untersuchung respiratorischer Infektionen im Menschen dar. / Mechanisms contributing to the different pathogenicity of low and highly pathogenic avian and seasonal influenza viruses in humans are currently only partially understood. Furthermore, underlying pathological mechanisms of the Middle East Respiratory Syndrome (MERS)-CoV infection in humans are widely unknown. In this study a human ex vivo lung culture model was established, which allowed investigating influenza virus and MERS-CoV infection. Replication and cellular tropism of the different viruses were compared systematically. While highly pathogenic avian, seasonal and pandemic influenza viruses replicated efficiently, low pathogenic avian viruses and a porcine virus propagated poorly. However, all viruses showed the same cellular tropism and infected only type II cells within the alveolar epithelium. Therefore, the different pathogenicity of these viruses cannot be attributed to different cellular tropisms. Nevertheless, the human and the avian influenza virus receptor could be detected on type II and type I cells. Low pathogenic avian influenza viruses are restricted in the human lung by the release of mostly non-infectious progeny virus particles. The MERS-CoV replicated with similar kinetics to a highly pathogenic H5N1 virus in the human lung. MERS-CoV antigen was detected in the bronchial epithelium, alveolar epithelium and endothelium. The functional receptor of MERS-CoV, dipeptidylpeptidase 4, was found in all infected cell types and in alveolar macrophages. Microscopic analysis of infected tissue samples indicated an alveolar damage provoked by MERS-CoV infection. This study contributes substantially to the pathophysiological understanding of the pulmonary influenza virus and MERS-CoV infection. The human ex vivo lung culture model represents a clinically relevant model to investigate human respiratory infections.

Cellular defense and metabolism are important biological processes in living cells. In this study, these two biological processes were investigated in two selected disease models: diabetes mellitus (DM) and severe acute respiratory syndrome associated coronavirus (SARS-CoV) infection by two-dimensional gel electrophoresis (2DE) coupled with Matrix-Assisted Laser Desorption Ionisation Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)-based proteomic approaches. The major findings are summarized as follows: / Our results on DM investigation can help to better understand the pathophysiological changes in patients with DM and the pathogenesis of hyperglycemia-caused complications. Data obtained from SARS-CoV studies provided novel insights into the molecular basis of the host cell response upon viral infection. / Protein profile of streptozotocin (STZ)-induced diabetic animal tissues, including mice liver, kidney and eye, and rats sera, indicated that DM has an impaired cellular defense system. These include the impairment in reactive oxygen species scavenging and the impairment in activation of complement system and innate immunity, and the enhancement in blood coagulation reaction. Our results also demonstrated that glycolysis and gluconeogenesis did not alter significantly in the liver of STZ-diabetic mice, while fatty acid oxidation and TCA cycle were attenuated under the same conditions. Moreover, we also detected other abnormal metabolism in aldehyde and amino acid, especially glutamate metabolism and the urea cycle. Abnormalities were also detected in lipid transport and metabolism. Besides, protein profile of mouse liver c37 cells indicated that high glucose may induce apoptosis in these cells, and this apoptotic effect may be mediated via the mitochondrial pathway. Furthermore, the proteomic results from the in vivo and in vitro diabetic models have prompted us to look for glucose responsive element on the promoters of these up-regulated hepatic genes. We found that the mouse aldolase 2 gene has glucose responsiveness in c37 cells treated with high glucose by semi-quantitative RT-PCR and promoter transfection assay. Finally, protein profile of Vero E6 cells strongly implicated that SARS-CoV can induce anti-apoptosis. This effect may be mediated via the mitochondrial pathway. Our data also suggested that the anti-apoptotic activity may be required for viral replication at the early stage of infection. While under the condition of long-term infection, this may be needed for viral survival. / Zhong Mingqi. / "October 2005." / Advisers: Sai Ming Ngai; Hon Ki Cheng. / Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6217. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 223-248). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

<p>The human coronavirus NL63 was discovered in 2004 by a team of researchers in Amsterdam. Since its discovery it has been shown to have worldwide spread and affects mainly children, aged 0-5 years old, the immunocompromised and the elderly. Infection with HCoV-NL63 commonly results in mild upper respiratory tract infections and presents as the common cold, with symptoms including fever, cough, sore throat and rhinorrhoea. Lower respiratory tract findings are less common but may develop into more serious complications including bronchiolitis, pneumonia and croup. The primary function of the HCoV-NL63 nucleocapsid (N) protein is the formation of theprotective ribonucleocapsid core. For this particle to assemble, the N-protein undergoes N-N dimerization and then interacts with viral RNA. Besides the primary structural role of the Nprotein, it is also understood to be involved in viral RNA transcription, translation and replication, including several other physiological functions. The N-protein is also highly antigenic and elicits a strong immune response in infected patients. For this reason the N-protein may serve as a target for the development of diagnostic assays. We have used bioinformatic analysis to analyze the HCoV-NL63 N-protein and compared it to coronavirus N-homologues. This bioinformatic analysis provided the data to generate recombinant clones for expression in a bacterial system. We constructed recombinant clones of the N-protein of SARS-CoV and HCoV-NL63 and synthesized truncated clones corresponding to the N- and C-terminal of the HCoV-NL63 N-protein. These heterologously expressed proteins will serve the basis for several post-expression studies including characterizing the immunogenic epitope of the N-protein as well identifying any antibody crossreactivity between coronavirus species.</p>

<p>The human coronavirus NL63 was discovered in 2004 by a team of researchers in Amsterdam. Since its discovery it has been shown to have worldwide spread and affects mainly children, aged 0-5 years old, the immunocompromised and the elderly. Infection with HCoV-NL63 commonly results in mild upper respiratory tract infections and presents as the common cold, with symptoms including fever, cough, sore throat and rhinorrhoea. Lower respiratory tract findings are less common but may develop into more serious complications including bronchiolitis, pneumonia and croup. The primary function of the HCoV-NL63 nucleocapsid (N) protein is the formation of theprotective ribonucleocapsid core. For this particle to assemble, the N-protein undergoes N-N dimerization and then interacts with viral RNA. Besides the primary structural role of the Nprotein, it is also understood to be involved in viral RNA transcription, translation and replication, including several other physiological functions. The N-protein is also highly antigenic and elicits a strong immune response in infected patients. For this reason the N-protein may serve as a target for the development of diagnostic assays. We have used bioinformatic analysis to analyze the HCoV-NL63 N-protein and compared it to coronavirus N-homologues. This bioinformatic analysis provided the data to generate recombinant clones for expression in a bacterial system. We constructed recombinant clones of the N-protein of SARS-CoV and HCoV-NL63 and synthesized truncated clones corresponding to the N- and C-terminal of the HCoV-NL63 N-protein. These heterologously expressed proteins will serve the basis for several post-expression studies including characterizing the immunogenic epitope of the N-protein as well identifying any antibody crossreactivity between coronavirus species.</p>

Made available in DSpace on 2014-06-11T19:27:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-10-03Bitstream added on 2014-06-13T20:16:25Z : No. of bitstreams: 1 teixeira_mcb_me_araca.pdf: 1608069 bytes, checksum: 5e594d70a730c7e0223fb2453f313c44 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O Complexo de Enterite de Perus (PEC) tem sido incriminado como uma das maiores causas de perdas econômicas em outros países. Neste estudo, foi demonstrado causando diarréia, perda de peso e na maioria das vezes alta mortalidade em perus acometidos de enterite com 30-120 dias de idade de uma determinada região produtora no Brasil. A RT-PCR foi aplicada em suspensões de intestinos (SI) (n=2), respectivos conteúdos intestinais (CI) (n=2), bursa de Fabrícius (BF), fezes (F) (n=5) e swabs cloacais (SC) (n=44), para amplificar a região conservada 3`UTR e gene do nucleocapsídeo de TCoV. Os exames de histopatologia e imunohistoquímica direta foram realizados para detectar o antígeno TCoV a partir de lâminas de intestinos e bursas infectados. Todos os resultados obtidos nos tecidos marcados, revelaram lesões sugestivas de terem sido causadas pela infecção por TCoV. A marcação positiva da imunohistoquímica direta estava presente em todas as lâminas de intestinos, entretanto, todas as BF analisadas foram negativas. Os achados de RT-PCR foram positivos para TCoV em todas as amostras de fezes e 27,27% das amostras de SC foram positivas para a região 3`UTR e região TCoV nucleocapsídeo. As amostras de soro (n=200), foram positivas para TCoV, com títulos variando de 2.0Log a 8.0Log usando o ELISA comercial IDEEX para IBV. Finalmente, o melhor material de campo para o diagnóstico de TCoV foram as fezes (F) e/ou suspensão de intestinos (SI), resultando na primeira descrição de perus com quadro agudo de enterite acometidos por coronavirus Grupo 3 no Brasil. / The Poult Enteritis Complex (PEC) has been incriminated as the major cause of losses in other countries, and especially, in this study, was described causing diarrhea, weight gain and most of the time, high mortality. In this study, it was performed the turkey coronavirus (TCoV) detection from 30-120 day old affected poults from a particular producer region in Brazil. The RT-PCR was applied in intestines suspensions (IS) (n=2), respective intestines contents (IC) (n=2), bursa of Fabrícius (BF), faecal droppings (FD) (n=5) and cloacal swabs (CS) (n=44) to amplify the 3þUTR conserved region and TCoV nucleocapsid gene. The histopathological and direct immunohistochemical examinations were performed to detect the TCoV antigen from infected intestine and bursa slides. All results obtained from stained tissues, revealed lesions described to be caused by TCoV infection. The direct immunohistochemical positive signal was present in all intestine slides, however all BF analysed were negative. RT-PCRs findings were positive for TCoV in all FD samples, and 27,27% of CS analysed were positive for 3þUTR and TCoV nucleocapsid region. The sera samples (n=200) were positive for TCoV, with titers range from d 2.0Log to 8.0Log using the IDEEX commercial ELISA for IBV. Finally, the best field material for TCoV diagnosis was FD and/or intestine suspensions (IS), resulting in a first describe of TCoV affecting poults in Brazil.

>Magister Scientiae - MSc / Acute respiratory infections (ARI) continue to be the leading cause of acute illnesses worldwide and remain the most important cause of infant and young children mortality. Many viruses such as rhinoviruses, influenza viruses, parainfluenza viruses, respiratory syncytial viruses, adenoviruses and coronaviruses are deemed to be the etiological agents responsible for ARI’s in children. The recently discovered coronaviruses HCoV-HKU1 and HCoV-NL63 contribute significantly to the hospitalization of children with ARI’s. HCoV-NL63 was first identified in 2004, as the pathogen responsible for the hospitalization of a 7 month old child presenting with coryza, conjunctivitis and fever. Since then a significant amount of knowledge has been gained in the clinical spectrum on this virus, however HCoV-NL63 is still not well characterized on the molecular and proteomic level. This dissertation focuses on bringing about this characterization by cloning the HCoV-NL63 Nucleocapsid gene to be expressed in a bacterial system and transfecting the Nucleocapsid, Membrane and Envelope genes into a Mammalian cell culture system in order for its respective proteins to be expressed. With the use of Bioinformatic analytic tools certain characteristics of HCoV-NL63 Nucleocapsid, Membrane and Envelope proteins are able to be identified, as well as certain motifs and/or regions that are important in the functioning of these proteins. By comparing the results obtained for HCoV-NL63 N,M and E to other well studied coronavirus homologous will enlighten us on the potential role(s) of these proteins in determining HCoV-NL63 pathogenicity and infectivity. vi Although certain functions of these proteins can be deduced by the means of bioinformatics analysis, it is still imperative for it to be extensively characterized In Vitro. This will therefore form a fundamental step in the development of many other projects, which unfortunately fall outside the scope of this M.Sc thesis.

Magister Scientiae (Medical Bioscience) - MSc(MBS) / The human coronavirus NL63 was discovered in 2004 by a team of researchers in Amsterdam. Since its discovery it has been shown to have worldwide spread and affects mainly children, aged 0-5 years old, the immunocompromised and the elderly. Infection with HCoV-NL63 commonly results in mild upper respiratory tract infections and presents as the common cold, with symptoms including fever, cough, sore throat and rhinorrhoea. Lower respiratory tract findings are less common but may develop into more serious complications including bronchiolitis, pneumonia and croup. The primary function of the HCoV-NL63 nucleocapsid (N) protein is the formation of theprotective ribonucleocapsid core. For this particle to assemble, the N-protein undergoes N-N dimerization and then interacts with viral RNA. Besides the primary structural role of the Nprotein, it is also understood to be involved in viral RNA transcription, translation and replication, including several other physiological functions. The N-protein is also highly antigenic and elicits a strong immune response in infected patients. For this reason the N-protein may serve as a target for the development of diagnostic assays. We have used bioinformatic analysis to analyze the HCoV-NL63 N-protein and compared it to coronavirus N-homologues. This bioinformatic analysis provided the data to generate recombinant clones for expression in a bacterial system. We constructed recombinant clones of the N-protein of SARS-CoV and HCoV-NL63 and synthesized truncated clones corresponding to the N- and C-terminal of the HCoV-NL63 N-protein. These heterologously expressed proteins will serve the basis for several post-expression studies including characterizing the immunogenic epitope of the N-protein as well identifying any antibody crossreactivity between coronavirus species. / South Africa