Other Talks in the Series: Respiratory Infection

Hello. My name is H. Rogier Van Doorn, I work as a Clinical Virologist at the Oxford University Clinical Research Unit in Ho Chi Minh City, Vietnam. My areas of interest are influenza and foot and mouth disease in pathogen discovery. In this talk, I will discuss pathogen discovery in the respiratory tract.
I will briefly talk about respiratory infections in general and the pathogens associated with them. I will discuss the rules for establishing a link between a pathogen or a sequence and disease as they have been applied since the late 19th century and the required adaptations to make them applicable in a molecular era too. I will give an overview of pathogens exclusively viruses that have been discovered using molecular techniques in this millennium. I will discuss the peculiarities of respiratory tract samples and the consequences for pathogen discovery attempts and discuss some of the technologies that are being used for pathogen detection or discovery in various settings. I advise you to also have a look at the Henry Stuart talks from Ron Fouchier on emerging respiratory viruses and from Ian Lipkin on novel approaches to viral diagnosis as these inevitably overlap with mine.
Acute respiratory infections are the most frequently occurring illness in all age groups globally. Infection is usually limited to the upper respiratory tract and presents as a mild and self-limiting illness like the common cold. A small percentage can progress to a lower respiratory tract infection as bronchiolitis or pneumonia. Annually, 450 million cases of pneumonia are recorded, of whom 4.2 million die. Young children and the elderly are at an increased risk, especially in developing countries. The most important etiologic agents of severe, lower respiratory illnesses are bacteria like Streptococcus pneumoniae and Haemophilus influenzae type B and viruses, as respiratory syncytial virus and influenza virus. Bacteria are the main cause of pneumonia, especially in adults and generally have a higher case fatality rate. Viruses are the predominant cause of bronchiolitis and episodic wheeze exacerbation in children and of uncomplicated upper respiratory tract infections in general. Apart from the usual suspects as pneumococcus, Haemophilus influenza viruses, and RSV, there is a myriad of pathogens that have been associated with respiratory infections. Among these are mostly endemic human pathogens, to a lesser extent environmental or zoonotic pathogens and pathogens that are exclusively related to certain geographic areas or to severely compromise of the immune system. Although many viruses have been added to the list of common endemic pathogens in the last few years, there may still be endemic pathogens that we haven't discovered yet. On top of that, novel viruses are continuously emerging in the animal reservoir and may cause anything from isolated sporadic infections to pandemics of severe disease. This slide shows the etiology

Pathogen discovery in the respiratory tract

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