Respiratory infections

Multiple viruses are responsible for respiratory infections and co-infections causing a variety of disease outcomes that range from a mild cold to life-threatening viral pneumonia. Occasionally, respiratory viruses result in emerging infections such as the swine-origin influenza A virus (that caused the 2009 pandemic) or the severe acute respiratory syndrome coronavirus that caused an extended outbreak in several countries in early 2000s. Molecular diagnostic assays are routinely used in the UK healthcare system and they can simultaneously test for the presence of multiple viruses. Databases with results from such diagnostic tests represent a rich source of information that can reveal insight into the epidemiology of viral respiratory infections in the patient population. Respiratory viruses are generally studied as single entities and not as a community. Since they are obligate intracellular pathogens that infect a well-defined ecological niche (the human respiratory tract), studying them as a community is a logical approach to capture the impact of their complex interactions on their infection dynamics. We propose to study the infection dynamics of a group of respiratory viruses in a large and well-defined population over an extended period of time. We will analyse the long-term trends in viral respiratory infections using information on diagnostic test results (and associated metadata) of the Greater Glasgow and Clyde Health Board (GGCHB, the largest Health Board in Scotland) patient population. We will sequence a large number of viruses from clinical specimens to determine their complete genomes, study their evolutionary dynamics and to identify mutations that might be associated with changes in their phenotype (virulence, seasonality, age group distribution, etc.). We will use mathematical and statistical models to infer interactions among viruses at the patient level and their impact at the epidemiological scale. Finally, we will develop bioinformatics tools to facilitate the future use of complex sequence data in diagnostic laboratories and public health bodies.