Pipeline for sequence data of hemagglutinin gene of influenza A

Advisor:
Zvonimir Poljak (Population Medicine)

The objective of these project is to create a bioinformatics pipeline that could be used in real time to extract nucleotide sequence data of hemagglutinin gene of influenza A virus of subtype H3Nx and subtype H1Nx from a database, classify the existing sequences into established clades and create data that could be used for interactive dashboards.

Swine influenza is a respiratory disease affecting pigs of different ages and is one of the diseases of highest priority for swine producers and veterinarians across the globe. The causative pathogen is influenza A virus and the exposure to IAV in swine populations is very high. IAV is an RNA virus with segmented genome, and consequently, the virus is prone to various mutations and recombination which can result in emergence of novel strains. These strains complicate design of control measures in swine system. Furthermore, their monitoring is of interest for public health because some swine-adapted strains of influenza A virus can be transmitted to people. Historically, monitoring of influenza A virus was based on summarizing relative frequency of subtypes, and most common subtypes of IAV in swine are H1N1, H3N2, and H1N2. Such monitoring is becoming increasingly limited because of increased genetic variability within important genes of each of these viruses. For this reason, both influenza surveillance and clinical decision making are based on sequence analysis of the hemagglutinin gene of IAV. To establish a pipeline, existing global databases of influenza viruses will be used as a source dataset, and project participants will be interacting with animal health experts who are involved in design and implementation of dashboards for surveillance of animal health data in Ontario.