West Nile virus (WNv) is an arbovirus and is transmitted by infected mosquitoes after feeding on the blood of birds carrying the virus. The Canadian WNv national surveillance system has just completed its tenth year of operation. The thesis is to evaluate the surveillance system and analyze multi-year human data. The evaluation includes the use of multiple lines of complementary methods such as the US CDC surveillance guidelines, Canadian Evaluation Framework, document review and a survey. Logistic and Poisson regressions were used for data analyses. WNv has become endemic in most parts of Canada since the virus occurred in 2001. The virus activity is peak around August. High numbers of human cases with WNv neurological syndrome identified pose a significant health concern due to the long term sequelae among affected patients. WNv national surveillance met its main objectives and there is a continual need for the surveillance.

West Nile virus (WNv) is an arbovirus and is transmitted by infected mosquitoes after feeding on the blood of birds carrying the virus. The Canadian WNv national surveillance system has just completed its tenth year of operation. The thesis is to evaluate the surveillance system and analyze multi-year human data. The evaluation includes the use of multiple lines of complementary methods such as the US CDC surveillance guidelines, Canadian Evaluation Framework, document review and a survey. Logistic and Poisson regressions were used for data analyses. WNv has become endemic in most parts of Canada since the virus occurred in 2001. The virus activity is peak around August. High numbers of human cases with WNv neurological syndrome identified pose a significant health concern due to the long term sequelae among affected patients. WNv national surveillance met its main objectives and there is a continual need for the surveillance.

West Nile virus (WNv) is an arbovirus and is transmitted by infected mosquitoes after feeding on the blood of birds carrying the virus. The Canadian WNv national surveillance system has just completed its tenth year of operation. The thesis is to evaluate the surveillance system and analyze multi-year human data. The evaluation includes the use of multiple lines of complementary methods such as the US CDC surveillance guidelines, Canadian Evaluation Framework, document review and a survey. Logistic and Poisson regressions were used for data analyses. WNv has become endemic in most parts of Canada since the virus occurred in 2001. The virus activity is peak around August. High numbers of human cases with WNv neurological syndrome identified pose a significant health concern due to the long term sequelae among affected patients. WNv national surveillance met its main objectives and there is a continual need for the surveillance.

abstract: Accounting for over a third of all emerging and re-emerging infections, viruses represent a major public health threat, which researchers and epidemiologists across the world have been attempting to contain for decades. Recently, genomics-based surveillance of viruses through methods such as virus phylogeography has grown into a popular tool for infectious disease monitoring. When conducting such surveillance studies, researchers need to manually retrieve geographic metadata denoting the location of infected host (LOIH) of viruses from public sequence databases such as GenBank and any publication related to their study. The large volume of semi-structured and unstructured information that must be reviewed for this task, along with the ambiguity of geographic locations, make it especially challenging. Prior work has demonstrated that the majority of GenBank records lack sufficient geographic granularity concerning the LOIH of viruses. As a result, reviewing full-text publications is often necessary for conducting in-depth analysis of virus migration, which can be a very time-consuming process. Moreover, integrating geographic metadata pertaining to the LOIH of viruses from different sources, including different fields in GenBank records as well as full-text publications, and normalizing the integrated metadata to unique identifiers for subsequent analysis, are also challenging tasks, often requiring expert domain knowledge. Therefore, automated information extraction (IE) methods could help significantly accelerate this process, positively impacting public health research. However, very few research studies have attempted the use of IE methods in this domain. This work explores the use of novel knowledge-driven geographic IE heuristics for extracting, integrating, and normalizing the LOIH of viruses based on information available in GenBank and related publications; when evaluated on manually annotated test sets, the methods were found to have a high accuracy and shown to be adequate for addressing this challenging problem. It also presents GeoBoost, a pioneering software system for georeferencing GenBank records, as well as a large-scale database containing over two million virus GenBank records georeferenced using the algorithms introduced here. The methods, database and software developed here could help support diverse public health domains focusing on sequence-informed virus surveillance, thereby enhancing existing platforms for controlling and containing disease outbreaks. / Dissertation/Thesis / Doctoral Dissertation Biomedical Informatics 2019