LEARNING OUTCOMES
The course aims to introduce students to modern methods of molecular epidemiology as well as to their applications in the epidemiological investigation of infectious diseases and the epidemics they cause
Objectives and expected learning outcomes
Upon completion of the course students will be able to:
• Know and understand the basic concepts and tools of molecular epidemiology.
• Apply molecular epidemiology methods to investigate infectious disease epidemics and their applications in public health issues (prevention and intervention policies).
• Know and understand modern tools and phylogenetic programs applied in molecular epidemiology methods.
• Use general texts, reference books and several other resources to further develop knowledge through continuous independent learning.
• Carry out a series of analyzes using pipelines and programs, which are applied in molecular epidemiology studies, proving development of practical scientific skills.
SYLLABUS
Lectures
1. Introduction to molecular epidemiology: Introductory concepts and applications of molecular epidemiology in the epidemiological study of infectious diseases and their relevant epidemics.
2. Basic principles of molecular Epidemiology. Molecular evolution and phylogenetic analysis. File types
3. Alignment of Biological Macromolecule Sequences and Alignment Algorithms.
4. Nucleotide replacement models
5. Phylogenetic Analysis Methods: Distance and maximum parsimony methods
6. Maximum likelihood method
7. Introduction Bayesian inference in phylogenetic analysis
8. Introduction to the concept of Molecular Clock in Phylogenetic Analysis
9. Phylodynamics and Phylogeny
10. Phylogenetic Analysis and Genetic Recombination
11. Applications of molecular epidemiology. Epidemiological investigation of infectious
diseases and study of epidemics.
Laboratory / tutorial exercises
1) Nucleotide sequence storage forms, 2) Alignment algorithms and nucleotide sequences alignments manipulation/trimming correction, 3)Phylogenetic analysis using various methods, Phylogenetic Molecular Clock Analysis (BEAUti/BEAST), Recombination Analysis Methods