Date 
Oct 4, 2016 
Speaker 
Kimihito Ito, Division of Bioinformatics,
Research Center for Zoonosis Control, Hokkaido University

Title 
Combining Population Genetics of Pathogens and Epidemiology of Infectious Diseases

Abstract 
The estimation of the basic reproduction number is essential to
understand epidemic dynamics, and time series data of infected
individuals are usually used for the estimation. However, such data
are not always available, and methods to estimate the basic
reproduction number using genealogy constructed from nucleotide
sequences of pathogens have been proposed so far. In my talk I will
introduce a new method that we recently developed to estimate
epidemiological parameters of outbreaks using the time series change
of Tajima’s D statistic on the nucleotide sequences of pathogens. To
relate the time evolution of Tajima’s D to the number of infected
individuals, we constructed a mathematical model describing both the
transmission process of pathogens among hosts and the evolutionary
process of the pathogens. As a case study we applied this method to
the field data of nucleotide sequences of pandemic influenza A (H1N1)
2009 viruses collected in Argentina. The Tajima’s Dbased method
estimated basic reproduction number, recovery rate, and mutation rate
to be 1.47 (95% highest posterior density (HPD): 1.1– 4.34), 0.12 per
day (95% HPD: 0.09– 0.84), and 0.000163 per site per day (95% HPD:
0.0000599–0.000423), respectively. The estimated basic reproduction
number was consistent with estimation by birth–death skyline plot and
estimation using the time series of the number of infected
individuals. These results suggested that Tajima’s D statistic on
nucleotide sequences of pathogens could be useful to estimate
epidemiological parameters of outbreaks.

