Application of phylogenetic analysis in the molecular epidemiological study of infectious diseases.
10.3760/cma.j.cn112338-20210701-00515
- Author:
Lu Qi WANG
1
;
Hai Yan XIONG
1
;
Wei Bing WANG
1
Author Information
1. Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China.
- Publication Type:Journal Article
- MeSH:
Bayes Theorem;
Communicable Diseases/genetics*;
Epidemiologic Studies;
Genomics;
Humans;
Phylogeny
- From:
Chinese Journal of Epidemiology
2022;43(2):282-285
- CountryChina
- Language:Chinese
-
Abstract:
The rapid development of sequencing technology brings the explosive growth of pathogen genetic data. The combination of genomic data and phylogenetic method is being used to elaborate the origin and evolution of pathogens, the time and space distribution and parameter changes in the prevalence process, and how phenotypes like antigen, virulence, and resistance change over time. This method is also being used to predict pathogen transmission trends. In this study, we described the aim of phylogeny and the process of the phylogenetic construction method. We elaborated the advantages and disadvantages and scope of application of tree-building methods including distance-based, maximum parsimony, maximum likelihood and bayesian methods. We have reviewed the application and the estimation methods of major epidemiological parameters of phylodynamics and phylogeography in domestic and foreign studies. We concluded that the time- and location-scaled phylogenetic trees are increasingly used for outbreak investigation and routine surveillance of infectious diseases.
