The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review.
Massimo CiccozziAlessia LaiGiangluglielmo ZehenderAlessandra BorsettiEleonora CellaCaterina SagnelliEvangelista SagnelliCaterina SagnelliSilvia AngelettiPublished in: Journal of medical virology (2019)
In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
Keyphrases
- infectious diseases
- human immunodeficiency virus
- sars cov
- hepatitis c virus
- zika virus
- risk factors
- genetic diversity
- antiretroviral therapy
- hiv infected
- genome wide
- dengue virus
- coronavirus disease
- gene expression
- single cell
- aedes aegypti
- dna methylation
- drug resistant
- electronic health record
- hiv aids
- methicillin resistant staphylococcus aureus
- solid state