The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review

• Published in: Journal of medical virology 2019-10, Vol.91 (10), p.1707-1724
• Main Authors: Ciccozzi, Massimo, Lai, Alessia, Zehender, Gianguglielmo, Borsetti, Alessandra, Cella, Eleonora, Ciotti, Marco, Sagnelli, Evangelista, Sagnelli, Caterina, Angeletti, Silvia
• Format: Article
• Language: English
• Subjects: Antibiotics; Epidemics; Epidemiology; Evolution; Hepatitis; HIV; Hospitals; Human immunodeficiency virus; Infections; Infectious diseases; Microorganisms; Nosocomial infection; Outbreaks; Pandemics; Phylogenetics; Phylogeny; Precision medicine; research and analysis methods; Vaccines; Vector-borne diseases; Virology; Viruses
• ISSN: 0146-6615; 1096-9071
• DOI: 10.1002/jmv.25526

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. Highlight Epidemiology is the first way to study viral epidemics. Phylogeny and phylodynamic are important supports for epidemic events analysis by the microorganism point of view. The integration between classical epidemiology and phylogenetic approaches provide a single analytical framework, called evolutionary epidemiology. This review showed the need to enrich the classical surveillance by the molecular phylogenetic analysis to analyse the spread of global infectious diseases in terms of regional epidemic or nosocomial outbreaks.