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Genotype I hepatitis A virus introduction in Italy: Bayesian phylogenetic analysis to date different epidemics
Author(s) -
Cella Eleonora,
Riva Elisabetta,
Angeletti Silvia,
Fogolari Marta,
Blasi Aletheia,
Scolamacchia Vittoria,
Spoto Silvia,
Bazzardi Riccardo,
Lai Alessia,
Sagnelli Caterina,
Sagnelli Evangelista,
Ciccozzi Massimo
Publication year - 2018
Publication title -
journal of medical virology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.782
H-Index - 121
eISSN - 1096-9071
pISSN - 0146-6615
DOI - 10.1002/jmv.25220
Subject(s) - most recent common ancestor , phylogenetic tree , clade , biology , population , genotype , virology , herd immunity , markov chain monte carlo , molecular clock , genetics , bayesian probability , demography , statistics , vaccination , mathematics , gene , sociology
Despite a significant decrease in acute hepatitis A in the last 2 decades in Italy, outbreaks were observed occurring mostly in southern Italy. In this study, Bayesian phylogenetic analysis was used to analyze the origin of these epidemics. With this aim, 5 different data sets of hepatitis A virus sequences were built to perform genotyping by the neighbor‐joining method to estimate the evolutionary rates by using a Bayesian Markov chain Monte Carlo approach and to investigate the demographic history by independent Markov chain Monte Carlo runs enforcing both a strict and relaxed clock. The estimated mean value of the evolutionary rate, representing Ia and Ib strains, was 1.21 × 10 −3 and 2.0 × 10 −3 substitutions/site/year, respectively. The Bayesian maximum clade credibility tree of hepatitis A virus (HAV) Ia and Ib strains showed that Italian sequences mostly formed separate clusters. The root of the time for the most recent common ancestor (tMRCA) for HAV Ia and Ib strains dated back to 1981 and to 1988, respectively, showing in both cases different epidemic entrances. Phylodynamic analysis showed that genotype Ia increased in 1997, when the Apulia epidemic started, then suffered a bottleneck, probably consequent to vaccination and to the herd immunity, followed by a new increase in virus population in the years 2013‐2014 consequent to the epidemic caused by the ingestion of mixed frozen berries. A similar trend without an evident bottleneck was observed also in the case of genotype Ib. In conclusion, the Bayesian phylogenetic analysis represents a good tool to measure the effectiveness of the public health plans used for HAV control.