Genotype I hepatitis A virus introduction in Italy: Bayesian phylogenetic analysis to date different epidemics

Abstract

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 and 2.0 × 10 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.

Hepatitis A Strain Linked to the European Outbreaks During Gay Events between 2016 and 2017, Identified in a Brazilian Homosexual Couple in 2017

“…Phylogenetic analysis showed a monophyletic cluster of genotype IA (aLRT = 0.94) enrolling the couple’s samples and sequences from the European MSM outbreaks, demonstrating that this strain (VRD_521_2016) is circulating in Rio de Janeiro, Brazil, and may or may not be limited to MSM. The mean evolutionary rate, estimated in 1.56 × 10 −3 substitutions/site/year (95% HPD, 6.76 × 10 −4 to 2.61 × 10 −3 ), is consistent with other studies on HAV genotype IA VP1-2A (1.21 × 10 −3 substitutions/site/year) and HAV genotype I VP3-VP1-2A (5.56 × 10 −4 substitutions/site/year) [18,19]. The Bayesian inference revealed that the most recent common ancestor of the strain VRD_521_2016 might have been originated around 2013 in Europe (root of the clade) and may be introduced in Brazil between the second half of 2016 and the beginning of 2017.…”

Origin of HAV strains responsible for 2016–2017 outbreak among MSM: Viral phylodynamics in Lazio region

“…The presence of both clusters was showed by Bayesian phylogenetic tree (Bayesian MCC), where was also confirmed by posterior probability > 0.80 (Fig 4). The evolutionary rate estimated on the this dataset was 4.41 � 10 −4 subst/site/year (95% HPD:3.28 � 10 −4 -5.4 � 10 −4 ), consistent with both previous root-to-tip analyses and estimated rates of HAV genotype IA [56][57][58][59][60]. The most common recent ancestor (tMRCA) in the root of the tree corresponded to 1826 (95% HPD:1754-1881).…”

Increase in Hepatitis A Cases Linked to Imported Strains to Rio de Janeiro, Brazil: A Cross-Sectional Study

“…Our findings showed that the imported viral strains may have been responsible for the increase in the number of HAV cases in Rio de Janeiro city and other cities in the southeastern and southern regions of Brazil. Other studies have acknowledged the introduction of new viral variants as possible sources for new outbreaks, especially associated with less common transmission routes [1,43,44].…”