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

PLoS One. 2020 May 29;15(5):e0234010. doi: 10.1371/journal.pone.0234010. eCollection 2020.

Abstract

In Europe HAV infection occurs mainly among specific risk groups, such as consumers of specific food. Sexual transmission of HAV has been demonstrated, particularly among Men-Who-Have-Sex-With-Men (MSM), causing MSM-specific outbreaksin Europe. Here we report a molecular epidemiologic and phylodynamic analysis on HAV sequences in Lazio (central Italy)to identify genetic background and the phylogenetic relations, and test the HAV infection dynamics during a large outbreak through phylodynamic model.Among all HAV sequences found during 2013-2018 in Lazio, low genetic diversity was observed in HAV population in 2016 and 2017, along with high frequenciesVRD_521_2016and RIVM-HAV16-090, suggesting a large expansion event of viral population. The initial expansion of both VRD_521_2016 and RIVM-HAV16-090 clusters dated back to 2012 (95% HPD:2006-2015). During the2016-2017outbreak in Lazio region, the Re peaked around mid-2016, with a value of 1.73 (95% HPD: 1.03-2.37), consistent with incidence trend of AHA cases in Lazio between 2016 and mid-2017. This study showed the magnitude of HAV outbreak in Lazio during 2016-2017, demonstrating the epidemic continuity to MSM-specific outbreak in Europe. The HAV dataset is available on interactive phylodynamic platform https://nextstrain.org to real-time update of future outbreaks.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Basic Reproduction Number
  • Bayes Theorem
  • Disease Outbreaks*
  • Genetic Variation
  • Genotype
  • Hepatitis A / epidemiology*
  • Hepatitis A / virology*
  • Hepatitis A virus / classification*
  • Hepatitis A virus / genetics
  • Homosexuality, Male*
  • Humans
  • Italy / epidemiology
  • Likelihood Functions
  • Male
  • Phylogeny*
  • Population Dynamics

Grants and funding

MRC- Italian Ministry of Health (Ricerca Corrente “Linea 1” and Ricerca Finalizzata) GI- the European Union’s Horizon 2020 research and innovation program, European Virus Archive (EVAg, grant no. 653316). https://cordis.europa.eu/project/id/653316 The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.