Phylodynamics and evolutionary epidemiology of African swine fever p72-CVR genes in Eurasia and Africa

PLoS One. 2018 Feb 28;13(2):e0192565. doi: 10.1371/journal.pone.0192565. eCollection 2018.

Abstract

African swine fever (ASF) is a complex infectious disease of swine that constitutes devastating impacts on animal health and the world economy. Here, we investigated the evolutionary epidemiology of ASF virus (ASFV) in Eurasia and Africa using the concatenated gene sequences of the viral protein 72 and the central variable region of isolates collected between 1960 and 2015. We used Bayesian phylodynamic models to reconstruct the evolutionary history of the virus, to identify virus population demographics and to quantify dispersal patterns between host species. Results suggest that ASFV exhibited a significantly high evolutionary rate and population growth through time since its divergence in the 18th century from East Africa, with no signs of decline till recent years. This increase corresponds to the growing pig trade activities between continents during the 19th century, and may be attributed to an evolutionary drift that resulted from either continuous circulation or maintenance of the virus within Africa and Eurasia. Furthermore, results implicate wild suids as the ancestral host species (root state posterior probability = 0.87) for ASFV in the early 1700s in Africa. Moreover, results indicate the transmission cycle between wild suids and pigs is an important cycle for ASFV spread and maintenance in pig populations, while ticks are an important natural reservoir that can facilitate ASFV spread and maintenance in wild swine populations. We illustrated the prospects of phylodynamic methods in improving risk-based surveillance, support of effective animal health policies, and epidemic preparedness in countries at high risk of ASFV incursion.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Africa / epidemiology
  • African Swine Fever / epidemiology*
  • African Swine Fever / virology
  • Animals
  • Asfarviridae / classification
  • Asfarviridae / genetics*
  • Asia / epidemiology
  • Europe / epidemiology
  • Genes, Viral
  • Molecular Epidemiology*
  • Phylogeny*
  • Swine

Grants and funding

CJ is the recipient of a Spanish Government-funded PhD fellowship for the Training of Future Scholars (FPU) given by the Spanish Ministry of Education, Culture and Sports. This work was partly supported under the EU project ASFRISK, Evaluating and Controlling the Risk of African Swine Fever in the EU (DG-Research, EC, 7FP Grant Agreement, KBBE211691), and the EU Reference laboratory for ASF (grant no UE- LR PPA/03). EU project ASFORCE (Grant Agreement n°311931, FP7 - KBBE.2012.1.3-02) and the Spanish National Project RTA-PPA (RTA201 1-00060-C02-02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.