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SHIC-Funded ASF Molecular Epidemiology Project Identifies Prevention and Control Gaps

April 7, 2021 — Paul Sundberg

A project to summarize current knowledge and remaining gaps regarding the molecular epidemiology of African swine fever (ASF) was funded by the Swine Health Information Center (SHIC). The unprecedented expansion of ASF during the last five years produced a 218% increase in the volume of scientific publications on the subject compared to the previous five years (2010 to 2014). Due to this volume, a critical need to synthesize available scientific evidence to support and facilitate translation of the new evidence into updates for regulations and policy framework, and management recommendations for the industry, was apparent. Staff at the Center for Animal Health and Food Safety (CAHFS) at the University of Minnesota College of Veterinary Medicine conducted a systematic review of current literature including, but not restricted to, genetic diversity of strains, the association between sequence data, and epidemiological or pathogenic features, and development and performance of molecular diagnostic tools.

Resulting information from this study will inform appropriate preparedness and control strategies in the US. This work found globally available data, and consequently, analytical approaches, show a strong asymmetry across genotypes. This gap demonstrates eastern and southern Africa's role as a major reservoir of virus diversity, from which new spillovers such as the one in 2007 could happen again, which needs to be continually addressed. It also reported several comprehensive lists of research priorities to be addressed to support more efficient control strategies on a global scale (Table 1). Identifying relevant research gaps in disease prevention and control informs the ultimate goal of supporting experiments and projects to fill those gaps.

Table 1

Field Gaps
GEONOMICS
  • Systematic collection of whole-genomic sequences of all genotypes from domestic and wild hosts.
    • 1-3 whole genomes per genotype
    • different virulence phenotypes
    • viruses from different host species
  • Evolutionary analysis of isolates from endemic areas in regard to both time and distance.
  • ASFV bioinformatics resource: specialized tools for genome annotation and analysis of ASFV genomes.
  • Harmonization and workflows for the characterization of field isolates of different virulence phenotypes through:
    • Transcriptomic of ASFV and of the host at various stages of infection.
    • Functional genomics of ASFV proteins
  • Identification of viral genetic patterns that correlate with homologous and heterologous protection.
  • Improve our understanding of the role of multigene families in antigenic variability and evasion of immune response.
MOLECULAR DIAGNOSIS and SURVEILLANCE
  • Comprehensive biological and molecular characterization of currently circulating isolates in Africa and Europe.
  • Identification of new phylogenetic markers associated with the evolution of virus virulence in endemic areas.
  • In a targeted approached, monitor ASF isolates' diversity in endemic areas
  • Need to expand virus detection, isolation and characterization of genetic diversity of isolates from sylvatic cycle hosts in Africa.
  • Need to intensify ongoing biological and molecular characterization of currently circulating isolates in Africa and Europe.
  • Automation and standardization of viral genome sequencing for subtyping ASFV strains.
  • Improved stability of reagents in commercial diagnostic kits ● Expanded field validation of novel assays, taking into consideration the worldwide scenarios.
  • Monitor the performance and overall accuracy of currently available tests.
  • Automation and standardization of viral genome sequencing for subtyping ASFV strains.
  • Field validation of new assays is needed taking into account fitness-for-purpose and the overall situation.
  • There is a need to intensify training and follow-up activities for international harmonization of diagnostic tests.

As the world deals with the COVID-19 pandemic, SHIC continues to focus efforts on prevention, preparedness, and response to novel and emerging swine disease for the benefit of US swine health. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. SHIC is funded by America's pork producers to fulfill its mission to protect and enhance the health of the US swine herd. For more information, visit http://www.swinehealth.org; or contact Dr. Sundberg at psundberg@swinehealth.

Paul Sundberg, Executive Director, Swine Health Information Center