A Deep Sequencing Strategy for Investigation of Virus Variants within African Swine Fever Virus-Infected Pigs
Camille Melissa Johnston,
Ann Sofie Olesen,
Louise Lohse,
Agnete le Maire Madsen,
Anette Bøtner,
Graham J. Belsham,
Thomas Bruun Rasmussen
Affiliations
Camille Melissa Johnston
Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
Ann Sofie Olesen
Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
Louise Lohse
Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
Agnete le Maire Madsen
Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
Anette Bøtner
Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Denmark
Graham J. Belsham
Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Denmark
Thomas Bruun Rasmussen
Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
African swine fever virus (ASFV) is the causative agent of African swine fever, an economically important disease of pigs, often with a high case fatality rate. ASFV has demonstrated low genetic diversity among isolates collected within Eurasia. To explore the influence of viral variants on clinical outcomes and infection dynamics in pigs experimentally infected with ASFV, we have designed a deep sequencing strategy. The variant analysis revealed unique SNPs at <10% frequency in several infected pigs as well as some SNPs that were found in more than one pig. In addition, a deletion of 10,487 bp (resulting in the complete loss of 21 genes) was present at a nearly 100% frequency in the ASFV DNA from one pig at position 6362-16849. This deletion was also found to be present at low levels in the virus inoculum and in two other infected pigs. The current methodology can be used for the currently circulating Eurasian ASFVs and also adapted to other ASFV strains and genotypes. Comprehensive deep sequencing is critical for following ASFV molecular evolution, especially for the identification of modifications that affect virus virulence.