Key result
Deep sequencing identifies 3 distinct SNPs and a large deletion in African swine fever virus.
Why the study?
To explore the influence of viral variants on clinical outcomes and infection dynamics in pigs experimentally infected with African swine fever virus, given the low genetic diversity observed among Eurasian isolates.
Deep sequencing can identify ASFV viral variants and modifications, such as large deletions, that may affect virus virulence.
Enables ASFV variant tracking in swine models; leaves open virulence and field relevance.
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. Variant analysis revealed 3 distinct SNPs present in the virus inoculum (at 2.4%, 0.7%, and 13% frequency, respectively) that were maintained within all infected pigs (1-6 % frequency, and the latter at 16-21%). Several pigs displayed other unique SNPs at <10% frequency. In addition, a deletion of 10487 bp (resulting in the complete loss of 21 genes) was present at 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 identification of modifications that affect virus virulence.
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Johnston et al. (2023) studied African swine fever virus (ASFV) infection. Deep sequencing strategy was evaluated on Identification of viral variants (SNPs and deletions). A deep sequencing strategy successfully identified 3 distinct SNPs and a 10487 bp deletion in African swine fever virus variants within experimentally infected pigs.
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