A Deep Sequencing Strategy for Investigation of Virus Variants within African Swine Fever Virus-Infected Pigs
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A Deep Sequencing Strategy for Investigation of Virus Variants within African Swine Fever Virus-Infected Pigs. / Johnston, Camille Melissa; Olesen, Ann Sofie; Lohse, Louise; le Maire Madsen, Agnete; Bøtner, Anette; Belsham, Graham J.; Rasmussen, Thomas Bruun.
In: Pathogens, Vol. 13, No. 2, 154, 2024.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A Deep Sequencing Strategy for Investigation of Virus Variants within African Swine Fever Virus-Infected Pigs
AU - Johnston, Camille Melissa
AU - Olesen, Ann Sofie
AU - Lohse, Louise
AU - le Maire Madsen, Agnete
AU - Bøtner, Anette
AU - Belsham, Graham J.
AU - Rasmussen, Thomas Bruun
N1 - Publisher Copyright: © 2024 by the authors.
PY - 2024
Y1 - 2024
N2 - 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.
AB - 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.
KW - African swine fever virus (ASFV)
KW - deep sequencing
KW - minority variant analysis
KW - nanopore sequencing
KW - next-generation sequencing (NGS)
U2 - 10.3390/pathogens13020154
DO - 10.3390/pathogens13020154
M3 - Journal article
C2 - 38392892
AN - SCOPUS:85185661743
VL - 13
JO - Pathogens
JF - Pathogens
SN - 2076-0817
IS - 2
M1 - 154
ER -
ID: 385214166