+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) from the country of Georgia



Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) from the country of Georgia



Virology Journal 15(1): 190



African swine fever virus (ASFV) causes an acute hemorrhagic infection in suids with a mortality rate of up to 100%. No vaccine is available and the potential for catastrophic disease in Europe remains elevated due to the ongoing ASF epidemic in Russia and Baltic countries. To date, intra-epidemic whole-genome variation for ASFV has not been reported. To provide a more comprehensive baseline for genetic variation early in the ASF outbreak, we sequenced two Georgian ASFV samples, G-2008/1 and G-2008/2, derived from domestic porcine blood collected in 2008. Genomic DNA was extracted directly from low-volume ASFV PCR-positive porcine blood samples and subjected to next generation sequencing on the Illumina Miseq platform. De novo and mapped sequence assemblies were performed using CLCBio software. Genomic illustrations, sequence alignments and assembly figures were generated using Geneious v10.2.4. Sequence repeat architecture was analyzed using DNASTAR GeneQuest 14.1.0. The G-2008/1 and G-2008/2 genomes were distinguished from each other by coding changes in seven genes, including MGF 110-1 L, X69R, MGF 505-10R, EP364R, H233R, E199L, and MGF 360-21R in addition to eight homopolymer tract variations. The 2008/2 genome possessed a novel allele state at a previously undescribed intergenic repeat locus between genes C315R and C147L. The C315R/C147L locus represents the earliest observed variable repeat sequence polymorphism reported among isolates from this epidemic. No sequence variation was observed in conventional ASFV subtyping markers. The two genomes exhibited complete collinearity and identical gene content with the Georgia 2007/1 reference genome. Approximately 56 unique homopolymer A/T-tract variations were identified that were unique to the Georgia 2007/1 genome. In both 2008 genomes, within-sample sequence read heterogeneity was evident at six homopolymeric G/C-tracts confined to the known hypervariable ~ 7 kb region in the left terminal region of the genome. This is the first intra-epidemic comparative genomic analysis reported for ASFV and provides insight into the intra-epidemic microevolution of ASFV. The genomes reported here, in addition to the G-2007/1 genome, provide an early baseline for future genome-level comparisons and epidemiological tracing efforts.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 066005183

Download citation: RISBibTeXText

PMID: 30547827

DOI: 10.1186/s12985-018-1099-z


Related references

The low-virulent African swine fever virus (ASFV/NH/P68) induces enhanced expression and production of relevant regulatory cytokines (IFNalpha, TNFalpha and IL12p40) on porcine macrophages in comparison to the highly virulent ASFV/L60. Archives of Virology 153(10): 1845-1854, 2008

Complete genome sequence of an African swine fever virus (ASFV POL/2015/Podlaskie) determined directly from pig erythrocyte-associated nucleic acid. Journal of Virological Methods 261: 14-16, 2018

Virus-specific CTL in SLA-inbred swine recovered from experimental African swine fever virus (ASFV) infection. Annals of the New York Academy of Sciences 532: 462-464, 1988

African swine fever virus Georgia isolate harboring deletions of 9GL and MGF360/505 genes is highly attenuated in swine but does not confer protection against parental virus challenge. Virus Research 221: 8-14, 2016

Comparison of the genome sequences of non-pathogenic and pathogenic African swine fever virus isolates. Journal of General Virology 89(Pt 2): 397-408, 2008

Swine monocytes macrophages can be stimulated by the murine macrophage growth factor csf 1 in vitro use in a virus cell model for investigating african swine fever virus asfv. Abstracts of the Annual Meeting of the American Society for Microbiology 89: 379, 1989

The low-virulent African swine fever virus induces enhanced expression and production of relevant regulatory cytokines on porcine macrophages in comparison to the highly virulent ASFV/L60. Archives Of Virology3: 10, 1845-1854, 2008

Structure of African swine fever virus (ASFV). Hog Cholera: sical Swine Fever and African Swine Fever, 543-554, 1977

Specific resistance to the african swine fever virus asfv. Revista Portuguesa de Ciencias Veterinarias 86(498): 76-82, 85-88, 1991

The non-haemadsorbing African swine fever virus isolate ASFV. Journal of general virology 82(3): 513-523, 2001

Some considerations on African swine fever virus (ASFV) infection. Revista Portuguesa de Ciencias Veterinarias 93(525): 3-23, 1998

A novel TLR3 inhibitor encoded by African swine fever virus (ASFV). Archives of Virology 156(4): 597-609, 2011

Antibody studies in animals infected with African swine fever virus (ASFV). Fedn Proc 26: 2, 482 p, 1967

Porcine immune responses to African swine fever virus (ASFV) infection. Veterinary Immunology and Immunopathology 43(1/3): 99-106, 1994

Molecular characterization of the non-haemadsorbing African swine fever virus isolate (ASFV/NH/P68). Revista Portuguesa de Ciencias Veterinarias 90(515): 120-130, 1995