Genomic Analysis of African Swine Fever Virus | CDC EID

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Volume 17, Number 4–April 2011
Research
Genomic Analysis of Highly Virulent Georgia 2007/1 Isolate of African Swine Fever Virus
David A.G. Chapman, Alistair C. Darby, Melissa Da Silva, Chris Upton, Alan D. Radford, and Linda K. Dixon

Author affiliations: Institute for Animal Health, Woking, UK (D.A.G. Chapman, L.K. Dixon); University of Liverpool, Neston, UK (A.C. Darby, A. Radford); and University of Victoria, Victoria, British Columbia, Canada (M. Da Silva, C. Upton)


Suggested citation for this article

Abstract
African swine fever is widespread in Africa but has occasionally been introduced into other continents. In June 2007, African swine fever was isolated in the Caucasus Region of the Republic of Georgia and subsequently in neighboring countries (Armenia, Azerbaijan, and 9 states of the Russian Federation). Previous data for sequencing of 3 genes indicated that the Georgia 2007/1 isolate is closely related to isolates of genotype II, which has been identified in Mozambique, Madagascar, and Zambia. We report the complete genomic coding sequence of the Georgia 2007/1 isolate and comparison with other isolates. A genome sequence of 189,344 bp encoding 166 open reading frames (ORFs) was obtained. Phylogeny based on concatenated sequences of 125 conserved ORFs showed that this isolate clustered most closely with the Mkuzi 1979 isolate. Some ORFs clustered differently, suggesting that recombination may have occurred. Results provide a baseline for monitoring genomic changes in this virus.

African swine fever (ASF) is a hemorrhagic fever in domestic pigs that causes serious economic losses and high mortality rates. ASF is currently endemic to many countries in sub-Saharan Africa and the island of Sardinia in Europe and was endemic to Spain and Portugal from 1960 until the mid 1990s. It is still endemic to Madagascar since its introduction in 1998. Sporadic ASF outbreaks have occurred in Brazil, the Caribbean region, the Indian Ocean island of Mauritius, and countries in Europe (1). There is no vaccine against ASF, and disease control relies on rapid diagnosis and implementation of quarantine and slaughter policies. African swine fever virus (ASFV) is a large, icosahedral, cytoplasmic, double-stranded DNA virus; it is the only member of the family Asfaviridae, although it shares similarities with other virus families in the superfamily of nucleo-cytoplasmic large DNA viruses (2–4).

In 2007, a new outbreak of ASF was confirmed in the Republic of Georgia, which is far from the usual geographic virus range in sub-Saharan Africa. Infections were first observed near the Black Sea port of Poti and are thought to have been introduced by improper disposal of waste from shipping. The disease rapidly spread throughout Georgia and was reported in Armenia and in wild boar in Chechnya in the Russian Federation in 2007 and Azerbaijan in 2008. ASF has since spread to 9 regions in the Russian Federation, including 2,000 km to St. Petersburg in October 2009. As of August 10, 2010, there have been 85 outbreaks reported within the Russian Federation, which have led to the deaths of ≈48,000 animals and an estimated cost to the Russian economy during 2009 of US$1 billion (5; World Organisation for Animal Health Information Database). There have been several reports of ASFV infection in wild boars in different locations in the Russian Federation, which led to fears that ASF may have become established in the wild boar population. This rapid transboundary spread of ASF emphasizes the serious risk for ASF to pig farming worldwide.

In its natural hosts (warthogs [Phacochoerus aethiopicus], bushpigs [Potamochoerus porcus], and Ornithodorous spp. soft ticks), ASFV causes a persistent but asymptomatic infection. In domestic swine, it causes an acute hemorrhagic infection with mortality rates <100%. European wild boars (Sus scrofa) are susceptible, and disease signs are similar to those in domestic pigs. The ASFV strain introduced to the Caucasus is highly virulent and resulted in a mortality rate of ≈100% during the early stages of the outbreak in Georgia; ≈90,000 animals died or were destroyed (http://web.oie.int/wahis/public.php?page=home). Experimental infections of pigs confirmed that isolates obtained after introduction of ASF into Armenia and the Russian Federation cause acute disease and result in high mortality rates (www.efsa.europa.eu/en/scdocs/scdoc/1556.htm). Genotyping of ASFV isolates by partial sequencing of the B646L gene that encodes the major capsid protein p72 has identified 22 genotypes (6). The Georgia 2007/1 isolate was grouped within genotype II by partial sequencing of the B646L and B602L genes and complete sequencing of the CP204L gene. Genotype II virus has been isolated in Mozambique and Zambia and was also introduced into the Indian Ocean islands of Madagascar (1998) and Mauritius (2007) (7). We analyzed the complete coding region of the genome of the Georgia 2007/1 strain of ASFV, which was isolated after its introduction to Georgia in 2007. This information provides a baseline for comparison with other isolates obtained during the continued spread of ASF in this region and provides information for vaccine and diagnostic test development. full-text: Genomic Analysis of African Swine Fever Virus | CDC EID


Suggested Citation for this Article
Chapman DAG, Darby AC, Da Silva M, Upton C, Radford AD, Dixon LK. Genomic analysis of highly virulent Georgia 2007/1 isolate of African swine fever virus. Emerg Infect Dis [serial on the Internet]. 2011 Apr [date cited].
http://www.cdc.gov/EID/content/17/4/599.htm


DOI: 10.3201/eid1704.101283


Comments to the Authors
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Linda K. Dixon, Institute for Animal Health, Pirbright Laboratory, Ash Rd, Pirbright, Woking, Surrey GU24 0NF, UK; email: linda.dixon@bbsrc.ac.uk