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African swine fever virus genotype II Eurasian spatiotemporal expansion and its origin and spread in Cambodia
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Edité par CCSD -
International audience. African swine fever (ASF) is a highly contagious haemorrhagic disease that affects domestic and wild pigs of all ages, causing up to 100% mortality in the absence of an effective vaccine. ASF is caused by a slow-evolving large dsDNA virus (ASFV) belonging to the Asfarviridae family that can be classified in 23 genotypes. ASFV originated from Southeast Africa and is endemic to sub-Saharan Africa. In 2007, first cases of ASFV genotype II were reported in Caucasus countries before spreading in the 2010s to several Baltic, Central and Southern European countries, causing important mortalities in pigs and wild boars. Since 2018, outbreaks of ASFV genotype II in China and several Eastern Asian countries have caused tremendous losses to the local swine industries. In Cambodia, from 2019 onwards, numerous outbreaks have occurred threatening the main livestock production sector in the country. To our knowledge, no phylodynamics studies have so far been conducted on ASFV although it can provide new insight into the spatiotemporal dynamics of the disease. In this study, we sequenced 54 ASFV genomes from Cambodia between 2020 and 2022 isolated from infected pigs originating from smallholders and commercial farms in different provinces. We applied Bayesian phylodynamic approaches to reconstruct the spatiotemporal Eurasian expansion of ASFV and uncover its origin and spread in Cambodia. The resulting phylogeny indicated that multiple introductions of ASFV around 2019, notably from China and Viet Nam, contributed to the Cambodian epidemic, with most of the introduced lineages spreading from Takeo province to bordering provinces. We estimated that the epidemic grows from 2019 to 2021 and begins to decline thereafter, corresponding to the first detection of the virus in the country in April 2019 and the start of mitigation measures. Finaly, we identified high viral migration rates from smallholders to commercial farms suggesting that the backyard farming sector may be a primary driver of the disease in Cambodia. ASFV continues to threaten many countries in Europe and Asia. Genomic-based studies are necessary along with epidemiological modelling to better understand this complex and devastating disease.
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