Mthombeni, Rivalani ForgetBastos, Armanda D.S.Van Schalkwyk, AntoinetteVan Emmenes, JuanitaHeath, Livio2024-09-102024-09-102023-09-04Mthombeni, R.F.; Bastos, A.D.; van Schalkwyk, A.; van Emmenes, J.; Heath, L. Phylogenomic Comparison of Seven African Swine Fever Genotype II Outbreak Viruses (1998–2019) Reveals the Likely African Origin of Georgia 2007/1. Pathogens 2023, 12, 1129. https://doi.org/10.3390/pathogens12091129.2076-0817 (online)10.3390/pathogens12091129http://hdl.handle.net/2263/98111DATA AVAILABILITY STATEMENT : All virus genome sequences generated in this study were submitted to Genbank and are available under the accession numbers indicated in Table 1.SUPPLEMENTARY MATERIALS : TABLE S1: Genome sequences included in this study and their corresponding Genbank accession numbers; TABLE S2: Synonymous SNPs of seven ASFVs under study compared to Georgia 2007/1 (FR682468.2), Tanzania/Rukwa/17/1 (LR813622) and MAL/19/Karonga (MW856068) with nucleotide substitutions on amino acids highlighted in grey; TABLE S3: Non-synonymous SNPs identified between nine ASFV genotype IIs from Africa compared to Georgia 2007/1; TABLE S4: SNPs observed within the intergenic regions of the nine African Isolates and Georgia 2007/1 with differences highlighted in grey.Since the initial report of African swine fever (ASF) in Kenya in 1921, the disease has predominantly been confined to Africa. However, in 2007, an ASF genotype II virus of unknown provenance was introduced to Georgia. This was followed by its rampant spread to 73 countries, and the disease is now a global threat to pig production, with limited effective treatment and vaccine options. Here, we investigate the origin of Georgia 2007/1 through genome sequencing of three viruses from outbreaks that predated the genotype II introduction to the Caucasus, namely Madagascar (MAD/01/1998), Mozambique (MOZ/01/2005), and Mauritius (MAU/01/2007). In addition, genome sequences were generated for viruses from East African countries historically affected by genotype II (Malawi (MAL/04/2011) and Tanzania (TAN/01/2011)) and newly invaded southern African countries (Zimbabwe (ZIM/2015) and South Africa (RSA/08/2019). Phylogenomic analyses revealed that MOZ/01/2005, MAL/04/2011, ZIM/2015 and RSA/08/2019 share a recent common ancestor with Georgia 2007/1 and that none contain the large (~550 bp) deletion in the MGT110 4L ORF observed in the MAD/01/1998, MAU/01/2007 and TAN/01/2011 isolates. Furthermore, MOZ/01/2005 and Georgia 2007/1 only differ by a single synonymous SNP in the EP402R ORF, confirming that the closest link to Georgia 2007/1 is a virus that was circulating in Mozambique in 2005.en2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.Genotype IIComplete genome sequencingPhylogeneticsAfrican swine fever virus (ASFV)Single nucleotide polymorphism (SNP)Article