Abstract
African swine fever (ASF) is a highly lethal disease of domestic pigs caused by the only known DNA arbovirus. It was first described in Kenya in 1921 and since then many isolates have been collected worldwide. However, although several phylogenetic studies have been carried out to understand the relationships between the isolates, no molecular dating analyses have been achieved so far. In this paper, comprehensive phylogenetic reconstructions were made using newly generated, publicly available sequences of hundreds of ASFV isolates from the past 70 years. Analyses focused on B646L, CP204L, and E183L genes from 356, 251, and 123 isolates, respectively. Phylogenetic analyses were achieved using maximum likelihood and Bayesian coalescence methods. A new lineage-based nomenclature is proposed to designate 35 different clusters. In addition, dating of ASFV origin was carried out from the molecular data sets. To avoid bias, diversity due to positive selection or recombination events was neutralized. The molecular clock analyses revealed that ASFV strains currently circulating have evolved over 300 years, with a time to the most recent common ancestor (TMRCA) in the early 18th century.
Highlights
African swine fever (ASF) is an infectious and contagious hemorrhagic disease of domestic pigs [1]
Additional sequences of Madagascar isolates were generated after virus isolation on pig alveolar macrophages from pigs sampled during outbreaks between 1998 and 2008. These sequences are interesting for the study of African swine fever virus (ASFV) evolution since they are considered to have derived from a unique introduction of the virus in 1998: twenty-one samples were selected to cover the whole territory and the 1998– 2008 period
Because the localization of the major capsid protein VP72 in the virus core prevents exposure to circulating neutralizing antibodies, the corresponding B646L gene is not expected to be submitted to immune system pressure
Summary
African swine fever (ASF) is an infectious and contagious hemorrhagic disease of domestic pigs [1]. It is highly lethal, causing up to 100% mortality in naive animals, with devastating effects on pig production and animal trade, and major economic losses in affected countries [2]. In Europe, ASF remained endemic in the Iberian Peninsula up to the middle of the 90s and the disease is still present in Sardinia [2]. No vaccine is available and disease control is based only on quarantine and animal slaughtering In this context, its great ability to spread makes the ASF virus one of the most important infectious threats for the domestic pig industry worldwide. ASFV shares characteristics with the other members of the Nucleo-Cytoplasmic
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