The first genotype II African swine fever virus isolated in Africa provides insight into the current Eurasian pandemic

Abstract

African swine fever (ASF) caused by the African swine fever virus (ASFV) is ranked by OIE as the most important source of mortality in domestic pigs globally and is indigenous to African wild suids and soft ticks. Despite two ASFV genotypes causing economically devastating epidemics outside the continent since 1961, there have been no genome-level analyses of virus evolution in Africa. The virus was recently transported from south-eastern Africa to Georgia in 2007 and has subsequently spread to Russia, eastern Europe, China, and south-east Asia with devastating socioeconomic consequences. To date, two of the 24 currently described ASFV genotypes defined by sequencing of the p72 gene, namely genotype I and II, have been reported outside Africa, with genotype II being responsible for the ongoing pig pandemic. Multiple complete genotype II genome sequences have been reported from European, Russian and Chinese virus isolates but no complete genome sequences have yet been reported from Africa. We report herein the complete genome of a Tanzanian genotype II isolate, Tanzania/Rukwa/2017/1, collected in 2017 and determined using an Illumina short read strategy. The Tanzania/Rukwa/2017/1 sequence is 183,186 bp in length (in a single contig) and contains 188 open reading frames. Considering only un-gapped sites in the pairwise alignments, the new sequence has 99.961% identity with the updated Georgia 2007/1 reference isolate (FR682468.2), 99.960% identity with Polish isolate Pol16_29413_o23 (MG939586) and 99.957% identity with Chinese isolate ASFV-wbBS01 (MK645909.1). This represents 73 single nucleotide polymorphisms (SNPs) relative to the Polish isolate and 78 SNPs with the Chinese genome. Phylogenetic analysis indicated that Tanzania/Rukwa/2017/1 clusters most closely with Georgia 2007/1. The majority of the differences between Tanzania/Rukwa/2017/1 and Georgia 2007/1 genotype II genomes are insertions/deletions (indels) as is typical for ASFV. The indels included differences in the length and copy number of the terminal multicopy gene families, MGF 360 and 110. The Rukwa2017/1 sequence is the first complete genotype II genome from a precisely mapped locality in Africa, since the exact origin of Georgia2007/1 is unknown. It therefore provides baseline information for future analyses of the diversity and phylogeography of this globally important genetic sub-group of ASF viruses.

Figure 1

A map showing the geographical distribution of the two genotypes that have escaped outside Africa into other continents. While genotype I has dominated the western, genotype II is more prevalent in the eastern part of Africa. This map was constructed using QGIS software version 2.18.14 freely downloaded from https://qgis.org/en/site/.

Figure 2

Circos plot representing the mapping of reads from the Tanzania/Rukwa/2017/1 genome to the recently corrected Georgia 2007/1 (FR682468.2) strain. The histogram shows log read depth values. The inner wheel gives approximate locations for the open reading frames.

Figure 3

Genome-wide pairwise sequence identities between genotype II viruses. The highly dissimilar isolate Estonia 2014 (accession number LS478113.1) is not included here. Gap-containing sites were ignored in sequence alignments in a pairwise manner.

Figure 4

Maximum-likelihood phylogenetic tree showing the relationship between the sequence of Tanzania/Rukwa/2017/1 determined in this study (highlighted in red), and 54 additional full-length ASFV sequences retrieved from the public databases. The branch length unit is the number of expected substitutions per site.

Figure 5

Maximum-likelihood phylogenetic tree of 29 complete genotype II genomes rooted with a genotype I outgroup sequence from Sardinia. The tree is represented as a cladogram instead of a phylogram for the sake of legibility. Branch lengths, expressed in number of expected substitutions per site, are displayed in scientific notation above the branches. Local Shimodaira-Hasegawa (SH-like) statistical branch supports calculated by FastTree are displayed as percentages in blue colour below the branches. We notice the high support (99%) attributed to the branch that makes Tanzania/Rukwa/2017/1 basal to the clade of all genotype II sequences. There was also a tendency for isolates to cluster according to their country/region of origin.

Figure 6

Map of Tanzania showing the location where ASFV samples were collected in this study. The map also shows other locations within South-eastern Africa from where other genotype II ASF viruses were reported. This map was constructed using QGIS software version 2.18.14 freely downloaded from https://qgis.org/en/site/.