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. 2021 Aug 17;53(4):438.
doi: 10.1007/s11250-021-02877-y.

Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

Jean N Hakizimana  1   2 , Jean B Ntirandekura  3 , Clara Yona  1   4 , Lionel Nyabongo  5 , Gladson Kamwendo  6 , Julius L C Chulu  6 , Désiré Ntakirutimana  5 , Olivier Kamana  7 , Hans Nauwynck  8 , Gerald Misinzo  9   10
Affiliations

Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

Jean N Hakizimana et al. Trop Anim Health Prod. .

Abstract

Several African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

Keywords: African swine fever virus; Asfarviridae; Burundi; Domestic pig; Malawi; Whole-genome sequencing.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Graphical display of African swine fever virus open reading frames (ORFs) of MAL/19/Karonga (a) and BUR/18/Rutana (b.) automatically annotated by Genome Annotation Transfer Utility (GATU) using corresponding very closely related African swine fever virus reference genomes. The direction of arrows indicates the 5′ to 3′orientation of ORFs
Fig. 2
Fig. 2
Maximum likelihood phylogenetic tree obtained after multiple sequence alignment of complete genomes of African swine fever virus strains from Africa and selected strains from Europe and Asia. The viruses described in this study are indicated by black squares and the scale bar indicates nucleotide substitution per site while the node values show percentage of bootstrap support. The analysis involved 22 nucleotide sequences with a total of 166,578 positions in the final dataset
Fig. 3
Fig. 3
A maximum likelihood phylogenetic tree of the ASFV EP402R (CD2v) gene indicating serogroups of selected ASFV strains. The strains responsible for the 2018 and 2019 ASF outbreak in Burundi and in Malawi are indicated by a black dot. The scale bar indicates the number of substitutions per site
See this image and copyright information in PMC

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