Target capture sequencing for the first Nigerian genotype I ASFV genome

Area of Science:

• Veterinary Virology
• Molecular Epidemiology
• Genomics

Background:

• African swine fever (ASF) causes significant global economic losses in pig populations.
• Nigeria has experienced frequent outbreaks of ASF since 1997.
• Understanding ASFV genotypes and phylogenetic relationships is crucial for disease control.

Purpose of the Study:

• To determine the near-complete genomes of two ASFV isolates from Nigeria.
• To perform genome-wide phylogenetic analysis of Nigerian ASFV isolates.
• To elucidate the origin and evolutionary relationships of Nigerian ASFV strains.

Main Methods:

• Detection of ASFV in Nigerian indigenous pig samples collected in 2016.
• Assembly of near-complete ASFV genomes using in-solution hybrid capture sequencing.
• Genome-wide phylogenetic analysis using p72 gene and whole genome data.

Main Results:

• Two ASFV-positive samples were identified from 150 Nigerian pig samples.
• The two Nigerian ASFV genomes were assigned to genotype I, closely related to the Benin 97/1 strain.
• High genomic sequence identity (99.94% and 99.92%) was observed between the Nigerian isolates and Benin 97/1.

Conclusions:

• This study provides the first near-complete genome sequences of ASFV from Nigeria.
• The findings indicate a close relationship between Nigerian ASFV isolates and strains from Benin and potentially Italy.
• In-solution hybrid capture sequencing is an effective method for ASFV genome determination, advancing the understanding of ASFVs global evolution.