Genome sequencing reveals variation of African swine fever virus in Nigerian outbreaks and identification of two major West African viral lineages.

African swine fever is a transboundary disease of wild boar and domestic pigs that is caused by the African swine fever virus (ASFV), with a mortality rate of 100 % in naïve animals. The ongoing spread poses a significant threat to food security and economic stability globally. In Nigeria, frequent outbreaks of the disease have been reported since 1997, and genetic analysis of Nigerian ASFV has defined virulent genotypes I and II. The disease has caused a significant impact in the pig-producing regions of the country, resulting in high economic losses. For improved control of the virus, a better knowledge of the virus's genetic diversity is required. Here, we report five complete genome assemblies of ASFV from Nigeria, four genomes assembled with hybrid sequencing platforms and one using the Oxford Nanopore Technology, from different outbreaks between 2020 and 2024. Phylogenetic analysis indicates that these outbreak strains are of genotypes I and II, showing a striking sequence similarity to Benin 97/1 and Nigeria-RV502 of ≥99.90 %. Evolutionary analysis identified CAM1994 and Mauritius MAU/01/2007 to be the closest to the common ancestor of the circulating virus strains in Nigeria. The study reports for the first time the simultaneous occurrence of genotypes I and II in Nigeria. The study documents the evolutionary pattern of the two circulating genotypes in Nigeria and the West African region, allowing monitoring of the transmission dynamics, which will help strengthen surveillance and disease control.

• Publication year

  2026

• Venue

  Microbial Genomics

• Publication date

  2026-02-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1099/mgen.0.001636PMID 41665619
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Genome-Wide Approach Identifies Natural Large-Fragment Deletion in ASFV Strains Circulating in Italy During 2023

  2025cited by this paper
• Complete Genome Sequencing and Comparative Phylogenomics of Nine African Swine Fever Virus (ASFV) Isolates of the Virulent East African p72 Genotype IX without Viral Sequence Enrichment

  2024cited by this paper
• The African swine fever virus gene MGF_360-4L inhibits interferon signaling by recruiting mitochondrial selective autophagy receptor SQSTM1 degrading MDA5 antagonizing innate immune responses

  2024cited by this paper
• African swine fever virus pB475L evades host antiviral innate immunity via targeting STAT2 to inhibit IFN-I signaling

  2024cited by this paper
• Advancements in long-read genome sequencing technologies and algorithms.

  2024cited by this paper
• Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool

  2024cited by this paper
• African swine fever virus NAM P1/95 is a mixture of genotype I and genotype VIII viruses

  2024cited by this paper
• Pig production in Africa: current status, challenges, prospects and opportunities

  2024cited by this paper
• Whole-genome sequencing of African swine fever virus from wild boars in the Kaliningrad region reveals unique and distinguishing genomic mutations

  2023cited by this paper
• A Re-Evaluation of African Swine Fever Genotypes Based on p72 Sequences Reveals the Existence of Only Six Distinct p72 Groups

  2023cited by this paper
• Seroimmunotyping of African swine fever virus

  2023cited by this paper
• The 2022 Outbreaks of African Swine Fever Virus Demonstrate the First Report of Genotype II in Ghana

  2023cited by this paper
• Target capture sequencing for the first Nigerian genotype I ASFV genome

  2023cited by this paper
• Characterization of a Novel African Swine Fever Virus p72 Genotype II from Nigeria

  2023cited by this paper
• Tracing the Origin of Genotype II African Swine Fever Virus in China by Genomic Epidemiology Analysis

  2023cited by this paper
• African Swine Fever Virus MGF505-7R Interacts with Interferon Regulatory Factor 9 to Evade the Type I Interferon Signaling Pathway and Promote Viral Replication

  2023cited by this paper
• An analysis of African Swine Fever consequences on rural economies and smallholder swine producers in Haiti

  2022cited by this paper
• Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming

  2022cited by this paper
• NanoPack2: population-scale evaluation of long-read sequencing data

  2022cited by this paper
• MGF360-9L Is a Major Virulence Factor Associated with the African Swine Fever Virus by Antagonizing the JAK/STAT Signaling Pathway

  2022cited by this paper
• African Swine Fever Virus MGF-110-9L-deficient Mutant Has Attenuated Virulence in Pigs

  2021cited by this paper
• African swine fever in the Dominican Republic.

  2021cited by this paper
• New strategies to improve minimap2 alignment accuracy

  2021cited by this paper
• First-Time Presence of African Swine Fever Virus Genotype II in Nigeria

  2021cited by this paper
• Rapid Identification for Serotyping of African Swine Fever Virus Based on the Short Fragment of the EP402R Gene Encoding for CD2-Like Protein

  2021cited by this paper
• VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

  2021cited by this paper
• African swine fever whole-genome sequencing—Quantity wanted but quality needed

  2020cited by this paper
• CheckV assesses the quality and completeness of metagenome-assembled viral genomes

  2020cited by this paper
• Using SPAdes De Novo Assembler

  2020cited by this paper
• Architecture of African swine fever virus and implications for viral assembly

  2019cited by this paper
• The evolution of African swine fever (ASF) in Europe and our country

  2019cited by this paper
• A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences

  2019cited by this paper
• IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

  2019cited by this paper
• BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

  2018cited by this paper
• Deletion at the 5’-end of Estonian ASFV strains associated with an attenuated phenotype

  2018cited by this paper
• Assembly of long, error-prone reads using repeat graphs

  2018cited by this paper
• BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines

  2018cited by this paper
• Emergence of African Swine Fever in China, 2018.

  2018cited by this paper
• The African swine fever epidemic in West Africa, 1996-2002.

  2018cited by this paper
• Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

  2018cited by this paper
• Fast and accurate de novo genome assembly from long uncorrected reads

  2016cited by this paper
• African swine fever virus ORF P1192R codes for a functional type II DNA topoisomerase.

  2015cited by this paper
• Molecular characterization of African swine fever virus from domestic pigs in northern Tanzania during an outbreak in 2013

  2014cited by this paper
• Trimmomatic: a flexible trimmer for Illumina sequence data

  2014cited by this paper
• Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

  2014cited by this paper
• AliView: a fast and lightweight alignment viewer and editor for large datasets

  2014cited by this paper
• MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

  2013cited by this paper
• Domestic Pigs in Africa

  2013cited by this paper
• African swine fever virus replication and genomics.

  2013cited by this paper
• QUAST: quality assessment tool for genome assemblies

  2013cited by this paper
• FUBAR: a fast, unconstrained bayesian approximation for inferring selection.

  2013cited by this paper
• African swine fever: an epidemiological update.

  2012cited by this paper
• Fast and accurate long-read alignment with Burrows–Wheeler transform

  2010cited by this paper
• trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

  2009cited by this paper
• Review of African swine fever: transmission, spread and control.

  2009cited by this paper
• African swine fever in the Caucasus

  2008cited by this paper
• Comparison of the genome sequences of non-pathogenic and pathogenic African swine fever virus isolates.

  2008cited by this paper
• Trends in Emerging Viral Infections of Swine: Zimmerman/Trends

  2008cited by this paper
• Pattern of spread of African swine fever in south-western Nigeria, 1997-2005.

  2007cited by this paper
• Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome

  2006cited by this paper
• Not so different after all: a comparison of methods for detecting amino acid sites under selection.

  2005cited by this paper
• An Outbreak of African Swine Fever in Nigeria: Virus Isolation and Molecular Characterization of the VP72 Gene of a First Isolate from West Africa

  2004cited by this paper
• Development of a TaqMan PCR assay with internal amplification control for the detection of African swine fever virus.

  2003cited by this paper
• Comparison of genomes of African swine fever virus isolates from Cameroon, other african countries and Europe

  2000cited by this paper
• On A Form of Swine Fever Occurring in British East Africa (Kenya Colony)

  year unknowncited by this paper

• No citing papers are available for this paper.