Pig farms in Southern Nigeria face recurrent threats from enzootic viral infections, yet active surveillance remains limited. This study implemented an active surveillance approach targeting African swine fever virus (ASFV) to assess its circulation across four states. We sampled 40 pig farms and two abattoirs, collecting swine blood and ticks for molecular and serological analysis. Sampling was conducted during both African swine fever (ASF) outbreak (n = 27 pigs) and non-outbreak (n = 204 pigs) periods, resulting in 231 samples tested for ASFV DNA. Additionally, 46 plasma samples from the non-outbreak period were screened for ASFV-specific antibodies. ASFV was detected in all pigs sampled during outbreak periods (27/27; 100%), whereas none of the pigs sampled during non-outbreak periods tested positive (0/204). Of the 27 positives, sequencing generated 7 genomes characterized as genotype II. Serological testing of the 46 plasma samples from non-outbreak pigs revealed no ASFV seropositivity. All tick samples were negative for ASFV DNA. Farm-level risk evaluations revealed widespread biosecurity lapses, suggesting these deficiencies as potential drivers of ASFV circulation. These findings underscore the urgent need to strengthen farm-level biosecurity and demonstrate the pivotal role of active surveillance and genome sequencing in detecting and characterizing ASF outbreaks.

Lumpy Skin Disease Virus (LSDV) is a transboundary pathogen that affects cattle, causing significant economic losses, particularly in Africa and Asia. While the virus was originally endemic to sub-Saharan Africa, it has rapidly spread to Europe, the Middle East, and Asia, necessitating comprehensive genomic surveillance. Despite LSDV’s African origins, genomic data from West and Central Africa remain scarce, limiting insights into regional viral evolution and vaccine compatibility. In this study, molecular detection of LSDV was carried out on cattle samples from Nigeria, Cameroon, and Benin. However, comparative genomic analysis was performed using two near-complete LSDV genomes obtained from Cameroon. Phylogenetic evaluation revealed that LSDV strains from Nigeria and Cameroon cluster within the classical 1.2 lineage. Furthermore, the two sequences from this study cluster with the only publicly available sequence from West and Central Africa, supporting earlier findings of the presence of a West/Central African sub-lineage. Functional genomic analysis identified mutations in genes encoding ankyrin repeat Kelch-like proteins, and envelope proteins involved in immune evasion and viral virulence, raising concerns about vaccine effectiveness. Furthermore, the detection of LSDV in flesh flies (Sarcophaga spp.) underlines their potential role in virus transmission. These findings highlight the importance of genomic monitoring and targeted surveillance.

Pig farms in Southern Nigeria face threats from both enzootic and emerging viral infec-tions, yet active surveillance remains limited. In this study, a dual-pathogen surveillance project targeting African swine fever virus (ASFV) and Japanese encephalitis virus (JEV) was undertaken to assess their circulation. Using serology, molecular testing of both swine blood as well as arthropods, 40 pig farms and two abattoirs across four states were assessed. ASFV was detected in 100% of pigs sampled during known African Swine Fever outbreaks, while no viral presence was found in pigs during periods in which no outbreak was recorded. Ticks were consistently negative for the presence of ASFV. Farm-level risk evaluations revealed widespread biosecurity lapses, identifying them as key drivers of ASFV circulation. For JEV, molecular tests failed to reveal the presence of the virus in any pigs or mosquitoes. However, a high degree of seropositivity (57.1%) was noted in the pig samples. In the absence of any positive detection of the virus, cross-reactivity with other flaviviruses cannot be excluded.

Lumpy Skin Disease Virus (LSDV) is a highly contagious, transboundary pathogen that affects cattle, causing sig-nificant economic losses, particularly in Africa and Asia. While the virus was originally endemic to sub-Saharan Africa, it has rapidly spread to Europe, the Middle East, and Asia, necessitating comprehensive genomic surveil-lance. Despite LSDV’s African origins, genomic data from West and Central Africa remain scarce, limiting insights into regional viral evolution and vaccine compatibility. In this study, we used molecular detection, sequencing, and comparative genomic analysis to characterise LSDV strains circulating in Nigeria, Cameroon, and the Republic of Benin. Phylogenetic evaluation revealed that LSDV strains from Nigeria and Cameroon cluster within the classical 1.2 lineage, but do not align with known sub-lineages, suggesting the presence of a novel West/Central African sub-lineage. Functional genomic analysis identified mutations in genes encoding ankyrin repeat kelch-like proteins, and envelope proteins known for immune evasion, as well as virulence-associated genes, raising concerns about vaccine effectiveness. Furthermore, the detection of LSDV in flesh flies (Sarcophaga spp.) underlines their potential role in virus transmission. These findings highlight the importance of genomic monitoring and targeted surveil-lance or polyvalent vaccines to address emerging variants, and improve disease control strategies.