Five years before the 2022 multi-country mpox outbreak, Nigeria and Cameroon reported their first cases in more than three decades^1,2. Whereas the outbreak in Nigeria is recognized as an ongoing human epidemic, the drivers of the resurgence in Cameroon remain unclear^3,4. The rate of zoonoses remains uncertain in both countries, and gaps in genomic data obscure the timing and zoonotic and geographic origin of monkeypox virus (MPXV) emergence in humans. Here, to address these uncertainties, we sequenced 118 MPXV genomes isolated from cases in Nigeria and Cameroon between 2018 and 2023. We show that in contrast to cases in Nigeria, cases in Cameroon are the result of repeated zoonoses, with two distinct zoonotic lineages circulating across the Nigeria–Cameroon border. Our findings suggest that shared animal populations in the cross-border forest ecosystems drive the emergence and spread of the virus. Accordingly, we identify the closest zoonotic outgroup to the Nigerian human epidemic lineage (hMPXV-1) in a southern Nigerian border state. We estimate that the shared ancestor of the zoonotic outgroup and hMPXV-1 circulated in animals in southern Nigeria in late 2013. We find that hMPXV-1 emerged in humans in August 2014 in the southern Rivers State and circulated undetected for three years. Rivers State was the main source of viral spread during the human epidemic. Our study sheds light on the recent establishment of MPXV in the human population and highlights the risk of persistent zoonotic emergence of MPXV in the complex border regions of Cameroon and Nigeria.

The ongoing outbreak of Marburg virus disease in Rwanda marks the third largest historically, although it has shown the lowest fatality rate. Genomic analysis of samples from 18 cases identified a lineage with limited internal diversity, closely related to a 2014 Ugandan case. Our findings suggest that the Rwandan lineage diverged decades ago from a common ancestor shared with diversity sampled from bats in Uganda. Our genomic data reveal limited genetic variation, consistent with a single zoonotic transmission event and limited human-to-human transmission. Investigations including contact tracing, clinical assessments, sequencing and serology, linked the index case to a mining cave inhabited by Rousettus aegyptiacus. Serology tests identified three individuals seropositive for immunoglobulin G and immunoglobulin M, further supporting the zoonotic origin of the outbreak through human–animal interactions.

Since SARS-CoV-2 caused the COVID-19 pandemic, records have suggested the occurrence of reverse zoonosis of pets and farm animals in contact with SARS-CoV-2-positive humans in the Occident. However, there is little information on the spread of the virus among animals in contact with humans in Africa. Therefore, this study aimed to investigate the occurrence of SARS-CoV-2 in various animals in Nigeria. Overall, 791 animals from Ebonyi, Ogun, Ondo, and Oyo States, Nigeria were screened for SARS-CoV-2 using RT-qPCR (n = 364) and IgG ELISA (n = 654). SARS-CoV-2 positivity rates were 45.9% (RT-qPCR) and 1.4% (ELISA). SARS-CoV-2 RNA was detected in almost all animal taxa and sampling locations except Oyo State. SARS-CoV-2 IgGs were detected only in goats from Ebonyi and pigs from Ogun States. Overall, SARS-CoV-2 infectivity rates were higher in 2021 than in 2022. Our study highlights the ability of the virus to infect various animals. It presents the first report of natural SARS-CoV-2 infection in poultry, pigs, domestic ruminants, and lizards. The close human–animal interactions in these settings suggest ongoing reverse zoonosis, highlighting the role of behavioral factors of transmission and the potential for SARS-CoV-2 to spread among animals. These underscore the importance of continuous monitoring to detect and intervene in any eventual upsurge.

The ongoing outbreak of Marburg virus disease (MVD) in Rwanda marks the third largest historically, though it has exhibited the lowest fatality rate. Genomic analysis has identified a lineage with limited internal diversity most closely related to a genome sequence from a sporadic case sampled in 2014 in Uganda, though the lineages have diverged from a common ancestor that was circulating for decades in the animal reservoir. Notably, the data also provide evidence that the outbreak resulted from a single zoonotic transmission event with limited human-to-human transmission, rather than multiple independent zoonotic transmission events. The Rwandan MVD outbreak prompted a thorough investigation that included contact tracing, clinical assessment, travel history, sequencing, and serology testing, to trace the virus’s origin. Results of investigations linked the index case to a mining cave inhabited by Rousettus aegyptiacus (the Egyptian fruit bat), where three individuals tested seropositive for IgG and IgM, further supporting the zoonotic origin of the outbreak through human-animal interactions.

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.

Zoonotic spillover events pose an ongoing threat to global health, with historic and recent viral diseases of international concern emerging from animal reservoirs 1–6. In Nigeria, limited surveillance of animal hosts at the human and animal interface continues to hinder our understanding of viruses that are cryptically circulating in animals near human dwellings with potential for consequential spillover events. We performed unbiased metagenomic next‑generation sequencing (mNGS) on tissue and swab samples collected from 240 individual animals across 11 taxa (rodents, shrews, bats, goats, sheep, pigs, dogs, cats, chickens, cattle egrets, and lizards) in two Lassa‑affected Nigerian states (Ondo and Ebonyi). Host‑depleted sequencing reads were assembled into contigs, taxonomically classified, and subjected to phylogenetic analyses to characterize viral diversity, host associations, and evidence of cross‑species transmission. Across all samples, we identified 214 distinct viral taxa spanning 33 families, of which 41% (n = 83) represent novel species by ICTV criteria. Positive‑sense RNA viruses dominated (Coronaviridae, Picornaviridae, Astroviridae), followed by negative‑sense RNA, single‑ and double‑stranded DNA, and double‑stranded RNA viruses. Notably, human‑associated enteroviruses—including Hepatitis A virus (genotype 1b), echoviruses, coxsackieviruses, and noroviruses—were detected in goats, pigs, dogs, and chickens, indicating cryptic circulation of human pathogens in peridomestic and domesticated animals. Phylogenetic reconstructions revealed multiple cross‑species viral sharing events, particularly among rodents, goats, sheep, and pigs, and extensive recombination within Nigerian Betacoronavirus 1 lineages. Interestingly we found a putative novel avian like coronavirus in rodents, goats and sheep. Ecological modelling demonstrated that host species identity, sample type, and sampling effort were primary drivers of viral richness and abundance, and that higher overall viral diversity strongly predicted cross‑species transmission potential. Our integrated mNGS approach uncovered a rich and dynamic virome within animals inhabiting human‑dominated environments in Nigeria, including undetected circulation of human enteric viruses. These findings underscore the importance of broad‑taxonomic, real‑time surveillance at human–animal interfaces to inform early‑warning systems and pandemic preparedness, particularly in low‑resource settings.