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.

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.

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.