Local and introduced lineages drive MERS-CoV recombination in Egyptian camels.

Dromedary camels are the primary reservoir for Middle East respiratory syndrome coronavirus (MERS-CoV), a zoonotic coronavirus responsible for sporadic human infections. While clade B predominates in the Arabian Peninsula and is frequently linked to zoonotic outbreaks and household secondary transmission, clade C circulates primarily in African camels, with limited evidence of human infections. The extent of MERS-CoV transmission, genetic diversity, and cross-species potential in North Africa remains poorly characterized. Here, we investigate MERS-CoV incidence, seroprevalence, and genomic recombination in dromedary camels and sympatric livestock across slaughterhouses and farms in Egypt. MERS-CoV was detected in 12% of camels sampled at slaughterhouses, with no evidence of infection in cattle, buffalo, sheep, or goats. Seroprevalence was higher in slaughtered camels (79%) than camels on farms (12%). Phylogenetic analyses of MERS-CoV genomes obtained from dromedary camels revealed an introduction of clade B into Egypt, originating from the Arabian Peninsula. Furthermore, we identified recombination events between clades B and C, in addition to events within each clade. This included at least one clade C virus that acquired multiple genomic regions from the newly introduced clade B viruses. These findings suggest that newly introduced MERS-CoV strains can recombine with locally circulating viruses, generating novel variants with potential zoonotic implications and challenging assumptions of limited cross-regional exchange. Enhanced surveillance, targeted control measures, and a One Health approach are crucial to mitigating MERS-CoV transmission and the emergence of recombinant strains. IMPORTANCE: This study highlights the importance of monitoring Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels, which are the main animal source of this virus that can occasionally infect humans. While most human cases have been linked to strains in the Arabian Peninsula, this research focused on Egypt, where the virus is less understood. Among surveyed dromedary camels and associated livestock, a significant number of camels at slaughterhouses were infected, and many had antibodies showing past exposure. Importantly, we discovered that a strain common in the Arabian Peninsula had recently entered Egypt and mixed genetically with local strains. This mixing, or recombination, can lead to new virus versions that may pose new risks to humans. The findings challenge the belief that MERS-CoV strains in different regions do not interact and highlight the need for stronger monitoring and prevention strategies. A One Health approach, linking animal, human, and environmental health, is key to managing future risks.