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Marek’s disease is caused by Mardivirus gallidalpha2, commonly known as Marek’s disease virus (MDV). This pathogen infects various bird species resulting in a range of clinical manifestations. The meq gene, which is crucial for oncogenesis, has been extensively studied, but molecular investigations of MDV in noncommercial South American birds are limited. This study detected MDV in backyard and ornamental birds from Brazil and Peru and characterized the meq gene. MDV was confirmed in all seven outbreaks examined. Three isoforms of meq (S-meq, meq, and L-meq) and two to seven proline repeat regions (PRRs) were detected among the sequenced strains. At the amino acid level, genetic profiles with low and high virulence potential were identified. Phylogenetic analysis grouped the sequences into three distinct clusters. Selection pressure analysis revealed 18 and 15 codons under positive and negative selection, respectively. The results demonstrate significant MDV diversity in the studied birds, with both high and low virulence potentials. This study highlights the importance of monitoring and characterizing circulating MDV in backyard and ornamental birds, as they can act as reservoirs for future epidemiological outbreaks.