Background: EBV Nuclear Antigen 1 (EBNA1) is a multifunctional protein of 641 amino acids. In host cells it is essential for the maintenance, replication and transcription of the EBV genome in expressed in both latent and lytic modes of infection. Objetive this study aimed to characterize the EBNA1 gene in cases of Infectious Mononucleosis (IM) in the metropolitan region of Belém/Pará/Brazil, period of 2005-2016.

Methods: The detection of the EBNA1 gene occurred in 26 positive cases of infectious mononucleosis were investigated by the Health Service of the Evandro Chagas Institute, using the Nested PCR and sequencing, these strains were analyzed, edited and compared with the prototype B95-8 (GenBank V01555.2) and MK540312.

Results: Phylogenetic analysis identified two EBNA1 variants, the P-ala with a rate of 23.1% (6/26) and V-Leu in 19.2% (5/26), and the subvariants V-LeuAg in 30.8% (8/26), P-Thr' in 11.5% (3/26), P-ala' in 7.7% (2/26) and V-alaiii in 7.7% (2/26). As for the origin of the sequenced cases, in the Belém strains (76.9% - 20/26) the presence of all types of EBNA1 was verified: P-ala and V-leu in 20% (4/20) each; V-LeuAg in 30.0% (6/20), P-Thr' in 15%, (3/20); P-ala' in 10% (2/20); and V-alaiii in 5% (1/20). Regarding the EBNA1 gene, of the 26 IM strains, six (23.1%) showed identical alignment to the B95-8 prototype sequence, with the others, a total of 17 amino acid alterations were observed.

Conclusion: The genetic identification of EBNA1 in the present study allowed for the first time to distinguish the molecular epidemiology and the circulation of these viral agents, highlighted its characteristic of viral persistence in clinical specimens of lymphocytes identified in IM strains coming from individuals of the northern Brazil.