The study examined factors influencing cutaneous leishmaniasis caused by the parasite Leishmania (Viannia) in the Brazilian Amazon. Among 113 confirmed patients, Leishmania RNA Virus 1 (LRV1) was detected in skin lesions in 34.51% of patients and in nasal mucosa in 24.13%. Leishmania DNA was found in healthy nasal mucosa in 12.38% of patients. The presence of LRV1 in skin lesions was associated with parasite detection in nasal mucosa. Higher parasite burden before treatment was most strongly associated with treatment failure in multivariate analysis. LRV1 detection in skin lesions suggests possible parasite dissemination to mucosal sites, although its clinical significance requires further investigation. Parasite burden emerged as an important prognostic factor for treatment outcome.