We describe the first, to our knowledge, cases of han-tavirus pulmonary syndrome in northeastern Argentina and eastern Paraguay. Andes and Juquitiba (JUQ) viruses were characterized. JUQV was also confirmed in 5 Oligoryzomys nigripes reservoir species from Misiones. A novel Akodon-borne genetic hantavirus lineage was detected in 1 rodent from the Biologic Reserve of Limoy.
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