Genetic Characterization of Hantaviruses Associated with Sigmodontine Rodents in an Endemic Area for Hantavirus Pulmonary Syndrome in Southern Brazil Renata Carvalho de Oliveira, 1 Paula J. Padula, 2 Raphael Gomes, 1 Valeria P. Martinez, 2 Carla Bellomo, 2 Cibele R. Bonvicino, 3,4 Danu ´ bia Ine ˆ s Freire e Lima, 4 Camila Bragagnolo, 1 Anto ˆ nio C.S. Caldas, 5 Paulo S. D’Andrea, 4 and Elba R.S. de Lemos 1 Abstract An ecological assessment of reservoir species was conducted in a rural area ( Jabora ´) in the mid-west of the state of Santa Catarina in southern Brazil, where hantavirus pulmonary syndrome is endemic, to evaluate the prevalence of hantavirus infection in wild rodents. Blood and tissue samples were collected from 507 rodents during seven field trips from March 2004 to April 2006. Some of the animals were karyotyped to confirm morphological identification. Phylogenetic reconstructions of rodent specimens, based on the mitochondrial DNA cytochrome b gene sequences, were also obtained. Hantavirus antibody was found in 22 (4.3%) of the 507 rodents: 5 Akodon montensis,2 Akodon paranaensis, 14 Oligoryzomys nigripes, and 1 Sooretamys angouya. Viral RNAs detected in O. nigripes and A. montensis were amplified and sequenced. O. nigripes virus genome was 97.5% (nt) and 98.4% (nt) identical to sequences published for Araucaria ( Juquitiba-like) virus based on N and G2 fragment sequences. Viral sequences from A. montensis strain showed 89% and 88% nucleotide identities in a 905-nt fragment of the nucleocapsid (N) protein-coding region of the S segment when it was compared with two other Akodontine rodent-associated viruses from Paraguay, A. montensis and Akodon cursor, respectively. Phylogenetic analysis showed the cocirculation of two genetic hantavirus lineages in the state of Santa Catarina, one from O. nigripes and the other from A. montensis, previously characterized in Brazil and Paraguay, respectively. The hantavirus associated with A. montensis, designed Jabora ´ virus, represents a distinct phylogenetic lineage among the Brazilian hantaviruses. Key Words: Endemic area—Hantavirus—Hantavirus pulmonary syndrome—Jabora ´ —Juquitiba—Sigmodontine rodents—Southern Brazil. Introduction H antaviruses native to the Americas include the eti- ologic agents of hantavirus pulmonary syndrome (HPS). Since the first identification of HPS cases in the United States in 1993, the number of known distinct hantavirus genotypes has grown significantly and an increasing number of cricetide rodents have been recognized as res- ervoir hosts of different hantaviruses throughout the American continent, mainly in South America (Nichol et al. 1993, Childs et al. 1994, Musser and Carleton 2005). The International Committee on Taxonomy of Viruses (ICTV) officially recognized 22 species, each closely related to a single rodent or insectivore host, although there appear to be occasional occurrences of spillover infections in related sympatric rodents (Hjelle and Yates 2001, Plyusnin and 1 Laborato ´ rio de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil. 2 INEI-ANLIS ‘‘Dr C.G. Malbra ´n,’’ Buenos Aires, Argentina. 3 Instituto Nacional de Ca ˆ ncer, Ministe ´rio da Sau ´ de, Rio de Janeiro, Brazil. 4 Laborato ´ rio de Biologia e Parasitologia de Mamı ´feros Silvestres Reservato ´ rios, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil. 5 Secretaria de Estado de Sau ´ de de Santa Catarina, Floriano ´ polis, SC, Brazil. VECTOR-BORNE AND ZOONOTIC DISEASES Volume 11, Number 3, 2011 ª Mary Ann Liebert, Inc. DOI: 10.1089/vbz.2010.0001 301