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Identifying rodent hantavirus reservoirs, Brazil.


We describe the genetic analysis of samples from hantavirus pulmonary syndrome hantavirus pulmonary syndrome An often fatal RTI caused by a hantavirus; the first cluster occurred in the Four Corners region of Southwestern US Epidemiology Mean age 32, 61% ♀, 72% Native American Case definition Unexplained bilateral interstitial  (HPS See Seer*HPS. ) patients from southern and southeastern states of Brazil Brazil is divided into twenty-six estados ("states"; singular estado) and one district, the Distrito Federal ("Federal District") which contains the capital city, Brasília.  and rodents captured at the presumed site of infection of these patients. A total of 65 samples that were antibody-positive for Sin Nombre or Laguna Negra virus by enzyme-linked immunosorbent assay enzyme-linked immunosorbent assay
n.
ELISA.


Enzyme-linked immunosorbent assay (ELISA)
A diagnostic blood test used to screen patients for AIDS or other viruses.
 were processed by nested reverse transcription-polymerase chain reaction (RT-PCR RT-PCR

reverse transcriptase-polymerase chain reaction. See PCR1.
) by using several primer combinations in the M and S genome segments. PCR PCR polymerase chain reaction.

PCR
abbr.
polymerase chain reaction


Polymerase chain reaction (PCR) 
 products were amplified and sequenced from samples from 11 HPS patient and 7 rodent samples. Phylogenetic phy·lo·ge·net·ic
adj.
1. Of or relating to phylogeny or phylogenetics.

2. Relating to or based on evolutionary development or history.
 analysis of nucleotide sequence differences showed the cocirculation of Araraquara and Juquitiba-like viruses, previously characterized from humans. Our genetic data indicate that Araraquara virus is associated with Bolomys lasiurus (hairy-tailed Bolo mouse The Hairy-tailed Bolo Mouse, Necromys lasiurus, is a rodent species from South America. It is found in Argentina, Bolivia, Brazil and Paraguay. References
  • Baillie, J. 1996. Bolomys lasiurus. 2006 IUCN Red List of Threatened Species.
) and the Juquitiba-like virus is associated with Oligoryzomys nigripes (black-footed pigmy rice rat).

**********

Hantaviruses are mainly rodentborne viruses of the family Bunyaviridae (1). Two clinical forms of infections by hantaviruses are known: hemorrhagic Hemorrhagic
A condition resulting in massive, difficult-to-control bleeding.

Mentioned in: Hantavirus Infections


hemorrhagic

pertaining to or characterized by hemorrhage.
 lever with renal syndrome (HFRS HFRS Hemorrhagic Fever With Renal Syndrome
HFRS Hampshire Fire and Rescue Service (UK)
HFRS Humberside Fire and Rescue Service (UK)
HFRS High-Float, Rapid-Setting (emulsion) 
) in the Old World and hantavirus pulmonary syndrome (HPS) in the American continent (2-4). Hantaviruses are enveloped en·vel·op  
tr.v. en·vel·oped, en·vel·op·ing, en·vel·ops
1. To enclose or encase completely with or as if with a covering: "Accompanying the darkness, a stillness envelops the city" 
, single-stranded, negative-sense RNA viruses, with a genome with three segments, designated small (S), medium (M), and large (L). The S segment encodes the nucleocapsid nucleocapsid /nu·cleo·cap·sid/ (noo?kle-o-kap´sid) a unit of viral structure, consisting of a capsid with the enclosed nucleic acid.

nu·cle·o·cap·sid
n.
 protein N, the M segment encodes a glycoprotein glycoprotein (glī'kōprō`tēn), organic compound composed of both a protein and a carbohydrate joined together in covalent chemical linkage.  precursor that is processed into the envelope glycoproteins G1 and G2, and the L segment encodes the RNA polymerase (5,6).

The hantaviruses that cause HPS are associated with wild rodents species of the subfamily subfamily /sub·fam·i·ly/ (sub´fam-i-le) a taxonomic division between a family and a tribe.

sub·fam·i·ly
n.
A taxonomic category ranking between a family and a genus.
 Sigmodontinae. They are transmitted mainly by contact or through aerosols of excrete excrete /ex·crete/ (eks-kret´) to throw off or eliminate by a normal discharge, such as waste matter.

ex·crete
v.
To eliminate waste material from the body.
 and secretions of infected rodents (7-9). Person-to-person transmission has been reported in the 1996 out break in Argentina, involving the Andes (AND) virus (10,11). In Chile, this kind of transmission is suggested by clusters of cases in household contacts (12).

In Brazil, during the 1980s and 1990s, virologic and serologic se·rol·o·gy  
n. pl. se·rol·o·gies
1. The science that deals with the properties and reactions of serums, especially blood serum.

2.
 studies conducted in humans and urban rodents showed the circulation of a hantavirus hantavirus, any of a genus (Hantavirus) of single-stranded RNA viruses that are carried by rodents and transmitted to humans when they inhale vapors from contaminated rodent urine, saliva, or feces. There are many strains of hantavirus.  related to Seoul virus (13-16). In 1993, cases of an acute respiratory illness were detected in a family cluster in Juquitiba County, approximately 80 km from Sao Paulo City, in southeastern Brazil. Three brothers were affected by the infection, and two of them died (17,18). Necropsy necropsy /nec·rop·sy/ (nek´rop-se) examination of a body after death; autopsy.

nec·rop·sy
n.
See autopsy.



necropsy

examination of a body after death. See also autopsy.
 material from one of them allowed the genetic characterization of a new hantavirus, later named Juquitiba (JUQ) virus, by sequencing a fragment of 139 nucleotides (nt) of the M genomic segment G2 encoding region (19). During 1995 and 1996, three more cases of HPS were confirmed by enzyme-linked immunosorbent assay (ELISA ELISA (e-li´sah) Enzyme-Linked Immuno-Sorbent Assay; any enzyme immunoassay using an enzyme-labeled immunoreactant and an immunosorbent.

ELISA
n.
); one patient was from the central western county of Vilarejo de Castelo dos Sonhos, in Mato Grosso State, and the remaining two patients were from Araraquara and Franca counties in Sao Paulo State. Molecular studies carried out on samples from those HPS patients identified two novel genetic lineages of hantaviruses, Castelo dos Sonhos (CAS) and Araraquara (ARA Ara or Arrah (both: ŭ`rə), city (1991 pop. 157,082), Bihar state, NE India, on the Son Canal. A major road and rail junction, it is the administrative center for a district that produces grain, sugarcane, and oilseed. ) viruses (20). In 1998, new cases of HPS were detected: two in Minas Gerais, four cases in Rio Grande do Sul Rio Grande do Sul (rē` grän`dĭ th s , and five in Sao Paulo State. Since then, an increasing number of HPS cases have been diagnosed annually in many states of Brazil. By March 2004, 342 HPS cases had been diagnosed on the basis of characteristic clinical syndrome, epidemiologic data, and Ig (immunoglobulin) M and IgG serologic response against Sin Nombre (SN), Laguna Negra (LN), or AND virus antigens by ELISA (9,21). Some of these cases were also diagnosed by immunohistochemistry. Most of the HPS cases occurred in the southern and southeastern states of Brazil (177 and 113, respectively). Paran5, reported the highest number of cases (n = 92), followed by Sao Paulo (n = 59), Minas Gerais (n = 54), Santa Catarina (n = 50), Rio Grande do Sul (n = 35), Mato Grosso (n = 33), Maranhao (n = 7), Para (n = 4), Goias (n = 3), Rio Grande do Norte Rio Grande do Norte (rē` grän`dĭ th nôr`tĭ), state (1996 pop.  (n = 1), and Bahia (n = 1) (M. Elkhoury, pers. comm.).

This study describes the genetic analysis carried out on samples from HPS-case patients from southern and southeastern states of Brazil and rodents captured at the presumed site of infection of the human case-patients. The primary aims were to identify the hantavirus lineages causing HPS in that area, because few reports were available on this topic, and to identify the potential rodent host reservoirs because genetic data were not available from hantavirus-positive rodents. Genetic analysis of the nucleotide sequences indicates that ARA and JUQ-like viruses are circulating in the studied area. We report the genetic identification of the putative primary rodent reservoirs for these viruses.

Material and Methods

Area of Study

The studied areas included two kinds of natural ecosystems: the Atlantic rainforest and "cerrado" at the southern states of Parana, Santa Catarina, and Rio Grande do Sul and at the southeastern states of Minas Gerais and Sao Paulo (Figure 1). Basically, the Atlantic rainforest extends along the Brazilian Atlantic Coast, and it is found as umbrofilous tropical forest of hillside or as its regional variation known as Araucaria araucaria

Any pinelike coniferous plant (see conifer) of the genus Araucaria (family Araucariaceae). Found in South America, the Phoenix Islands, and Australia, araucaria trees are magnificent evergreens, with whorled branches and stiff, flattened, pointed leaves.
 forest. The cerrado occurs in the Brazilian central plateau and part of northeastern region, and it is characterized by small trees, and grass vegetation, adapted to climates with long dry periods. Both kinds of ecosystems are found in Silo silo, watertight and airtight structure for making and storing silage. Silos vary in form from a covered pit, such as was used by the early Romans, to the modern storage tower, dating from the 19th cent.  Paulo and Minas Gerais States.

[FIGURE 1 OMITTED]

Patient and Rodent Samples

We studied samples from HPS patients and from rodents captured at the potential sites where HPS exposures occurred. All samples included in the present study had tested positive to hantavirus by ELISA (9) by using SN virus and LN virus antigens (provided by T.G. Ksiazek, Centers for Disease Control and Prevention Centers for Disease Control and Prevention (CDC), agency of the U.S. Public Health Service since 1973, with headquarters in Atlanta; it was established in 1946 as the Communicable Disease Center. , Atlanta, GA).

Patients

A total of 40 blood and serum samples of HPS patients from five different states of Brazil were processed by nested RT-PCR: 6 samples from Minas Gerais (Patrocinio, Uberaba, Araxa, and Passos); 10 samples from Sao Paulo (Florida Paulista, Batatais, Franca, Sao Carlos, Jau, Cotia, Barra do Turvo Barra do Turvo is a municipality in the state of São Paulo in Brazil. The population in 2003 is 8,613 and the area is 1007.3 km². The elevation is 158 m. , and Tupi Paulista); 7 samples from Parana (General Carneiro, Bituruna, Ponta Grossa, Catanduvas, Curitiba, and Guarapuava); 7 samples from Santa Catarina (Seara, Arroio Trinta, and Lindoia do Sul); 10 samples from Rio Grande do Sul (Vacaria, Pelotas Pelotas (pəlô`təsh), city (1991 pop. 291,100), Rio Grande do Sul state, S Brazil, an inland port on the São Gonçalo canal. , Marcelino Ramos, Sio Lourenco do Sul, Capao Canoa, Santana do Livramento This article or section needs copy editing for grammar, style, cohesion, tone and/or spelling.
You can assist by [ editing it] now.
, Santa Cruz do Sul Santa Cruz do Sul is a city in central Rio Grande do Sul, Brazil. The city has approximately 117,000 inhabitants and sits about 150 km (about 93 miles) from the capital city of the state, Porto Alegre. The city enjoys a high standard of living and Gross Income per Capita is 2. , Novo Hamburgo, and Arvorezinha). Of seven samples from HPS patients from Santa Catarina, five samples were from a family cluster reported by Seara (22).

Rodents

Rodents were captured by using Sherman live-capture traps (Sherman Traps Inc., Tallahassee, FL) set in rural or sylvan sylvan

emanating from or pertaining to woods. See also sylvatic.
 environments, around the presumed sites of HPS infection. The rodents were processed in the field; biologic samples (blood, liver, kidneys, spleen, heart, and lung) were obtained according to established biosafety guidelines (23) and stored in liquid nitrogen for further processing. The carcasses of the rodents were brought to the laboratory; the skins and craniums were used for further identification of the positive specimens. Samples of carcasses were deposited at Museu de Zoologia--Universidade de Sao Paulo, Sao Paulo, Sao Paulo State, and Museum of Southwestern Biology, University of New Mexico The University of New Mexico (UNM) is a public university in Albuquerque, New Mexico. It was founded in 1889. It also offers multiple bachelor's, master's, doctoral, and professional degree programs in all areas of the arts, sciences, and engineering. , Division of Mammals, Albuquerque, New Mexico “Albuquerque” redirects here. For other uses, see Albuquerque (disambiguation).
Albuquerque (pronounced [ˈæl.bə.kɚ.kiː], Spanish: [al.βu.
, and most of the specimens were deposited in the Vertebrates Collection at Instituto Adolfo Lutz--Secao de Virus Transmitidos por Artropodos in Sao Paulo, SP.

A total of 25 rodent samples (subfamily Sigmodontinae) were studied by nested RT-PCR: 3 samples were from Uberlandia (2 Bolomys lasiurus) and Uberaba (1 B. lasiurus), in Minas Gerais; 13 samples were from Araraquara (1 B. lasiurus), Batatais (2 B. lasiurus), Franca (1 B. lasiurus and 1 Calomys tener), Cassia cassia (kăsh`ə): see cinnamon; senna.
cassia

Spice, also called Chinese cinnamon, consisting of the aromatic bark of the Cinnamomum cassia plant, of the laurel family.
 dos Coqueiros (1 Oximycterus rutilans), Cravinhos (1 B. lasiurus), Fartura (1 Akodon sp.), Mariapolis (2 B. lasiurus), Nuporanga (1 B. lasiurus and 1 Oligoryzomys nigripes), and Sao Carlos (1 B. lasiurus), in Sao Paulo; 3 samples from General Carneiro (2 O. nigripes and 1 Akodon sp.) in Parana; 3 samples from Seara (2 O. nigripes and 1 Bolomys sp.) in Santa Catarina; 3 samples from Marcelino Ramos (1 O. nigripes and 1 Akodon sp.) and Sao Lourenco do Sul (1 Akodon sp.), in Rio Grande do Sul.

RNA RNA: see nucleic acid.
RNA
 in full ribonucleic acid

One of the two main types of nucleic acid (the other being DNA), which functions in cellular protein synthesis in all living cells and replaces DNA as the carrier of genetic
 Extraction and Nested RT-PCR

Total RNA was extracted from human blood samples and rodent lung samples by using the RNaid (PLUS) Kit (BIO 101 Inc., La Jolla, CA) as described elsewhere (24). Briefly, approximately 100 mg of tissue was mixed with 300 [micro]L of cell lysis lysis /ly·sis/ (li´sis)
1. destruction or decomposition, as of a cell or other substance, under influence of a specific agent.

2. mobilization of an organ by division of restraining adhesions.

3.
 solution containing guanidine guanidine /gua·ni·dine/ (gwah´ni-den) the compound NHdbondC(NH2)2, a strong base found in the urine as a result of protein metabolism and used in the laboratory as a protein denaturant.  thiocyanate thiocyanate /thio·cy·a·nate/ (-si´ah-nat) a salt analogous in composition to a cyanate, but containing sulfur instead of oxygen.  extracted with phenol/chloroform and purified with RNA matrix beads. From some tissue samples, RNA was extracted with Trizol LS reagent (Invitrogen Co., Carlsbad, CA), following the manufacturer's recommendations. When human serum specimens were used as source of viral RNA, the QIAmp Viral RNA Kit (Qiagen, Chastworth, CA) was used according to the manufacturer's instructions. Amplification of virus RNA was performed by "RT-PCR-one step," followed by a second PCR amplification as described previously (4). Numerous primer combinations in the M and S segments were used in nested RT-PCR reactions, including oligonucleotide sequences published (4,25,26) and unpublished that were designed to amplify conserved fragments of the S and M genome segments of South American hantaviruses.

Genetic and Phylogenetic Analysis

The DNA DNA: see nucleic acid.
DNA
 or deoxyribonucleic acid

One of two types of nucleic acid (the other is RNA); a complex organic compound found in all living cells and many viruses. It is the chemical substance of genes.
 products of the nested PCR reactions were separated from an agarose agarose

more highly purified form of agar with similar uses to agar and widely used in the separation of nucleic acid fragments.
 gel, and bands of the correct predicted size were purified from gel slices with a GeneClean kit (BIO 101 Inc.) or GFXTM PCR DNA and Gel Band Purification Kit (Amersham Pharmacia Biotech, Inc., Piscataway, NJ). The nucleotide sequence of these products was determined on an ABI Abi (ā`bī) [short for Abijah], in the Bible, King Hezekiah's mother.


(Application Binary Interface) A specification for a specific hardware platform combined with the operating system.
 PRISM 377 Genetic Analyzer (Applied Biosystems, Foster City, CA.) using the dydeoxy cycle sequencing technique (4). Sequences were aligned with those of previously described hantaviruses by using BioEdit version 5.0.9 (North Carolina State University History

Main article: History of North Carolina State University
The North Carolina General Assembly founded NC State on March 7, 1887 as a land-grant college under the name North Carolina College of Agriculture and Mechanic Arts.
, Raleigh, NC) and the computer software package Clustal W 1.4 (27). Primer sequences were removed from sample sequences before being aligned. Phylogenetic analysis was carried out on the multiple nucleotide and amino acid sequence alignments by using maximum parsimony (PAUP PAUP Phylogenetic Analysis Using Parsimony * version 4.0b4a Macintosh computer software programs) (28) and the distance-based neighbor-joining method. Phylogenetic analysis by maximum parsimony was obtained by the heuristic search method. Pairwise genetic distances were computed by using the Kimura-2 parameter, as implemented in the computer program MEGA version 2.1 software (29). The bootstrap See boot.

(operating system, compiler) bootstrap - To load and initialise the operating system on a computer. Normally abbreviated to "boot". From the curious expression "to pull oneself up by one's bootstraps", one of the legendary feats of Baron von Munchhausen.
 support for the results of the phylogenetic analysis was based on 500 replicates. GenBank accession numbers of the previously published sequences of the hantaviruses used in this study are listed in figure legends.

Results

PCR products of the expected size were amplified from 11 of 40 HPS patient samples (Table 1) and 7 of 25 rodent samples studied (Table 2). A 303-nt fragment of the G2 gene was amplified and sequenced (bases corresponding to position 2807 to 3109 of Lechiguanas [LEC (1) (LAN Emulation Client) A software driver that provides LAN emulation (LANE) in an ATM network. It resides in an ATM end station or in a computer system that provides the LAN to ATM conversion, often known as a LAN access device. See LANE. ] virus). Phylogenetic analysis of nucleotide sequence differences showed the cocirculation of two genetic hantavirus lineages previously characterized from humans only: ARA virus and a genotype compatible with the previously identified JUQ virus. ARA virus sequences were derived from eight samples: from three HPS patients and three rodents (Bolomys lasiurus) from the state of Sao Paulo, and 1 HPS case-patient and one rodent (B. lasiurus) from Minas Gerais. Pairwise comparisons of the sequences of ARA virus strains from HPS patients and B. lasiurus showed an 85.1%-99.7% nt and 95%-99% amino acid (aa) identity. The viral sequence from the HPS patient Hu237251 from Patrocinio, Minas Gerais, the northernmost location included in this study, was most divergent from the other members of this group (16.7%). The second hantavirus genetic lineage identified was closely related to JUQ virus. Samples from seven HPS patients and three Oligoryzomys nigripes from the states of Rio Grande do Sul, Santa Catarina, Parana, and Sao Paulo fall into this group (Figure 2).

[FIGURE 2 OMITTED]

Sequence comparison with JUQ virus, limited to an overlapping piece of 139 nt of the G2 encoding region, the only available from this virus (19), showed 85.7%-97.7% nt identity (Figure 3). The maximum identity with the prototype JUQ virus was found to correspond to the viral RNA from the patient Hu239727 (97.7%) from Barra do Turvo, Sao Paulo, the closest location to the site of infection of the fatal HPS case from which JUQ virus was originally characterized in Juquitiba in 1993. Sequences in JUQ-like clade clade Cladus, subtype Genetics A branch of biological taxa or species that share features inherited from a common ancestor; a single phylogenetic group or line. See Inheritance, Species.  group in two subclades, one including JUQ prototype strain and Hu239727, and the other one comprising six human and the three O. nigripes sequences (distance 0.273). The distance observed between these two subclades is intermediate between in-group and between group distances (Table 3).

[FIGURE 3 OMITTED]

Comparison of the 303-nt G2-encoding region sequences derived from HPS-patient and O. nigripes samples of this group showed 86.6%-99.7% nt identity. Sequence comparison with the corresponding to ARA group showed 20.8% nt and 4.9% amino acid (aa) divergence. Genetic distances between the sequences studied are shown in Table 3. The general time reversible model (GTR GTR Guitar
GTR Gamertag Radio (gaming community radio show)
GTR Guided Tissue Regeneration
GTR General Theory of Relativity (physics)
GTR Génie des Télécommunications et Réseaux
) with a 0.2479 proportion of invariable in·var·i·a·ble  
adj.
Not changing or subject to change; constant.



in·vari·a·bil
 sites and [gamma] = 0.4121, was used in analysis. AND virus resulted in ARA closest sequence (mean distance 0.516) and Hu39694, JUQ-like closest sequence (0.723). Mean distances between ARA and JUQ-like sequences further support that they are different viruses.

A longer fragment of 1,239 nt of the G2 encoding region of the M segment (Figure 4), as well as a fragment of 259 nt of the nucleoprotein nucleoprotein

Macromolecular complex consisting of a protein linked to a nucleic acid, either DNA or RNA. The proteins that combine with DNA are generally of characteristic types called histones and protamines.
 encoding region of the S segment, was generated by one representative strain of each hantavirus group (B1194307 for ARA virus and On193576 for JUQ-like virus). Comparison of viral RNA from B. lasiurus sequences with ARA virus showed a 96.8%-nt and 99.3%-aa identity for the 1,239-nt G2-M piece, and 98.8% nt and 100% aa identity for the S segment piece. When RNA viral sequences from B. lasiurus were compared with those from O. nigripes, 77.8% nt and 93.4% aa identity for the 1,239-nt G2-M piece, and 84.1% nt and 98.8% aa identity for the S segment piece were observed.

[FIGURE 4 OMITTED]

The phylogenetic relationship of ARA and JUQ-like genotypes to other hantaviruses of South America was****** determined on the nucleotide sequences of the 303-nt and 1,239-nt G2-encoding region of the M segment genomes by using maximum parsimony and neighbor-joining analysis. Both trees showed a similar topology, except for the altered placement of certain genotypes that displayed low bootstrap support. Phylogenetic analysis performed on the 303-nt sequence fragment (Figure 2) showed that all samples from B. lasiurus fell into the ARA virus group, whereas all samples from O. nigripes fell into the JUQ-like genetic group. The nodes separating these groups had high bootstraps values (72% and 91%, respectively); however, the exact branching order among the Brazilian and the other hantaviruses cannot be resolved by the present phylogenetic analysis. The phylogenetic tree, based on the analysis of the 1,239-nt M segment sequence differences, showed the same topology of the 303-nt sequence, data-based tree. Both maximum parsimony (Figure 2) and neighbor-joining (data not shown) analysis demonstrated that the divergent ARA and JUQ-like viruses form a unique monophyletic monophyletic /mono·phy·let·ic/ (mon?o-fi-let´ik) descended from a common ancestor or stem cell.

mon·o·phy·let·ic
adj.
1. Descended or derived from one original stock or source.
 clade with the other South American hantaviruses (71% bootstrap support).

[FIGURE 2 OMITTED]

Within this clade the ARA virus forms a subclade with other two akodontine-borne Argentinean hantaviruses, Maciel (MAC) from Neovmys benefactus and Pergamino (PRG PRG Parti Radical de Gauche (French: Left Radical Party)
PRG Purge
PRG Programming Research Group (Oxford University)
PRG Preliminary Remediation Goal
PRG People's Revolutionary Government
) from Akodon azarae, although with a low bootstrap support (66%). The JUQ-like virus from O. nigripes 193576 is ambiguously placed within the South American viruses, together with CAS virus from Brazil and the rest of the Oligowzomys-borne Argentinean hantaviruses (LEC, Orfin, Hu39694, Bermejo, AND virus), as well as LN virus from Paraguay. A slight difference in the topology of this 1,239-nt database tree was observed when neighbor-joining analysis was used; the grouping of this Oligoryzomys-borne Argentinean hantavirus clustered in a subclade with a bootstrap support of 79% (data not shown).

Discussion

Eleven (27.5%) of 40 human samples and 7 (28.0%) of 25 rodent samples studied tested positive for hantavirus by RT-PCR. Previous studies have characterized three different hantavirus genetic lineages associated with HPS cases in Brazil: CAS, ARA, and JUQ (20,30,31).

Previous serologic studies detected IgG antibodies in rodent biologic samples: in B. lasiurus and Akodon spp. captured in the state of Sao Paulo (32), as well as B. lasiurus from Sao Paulo and Minas Gerais States, and O. nigripes from Sao Paulo, Rio Grande do Sul, Santa Catarina, and Paranfi States (33).

The data we report on the phylogenetic analysis of viral M and S genome segment fragments, from HPS patients and rodent samples from different locations of southern and southeastern Brazil, showed the circulation of two distinct hantaviruses, closely related to ARA and JUQ viruses, previously characterized only from humans. Our data on the phylogenetic analysis of a 303-nt G2 encoding region of the M genome segment represents the first genetic evidence of the role of B. lasiurus as rodent host reservoir for ARA virus, as well as O. nigripes as rodent host reservoir for the JUQ-like virus in the region under study. The nodes separating each group of virus within the South American hantaviruses clade were highly supported (72% and 91% bootstrap for ARA and JUQ-like lineages, respectively). The two subclades observed in Figure 3 (i.e., 139nt tree), and the intermediate distance between them suggested the possibility of some geographic isolation. More extensive sequencing of JUQ prototype and JUQ-like sequences is needed to clarify this point.

[FIGURE 3 OMITTED]

Comparison of the sequences of ARA virus strains obtained from rodents (B. lasiurus) and HPS patient samples showed an identity of up to 99.7% at the nucleotide level, while within the JUQ-like virus group, the comparison between O. nigripes and HPS patient virus strains showed an identity of up to 97.7%. However, the phylogenetic relationship of JUQ-like hantavirus to other members of the South American hantavirus lineages, determined on the nucleotide sequences of the 303-nt sequence, as well as on a longer fragment of a 1,239-nt piece of the M segment performed for one representative strain derived from one O. nigripes, systematically tailed to resolve the branching order.

In South America, human illnesses associated with hantaviruses have been linked to viruses from the Oryzomyini and Phyllotini tribes. Known akodontine-borne hantaviruses have not been associated with human illnesses. Thus, the data reported here on ARA rodent reservoir constitute the first evidence that a hantavirus associated with an akodontine rodent can cause HPS. Phylogenetic tree based on a 1,239-nt G2 sequence fragment places together the akodontine-borne ARA virus from B. lasiurus in Brazil, MAC from N. benefactus, and PRG from A. azarae in Argentina (34). Although the bootstrap support displayed was low (66%), this finding is in accordance with previous observations based on the S genome phylogeny of Argentinean hantaviruses (35). This would support the hypothesis of cospeciation of hantaviruses with their specific rodent hosts. As it has been described with other hantaviruses, biogeographic bi·o·ge·og·ra·phy  
n.
The study of the geographic distribution of organisms.



bio·ge·og
 factors are also involved in the evolution of hantavirus lineages (36,37). The human- and rodent-derived ARA strains analyzed in the current study were distributed at a distance of approximately 650 kin. As expected, ARA virus strains originated from the more distant localities displayed the highest genetic divergence, as shown between samples from Patrocinio (Hu237251) and Uberlfindia (B1235018) in Minas Gerais State, and Fl6rida Paulista (Hu196618) in Sao Paulo (16.7%-nt difference). Similarly, the divergent JUQ-like virus sample Hu239727 originated from Barra do Turvo, Sao Paulo, in relation to the rest of the human and rodent JUQ-like virus samples included in this group from locations in Santa Catarina, Parana, and Rio Grande do Sul may be associated with the geographic distance between them (500 km on average).

Although the data from serologic testing by ELISA indicated four positive Akodon spp., one C. tenet; and one Or. rutilans, specific viral sequences could not be amplified from those specimens. Thus, additional studies are needed to determine the possible role of these species in the epidemiology of hantavirus in Brazil.

The habitats and behavior of the rodents are important aspects to consider in elucidating the reservoirs of etiologic agents. ARA virus was recovered mostly from HPS patients as well as B. lasiurus samples from the ecosystem called cerrado, while JUQ-like virus was recovered mostly from human and O. nigripes samples from the ecosystem called Atlantic rainforest. Geographic distribution of B. lasiurus in Brazil includes the original areas of cerrado and "caatinga." This environment is typical in northeastern Brazil, characterized by deciduous trees and cactus and an extremely prolonged dry season. The B. lasiurus distribution shows its ability to adapt to anthropic environments, especially grasses (Brachiaria) and sugar cane cultures. These rodents are aggressive and usually dominate the areas they infest in·fest
v.
1. To live as a parasite in or on tissues or organs or on the skin and its appendages.

2. To inhabit or overrun in numbers large enough to be harmful, threatening, or obnoxious.
 (38); they do not colonize col·o·nize  
v. col·o·nized, col·o·niz·ing, col·o·niz·es

v.tr.
1. To form or establish a colony or colonies in.

2. To migrate to and settle in; occupy as a colony.

3.
 human dwellings, although occasionally they can invade houses.

O. nigripes is adapted to live in the primary and secondary forests, especially in the Atlantic rainforest and Araucaria forest. It is primarily found in anthropic environment, such as the lineal That which comes in a line, particularly a direct line, as from parent to child or grandparent to grandchild.


LINEAL. That which comes in a line. Lineal consanguinity is that which subsists between persons, one of whom is descended in a direct line from the other.
 natural habitats bordering cultivated areas, especially those with corn, where it is the most abundant species. These rodents can easily invade dwelling houses and barns to search for food, and they can nest in the domestic habitats.

Among the rodents captured in the cerrado, B. lasiurus was the most abundant species (44%) and showed the highest prevalence of antibodies to hantavirus (11%). Akodon spp. and O. nigripes were the two most abundant among those rodents captured in the transition area between cerrado and the Atlantic rainforest, but the highest prevalence of antibodies to hantavirus was found in O. nigripes specimens (8%) (33). These data help incriminate To charge with a crime; to expose to an accusation or a charge of crime; to involve oneself or another in a criminal prosecution or the danger thereof; as in the rule that a witness is not bound to give testimony that would tend to incriminate him or her.  B. lasiurus and O. nigripes in the transmission of ARA and JUQ-like viruses, respectively, to humans.
Table 1. Sequenced viral RNA samples and epidemiologic data of
hantavirus pulmonary syndrome case-patients, Brazil

Specimen    Age (y)    Onset of symptoms   Sample date

Hu193054      25         Oct 18, 2000           NA
Hu193256      22          Nov 5, 2000           NA
Hu196618      NA          Mar 5, 2001           NA
Hu199084      39          Apr 8, 2001      Apr 13, 2001
Hu201444      28              NA           May 8, 2001
Hu205597      40         Aug 28, 2001      Sep 2, 2001
Hu206776      NA              NA            Nov, 2001
Hu237251      22          Jul 1, 2002      Jul 17, 2002
Hu238063      39              NA           Aug 12, 2002
Hu239727      32          Oct 8, 2002           NA
NiOOR1W       59              NA           SeD 27 2001

Specimen        County/State       Outcome

Hu193054       Seara, SC (a)       Survived
Hu193256         Seara, SC         Survived
Hu196618    Florida Paulista, SP     Died
Hu199084        Batatais, SP       Survived
Hu201444       Arvorezinha,RS      Survived
Hu205597     Tupi Paulista, SP     Survived
Hu206776     Arroio Trinta, SC       Died
Hu237251       Patrocinio, MG      Survived
Hu238063    General Carneiro, PR     Died
Hu239727     Barra do Turvo, SP      Died
NiOOR1W     Marcelino Ramos. RS      Died

(a) SC, Santa Catarina; SP, Sao Paulo; RS, Rio Grande do Sul; MG, Minas
Gerais; PR, Parana; NA, not available.

Table 2. Rodent samples hantavirus positive by RT-PCR according to
location and original ecosystem, Brazila

Specimen                       Original
code        Rodent species    ecosystem          County/state

On193576     Oligoryzomys      Atlantic    General Carneiro, PR (a)
               nigripes       rainforest
B1194307   Bolomys lasiurus    Cerrado            Franca, SP
B1235018     B. lasiurus       Cerrado          Uberlandia, MG
B1235518     B. lasiurus       Cerrado          Mariapolis, SP
B1236546     B. lasiurus       Cerrado          Nuporanga, SP
On238341     O. nigripes       Atlantic           Seara, SC
                              rainforest
On238477     O. nigripes       Atlantic           Seara. SC
                              rainforest

(a) RT-PCR, reverse transcription-polymerase chain reaction, PR,
Parana, SP, Sao Paulo; MG, Minas Gerais, SC, Santa Catarina.

Table 3. Mean distance between sequences (a)

                         ARA Glade       JUQ-like clade

Distance from            Mean     SD     Mean     SD

Laguna Negra             0.683   0.037   1.135   0.060
Oran                     0.642   0.077   0.785   0.071
Pergamino                0.608   0.019   0.770   0.056
Maciel                   0.747   0.042   1.105   0.127
Castelo dos Sonhos       0.555   0.047   0.970   0.046
Hu39694                  0.742   0.100   0.723   0.057
Lechiguanas              0.642   0.081   0.798   0.069
Andes                    0.516   0.054   0.862   0.044
JUQ-like clade           0.924   0.138    --      --
ARA clade                 --      --     0.924   0.138
Inside clade distances   0.149   0.087   0.111   0.089

(a) ARA, Araraquara virus; SD, standard deviation; JUQ, Juquitiba
virus.


Acknowledgments

We thank the staff of Secao de Virus Transmitidos por Artropodos, Sao Paulo State Health Secretary and A. Degleue, S. Bourda, and V. Fasciani for their laboratory help. We also thank the personnel of Brazilian Ministry of Health, State and Municipal Health Secretaries in the States of Sao Paulo, Minas Gerais, Parana, Santa Catarina, and Rio Grande do Sul for their efforts in the surveillance of notifiable diseases.

This work was supported in part by VIGISUS/ FUNASA/MS Project no. 914/BRA/02. The work was done at Instituto Adolfo Lutz-Secretaria de Estado da Saude de Sao Paulo, Sao Paulo/SP, Brazil, and Instituto Nacional de Enfermedades Virales Humanas Dr. Julio I. Maiztegui, Pergamino, Argentina.

Dr. Suzuki is chief of the Secao de Virus Transmitidos por Artropodos at Instituto Adolfo Lutz, Sao Paulo State Health Secretary. Her research interests include the epidemiology and ecology of arboviruses arboviruses (ar´bōvī´rsz),
n.
, hantaviruses, and arcnaviruses, and the laboratory diagnosis of infections by these agents.

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Akemi Suzuki, * Ivani Bisordi, * Silvana Levis, ([dagger]) Jorge Garcia, ([dagger]) Luiz E. Pereira, * Renato P. Souza, * Teresa K.N. Sugahara, * Noemi Pini, ([dagger]) Delia Enria, ([dagger]) and Luiza T.M. Souza *

* Institute Adolfo Lutz-Sao Paulo, Sao Paulo, Brazil; and ([dagger]) Instituto Nacional de Enfermedades Virales Humanas Dr. Julio I. Maiztegui, Pergamino, Argentina

Address for correspondence: Akemi Suzuki, Secao de Virus Transmitidos por Artropodos--Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 355--CEP 01246-902--Sao Paulo/SP, Brazil; fax: 5511-3088-3753; email: aksuzuki @ial.sp.gov.br

Use of trade names is for identification only and does not imply endorsement by the Public Health Service or by the U.S. Department of Health and Human Services Noun 1. Department of Health and Human Services - the United States federal department that administers all federal programs dealing with health and welfare; created in 1979
Health and Human Services, HHS
.
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