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Geographic Distribution and Genetic Diversity of Whitewater Arroyo Virus in the Southwestern United States.


The purpose of this study was to extend our knowledge of the geographic distribution and genetic diversity of the arenavirus arenavirus /are·na·vi·rus/ (ah-re´nah-vi?rus) any virus of the family Arenaviridae.
Arenavirus /Are·na·vi·rus/ (ah-re´nah-vi?rus 
(es) associated with Neotoma species (woodrats) in the southwestern United States. Infectious arenavirus was recovered from 14 (3.3%) of 425 woodrats. The virus-positive species included N. albigula in New Mexico and Oklahoma, N. cinerea in Utah, N. mexicana in New Mexico and Utah, and N. micropus in Texas. Analyses of viral 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 gene sequence data indicated that all the isolates were strains of the Whitewater Arroyo virus, an arenavirus previously known only from northwestern New Mexico. Analyses of the sequence data also indicated that there can be substantial genetic diversity among strains of Whitewater Arroyo virus from conspecific con·spe·cif·ic  
adj.
Of or belonging to the same species.

n.
An organism belonging to the same species as another.

Noun 1.
 woodrats collected from different localities and substantial genetic diversity among strains from different woodrat species collected from the same locality.

The virus family Arenaviridae comprises two serocomplexes. The lymphocytic choriomeningitis-Lassa (Old World) complex includes lymphocytic choriomeningitis Lymphocytic Choriomeningitis Definition

Lymphocytic choriomeningitis (LCM) is a viral infection of the membranes surrounding the brain and spinal cord and of the cerebrospinal fluid.
 (LCM (Liquid Crystal Monitor) A flat panel display that uses the liquid crystal (LCD) technology. See flat panel display. ), Lassa, Mopeia, Mobala, and Ippy viruses. The Tacaribe (New World) complex includes Tamiami (TAM), Whitewater Arroyo (WWA WWA World Waterpark Association
WWA Who We Are (album title)
WWA World Wakeboard Association
WWA World Wrestling Alliance (game)
WWA Western Writers of America
), Pichinde (PIC), Amapari, Flexal, Guanarito, Junin, Latino, Machupo, Oliveros, Parana, Pirital, Sabia, and Tacaribe viruses.

The arenaviruses have bipartite BIPARTITE. Of two parts. This term is used in conveyancing as, this indenture bipartite, between A, of the one part, and B, of the other part. But when there are only two parties, it is not necessary to use this word. , single-stranded 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
 genomes (1). The large (L) genomic segment encodes the viral RNA-dependent RNA polymerase RNA polymerase
n.
A polymerase that catalyzes the synthesis of RNA from a DNA or RNA template.
 and a zinc-binding protein. The small (S) genomic segment encodes the nucleocapsid (N) protein and glycoprotein glycoprotein (glī'kōprō`tēn), organic compound composed of both a protein and a carbohydrate joined together in covalent chemical linkage.  precursor. The most comprehensive knowledge of the phylogeny of the family Arenaviridae is based on a fragment of the N protein gene (2-4).

Six arenaviruses are known to cause severe disease in humans. LCM virus is an agent of acute central nervous system disease (5) and congenital malformations (6). Lassa, Junin, Machupo, Guanarito, and Sabia viruses are etiologic agents of hemorrhagic fever hemorrhagic fever (hĕm'ərăj`ĭk), any of a group of viral diseases characterized by sudden onset, muscle and joint pain, fever, bleeding, and shock from loss of blood.  in western Africa, Argentina, Bolivia, Venezuela, and Brazil, respectively (7).

The arenaviruses known to occur in North America are LCM, TAM, and WWA. LCM virus was introduced into the Americas along with its principal rodent host, Mus musculus (house mouse) (8). TAM virus is known only from Sigmodon hispidus (hispid cotton rat The Hispid Cotton Rat, Sigmodon hispidus, is a rodent species long thought to occur in parts of South America, Central America, and southern North America. However, recent taxonomic revisions, based on mitochondrial DNA sequence data, have split this widely distributed ) in southern Florida (9-11). WWA virus was originally recovered from Neotoma albigula (white-throated woodrat) collected from northwestern New Mexico (12).

In a recent study (13), antibody to an arenavirus was found in five Neotoma species in the southwestern United States: N. albigula in Arizona, Colorado, and New Mexico; N. stephensi (Stephen's woodrat) in Arizona and New Mexico; N. mexicana (Mexican woodrat) in Arizona and Utah; and N. fuscipes (dusky-footed woodrat) and N. lepida (desert woodrat) in California. The purpose of the present study was to extend our knowledge of the geographic distribution and genetic diversity of the arenavirus(es) associated with Neotoma rodents in the southwestern United States.

Materials and Methods

All work with rodent tissues and infectious arenavirus was performed in a biosafety level biosafety level Epidemiology A classification for the degree of caution required when working with specific groups of pathogens. See Maximum containment facility.  3 laboratory at the 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) or University of Texas Medical Branch "UTMB" redirects here. For other system schools, see University of Texas System.
The University of Texas Medical Branch (UTMB) is a component of the University of Texas System located in Galveston, Texas, about 50 miles (80 km) southeast of downtown Houston.
, Galveston.

Rodent Tissues

Five hundred sixty-six tissue specimens (74 spleen, 225 liver, and 267 kidney) from 425 woodrats were tested for infectious arenavirus. The specimens were from the Museum of Texas Tech University (Lubbock, TX) or 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. , Albuquerque, NM). The specimens from the Museum of Southwestern Biology were chosen to represent localities in which antibody to an arenavirus was found in one or more Neotoma species in a previous study (13).

Virus Assay

Tissue specimens were tested for infectious arenavirus as described previously (12). Briefly, 0.2 mL of a 10% w/v crude tissue homogenate homogenate /ho·mog·e·nate/ (ho-moj´in-at) material obtained by homogenization.

homogenate

material obtained by homogenization.
 was inoculated onto a monolayer mon·o·lay·er
n.
1. A film or layer one molecule thick formed at the interface between water and either oil or air by a substance such as a partially esterified fatty acid that contains both hydrophobic and hydrophilic groups in the same
 of Vero E6 cells in a 25-[cm.sup.2] plastic culture flask (Corning, Inc., Corning, NY). The inoculum inoculum /in·oc·u·lum/ (-ok´u-lum) pl. inoc´ula   material used in inoculation.

in·oc·u·lum
n. pl.
 was incubated on the cell monolayer at 37 [degrees] C for 60 minutes; then the monolayer was overlaid with 7.0 mL of a minimum essential medium containing Earle's salts, 1.5 mg/mL sodium bicarbonate sodium bicarbonate or sodium hydrogen carbonate, chemical compound, NaHCO3, a white crystalline or granular powder, commonly known as bicarbonate of soda or baking soda. It is soluble in water and very slightly soluble in alcohol. , 2% v/v heat-inactivated (56 [degrees] C for 30 minutes) fetal bovine serum Fetal bovine serum ( or foetal bovine serum) is serum taken from the fetuses of cows. Fetal Bovine Serum (or FBS) is the most widely used serum in the culturing of cells. In some papers the expression foetal calf serum is used. , 0.29 mg/mL L-glutamine, 100 U/mL penicillin G penicillin G
n.
The most commonly used penicillin compound, used primarily in the form of its stable salts. Also called benzylpenicillin.
, 100 [micro]g/mL streptomycin sulfate streptomycin sulfate

Pharmacologic class: Aminoglycoside

Therapeutic class: Anti-infective

Pregnancy risk category D

FDA Boxed Warning

, and 100 U/mL nystatin nystatin /ny·sta·tin/ (ni-stat´in) an antifungal produced by growth of Streptomyces noursei; used in treatment of infections caused by Candida albicans and other Candida species. . The cell culture was maintained at 37 [degrees] C in a humidified atmosphere of 5% CO2 in air for 13 days. Half the culture medium was replaced with fresh maintenance medium on day 6 or 7 after inoculation. Cells were scraped from the monolayer on day 13 after inoculation and coated onto 12-well glass microscope slides (Cel-Line Associates, Inc., Newfield, NJ). The cell spots were air-dried, fixed in cold acetone acetone (ăs`ĭtōn), dimethyl ketone (dīmĕth`əl kē`tōn), or 2-propanone (prō`pənōn), CH3COCH3 , and then tested for arenaviral antigen by using an indirect fluorescent antibody test Fluorescent antibody test (FA test)
A test in which a fluorescent dye is linked to an antibody for diagnostic purposes.

Mentioned in: Rabies
 (12). In that test, cell spots were stained with a hyperimmune hyperimmune /hy·per·im·mune/ (hi?per-i-mun´) possessing very large quantities of specific antibodies in the serum.

hyperimmune

possessing very large quantities of specific antibodies in the serum.
 mouse ascitic as·ci·tes  
n. pl. ascites
An abnormal accumulation of serous fluid in the abdominal cavity.



[Middle English aschites, from Late Latin asc
 fluid prepared against the WWA virus prototype strain AV 9310135, and mouse immunoglobulin G immunoglobulin G
n. Abbr. IgG
The most abundant class of antibodies found in blood serum and lymph and active against bacteria, fungi, viruses, and foreign particles. Immunoglobulin G antibodies trigger action of the complement system.
 (IgG) bound to cell-associated arenaviral antigen was detected by using a goat anti-mouse IgG fluorescein isothiocyanate conjugate conjugate /con·ju·gate/ (kon´jdbobr-gat)
1. paired, or equally coupled; working in unison.

2. a conjugate diameter of the pelvic inlet; used alone usually to denote the true conjugate diameter; see
 (Cappel Laboratories, West Chester, PA).

Genetic Characterization of Viral Isolates

The nucleotide sequence of a fragment of the N protein gene of each of 12 isolates was determined. Four of the 12 isolates were from the spleens and kidneys of two animals, rodents 62425 and 62439 (Table 1). Total RNA was extracted from monolayers of infected Vero E6 cells by using TRIzol Reagent (Life Technologies, Inc., Grand Island, NY). Reverse transcription reverse transcription
n.
The process by which DNA is synthesized from an RNA template.
 of RNA from isolates AV 96010149, AV 96010151, AV 96010025, and AV 96010024 was carried out by using Superscript Any letter, digit or symbol that appears above the line. For example, 10 to the 9th power is written with the 9 in superscript (109). Contrast with subscript.  II RTase (Life Technologies) in conjunction with oligonucleotide ARE-3'END (14). This oligonucleotide apparently is complementary to the 19-nt fragment at the 3' terminus of the S genomic segment of all arenaviruses. Polymerase chain reaction polymerase chain reaction (pŏl`ĭmərās') (PCR), laboratory process in which a particular DNA segment from a mixture of DNA chains is rapidly replicated, producing a large, readily analyzed sample of a piece of DNA; the process is  (PCR PCR polymerase chain reaction.

PCR
abbr.
polymerase chain reaction


Polymerase chain reaction (PCR) 
) amplification of the first-strand cDNA was carried out by using Taq DNA polymerase DNA polymerase /DNA po·lym·er·ase/ (pah-lim´er-as) any of various enzymes catalyzing the template-directed incorporation of deoxyribonucleotides into a DNA chain, particularly one using a DNA template.  (Promega Corp., Madison, WI) in conjunction with oligonucleotides 1010C and NW1696R (2-3), which flank a 616-nt region of the N protein gene of WWA virus prototype strain AV 9310135 (12). Reverse transcription and PCR (RT-PCR RT-PCR

reverse transcriptase-polymerase chain reaction. See PCR1.
) amplification of a fragment of the N protein gene of each of the eight other isolates was carried out by using the Access RT-PCR Kit (Promega Corp.) in conjunction with oligonucleotides AVNP1 (5'-CCCTTCTTYTTNYTCTTRATGACTA-3') and AVNP2 (5'-GGKAGRGCNTGGGAYAACAC-3'). AVNP1 and AVNP2 flank a 518mt region in the fragment of the WWA virus N protein gene that is amplified by using oligonucleotides 1010C and NW1696R. They were designed based on N protein gene sequence data for the WWA virus prototype strain AV 9310135 (GenBank Accession No. U52180), WWA virus strains AV 96010149, AV 96010151, AV 96010025, and AV 96010024, TAM virus strain W-10777 (U43690), and PIC virus strain An 3739 (K02734). Size separation of PCR products was done by agarose gel electrophoresis Agarose gel electrophoresis is a method used in biochemistry and molecular biology to separate DNA, RNA, or protein molecules by size. This is achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field (electrophoresis). ; the products of the expected size were purified from gel slices by using QIAquick Gel Extraction Kit (Qiagen, Inc., Valencia, CA). One strand of each 1010C-NW1696R PCR product was sequenced directly by using the dye termination cycle sequencing technique (Applied Biosystems, Inc., Foster City, CA) in conjunction with oligonucleotide 1010C. The sequence of the other (i.e., complementary) strand of each of these products was determined by cloning the PCR product in the TA cloning vector cloning vector
n.
An autonomously replicating plasmid having regions into which foreign DNA can be inserted.
 PCRII (Invitrogen Corp., Carlsbad, CA) and then using a plasmid-specific oligonucleotide (M13) to initiate the cycle sequencing reaction. Both strands of the AVNP1-AVNP2 PCR products were sequenced directly by using the same oligonucleotides that were used to prime the RT-PCR, i.e., AVNP1 and AVNP2. The 12 nucleotide sequences generated in this study were deposited with the GenBank nucleotide sequence database under Accession Nos. AY012710-AY012721.
Table 1. Recovery of infectious arenavirus from tissues
of virus-positive woodrats (Neotoma species)

                                    Collected from
                         Date
Rodent     Species     collected    County    State

1627     N. albigula   07/15/93    McKinley    NM
1626     N. albigula   07/15/93    McKinley    NM
62415    N. mexicana   09/24/94    Socorro     NM
62425    N. mexicana   09/24/94    Socorro     NM
62439    N. mexicana   09/24/94    Socorro     NM
28731    N. albigula   10/12/85    Cimarron    OK
28742    N. albigula   10/12/85    Cimarron    OK
84648    N. micropus   07/18/99    Dimmit      TX
84703    N. micropus   07/19/99    Dimmit      TX
84708    N. micropus   07/19/99    Dimmit      TX
84761    N. micropus   07/18/99    Dimmit      TX
84816    N. micropus   07/20/99    La Salle    TX
36287    N. cinerea    07/06/94    San Juan    UT
36282    N. mexicana   07/05/94    San Juan    UT

                        Virus (strain) recovered from(a)

Rodent     Species       Spleen        Kidney         Liver

1627     N. albigula   AV 9310041    AV 9310135        nt
1626     N. albigula       nt        AV 9310040        nt
62415    N. mexicana       nt        AV 96010149       nt
62425    N. mexicana       nt        AV 96010151   AV 98360019
62439    N. mexicana       nt        AV 96010154   AV 98360020
28731    N. albigula       nt        AV 98490013    Negative
28742    N. albigula       nt        AV 97130039    TVP-6038
84648    N. micropus     Negative    AV A0400098       nt
84703    N. micropus   AV A0400337   AV A0400135       nt
84708    N. micropus       nt        AV A0400140       nt
84761    N. micropus   AV A0400373   AV A0400174       nt
84816    N. micropus   AV A0400412   AV A0400212       nt
36287    N. cinerea        nt        AV 96010025   AV 96010206
36282    N. mexicana       nt        AV 96010024   AV 96010205

(a) nt = not tested. The WWA virus prototype strain is bolded.
Isolates (strains) included in the (phylo-) genetic analyses
are underlined.


Data Analysis

The analyses of nucleotide sequence data were restricted to the 518-nt fragment of the WWA virus N protein gene that is flanked by oligonucleotides AVNP1 and AVNP2. The GenBank database sequences included in the analyses were Accession Nos. U52180 (WWA virus, strain AV 9310135), U43690 (TAM, W-10777), K02734 (PIC, An 3739), U43689 (Parana, 12056), U43687 (Flexal, BeAn 293022), U62561 (Pirital, VAV-488), U43688 (Latino, 10924), U34248 (Oliveros, 3229-1), U70802 (Junin, XJ), X62616 (Machupo, AA288-77), U43686 (Guanarito, INH-95551), U41071 (Sabia, SPH sph
abbr.
spherical lens
 114202), U43685 (Amapari, BeAn 70563), M20304 (Tacaribe, TRVL 11573), M20869 (LCM, Armstrong), and U80004 (Lassa, LP). The computer software package CLUSTAL W1.7 (15) was used to construct an alignment of the predicted amino acid amino acid (əmē`nō), any one of a class of simple organic compounds containing carbon, hydrogen, oxygen, nitrogen, and in certain cases sulfur. These compounds are the building blocks of proteins.  sequences, and the computer program TransAlign (16) was used to generate a multiple nucleotide sequence alignment from the amino acid sequence alignment. Pairwise genetic distances were computed by using the p distance model as implemented in the computer program MEGA, version 1.02 (17). Percent sequence identities were calculated by subtracting the genetic distances from 1.0 and multiplying by 100. 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 was carried out on the multiple amino acid sequence alignment by using the neighbor-joining method (gamma model, alpha = 2) as implemented in MEGA, version 1.02. 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 (18) for the results of the phylogenetic analysis was based on 500 pseudoreplicate datasets generated from the original multiple amino acid sequence alignment.

Results

Viral Isolates

Twenty-three arenaviral isolates were recovered from tissues of 14 (3.3%) of 425 Neotoma rodents (Table 1). The 23 isolates included three WWA virus strains (AV 9310135, AV 9310041, and AV 9310040) that were reported previously (12).

The virus-positive animals included two N. albigula from McKinley County, northwestern New Mexico; two N. albigula from Cimarron County, western Oklahoma; three N. mexicana from Socorro County, central New Mexico The center of the U.S. state New Mexico. In the center of this region is Albuquerque, the largest city and only metropolitan area. External links
  • New Mexico Tourism Department Website for Central New Mexico
; five N. micropus from the Chaparral Wildlife Management Area (Dimmit and La Salle counties), southern Texas; and one N. mexicana and one N. cinerea from San Juan County San Juan County is the name of four counties in the United States:
  • San Juan County, Colorado
  • San Juan County, New Mexico
  • San Juan County, Utah
  • San Juan County, Washington
, southeastern Utah (Table 2, Figure 1). The virus-positive animals from McKinley County were two (50%) of four woodrats (all N. albigula) collected on July 15, 1993, from Whitewater Arroyo. The positive N. albigula from Cimarron County were two (22.2%) of nine woodrats (seven N. albigula and two N. mexicana) collected on October 12, 1985, from a site near Kenton. The positive N. mexicana from Socorro County were three (42.9%) of seven woodrats (all N. mexicana) collected on September 24, 1994, from a site in the Magdalena Mountains. The positive N. micropus from Dimmit County were 4 (13.8%) of 29 woodrats (all N. micropus) collected in a 3-day period (July 17 through July 19, 1999) from the western region of the Chaparral Wildlife Management Area. The positive N. micropus from La Salle County was one (25.0%) of four woodrats (all N. micropus) collected on July 20, 1999, from the eastern region of the Chaparral Wildlife Management Area. The positive N. mexicana and N. cinerea from San Juan County were 2 (12.5%) of 16 woodrats (11 N. mexicana, 2 N. cinerea, and 3 N. albigula) collected in an 8-day period (June 29 through July 6, 1994) from Natural Bridges National Monument Natural Bridges National Monument, 7,636 acres (3,093 hectares), SE Utah; est. 1908. Located in an area of colored cliffs and box canyons, the monument contains three huge natural sandstone bridges: Owachomo (also called Rock Mound), 106 ft (32 m) high with a span of . Information from the Museum of Southwestern Biology indicated that the positive N. mexicana and N. cinerea were collected from different sites in Natural Bridges National Monument.

[Illustration omitted]
Table 2. Results of virus isolation
attempts on tissues from 425 woodrats

                        Neotoma species(a)

County(b)          State   Nalb    Ncin   Nflo

Apache (1)          AZ     --      --     --
Cochise (2)         AZ     0/31    --     --
Coconino (2)        AZ     0/6     --     --
Maricopa (1)        AZ     0/23    --     --
Navajo (1)          AZ     0/29    0/1    --
Yavapai (2)         AZ     0/5     --     --
McKinley (3)        NM     2/16    --     --
Otero (9)           NM     0/33    --     --
Socorro (3)         NM     0/31    --     --
Cimarron (4)        OK     2/11    --     --
Major (4)           OK     --      --     0/45
McIntosh (2)        OK     --      --     0/12
Pottawatomie (2)    OK     --      --     0/7
Dimmit (1)          TX     --      --     --
La Salle (1)        TX     --      --     --
San Juan (8)        UT     0/3     1/2    --
Total                      4/188   1/3    0/64

                       Neotoma species(a)

County(b)          Nme    Nmic    Nste   Total

Apache (1)         0/6    --      0/5     0/11
Cochise (2)        --     --      --      0/31
Coconino (2)       --     --      0/3     0/9
Maricopa (1)       --     --      --      0/23
Navajo (1)         0/5    --      0/7     0/42
Yavapai (2)        0/2    --      --      0/7
McKinley (3)       --     --      --      2/16
Otero (9)          0/9    0/35    --      0/77
Socorro (3)        3/10   0/1     --      3/42
Cimarron (4)       0/5    --      --      2/16
Major (4)          --     0/38    --      0/83
McIntosh (2)       --     --      --      0/12
Pottawatomie (2)   --     --      --      0/7
Dimmit (1)         --     4/29    --      4/29
La Salle (1)       --     1/4     --      1/4
San Juan (8)       1/11   --      --      2/16
Total              4/48   5/107   0/15   14/425

(a) Nalb = Neotoma albigula, Ncin = N. cinerea, Nflo = N.
floridana, Nmex = N. mexicana, Nmic = N. micropus,
Nste = N. stephensi. Values are the number positive/number
tested; "-" = none tested.

(b) Number in parentheses indicates the number
of sites sampled in the county.


The nucleotide sequences of the isolates from rodent 62425 (one isolate each from kidney and liver; strains AV 96010151 and AV 98360019, respectively) were identical. In contrast, the nucleotide sequences of the isolates from rodent 62439 (again, one isolate each from kidney and liver; strains AV 96010154 and AV 98360020, respectively) were 99.6% identical. Further study is needed to determine whether the differences between the isolates from rodent 62439 represent the coexistence of multiple virus genotypes (alleles) in the same rodent. An alternative explanation is that the sequence differences are the result of adaptation of the isolates to growth in cultured (Vero E6) cells or manipulation of viral nucleic acid nucleic acid, any of a group of organic substances found in the chromosomes of living cells and viruses that play a central role in the storage and replication of hereditary information and in the expression of this information through protein synthesis.  extracted from cultured cells.

Nucleotide and amino acid sequence identities among WWA virus prototype strain AV 9310135 and 12 other isolates from Neotoma rodents ranged from 74.7% to 100.0% and 84.9% to 100.0%, respectively (Table 3). When compared with other arenaviruses, the isolates from the Neotoma rodents exhibited 69.9% to 73.7% nucleotide sequence identity with TAM virus, 61.0% to 63.3% identity with PIC virus, and less than 62.0% sequence identity with all other arenaviruses.
Table 3. Nucleotide and amino acid sequence identities
among 13 arenavirus isolates recovered from
11 woodrats and Tamiami virus(a)

                                Virus or strain

                         AV 93   AV 93   AV 96   AV 96
Virus(b)     Strain      10135   10040   10149   10151

WWA        AV 9310135       --   100.0    86.5    86.5
WWA        AV 9310040    100.0      --    86.5    86.5
WWA        AV 96010149    95.3    95.3      --   100.0
WWA        AV 96010151    95.3    95.3   100.0      --
WWA        AV 98360019    95.3    95.3   100.0   100.0
WWA        AV 96010154    94.8    94.8    98.8    98.8
WWA        AV 98360020    95.3    95.3    99.4    99.4
WWA        AV 98490013    91.9    91.9    90.7    90.7
WWA        TVP-6038       91.9    91.9    90.7    90.7
WWA        AV A0400212    88.4    88.4    88.9    88.9
WWA        AV A0400174    88.9    88.9    89.5    89.5
WWA        AV 96010025    90.7    90.7    91.3    91.3
WWA        AV 96010024    93.0    93.0    94.2    94.2
TAM        W-10777        77.9    77.9    78.5    78.5

                        Virus or strain

           AV 98    AV 96   AV 98    AV 98    TVP-
Virus(b)   360019   10154   360020   490013   6038

WWA          86.5    85.3    85.3     82.3    82.6
WWA          86.5    85.3    85.3     82.3    82.6
WWA         100.0    98.1    98.5     80.1    80.3
WWA         100.0    98.1    98.5     80.1    80.3
WWA            --    98.1    98.5     80.1    80.3
WWA          98.8      --    99.6     81.3    81.5
WWA          99.4    99.4      --     81.3    81.5
WWA          90.7    90.7    91.3       --    99.4
WWA          90.7    90.7    91.3     98.8      --
WWA          88.9    88.9    89.5     86.6    86.6
WWA          89.5    89.5    88.9     85.5    85.5
WWA          91.3    91.3    91.3     87.8    87.8
WWA          94.2    94.2    94.2     88.4    88.4
TAM          78.5    78.5    78.5     78.5    78.5

                        Virus or strain

           AV A0    AV A0    AV 96   AV 96   TAM
Virus(b)   400212   400174   10025   10024

WWA         79.1     79.1     83.4    85.1   71.6
WWA         79.1     79.1     83.4    85.1   71.6
WWA         79.5     78.8     84.4    85.5   73.7
WWA         79.5     78.8     84.4    85.5   73.7
WWA         79.5     78.8     84.4    85.5   73.7
WWA         79.3     78.6     84.4    85.1   73.2
WWA         79.5     78.8     84.4    85.1   73.4
WWA         79.0     77.8     80.9    80.7   72.2
WWA         79.1     78.0     81.1    80.1   72.4
WWA           --     95.7     77.2    77.0   69.9
WWA         98.3       --     74.7    75.5   69.9
WWA         84.9     84.9       --    82.8   71.6
WWA         86.0     86.0     89.5      --   72.2
TAM         80.2     80.2     77.3    78.5     --

(a) Nucleotide and amino acid sequence identities
are listed above and below the dashes, respectively.

(b) WWA = Whitewater Arroyo, TAM = Tamiami.


Phylogenetic analysis of N protein amino acid sequence data indicated that isolates from Neotoma rodents represent a phylogenetic lineage (viral species) that is in a sister relationship to the lineage represented by TAM virus (Figure 2). We concluded that all isolates recovered from the Neotoma rodents were strains of WWA virus.

[Illustration omitted]

Discussion

Before the present study, WWA virus was known only from N. albigula in northwestern New Mexico (12). The present work provides unequivocal evidence that the virus also is naturally associated with N. cinerea, N. mexicana, and N. micropus, and that it occurs in Utah, central New Mexico, Oklahoma, and Texas. The recovery of WWA virus strains AV 98490013 and TVP-6083 from N. albigula is the first evidence that a Tacaribe complex virus occurs in Oklahoma. Likewise, the recovery of strains AV A0400174 and AV A0400212 from woodrats collected from southern Texas (Chaparral Wildlife Management Area) is the first evidence that N. micropus is naturally associated with a Tacaribe complex virus and that WWA virus occurs in Texas.

In a previous study (13), antibody to an arenavirus was found in N. fuscipes and N. lepida in southern California; N. albigula, N. mexicana, and N. stephensi in Arizona; and N. albigula in southwestern Colorado. Although the results of the present study indicate that WWA virus is geographically widely distributed in association with Neotoma rodents, further work is needed to determine whether the arenavirus associated with Neotoma rodents in California, Arizona, and Colorado is in fact WWA virus.

The results of the present study indicate that there can be substantial genetic heterogeneity among strains of WWA virus from different woodrat species from the same locality and among strains from conspecific woodrats collected from different localities. For example, nucleotide sequence identity between the strains recovered from N. mexicana and N. cinerea from Natural Bridges National Monument (San Juan County, Utah San Juan County is a county located in the U.S. state of Utah. In area it is the largest county in the state. In 2000 its population was 14,413; by 2005 the population has been estimated to have decreased to 14,104. ; strains AV 96010024 and AV 96010025, respectively) was 82.8%, and nucleotide sequence identity between strain AV 96010024 and the three strains recovered from N. mexicana collected from the Magdalena Mountains (Socorro County, New Mexico Socorro County is a county located in the U.S. state of New Mexico, United States. As of 2000, the population is 18,078. The county seat is Socorro. Socorro was originally the name given to a Native American village (see: Pueblo Indians) by Don Juan de Oñate in 1598. ; strains AV 96010149, AV 96010151, and AV 96010154) was from 85.1% to 85.5%. In contrast, nucleotide sequence identity in strains recovered from conspecific rodents collected from the same locality (e.g., strains AV 9310135 and AV 9310040 from N. albigula from Whitewater Arroyo, and strains AV A0400174 and AV A0400212 from N. micropus from the Chaparral Wildlife Management Area) was [is greater than] 95.0%.

The results of previous studies (3,19,20) suggested that the present-day diversity of the arenaviruses is a product of long-term coevolution co·ev·o·lu·tion  
n.
The evolution of two or more interdependent species, each adapting to changes in the other. It occurs, for example, between predators and prey and between insects and the flowers that they pollinate.
 of the various viruses with their respective principal rodent hosts. In the present study, WWA viral strains AV 9310135 and AV 9310040 (both from N. albigula, northwestern New Mexico) appeared to be phylogenetically phy·lo·ge·net·ic  
adj.
1. Of or relating to phylogeny or phylogenetics.

2. Relating to or based on evolutionary development or history: a phylogenetic classification of species.
 more closely related to strain AV 96010024 (N. mexicana, southeastern Utah) than to strains AV 98490013 and TVP-6038 (both from N. albigula, western Oklahoma). This situation suggests that the present-day association of WWA virus with N. albigula and N. mexicana does not represent a long-term shared evolutionary relationship between virus and rodent species. However, this conclusion assumes that recovery of WWA virus from a rodent represents a principal virus-host relationship. Perhaps some of the virus-positive rodents in the present study were infected by contact with other Neotoma species or even non-Neotoma rodent species.

The geographic range of the genus Neotoma extends from western Canada south to Guatemala, Honduras, and Nicaragua, and includes 33 states in the contiguous United States and 26 of the 32 states in Mexico (21). Thus, if the present-day association of WWA virus with the genus Neotoma represents a long-term shared evolutionary relationship between virus and rodent host, the geographic range of the virus may extend far beyond the southwestern United States. WWA virus recently was associated with several human deaths in California (22). Further study is needed to assess the human health significance of this virus in the southwestern United States and other regions in North America in which woodrats are indigenous.

Acknowledgments

Robert Baker and Terry Yates provided the tissue specimens that were tested for infectious arenavirus; Wen Li Kang amplified and cloned the PCR products generated from isolates AV 96010149, AV 96010151, AV 96010025, and AV 96010024.

This research was supported by the National Institutes of Health grant AI-41435 ("Ecology of emerging arenaviruses in the southwestern United States").

Dr. Fulhorst is assistant professor and member of the World Health Organization Collaborating Center for Tropical Diseases, University of Texas Medical Branch, Galveston. His research interests include the epidemiology of the arenaviruses, hantaviruses, and other viral zoonoses Zoonoses

Infections of humans caused by the transmission of disease agents that naturally live in animals. People become infected when they unwittingly intrude into the life cycle of the disease agent and become unnatural hosts.
.

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(11.) Jennings WL, Lewis AL, Sather GE, Pierce LV, Bond JO. Tamiami virus in the Tampa Bay area. Am J Trop Med Hyg 1970;19:527-36.

(12.) Fulhorst CF, Bowen MD, Ksiazek TG, Rollin PE, Nichol ST, Kosoy MY, et al. Isolation and characterization of Whitewater Arroyo virus, a novel North American North American

named after North America.


North American blastomycosis
see North American blastomycosis.

North American cattle tick
see boophilusannulatus.
 arenavirus. Virology 1996;224:114-20.

(13.) Kosoy MY, Elliot LH, Ksiazek TG, Fulhorst CF, Rollin PE, Childs JE, et al. Prevalence of antibodies to arenaviruses in rodents from the southern and western United States Noun 1. western United States - the region of the United States lying to the west of the Mississippi River
West

Santa Fe Trail - a trail that extends from Missouri to New Mexico; an important route for settlers moving west in the 19th century
: evidence for an arenavirus associated with the genus Neotoma. Am J Trop Med Hyg 1996;54:570-5.

(14.) Gonzalez JP, Sanchez A, Ricco-Hesse R. Molecular phylogeny of Guanarito virus, an emerging arenavirus affecting humans. Am J Trop Med Hyg 1995;53:1-6.

(15.) Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In general, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a  through sequence weighting, position-specific gap penalties and weight matrix choices. Nucleic Acids Nucleic acids
The cellular molecules DNA and RNA that act as coded instructions for the production of proteins and are copied for transmission of inherited traits.
 Res 1994;22:4673-80.

(16.) Weiller GF. TransAlign, version 1.0. Canberra, Australia: Research School of Biological Sciences; 1999.

(17.) Kumar S, Tamura K, Nei M. MEGA: Molecular Evolutionary Genetics Analysis package, version 1.02. University Park (PA): Pennsylvania State University Pennsylvania State University, main campus at University Park, State College; land-grant and state supported; coeducational; chartered 1855, opened 1859 as Farmers' High School. ; 1993.

(18.) Felsentein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783-91.

(19.) Gonzalez JP, Georges AJ, Kiley MP, Meunier DM, Peters CJ, McCormick JB. Evolutionary biology of a Lassa virus complex. Med Microbiol Immunol 1986;175:157-9.

(20.) Johnson KM, Webb PA, Justines G. Biology of Tacaribe-complex viruses. In: Lehman-Grebe F, editor. Lymphocytic choriomeningitis virus and other arenaviruses. Berlin: Springer-Verlag; 1973. p. 241-58.

(21.) Musser GG, Carleton MD. Family Muridae. In: Wilson DE, Reeder DM, editors. Mammal species of the world Mammal Species of the World, now in its 3rd edition, is a standard reference work in zoology giving descriptions and bibliographic data for the known species of mammals,

An updated Third Edition of Mammal Species of the World was published late in 2005: Wilson, D. E.
. A taxonomic and geographic reference. Washington: Smithsonian Institution Press; 1993. p. 501-755.

(22.) Centers for Disease Control and Prevention. Fatal illnesses associated with a New World arenavirus-California, 1999-2000. MMWR MMWR Morbidity & Mortality Weekly Report Epidemiology A news bulletin published by the CDC, which provides epidemiologic data–eg, statistics on the incidence of AIDS, rabies, rubella, STDs and other communicable diseases, causes of mortality–eg,  Morb Mortal Wkly Rep 2000;49:709-11.

Charles F. Fulhorst,(*) Remi N. Charrel,(*)([dagger]) Scott C. Weaver,(*) Thomas G. Ksiazek,([double dagger]) Robert D. Bradley,([sections]) Mary L. Milazzo,(*) Robert B. Tesh,(*) and Michael D. Bowen([double dagger])

(*) University of Texas Medical Branch, Galveston, Texas, USA; ([dagger]) Faculte de Medecine, Marseille, France; Centers for Disease Control and Prevention, Atlanta, Georgia, USA; and ([sections]) Texas Tech University, Lubbock, Texas, USA

Address for correspondence: Charles F. Fulhorst, Department of Pathology, Route 0609, University of Texas Medical Branch, Galveston, Texas 77555-0609, USA; fax: 409-747-2415; e-mail: cfulhors@utmb.edu
COPYRIGHT 2001 U.S. National Center for Infectious Diseases
No portion of this article can be reproduced without the express written permission from the copyright holder.
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Author:Bowen, Michael D.
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Date:May 1, 2001
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