Distribution and prevalence of Sin Nombre hantavirus in rodent species in eastern New Mexico

Orthohantaviruses are diverse zoonotic RNA viruses. Small mammals, such as mice and rats are common chronic, asymptomatic hosts that transmit the virus through their feces and urine. In North America, hantavirus infection primarily causes hantavirus cardiopulmonary syndrome (HCPS), which has a mortality rate of nearly 36%. In the United States of America, New Mexico (NM) is leading the nation in the number of HCPS-reported cases (N = 129). However, no reported cases of HCPS have occurred within eastern NM. In this study, we assessed the prevalence of Sin Nombre virus (SNV) in rodent assemblages across eastern NM, using RT-qPCR. We screened for potential rodent hosts in the region, as well as identified areas that may pose significant infection risk to humans. We captured and collected blood and lung tissues from 738 rodents belonging to 23 species. 167 individuals from 16 different species were positive for SNV RNA by RT-qPCR, including 6 species unreported in the literature: Onychomys leucogaster (Northern grasshopper mouse), Dipodomys merriami (Merriam's kangaroo rat), Dipodomys ordii (Ord's kangaroo rat), Dipodomys spectabilis (Banner-tailed kangaroo rat), Perognathus flavus (Silky pocket mouse), and Chaetodipus hispidus (Hispid pocket mouse). The infection rates did not differ between sexes or rodent families (i.e., Cricetidae vs. Heteromyidae). Generalized linear model showed that disturbed habitat types positively influenced the prevalence of SNV at sites of survey. Overall, the results of this study indicate that many rodent species in east New Mexico have the potential to maintain SNV in the environment, but further research is needed to assess species specific infectivity mechanisms and potential risk to humans.

Structural and functional characterization of the Sin Nombre virus L protein

The Bunyavirales order is a large and diverse group of segmented negative-strand RNA viruses. Several virus families within this order contain important human pathogens, including Sin Nombre virus (SNV) of the Hantaviridae. Despite the high epidemic potential of bunyaviruses, specific medical countermeasures such as vaccines or antivirals are missing. The multifunctional ~250 kDa L protein of hantaviruses, amongst other functional domains, harbors the RNA-dependent RNA polymerase (RdRp) and an endonuclease and catalyzes transcription as well as replication of the viral RNA genome, making it a promising therapeutic target. The development of inhibitors targeting these key processes requires a profound understanding of the catalytic mechanisms. Here, we established expression and purification protocols of the full-length SNV L protein bearing the endonuclease mutation K124A. We applied different biochemical in vitro assays to provide an extensive characterization of the different enzymatic functions as well as the capacity of the hantavirus L protein to interact with the viral RNA. By using single-particle cryo-EM, we obtained a 3D model including the L protein core region containing the RdRp, in complex with the 5' promoter RNA. This first high-resolution model of a New World hantavirus L protein shows striking similarity to related bunyavirus L proteins. The interaction of the L protein with the 5' RNA observed in the structural model confirms our hypothesis of protein-RNA binding based on our biochemical data. Taken together, this study provides an excellent basis for future structural and functional studies on the hantavirus L protein and for the development of antiviral compounds.

Experimental Infection of Peromyscus Species Rodents with Sin Nombre Virus

We demonstrate that 6 distinct Peromyscus rodent species are permissive to experimental infection with Sin Nombre orthohantavirus (SNV). Viral RNA and SNV antibodies were detected in members of all 6 species. P. leucopus mice demonstrated markedly higher viral and antibody titers than P. maniculatus mice, the established primary hosts for SNV.

Tracing Transmission of Sin Nombre Virus and Discovery of Infection in Multiple Rodent Species

Sin Nombre orthohantavirus (SNV), a negative-sense, single-stranded RNA virus that is carried and transmitted by the North American deer mouse Peromyscus maniculatus, can cause infection in humans through inhalation of aerosolized excreta from infected rodents. This infection can lead to hantavirus cardiopulmonary syndrome (HCPS), which has an ∼36% case-fatality rate. We used reverse transcriptase quantitative PCR (RT-qPCR) to confirm SNV infection in a patient and identified SNV in lung tissues in wild-caught rodents from potential sites of exposure. Using viral whole-genome sequencing (WGS), we identified the likely site of transmission and discovered SNV in multiple rodent species not previously known to carry the virus. Here, we report, for the first time, the use of SNV WGS to pinpoint a likely site of human infection and identify SNV simultaneously in multiple rodent species in an area of known host-to-human transmission. These results will impact epidemiology and infection control for hantaviruses by tracing zoonotic transmission and investigating possible novel host reservoirs. IMPORTANCE Orthohantaviruses cause severe disease in humans and can be lethal in up to 40% of cases. Sin Nombre orthohantavirus (SNV) is the main cause of hantavirus disease in North America. In this study, we sequenced SNV from an infected patient and wild-caught rodents to trace the location of infection. We also discovered SNV in rodent species not previously known to carry SNV. These studies demonstrate for the first time the use of virus sequencing to trace the transmission of SNV and describe infection in novel rodent species.

New Exposure Location for Hantavirus Pulmonary Syndrome Case, California, USA, 2018

We describe a case of hantavirus pulmonary syndrome in a patient exposed to Sin Nombre virus in a coastal county in California, USA, that had no previous record of human cases. Environmental evaluation coupled with genotypic analysis of virus isolates from the case-patient and locally trapped rodents identified the likely exposure location.

Novel Focus of Sin Nombre Virus in Peromyscus eremicus Mice, Death Valley National Park, California, USA

The deer mouse (Peromyscusmaniculatus) is the primary reservoir for Sin Nombre virus (SNV) in the western United States. Rodent surveillance for hantavirus in Death Valley National Park, California, USA, revealed cactus mice (P. eremicus) as a possible focal reservoir for SNV in this location. We identified SNV antibodies in 40% of cactus mice sampled.

Transcriptome markers of viral persistence in naturally-infected andes virus (bunyaviridae) seropositive long-tailed pygmy rice rats

Long-tailed pygmy rice rats (Oligoryzomys longicaudatus) are principal reservoir hosts of Andes virus (ANDV) (Bunyaviridae), which causes most hantavirus cardiopulmonary syndrome cases in the Americas. To develop tools for the study of the ANDV-host interactions, we used RNA-Seq to generate a de novo transcriptome assembly. Splenic RNA from five rice rats captured in Chile, three of which were ANDV-infected, was used to generate an assembly of 66,173 annotated transcripts, including noncoding RNAs. Phylogenetic analysis of selected predicted proteins showed similarities to those of the North American deer mouse (Peromyscus maniculatus), the principal reservoir of Sin Nombre virus (SNV). One of the infected rice rats had about 50-fold more viral burden than the others, suggesting acute infection, whereas the remaining two had levels consistent with persistence. Differential expression analysis revealed distinct signatures among the infected rodents. The differences could be due to 1) variations in viral load, 2) dimorphic or reproductive differences in splenic homing of immune cells, or 3) factors of unknown etiology. In the two persistently infected rice rats, suppression of the JAK-STAT pathway at Stat5b and Ccnot1, elevation of Casp1, RIG-I pathway factors Ppp1cc and Mff, and increased FC receptor-like transcripts occurred. Caspase-1 and Stat5b activation pathways have been shown to stimulate T helper follicular cell (T_FH) development in other species. These data are also consistent with reports suggestive of T_FH stimulation in deer mice experimentally infected with hantaviruses. In the remaining acutely infected rice rat, the apoptotic pathway marker Cox6a1 was elevated, and putative anti-viral factors Abcb1a, Fam46c, Spp1, Rxra, Rxrb, Trmp2 and Trim58 were modulated. Transcripts for preproenkephalin (Prenk) were reduced, which may be predictive of an increased T cell activation threshold. Taken together, this transcriptome dataset will permit rigorous examination of rice rat-ANDV interactions and may lead to better understanding of virus ecology.

Twenty-year summary of surveillance for human hantavirus infections, United States

In the past 20 years of surveillance for hantavirus in humans in the United States, 624 cases of hantavirus pulmonary syndrome (HPS) have been reported, 96% of which occurred in states west of the Mississippi River. Most hantavirus infections are caused by Sin Nombre virus, but cases of HPS caused by Bayou, Black Creek Canal, Monongahela, and New York viruses have been reported, and cases of domestically acquired hemorrhagic fever and renal syndrome caused by Seoul virus have also occurred. Rarely, hantavirus infections result in mild illness that does not progress to HPS. Continued testing and surveillance of clinical cases in humans will improve our understanding of the etiologic agents involved and the spectrum of diseases.

Increased detection of Sin Nombre hantavirus RNA in antibody-positive deer mice from Montana, USA: evidence of male bias in RNA viremia

Hantaviruses are widespread emergent zoonotic agents that cause unapparent or limited disease in their rodent hosts, yet cause acute, often fatal pulmonary or renal infections in humans. Previous laboratory experiments with rodent reservoir hosts indicate that hantaviruses can be cleared from host blood early in the infection cycle, while sequestered long term in various host organs. Field studies of North American deer mice (Peromyscus maniculatus), the natural reservoir of Sin Nombre hantavirus, have shown that viral RNA can be transiently detected well past the early acute infection stage, but only in the minority of infected mice. Here, using a non-degenerate RT-PCR assay optimized for SNV strains known to circulate in Montana, USA, we show that viral RNA can be repeatedly detected on a monthly basis in up to 75% of antibody positive deer mice for periods up to 3–6 months. More importantly, our data show that antibody positive male deer mice are more than twice as likely to have detectable SNV RNA in their blood as antibody positive females, suggesting that SNV-infected male deer mice are more likely to shed virus and for longer periods of time.

Selection and characterization of scFv antibodies against the Sin Nombre hantavirus nucleocapsid protein

Rodent-borne hantaviruses cause hemorrhagic fever with renal syndrome (HFRS) in the old world and hantavirus cardio-pulmonary syndrome (HCPS) in the new. Most cases of HCPS in North America are caused by Sin Nombre Virus (SNV). Current viral detection technologies depend upon the identification of anti-viral antibodies in patient serum. Detection of viral antigen may facilitate earlier detection of the pathogen. We describe here the characterization of two single-chain Fv antibodies (scFvs), selected from a large naïve phage antibody library, which are capable of identifying the Sin Nombre Virus nucleocapsid protein (SNV-N), with no cross reactivity with the nucleocapsid protein from other hantaviruses. The utility of such selected scFvs was increased by the creation of an scFv-alkaline phosphatase fusion protein which was able to directly detect virally produced material without the need for additional reagents.

Recombinant adenovirus vector vaccine induces stronger cytotoxic T-cell responses than recombinant vaccinia virus vector, plasmid DNA, or a combination of these

The efficiency of prime-boost vaccinations on the induction of T-cell responses to Sin Nombre virus nucleocapsid protein expressed by recombinant vaccinia virus, replication-deficient adenovirus, and plasmid DNA in mice was quantitated by the number of epitope-specific interferon-gamma-producing T cells and cytotoxic T-lymphocyte activity induced. In prime-boost immunizations, all combinations that included the recombinant adenovirus induced a much higher number of epitope-specific interferon-gamma-producing T cells than did other combinations. A single immunization of the recombinant adenovirus was able to induce similarly high levels of epitope-specific interferon-gamma-producing cells, despite the fact that the recombinant adenovirus produces less amount of the Sin Nombre virus nucleocapsid protein.

A preliminary study of the patterns of Sin Nombre viral infection and shedding in naturally infected deer mice (Peromyscus maniculatus)

Deer mice (Peromyscus maniculatus) were trapped in southern Manitoba, Canada and tested for evidence of Sin Nombre virus infection. Viral genome was amplified from tissues as well as saliva/oropharyngeal fluid, and urine samples were collected from seropositive animals. Detection of viral RNA in tissue samples and excreta/secreta from mice suggest that differences may exist between naturally infected rodents with respect to viral shedding.

Development of reassortant viruses between pathogenic hantavirus strains

Segment reassortment of negative strand viruses is an important mechanism for the development of new virus strains with altered pathogenicity. This study reports on in vitro generation of reassortants between Andes (ANDV) and Sin Nombre (SNV) viruses. Although they both cause hantavirus pulmonary syndrome (HPS), ANDV is the only hantavirus that has been transmitted from person to person (). Following dual infection of cells with ANDV and SNV, 8.9% of 337 progeny plaques contained reassortants, of which 66% were diploid, and 34% were monoploid. The monoploid reassortants contained the S and L segments of SNV and ANDV M segment. Analysis of replication of the monoploid reassortant indicated its efficiency was similar to ANDV rather than SNV. Results described in this study illustrate the ability to rapidly generate new hantavirus genotypes between genetically unrelated viruses by gene reassortment and provide a tool to dissect the pathogenesis of these important viruses.

Andes virus M genome segment is not sufficient to confer the virulence associated with Andes virus in Syrian hamsters

Sin Nombre virus (SNV) and Andes virus (ANDV), members of the genus Hantavirus, in the family Bunyaviridae, are causative agents of hantavirus pulmonary syndrome (HPS) in North and South America, respectively. Although ANDV causes a lethal HPS-like disease in hamsters, SNV, and all other HPS-associated hantaviruses that have been tested, cause asymptomatic infections of laboratory animals, including hamsters. In an effort to understand the pathogenicity of ANDV in the hamster model, we generated ANDV/SNV reassortant viruses. Plaque isolation of viruses from cell cultures infected with both parental viruses yielded only one type of stable reassortant virus: large (L) and small (S) segments of SNV and M segment of ANDV. This virus, designated SAS reassortant virus, had in vitro growth and plaque morphology characteristics similar to those of ANDV. When injected into hamsters, the SAS reassortant virus was highly infectious and elicited high-titer, ANDV-specific neutralizing antibodies; however, the virus did not cause HPS and was not lethal. These data indicate that the ANDV M genome segment is not sufficient to confer the lethal HPS phenotype associated with ANDV.

Neutralizing antibodies and Sin Nombre virus RNA after recovery from hantavirus cardiopulmonary syndrome

Patients who later have a mild course of hantavirus cardiopulmonary syndrome (HCPS) are more likely to exhibit a high titer of neutralizing antibodies against Sin Nombre virus (SNV), the etiologic agent of HCPS, at the time of hospital admission. Because administering plasma from patients who have recovered from HCPS to those in the early stages of disease may be an advantageous form of passive immunotherapy, we examined the neutralizing antibody titers of 21 patients who had recovered from SNV infection. Even 1,000 days after admission to the hospital, 6 of 10 patients had titers of 800 or higher, with one sample retaining a titer of 3,200 after more than 1,400 days. None of the convalescent-phase serum samples contained detectable viral RNA. These results confirm that patients retain high titers of neutralizing antibodies long after recovery from SNV infection.

Microarray technology for identification and distinction of hantaviruses

DNA microarrays combine high-precision technology with advanced molecular biology to achieve high-throughput screening of DNA fragments. In this study, we investigated the potential of the cDNA microarray technique to identify and discriminate PCR derived amplicons from genetically highly similar viruses. The wide range of sequence variation among hantaviruses makes them suitable as a model for this purpose. The hantaviruses, carried by rodents, cause several hundred thousand cases of severe human disease every year in many parts of the world. A hantavirus-specific microarray, including DNA fragments from 12 viral isolates of six different hantaviruses, was designed. The S and M genome segments were represented by 500-nucleotide overlapping and 250-nucleotide non-overlapping fragments. A considerable ability to distinguish between different hantaviruses was demonstrated using a novel analysis method. Even different isolates of a single virus, were identified correctly despite 90% sequence similarity. The distinction ability was accompanied by a tolerance for smaller sequence differences, which makes the microarray suitable for testing samples containing unknown viruses. Viral genetic material found in samples from the lungs of bank voles caught in the wild was identified precisely, which demonstrated further the potential for this technology.

Quantitation of antibody-bound and unbound Sin Nombre virus in the plasma of patient with hantavirus pulmonary syndrome

Hantavirus pulmonary syndrome (HPS) is a rare but acute fulminant disease caused by Sin Nombre virus and other related hantaviruses. We reported earlier that HPS patients had high levels of viremia and the levels of viremia correlated with the severity of the disease. To determine whether the viruses are free in plasma or bound to antibodies to form immune complexes, we established a method to quantitate viral genomic RNA in antibody-bound viruses and in unbound viruses separately. To isolate immune complexes from plasma we used protein L, which binds to all classes of immunoglobulins and all subclasses of IgG, and we measured viral RNA copy number in antibody-bound viruses and unbound viruses by quantitative RT-PCR. We analyzed plasma samples collected on admission from 15 patients with HPS in the acute phase. The percentage of viral RNA in immune complexes versus total viral RNA varied from 9 to 91% among patients, and correlated with the total viral RNA copy numbers (P<0.05) and the neutralizing antibody titers of plasma (P<0.05). This quantitative method may be useful to examine diseases where immune complex formation or antibody-dependent enhancement may be involved in pathogenesis.

Rapid and simple method for screening wild rodents for antibodies to Sin Nombre hantavirus

Sin Nombre hantavirus (SNV) is the primary etiologic agent of hantavirus cardiopulmonary syndrome (HCPS) in the United States and Canada. Hantavirus cardiopulmonary syndrome is a zoonotic disease. The most common reservoir is the deer mouse (Peromyscus maniculatus), although numerous other species of wild rodent can carry the viruses that cause HCPS throughout the Americas. Infected rodents show no signs of clinical disease but they develop persistent infection. Sin Nombre virus can be contracted by exposure to feces, urine, or saliva of its rodent reservoirs. Detection of infection in rodents is most often based upon detection of specific antibodies; many laboratories use enzyme linked immunosorbent assays (ELISAs), which require a specialized electrical ELISA reader. Enzyme linked immunosorbent assay readers are not readily amenable to field usage. We describe a portable test, the strip immunoblot assay (SIA), which we have utilized in field diagnosis. The test can be conducted in approximately 6 hr during the day or can be conducted overnight. The test can be used to detect rodents positive for SNV antibody while they are in traps. We show that results with the SIA have excellent concordance with western blot and reverse transcriptase polymerase chain reaction tests.

Infection dynamics of Sin Nombre virus after a widespread decline in host populations

Many researchers have speculated that infection dynamics of Sin Nombre virus are driven by density patterns of its major host, Peromyscus maniculatus. Few, if any, studies have examined this question systematically at a realistically large spatial scale, however. We collected data from 159 independent field sites within a 1 million-hectare study area in Nevada and California, from 1995-1998. In 1997, there was a widespread and substantial reduction in host density. This reduction in host density did not reduce seroprevalence of antibody to Sin Nombre virus within host populations. During this period, however, there was a significant reduction in the likelihood that antibody-positive mice had detectable virus in their blood, as determined by reverse-transcriptase polymerase chain reaction. Our findings suggest 2 possible causal mechanisms for this reduction: an apparent change in the age structure of host populations and landscape-scale patterns of host density. This study indicates that a relationship does exist between host density and infection dynamics and that this relationship concurrently operates at different spatial scales. It also highlights the limitations of antibody seroprevalence as a metric of infections, especially during transient host-density fluctuations.

Genetic vaccines protect against Sin Nombre hantavirus challenge in the deer mouse (Peromyscus maniculatus)

We used a deer mouse (Peromyscus maniculatus) infection model to test the protective efficacy of genetic vaccine candidates for Sin Nombre (SN) virus that were known to provoke immunological responses in BALB/c mice (Bharadwaj et al., Vaccine 17, 2836-2843, 1999 ). Protective epitopes were localized in each of four overlapping cDNA fragments that encoded portions of the SN virus G1 glycoprotein antigen; the nucleocapsid gene also was protective. The protective efficacy of glycoprotein gene fragments correlated with splenocyte proliferation in the presence of cognate antigen, but none induced neutralizing antibodies. Genetic vaccines against SN virus can protect outbred deer mice from infection even in the absence of a neutralizing antibody response.