Genetically distinct hantavirus in deer mice

Sin Nombre Virus and the Emergence of Other Hantaviruses: A Review of the Biology, Ecology, and Disease of a Zoonotic Pathogen

Sin Nombre virus (SNV) is an emerging virus that was first discovered in the Four Corners region of the United States in 1993. The virus causes a disease known as Hantavirus Pulmonary Syndrome (HPS), sometimes called Hantavirus Cardiopulmonary Syndrome (HCPS), a life-threatening illness named for the predominance of infection of pulmonary endothelial cells. SNV is one of several rodent-borne hantaviruses found in the western hemisphere with the capability of causing this disease. The primary reservoir of SNV is the deer mouse (Peromyscus maniculatus), and the virus is transmitted primarily through aerosolized rodent excreta and secreta. Here, we review the history of SNV emergence and its virus biology and relationship to other New World hantaviruses, disease, treatment, and prevention options.

Comparative Analysis of Molecular Pathogenic Mechanisms and Antiviral Development Targeting Old and New World Hantaviruses

Background

Hantaviruses - dichotomized into New World (i.e. Andes virus, ANDV; Sin Nombre virus, SNV) and Old-World viruses (i.e. Hantaan virus, HTNV) - are zoonotic viruses transmitted from rodents to humans. Currently, no FDA-approved vaccines against hantaviruses exist. Given the recent breakthrough to human-human transmission by the ANDV, an essential step is to establish an effective pandemic preparedness infrastructure to rapidly identify cell tropism, infective potential, and effective therapeutic agents through systematic investigation.

Methods

We established human cell model systems in lung (airway and distal lung epithelial cells), heart (pluripotent stem cell-derived (PSC-) cardiomyocytes), and brain (PSC-astrocytes) cell types and subsequently evaluated ANDV, HTNV and SNV tropisms. Transcriptomic, lipidomic and bioinformatic data analyses were performed to identify the molecular pathogenic mechanisms of viruses in different cell types. This cell-based infection system was utilized to establish a drug testing platform and pharmacogenomic comparisons.

Results

ANDV showed broad tropism for all cell types assessed. HTNV replication was predominantly observed in heart and brain cells. ANDV efficiently replicated in human and mouse 3D distal lung organoids. Transcriptomic analysis showed that ANDV infection resulted in pronounced inflammatory response and downregulation of cholesterol biosynthesis pathway in lung cells. Lipidomic profiling revealed that ANDV-infected cells showed reduced level of cholesterol esters and triglycerides. Further analysis of pathway-based molecular signatures showed that, compared to SNV and HTNV, ANDV infection caused drastic lung cell injury responses. A selective drug screening identified STING agonists, nucleoside analogues and plant-derived compounds that inhibited ANDV viral infection and rescued cellular metabolism. In line with experimental results, transcriptome data shows that the least number of total and unique differentially expressed genes were identified in urolithin B- and favipiravir-treated cells, confirming the higher efficiency of these two drugs in inhibiting ANDV, resulting in host cell ability to balance gene expression to establish proper cell functioning.

Conclusions

Overall, our study describes advanced human PSC-derived model systems and systems-level transcriptomics and lipidomic data to better understand Old and New World hantaviral tropism, as well as drug candidates that can be further assessed for potential rapid deployment in the event of a pandemic.

Reconstructing the evolutionary origins and phylogeography of hantaviruses

Rodents have long been recognized as the principal reservoirs of hantaviruses. However, with the discovery of genetically distinct and phylogenetically divergent lineages of hantaviruses in multiple species of shrews, moles, and insectivorous bats from widely separated geographic regions, a far more complex landscape of hantavirus host distribution, evolution, and phylogeography is emerging. Detailed phylogenetic analyses, based on partial and full-length genomes of previously described rodent-borne hantaviruses and newly detected non-rodent-borne hantaviruses, indicate an Asian origin and support the emerging concept that ancestral non-rodent mammals may have served as the hosts of primordial hantaviruses.

Hantaviruses: rediscovery and new beginnings

Virus and host gene phylogenies, indicating that antigenically distinct hantaviruses (family Bunyaviridae, genus Hantavirus) segregate into clades, which parallel the molecular evolution of rodents belonging to the Murinae, Arvicolinae, Neotominae and Sigmodontinae subfamilies, suggested co-divergence of hantaviruses and their rodent reservoirs. Lately, this concept has been vigorously contested in favor of preferential host switching and local host-specific adaptation. To gain insights into the host range, spatial and temporal distribution, genetic diversity and evolutionary origins of hantaviruses, we employed reverse transcription-polymerase chain reaction to analyze frozen, RNAlater(®)-preserved and ethanol-fixed tissues from 1546 shrews (9 genera and 47 species), 281 moles (8 genera and 10 species) and 520 bats (26 genera and 53 species), collected in Europe, Asia, Africa and North America during 1980-2012. Thus far, we have identified 24 novel hantaviruses in shrews, moles and bats. That these newfound hantaviruses are geographically widespread and genetically more diverse than those harbored by rodents suggests that the evolutionary history of hantaviruses is far more complex than previously conjectured. Phylogenetic analyses indicate four distinct clades, with the most divergent comprising hantaviruses harbored by the European mole and insectivorous bats, with evidence for both co-divergence and host switching. Future studies will provide new knowledge about the transmission dynamics and pathogenic potential of these newly discovered, still-orphan, non-rodent-borne hantaviruses.

Seewis virus: phylogeography of a shrew-borne hantavirus in Siberia, Russia

BACKGROUND

Hantaviral antigens were originally reported more than 20 years ago in tissues of the Eurasian common shrew (Sorex araneus), captured in European and Siberian Russia. The recent discovery of Seewis virus (SWSV) in this soricid species in Switzerland provided an opportunity to investigate its genetic diversity and geographic distribution in Russia.

METHODS

Lung tissues from 45 Eurasian common shrews, 4 Laxmann's shrews (Sorex caecutiens), 3 Siberian large-toothed shrews (Sorex daphaenodon), 9 pygmy shrews (Sorex minutus), 28 tundra shrews (Sorex tundrensis), and 6 Siberian shrews (Crocidura sibirica), captured in 11 localities in Western and Eastern Siberia during June 2007 to September 2008, were analyzed for hantavirus RNA by reverse transcription-polymerase chain reaction.

RESULTS

Hantavirus L and S segment sequences, detected in 11 S. araneus, 2 S. tundrensis, and 2 S. daphaenodon, were closely related to SWSV, differing from the prototype mp70 strain by 16.3-20.2% at the nucleotide level and 1.4-1.7% at the amino acid level. Alignment and comparison of nucleotide and amino acid sequences showed an intrastrain difference of 0-11.0% and 0% for the L segment and 0.2-8.5% and 0% for the S segment, respectively. Phylogenetic analysis, using neighbor-joining, maximum-likelihood, and Bayesian methods, showed geographic-specific clustering of SWSV strains in Western and Eastern Siberia.

CONCLUSIONS

This is the first definitive report of shrew-borne hantaviruses in Siberia, and demonstrates the impressive distribution of SWSV among phylogenetically related Sorex species. Coevolution and local adaptation of SWSV genetic variants in specific chromosomal races of S. araneus may account for their geographic distribution.

Genetic and phylogenetic analyses of hantaviral sequences amplified from archival tissues of deer mice (Peromyscus maniculatus nubiterrae) captured in the eastern United States

The S and M segments of a hantavirus, enzymatically amplified from tissues of Cloudland deer mice (Peromyscus maniculatus nubiterrae) captured during 1985 in West Virginia, diverged from strains of Four Corners virus from the southwestern United States by more than 16% and 6% at the nucleotide and amino acid levels, respectively. Phylogenetic analysis suggested that this virus strain (designated Monongahela) forms a possible evolutionary link between the Four Corners and New York hantaviruses.

Hantavirus infections in the United States: diagnosis and treatment

Definitive diagnosis of acute hantavirus infection requires demonstration of specific IgG and IgM antibodies and a compatible clinical course; most persons with acute illness will also have viral RNA in PBMC which can be detected after RT-PCR amplification. Characteristic hematologic and hemodynamic findings are helpful in establishing a presumptive diagnosis of HPS in persons with cardiopulmonary symptoms and signs while awaiting the results of serologic testing and PCR. Diagnosis during the prodromal phase is difficult although very limited data suggest that most these patients also have hantavirus IgG and IgM antibodies. Patients with suspected hantavirus infection should be treated in a critical care unit, as sudden hemodynamic deterioration can occur at any time. Hemodynamic monitoring is encouraged in patients with cardiopulmonary symptoms and signs, and inotropic support and vasopressors should be used rather than fluids. An uncontrolled study of ribavirin therapy was inconclusive and a placebo-controlled trial is therefore planned. The latter study aims to enroll persons with prodromal findings and early cardiopulmonary disease.

Hantaviruses: clinical, microbiologic, and epidemiologic aspects

Hantaviruses comprise a genus of the family Bunyaviridae. Bunyaviruses are enveloped viruses with a negative-sense, tripartite RNA genome. Hantaviruses are etiologic agents for two acute and severe illnesses of man, hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). Each hantavirus is primarily associated with a single rodent host species or genus, and is transmitted to man through accidental inhalation or ingestion of virus-contaminated rodent excreta. The distribution of hantaviruses is worldwide. HFRS is caused by infection with Hantaan, Seoul, Dobrava/Belgrade, and Puumala hantaviruses, all of which are enzootic in murid rodents of Old World origin. HPS is caused by any of several hantavirus species associated with indigenous New World rodents of the subfamily Sigmodontinae, family Muridae. HFRS and HPS have numerous common epidemiologic, clinical, and laboratory characteristics. Common features include fever, myalgia, thrombocytopenia, neutrophilia, and a profound capillary leak syndrome associated with hypotension, decreased cardiac output, and shock. Worldwide, HPS is much less common than HFRS but is associated with a higher mortality rate. Recovery from hantavirus disease is generally complete, although chronic renal insufficiency may be a rare sequel of HFRS.

Hantavirus pulmonary syndrome: the Four Corners disease

OBJECTIVE

To review the epidemiology, pathogenesis, clinical features, diagnosis, and treatment of hantavirus infections, focusing on the recent outbreak of hantavirus pulmonary syndrome in the US.

DATA SOURCES

A MEDLINE search (1966 to present) of English language literature pertaining to hantaviruses was performed. Additional literature was obtained from reference lists of pertinent articles identified through the search.

STUDY SELECTION AND DATA EXTRACTION

All articles were considered for possible inclusion in the review. Pertinent information, as judged by the authors, was selected for discussion.

DATA SYNTHESIS

Hemorrhagic fever with renal syndrome (HFRS) has long been recognized in Eurasia and is the predominant disease manifestation of hantavirus infection worldwide. Hantavirus pulmonary syndrome (HPS) recently has been described in the US and exhibits greater pulmonary involvement and mortality than HFRS. Historically, 4 hantavirus serotypes (Hantaan, Seoul, Puumala, Prospect Hill) are recognized; however, additional serotypes have been proposed as distinct serogroups, including the serotype responsible for HPS in the Four Corners area: the Four Corners virus (FCV). Phylogenetic analysis shows that FCV is most closely related to Prospect Hill virus, another hantavirus previously isolated in the US that has not yet been identified with human disease. Additional hantavirus serotypes isolated in the US may provide insight into the prevalence of hantavirus infection and disease in this country. Inhalation of aerosolized virus is the predominant mechanism of hantavirus infection. Diagnosis is based primarily on clinical findings and serologic evidence of hantavirus antibody or direct evidence in clinical tissue specimens. Limited clinical studies evaluating ribavirin as a therapeutic modality demonstrated that the agent improves clinical outcome in HFRS. However, the role of ribavirin in the treatment of HPS remains to be determined.

CONCLUSIONS

Hantavirus infections are becoming increasingly recognized as a cause of disease worldwide. Recognition of hantavirus disease in the US suggests enzoonosis of pathogenic hantaviruses. In the absence of a well-established cure, early diagnosis is imperative so that aggressive supportive care can be initiated.

Tula virus: a newly detected hantavirus carried by European common voles

A novel hantavirus has been discovered in European common voles, Microtus arvalis and Microtus rossiaemeridionalis. According to sequencing data for the genomic RNA S segment and nucleocapsid protein and data obtained by immunoblotting with a panel of monoclonal antibodies, the virus, designated Tula virus, is a distinct novel member of the genus Hantavirus. Phylogenetic analyses of Tula virus indicate that it is most closely related to Prospect Hill, Puumala, and Muerto Canyon viruses. The results support the view that the evolution of hantaviruses follows that of their primary carriers. Comparison of strains circulating within a local rodent population revealed a genetic drift via accumulation of base substitutions and deletions or insertions. The Tula virus population from individual animals is represented by quasispecies, indicating the potential for rapid evolution of the agent.

Genetic identification of a novel hantavirus of the harvest mouse Reithrodontomys megalotis

We have cloned the S genomic segment of a novel hantavirus of the harvest mouse Reithrodontomys megalotis. The virus is phylogenetically distinct from other hantaviruses. The new hantavirus was identified in harvest mice separated by approximately 1,000 km. A wood rat (Neotoma mexicana) was found to be infected with the harvest mouse hantavirus.

Hantavirus: an increasing problem?

Hantaviruses are enveloped RNA viruses and members of the Bunyaviridae family. They are transmitted from various rodent hosts by inhalation of infected urine, saliva or faeces. Infection in rodent hosts is inapparent but persists for life. Person-to-person spread of hantavirus has not been described. Two main presentations of the disease occur. Haemorrhagic fever with renal syndrome (HFRS) is due to Hantaan, Seoul, Puumala, Porogia and Belgrade viruses. In general HFRS due to Hantaan, Porogia and Belgrade viruses is more severe and has higher mortality than that due to Puumala (nephropathia epidemica) or Seoul viruses. Hantaan is predominant in the Far East (Korea, Japan, China), Porogia and Belgrade in the Balkans, and Puumala in Western Europe; Seoul has a world-wide distribution. Hantavirus pulmonary syndrome (HPS) is a recently described infection with high mortality (60%) due to adult respiratory distress syndrome. The virus (Muerto Canyon Virus) is a hantavirus but different genotypically from previous strains. Management of hantavirus infections may require bed-rest, sedation, circulatory and ventilatory support and renal dialysis. Ribavirin if administered early in the illness may be of benefit.