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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Crop‐associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection

Summary To understand the eco‐evolutionary significance of plant viruses in nature, we must (i) quantify the effects of infection on plant fitness and (ii) recognize that native plants are increasingly exposed to crop‐associated viruses. Studies of perennials are particularly needed: most of our knowledge of plant‐virus interactions is from annuals, yet long‐lived species dominate landscapes. Here we used aster models for life‐history analysis and longitudinal measures of plant virus status to evaluate multi‐year consequences of crop virus infection in a native perennial. We used Barley yellow dwarf virus acquired from wheat to inoculate seedlings of P anicum virgatum L. (switchgrass), a North American prairie grass. We grew inoculated and mock‐inoculated individuals of two ecotypes for 3 years in the field. We measured plant size, infection status and fitness components. Aster modelling provided integrated multi‐year measures of fitness. Crop virus inoculation reduced multi‐year native plant fitness by 30% over 2 years despite generally asymptomatic infection and evidence of resistance. This reduction was greater than predicted from individual fitness components or most size measures. Ecotypes differed in response, with the lowland ecotype experiencing higher apparent recovery from infection. Virus treatment in the upland ecotype delayed flowering phenology and reduced seed filling. Synthesis . Our use of field experimentation, surveys of plant infection status and aster modelling demonstrates a rigorous and broadly applicable approach for quantifying the effects of viruses and other microbes on multi‐year plant fitness. We found that a crop virus had negative multi‐year effects on native plant fitness even after infection was no longer detected. Viruses may have substantial effects on native vegetation with domestication of landscapes and agricultural expansion.

Alexander, Helen M.↗
DOE OSTI2012

Interim Report on SNP analysis and forensic microarray probe design for South American hemorrhagic fever viruses, tick-borne encephalitis virus, henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever viruses, Rift Valley fever

The goal of this project is to develop forensic genotyping assays for select agent viruses, enhancing the current capabilities for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the whole genome wide SNP analysis and microarray probe design for forensics characterization of South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)

Abstract The 56th meeting of the Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) was held in Bari, Italy, in July/August, 2024, and 115 submitted taxonomy proposals were reviewed. A total of 112 were subsequently ratified by the ICTV membership. An additional 9 error correction proposals were also approved in August 2025. This article lists the taxonomy proposals that have now been incorporated into release 40 version v2 of the Master Species List ( https://ictv.global/msl ), the Virus Metadata Resource ( https://ictv.global/vmr ), and associated ICTV databases. In addition to the assignments of 1,563 new virus species, 243genera, 55 families, 11 orders, and 8 classes, there were substantial additions to higher taxonomic ranks. These include the creation of a new realm ( Singelaviria ), which is based on the recognition of a separate evolutionary origin for the hallmark capsid genes of members of the kingdom Helvetiavirae. These express capsid proteins forming a single jelly-roll fold that is structurally and evolutionarily distinct from those of members of the family Bamfordvirae , assigned to the realm Varidnaviria . Furthermore, the realm Varidnaviria underwent a major reorganization, including the addition of a new kingdom, Abadenavirae . Another notable change was the classification of the vertebrate-infecting single-stranded DNA anellovirids into a new phylum Commensaviricota (kingdom Shotokuvirae , realm Monodnaviria ). Archaeal viruses infecting the hyperthermophilic Archaeoglobi were assigned to a new phylum Calorviricota , in the kingdom Trapavirae (realm Monodnaviria ), whereas RNA viruses infecting hyperthermophilic bacteria were classified into a new phylum Artimaviricota (realm Riboviria ). In recognition of his extensive and valuable contributions to virus taxonomic developments in Study Groups and over the period of his EC membership, Stuart Siddell was honoured as a new life member of the ICTV. The ICTV has created a new strategy for disseminating information on taxonomy advances through annual open-access publication of citeable taxonomy proposal summaries from each ICTV Subcommittee. A collective total of 354 co-authors of the seven summaries were drawn from members of each Subcommittee, the EC, and a very large number of contributors from the wider virology community.

Simmonds, Peter (ORCID:0000000279644700)↗
DOE OSTI2016

Influenza B virus M2 protein can functionally replace its influenza A virus counterpart in promoting virus replication

The M2 protein (AM2 and BM2) of influenza A and B viruses function as a proton channel essential for viral replication. They also carry a cytoplasmic tail whose functions are not fully delineated. It is currently unknown whether these proteins could be replaced functionally in a viral context. Here, we generated single-cycle influenza A viruses (scIAV-ΔHA) carrying various M2-2A-mCherry constructs in the segment 4 (HA) and evaluated their growth in complementing cells. Intriguingly, the scIAV-ΔHA carrying AM2 and that bearing BM2 grew comparably well in MDCK-HA cells. Furthermore, while the virus carrying chimeric B-AM2 in which the BM2 transmembrane fused with the AM2 cytoplasmic tail produced robust infection, the one bearing the AM2 transmembrane fused with the BM2 cytoplasmic tail (A-BM2) exhibited severely impaired growth. Altogether, we demonstrate that AM2 and BM2 are functionally interchangeable and underscore the role of compatibility between transmembrane and cytoplasmic tail of the M2 protein. -- Highlights: •Flu A M2 protein (AM2) can be functionally replaced by that of Flu B (BM2). •Both AM2 and BM2 with extended cytoplasmic tail are functional. •Compatibility between the ion channel and the cytoplasmic tail is critical for M2 function. •M2 with higher ion channel activity may augment influenza virus replication.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

A humanised murine monoclonal antibody protects mice from Venezuelan equine encephalitis virus, Everglades virus and Mucambo virus when administered up to 48 h after airborne challenge

Currently there are no licensed antiviral treatments for the Alphaviruses Venezuelan equine encephalitis virus (VEEV), Everglades virus and Mucambo virus. We previously developed a humanised version of the mouse monoclonal antibody 1A3B-7 (Hu1A3B-7) which exhibited a wide range of reactivity in vitro and was able to protect mice from infection with VEEV. Continued work with the humanised antibody has now demonstrated that it has the potential to be a new human therapeutic. Hu1A3B-7 successfully protected mice from infection with multiple Alphaviruses. The effectiveness of the humanisation process was determined by assessing proliferation responses in human T-cells to peptides derived from the murine and humanised versions of the V{sub H} and V{sub L} domains. This analysis showed that the number of human T-cell epitopes within the humanised antibody had been substantially reduced, indicating that Hu1A3B-7 may have reduced immunogenicity in vivo.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Virus-like particle vaccine primes immune responses preventing inactivated-virus vaccine-enhanced disease against respiratory syncytial virus

Formalin inactivated respiratory syncytial virus (FI-RSV) vaccination caused vaccine-enhanced respiratory disease (ERD) upon exposure to RSV in children. Virus-like particles presenting RSV F fusion protein (F VLP) are known to increase T helper type-1 (Th1) immune responses and avoid ERD in animal models. We hypothesized that F VLP would prime immune responses preventing ERD upon subsequent exposure to ERD-prone FI-RSV. Here, we demonstrated that heterologous F VLP priming and FI-RSV boosting of mice prevented FI-RSV vaccine-enhanced lung inflammation and eosinophilia upon RSV challenge. F VLP priming redirected pulmonary T cells toward effector CD8 T cells producing Th1 cytokines and significantly suppressed pulmonary Th2 cytokines. This study suggests that RSV F VLP priming would modulate and shift immune responses to subsequent exposure to ERD-prone FI-RSV vaccine and RSV infection, suppressing Th2 immune-mediated pulmonary histopathology and eosinophilia. - Highlights: • RSV F VLP priming dictates the type of subsequent immune responses to FI-RSV. • F VLP priming redirects pulmonary T cells toward effector CD8 T cells. • F VLP priming suppresses Th2 immune-mediated pulmonary histopathology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A Novel Recombinant Influenza Virus Neuraminidase Vaccine Candidate Stabilized by a Measles Virus Phosphoprotein Tetramerization Domain Provides Robust Protection from Virus Challenge in the Mouse Model

Influenza virus infections remain a high risk to human health, causing up to 650,000 deaths worldwide every year, with an enormous burden on the health care system. Since currently available seasonal vaccines are only partially effective and often mismatched to the circulating strains, a broader protective influenza virus vaccine is needed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Inhibition of influenza A virus replication by influenza B virus nucleoprotein: An insight into interference between influenza A and B viruses

Given that co-infection of cells with equivalent titers of influenza A and B viruses (FluA and FluB) has been shown to result in suppression of FluA growth, it is possible that FluB-specific proteins might hinder FluA polymerase activity and replication. We addressed this possibility by individually determining the effect of each gene of FluB on the FluA polymerase assay and found that the nucleoprotein of FluB (NP{sub FluB}) inhibits polymerase activity of FluA in a dose-dependent manner. Mutational analyses of NP{sub FluB} suggest that functional NP{sub FluB} is necessary for this inhibition. Slower growth of FluA was also observed in MDCK cells stably expressing NP{sub FluB}. Further analysis of NP{sub FluB} indicated that it does not affect nuclear import of NP{sub FluA}. Taken together, these findings suggest a novel role of NP{sub FluB} in inhibiting replication of FluA, providing more insights into the mechanism of interference between FluA and FluB and the lack of reassortants between them.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors

ABSTRACT The clinical severity and annual occurrence of influenza virus epidemics, combined with the availability of just a single class of antivirals to treat infections, underscores the urgent need to develop new anti-influenza drugs. The endonuclease activity within the viral acidic polymerase (PA) protein is an attractive target for drug discovery due to the critical role it plays in viral gene transcription. RO-7 is a next-generation PA endonuclease inhibitor of influenza A and B viruses, but its drug resistance potential is unknown. Through serial passage of influenza A(H1N1) viruses in MDCK cells under selective pressure of RO-7, we identified an I38T substitution within the PA endonuclease domain that conferred in vitro resistance to RO-7 (up to a 287-fold change in 50% effective concentration [EC 50 ]). I38T emerged between 5 and 10 passages, and when introduced into recombinant influenza A(H1N1) viruses, alone conferred RO-7 resistance (up to an 81-fold change in EC 50 ). Cocrystal structures of mutant and wild-type endonuclease domains with RO-7 provided the structural basis of resistance, where a key hydrophobic interaction between RO-7 and the Ile38 side chain is compromised when mutated to the polar threonine. While Ile38 does not have a crucial role in coordinating the endonuclease active site, the switch to threonine does affect the polymerase activity of some viruses and influences RO-7 affinity for the PA N target (i.e., the ≈200-residue N-terminal domain of PA). However, the change does not lead to a complete loss of replication activity in vitro . Our results predict that RO-7-resistant influenza viruses carrying the I38T substitution may emerge under treatment. This should be taken into consideration for clinical surveillance and in refinement of these drugs. IMPORTANCE The effectiveness of antiviral drugs can be severely compromised by the emergence of resistant viruses. Therefore, determination of the mechanisms by which viruses become resistant is critical for drug development and clinical use. RO-7 is a compound that potently inhibits influenza virus replication and belongs to a new class of drugs in late-stage clinical trials for treatment of influenza virus infection. Here we demonstrate that a single amino acid change acquired under prolonged virus exposure to RO-7 renders influenza viruses significantly less susceptible to its inhibitory effects. We have discovered how the mutation can simultaneously interfere with drug activity and still maintain efficient virus replication. These findings have important implications for the development of more effective derivatives of RO-7-like drugs and provide guidance for how to monitor the emergence of resistance.

Jones, Jeremy C.↗
DOE OSTI2014

Initial characterization of Vaccinia Virus B4 suggests a role in virus spread

Currently, little is known about the ankyrin/F-box protein B4. Here, we report that B4R-null viruses exhibited reduced plaque size in tissue culture, and decreased ability to spread, as assessed by multiple-step growth analysis. Electron microscopy indicated that B4R-null viruses still formed mature and extracellular virions; however, there was a slight decrease of virions released into the media following deletion of B4R. Deletion of B4R did not affect the ability of the virus to rearrange actin; however, VACV811, a large vaccinia virus deletion mutant missing 55 open reading frames, had decreased ability to produce actin tails. Using ectromelia virus, a natural mouse pathogen, we demonstrated that virus devoid of EVM154, the B4R homolog, showed decreased spread to organs and was attenuated during infection. This initial characterization suggests that B4 may play a role in virus spread, and that other unidentified mediators of actin tail formation may exist in vaccinia virus. - Highlights: • B4R-null viruses show reduced plaque size, and decreased ability to spread. • B4R-null viruses formed mature and extracellular virions; and rearranged actin. • Virus devoid of EVM154, the B4R homolog, was attenuated during infection. • Initial characterization suggests that B4 may play a role in virus spread. • Unidentified mediators of actin tail formation may exist in vaccinia virus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Molecular determinants of dengue virus 2 envelope protein important for virus entry in FcγRIIA-mediated antibody-dependent enhancement of infection

Antibody-dependent enhancement (ADE) of infection may cause severe illness in patients suffering a secondary infection by a heterologous dengue virus (DENV) serotype. During ADE of infection, cross-reactive non- or poorly-neutralizing antibodies form infectious virus-Ab complexes with the newly infecting serotype and enhance virus infection by binding to the Fcγ receptors (FcγR) on FcγR-bearing cells. In this study, we determined that molecular determinants of DENV2 envelope protein critical for virus entry during non-ADE infection are also required for ADE infection mediated by FcγRIIA, and binding of virus-Ab complexes with FcγRIIA alone is not sufficient for ADE of infection. The FcγRIIA mainly plays an auxiliary role in concentrating the virus–Ab complex to the cell surface, and other primary cellular receptors are required for virus entry. Understanding the viral entry pathway in ADE of DENV infection will greatly facilitate rational designs of anti-viral therapeutics against severe dengue disease associated with ADE. - Highlights: • KKK305/307/310 in DENV2 E-DIII is critical for virus attachment in ADE and non-ADE infection. • Binding of DENV2–Ab complex with FcγRII alone is not sufficient for virus entry in ADE infection. • Other primary receptors were required for DENV2 internalization during FcγRII–mediated ADE. • G104 and L135 of DENV2 E are critical for virus-mediated membrane fusion. • DENV2 virus-mediated membrane fusion is required for both ADE and non-ADE infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Data from: Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection

To understand the eco-evolutionary significance of plant viruses in nature, we must (i) quantify the effects of infection on plant fitness and (ii) recognize that native plants are increasingly exposed to crop-associated viruses. Studies of perennials are particularly needed: most of our knowledge of plant-virus interactions is from annuals, yet long-lived species dominate landscapes. Here we used aster models for life-history analysis and longitudinal measures of plant virus status to evaluate multi-year consequences of crop virus infection in a native perennial. We used Barley yellow dwarf virus acquired from wheat to inoculate seedlings of Panicum virgatum L. (switchgrass), a North American prairie grass. We grew inoculated and mock-inoculated individuals of two ecotypes for 3 years in the field. We measured plant size, infection status and fitness components. Aster modelling provided integrated multi-year measures of fitness. Crop virus inoculation reduced multi-year native plant fitness by 30% over 2 years despite generally asymptomatic infection and evidence of resistance. This reduction was greater than predicted from individual fitness components or most size measures. Ecotypes differed in response, with the lowland ecotype experiencing higher apparent recovery from infection. Virus treatment in the upland ecotype delayed flowering phenology and reduced seed filling. Synthesis. Our use of field experimentation, surveys of plant infection status and aster modelling demonstrates a rigorous and broadly applicable approach for quantifying the effects of viruses and other microbes on multi-year plant fitness. We found that a crop virus had negative multi-year effects on native plant fitness even after infection was no longer detected. Viruses may have substantial effects on native vegetation with domestication of landscapes and agricultural expansion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Epstein–Barr virus glycoprotein gM can interact with the cellular protein p32 and knockdown of p32 impairs virus

The Epstein–Barr virus glycoprotein complex gMgN has been implicated in assembly and release of fully enveloped virus, although the precise role that it plays has not been elucidated. We report here that the long predicted cytoplasmic tail of gM is not required for complex formation and that it interacts with the cellular protein p32, which has been reported to be involved in nuclear egress of human cytomegalovirus and herpes simplex virus. Although redistribution of p32 and colocalization with gM was not observed in virus infected cells, knockdown of p32 expression by siRNA or lentivirus-delivered shRNA recapitulated the phenotype of a virus lacking expression of gNgM. A proportion of virus released from cells sedimented with characteristics of virus lacking an intact envelope and there was an increase in virus trapped in nuclear condensed chromatin. The observations suggest the possibility that p32 may also be involved in nuclear egress of Epstein–Barr virus. - Highlights: • The predicted cytoplasmic tail of gM is not required to complex with gN. • Cellular p32 can interact with the predicted cytoplasmic tail of EBV gM. • Knockdown of p32 recapitulates the phenotype of virus lacking the gNgM complex.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

A protein kinase binds the C-terminal domain of the readthrough protein of Turnip yellows virus and regulates virus accumulation

Turnip yellows virus (TuYV), a phloem-limited virus, encodes a 74 kDa protein known as the readthrough protein (RT) involved in virus movement. We show here that a TuYV mutant deleted of the C-terminal part of the RT protein (TuYV-∆RT{sub Cter}) was affected in long-distance trafficking in a host-specific manner. By using the C-terminal domain of the RT protein as a bait in a yeast two-hybrid screen of a phloem cDNA library from Arabidopsis thaliana we identified the calcineurin B-like protein-interacting protein kinase-7 (AtCIPK7). Transient expression of a GFP:CIPK7 fusion protein in virus-inoculated Nicotiana benthamiana leaves led to local increase of wild-type TuYV accumulation, but not that of TuYV-∆RT{sub Cter}. Surprisingly, elevated virus titer in inoculated leaves did not result in higher TuYV accumulation in systemic leaves, which indicates that virus long-distance movement was not affected. Since GFP:CIPK7 was localized in or near plasmodesmata, CIPK7 could negatively regulate TuYV export from infected cells. - Highlights: • The C-terminal domain of TuYV-RT is required for long-distance movement. • CIPK7 from Arabidopsis interacts with RT{sub Cter} in yeast and in plants. • CIPK7 overexpression increases virus titer locally but not virus systemic movement. • CIPK7 localizes to plasmodesmata. • CIPK7 could be a defense protein regulating virus export.

60 APPLIED LIFE SCIENCES↗