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PubMed1989

Extension of JC virus host range to monkey cells by insertion of a simian virus 40 enhancer into the JC virus regulatory region.

A chimeric polyomavirus genome was constructed by inserting the 72- and the 21-bp repeats of simian virus 40 (SV40) into the JC virus (JCV) regulatory region on the late side of the JCV 98-bp repeats. Although the chimeric polyomavirus DNA was able to replicate very well in human fetal glial cells, deletions were found in sequences of the regulatory region. DNA sequence analysis of a selected clone indicated a 294-bp deletion from the original construction that retained the sequences for the JCV replication origin, 78 bp of one 98-bp repeat, 33 bp of one SV40 72-bp repeat, and one intact 72-bp repeat. Of significant interest was that this genome demonstrated an extended species and cell-type host range, producing infectious virus in human fetal brain and embryonic kidney as well as in rhesus monkey fetal and adult glial cells. However, the species host range was not extended beyond primate cells since the chimeric polyomavirus was unable to multiply in rodent glial cells. Analysis of the viral RNA transcripts from either kidney or glial cells indicated that the major start sites for early RNA mapped within the JCV sequences of the regulatory region and major start sites for late RNA mapped within the JCV and SV40 sequences. This extension of the JC virus host range was most likely attributable to changes in the regulatory region and not the viral T protein since a recombinant DNA clone which placed the coding sequences for the wild-type JCV T protein subject to regulation by the deleted chimeric regulatory region showed a similar extension of host range.

Animals↗

PubMed2026

AI-enabled viral genomics: from virus discovery to host prediction and emerging variant forecasting.

The rapid expansion of metagenomic sequencing has generated vast repositories of viral sequence data that far outpace our capacity to interpret them using conventional approaches. Highly divergent sequences, sparse functional annotation, and taxonomically uneven sampling present fundamental challenges for reference-dependent methods, which lose sensitivity precisely for novel and understudied viruses with high public health relevance. Artificial intelligence (AI) provides a new avenue to address these challenges by enabling predictive inference from viral genomes and proteins while reducing dependence on sequence similarity. In this Review, we discuss representative advances in AI for virus discovery, taxonomic classification and functional annotation, prediction of host range and zoonotic potential, and efforts toward forecasting emerging variants. These advances are transforming viral genomics from a largely descriptive discipline into one with increasing predictive capability. We also critically assess the major challenges that constrain current approaches, including the availability of high-quality and representative datasets, rigorous model evaluation, biological interpretability and responsible governance for increasingly capable AI models.

Artificial Intelligence↗

PubMed1993

Specificity of bipartite geminivirus movement proteins.

Pseudorecombinants produced by exchanging genome components (DNAs A and B) of the geminiviruses African cassava mosaic virus (ACMV) and Indian cassava mosaic virus (ICMV), ACMV, and tomato golden mosaic virus (TGMV), and TGMV and abutilon mosaic virus (AbMV) are not infectious in their common host Nicotiana benthamiana. In each case, DNA A was unable to trans-replicate the heterogenomic DNA B component in a N. benthamiana leaf disc assay. The non-viability of the pseudorecombinants has been exploited to investigate the specificity of geminivirus movement proteins, encoded by DNA B, by co-inoculating N. benthamiana with both genome components of one virus and DNA A of a second virus. We demonstrate that ACMV can mediate the systemic movement of ICMV, TGMV and AbMV DNA A components. In reciprocal experiments, neither TGMV nor AbMV can mediate the systemic movement of ACMV DNA A although they can support the movement of each other's DNA A. The variation in movement protein specificity suggests evolutionary divergence of New and Old World geminiviruses. Co-inoculation of combinations of ACMV and ICMV genome components into discriminating hosts and comparison of their behavior in N. benthamiana and N. tabacum leaf disc assays suggests that the host range of ICMV, a subset of that of ACMV, is restricted by impaired viral DNA replication rather than the inability of the virus to spread in non-host backgrounds.

DNA Replication↗

PubMedDate not supplied

Viral control of phytoplankton populations--a review.

Phytoplankton population dynamics are the result of imbalances between reproduction and losses. Losses include grazing, sinking, and natural mortality. As the importance of microbes in aquatic ecology has been recognized, so has the potential significance of viruses as mortality agents for phytoplankton. The field of algal virus ecology is steadily changing and advancing as new viruses are isolated and new methods are developed for quantifying the impact of viruses on phytoplankton dynamics and diversity. With this development, evidence is accumulating that viruses can control phytoplankton dynamics through reduction of host populations, or by preventing algal host populations from reaching high levels. The identification of highly specific host ranges of viruses is changing our understanding of population dynamics. Viral-mediated mortality may not only affect algal species succession, but may also affect intraspecies succession. Through cellular lysis, viruses indirectly affect the fluxes of energy, nutrients, and organic matter, especially during algal bloom events when biomass is high. Although the importance of viruses is presently recognized, it is apparent that many aspects of viral-mediated mortality of phytoplankton are still poorly understood. It is imperative that future research addresses the mechanisms that regulate virus infectivity, host resistance, genotype richness, abundance, and the fate of viruses over time and space.

Biodiversity↗

PubMed1993

Apoptosis reduces both the in vitro replication and the in vivo infectivity of a baculovirus.

Apoptotic programmed cell death occurs when the insect cell line SF-21, derived from Spodoptera frugiperda, is infected with mutants of the baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) which lack a functional p35 gene. However, infection of the Trichoplusia ni TN-368 cell line with p35 mutants does not result in apoptosis (R. Clem, M. Fechheimer, and L. Miller, Science 254:1388-1390, 1991). We have examined the effect of apoptosis on AcMNPV infections in cell lines and larvae of these two insect species. Production of viral progeny was significantly lower in SF-21 cells infected with p35 mutants than in cells infected with wild-type (wt) or revertant viruses. Viral gene expression was abnormal in SF-21 cells infected with p35 mutants; there was a delay in the transcription and translation of early and late viral genes, a lack of expression of very late genes, and a total cessation of protein synthesis late in the apoptotic process. In vivo analysis revealed that the dose of budded virus required for 50% lethality in S. frugiperda larvae was approximately 1,000-fold higher for p35 mutants than for wt or revertant viruses. In contrast, the replication and infectivity of p35 mutant viruses was equivalent to that of wt AcMNPV during infection of both TN-368 cells and T. ni larvae. Thus, the data indicate that a host apoptotic response provides protection against viral infection at the organismal level and that the p35 gene constitutes a host range determinant for AcMNPV infection.

Animals↗

PubMed2004

African swine fever virus multigene family 360 genes affect virus replication and generalization of infection in Ornithodoros porcinus ticks.

Recently, we reported that African swine fever virus (ASFV) multigene family (MGF) 360 and 530 genes are significant swine macrophage host range determinants that function by promoting infected-cell survival. To examine the function of these genes in ASFV's arthropod host, Ornithodoros porcinus porcinus, an MGF360/530 gene deletion mutant (Pr4Delta35) was constructed from an ASFV isolate of tick origin, Pr4. Pr4Delta35 exhibited a significant growth defect in ticks. The deletion of six MGF360 and two MGF530 genes from Pr4 markedly reduced viral replication in infected ticks 100- to 1,000-fold. To define the minimal set of MGF360/530 genes required for tick host range, additional gene deletion mutants lacking individual or multiple MGF genes were constructed. The deletion mutant Pr4Delta3-C2, which lacked three MGF360 genes (3HL, 3Il, and 3LL), exhibited reduced viral growth in ticks. Pr4Delta3-C2 virus titers in ticks were significantly reduced 100- to 1,000-fold compared to control values at various times postinfection. In contrast to the parental virus, with which high levels of virus replication were observed in the tissues of infected adults, Pr4Delta3-C2 replication was not detected in the midgut, hemolymph, salivary gland, coxal gland, or reproductive organs at 15 weeks postinfection. These data indicate that ASFV MGF360 genes are significant tick host range determinants and that they are required for efficient virus replication and generalization of infection. The impaired virus replication of Pr4Delta3-C2 in the tick midgut likely accounts for the absence of the generalized infection that is necessary for the natural transmission of virus from ticks to pigs.

African Swine Fever↗

PubMed1993

The parvovirus H-1 NS2 protein affects viral gene expression through sequences in the 3' untranslated region.

We reported previously that an NS2 null mutant of parvovirus H-1 (H-1SA) was capable of lytic growth in human and hamster cells, but not in rat cells (Li and Rhode, 1991). The host-range phenotype of H-1SA was also manifested in newborn rats and was associated with a reduction of viral protein synthesis to about 10% of wild-type virus and an absence of virions in cultured rat fibroblasts. However, the H-1SA mRNAs for NS1 and capsid proteins, R1 and R3, accumulated to wild-type levels and translated well with a cell free rabbit reticulocyte lysate. These results indicate that NS2 plays an important role in the regulation of viral protein synthesis in rat cells in vivo and in vitro, but NS2 is largely dispensable in other types of cells, such as human and hamster cells. To analyze whether the 5' and 3' untranslated regions (UTR) of viral RNA are involved in the regulation by NS2, the viral VP2 gene was replaced by a reporter gene, firefly luciferase, in a plasmid clone of viral sequences and the protein synthesis under the control of P38 was evaluated by luciferase assay. Cells were transfected with luciferase expressing plasmids and subsequently infected with wild-type H-1 or H-1SA. We were able to mimic the defect in expression that we observed in cultured cells and animals with virus infection. Luciferase activity in H- 1SA-infected rat cells was about 10-fold lower than that in H-1-infected rat cells, but only 2-fold lower or less in H-1SA-infected human cells and hamster cells compared to wild-type H-1. These results are consistent with our previous data that NS2 has a host-range phenotype in the natural host of H-1, the rat. Deletion of 5' UTR sequences from P38 transcripts reduced the overall P38-luc expression but expression was NS2 independent, whereas deletion of the terminal 3' UTR sequences of viral RNA reduced NS2-dependent expression in rat cells. These results suggest that the regulation of viral protein synthesis by NS2 depends on RNA sequences in the 3' UTR.

Animals↗

PubMed1998

Adaptation to promiscuous usage of CC and CXC-chemokine coreceptors in vivo correlates with HIV-1 disease progression.

OBJECTIVE: To study coreceptor usage of sequential primary HIV-1 isolates in a longitudinal follow-up cohort of HIV-1-infected men to understand its contribution to pathogenesis of HIV disease. DESIGN: Viral coreceptor usage of sequential primary isolates from HIV-1-infected individuals was examined at various timepoints and data was compared with CD4 cell counts, rates of disease progression and beta-chemokine production. METHODS: Fifty-eight sequential primary isolates were obtained from four rapid progressors, six late progressors, and three long-term nonprogressors (LTNP) and their coreceptor usage was examined by infection of peripheral blood mononuclear cells (PBMC) from donors with wild-type or non-functional CC-chemokine receptor (CCR)-5, and by infection of GHOST4 cells expressing CD4 and various chemokine receptors [CCR-1-CCR-5, CXC-chemokine receptor (CXCR)-4, BOB/GPR15, BONZO/STRL33]. Production of RANTES and macrophage inflammatory protein (MIP)-1beta was examined using unstimulated or phytohemagglutinin (PHA)-stimulated PBMC isolated from these individuals at multiple timepoints during infection. RESULTS: A switch from single CCR-5 coreceptor usage to multiple coreceptor usage occurred in all four rapid progressors and three out of six late progressors. In addition to the commonly used coreceptors CXCR-4, CCR-5, and CCR-3, some of the viruses isolated from patients in the terminal stage of infection also used CCR-1, CCR-2b, CCR-4, and BOB as coreceptors. The emergence of viral variants capable of utilizing multiple coreceptors generally preceded CD4 cell decline to < 200 x 10(6)/l and correlated with the onset of AIDS. In contrast, three LTNP maintained exclusive usage of CCR-5 over a period of 7-12 years post-infection. Endogenous production of RANTES and MIP-1beta by PBMC from LTNP was not significantly different from rapid and late progressors. However, PHA-driven production of both chemokines was significantly higher in LTNP, suggesting that in vivo activating stimuli might curtail HIV replication by inducing these chemokines. CONCLUSIONS: Viral variants capable of utilizing a broad range of coreceptors correlated with HIV-1 disease progression. In contrast, LTNP maintain exclusive usage of CCR-5 and produce higher levels of beta-chemokines. Thus, both viral and host determinants leading to the emergence of viral variants capable of using an expanded range of coreceptors may be likely determinants of disease progression.

Adaptation, Physiological↗

PubMed2004

Cytotoxic activity of the lymphocyte toxin granzyme B.

Cytotoxic lymphocytes protect their host from viral infection and cellular transformation by delivering a range of toxins stored within intracellular granules. One of the most potent of these toxins is the serine protease granzyme B. This review will discuss mechanisms used by granzyme B to enter target cells and the ways in which it synergizes with other granule toxins to cause cell death.

Animals↗

PubMed2002

Sialic acid functions in enterovirus 70 binding and infection.

The interaction of viruses with host cell receptors is the initial step in viral infection and is an important determinant of virus host range, tissue tropism, and pathogenesis. The complement regulatory protein decay-accelerating factor (DAF/CD55) is an attachment receptor for enterovirus 70 (EV70), a member of the Picornaviridae, commonly associated with an eye infection in humans known as acute hemorrhagic conjunctivitis. In early work, the EV70 receptor on erythrocytes, responsible for its hemagglutinating activity, was shown to be sensitive to neuraminidase, implying an essential role for sialic acid in virus attachment. Here, we extend these results to show that cell surface sialic acid is required for EV70 binding to nucleated cells susceptible to virus infection and that sialic acid binding is important in productive infection. Through the use of site-directed mutagenesis to eliminate the single N-linked glycosylation site of DAF and of a chimeric receptor protein in which the O-glycosylated domain of DAF was replaced by a region of the HLA-B44 molecule, a role in EV70 binding for the sialic acid residues of DAF was excluded, suggesting the existence of at least one additional, sialylated EV70-binding factor at the cell surface. Treatment of cells with metabolic inhibitors of glycosylation excluded a role for the N-linked oligosaccharides of glycoproteins but suggested that O-linked glycosylation is important for EV70 binding.

Animals↗

PubMed2005

Complex determinants in human immunodeficiency virus type 1 envelope gp120 mediate CXCR4-dependent infection of macrophages.

Host cell range, or tropism, combined with coreceptor usage defines viral phenotypes as macrophage tropic using CCR5 (M-R5), T-cell-line tropic using CXCR4 (T-X4), or dually lymphocyte and macrophage tropic using CXCR4 alone or in combination with CCR5 (D-X4 or D-R5X4). Although envelope gp120 V3 is necessary and sufficient for M-R5 and T-X4 phenotypes, the clarity of V3 as a dominant phenotypic determinant diminishes in the case of dualtropic viruses. We evaluated D-X4 phenotype, pathogenesis, and emergence of D-X4 viruses in vivo and mapped genetic determinants in gp120 that mediate use of CXCR4 on macrophages ex vivo. Viral quasispecies with D-X4 phenotypes were associated significantly with advanced CD4+-T-cell attrition and commingled with M-R5 or T-X4 viruses in postmortem thymic tissue and peripheral blood. A D-X4 phenotype required complex discontinuous genetic determinants in gp120, including charged and uncharged amino acids in V3, the V5 hypervariable domain, and novel V1/V2 regions distinct from prototypic M-R5 or T-X4 viruses. The D-X4 phenotype was associated with efficient use of CXCR4 and CD4 for fusion and entry but unrelated to levels of virion-associated gp120, indicating that gp120 conformation contributes to cell-specific tropism. The D-X4 phenotype describes a complex and heterogeneous class of envelopes that accumulate multiple amino acid changes along an evolutionary continuum. Unique gp120 determinants required for the use of CXCR4 on macrophages, in contrast to cells of lymphocytic lineage, can provide targets for development of novel strategies to block emergence of X4 quasispecies of human immunodeficiency virus type 1.

Adolescent↗

PubMed1989

Acquisition and retention of viruses by Trichomonas vaginalis.

Recently described occurrence of virus-like particles (VLP) in some strains of Trichomonas vaginalis suggests the possibility that the pathogenic significance of this organism may be broadened by its potential for viral transmission. Inasmuch as neither the source nor the host range of the VLP are known, any hazard which they may present for man cannot be estimated. A model has been established for the study of acquisition of known human viruses by T vaginalis. Tissue cultures were infected with two reoviruses and a fresh isolate of genital herpes simplex virus (HSV). A squirrel monkey reovirus was also included in the study. T vaginalis was inoculated into the virus cultures three days later. The progress of virus acquisition by the trichomonads was monitored by transmission electron microscopy and by culture. Virus-containing cell fragments were engulfed by trichomonads and internalised in vacuoles. After digestion of cellular debris only virus particle aggregates were retained. Viable reoviruses were recovered from the trichomonads for nine days, and HSV for six days. The results suggest the possibility of transmission of at least some viruses by T vaginalis.

Animals↗

PubMed2004

Recent advances in the understanding of HIV-1 Vpu accessory protein functions.

HIV-1 encodes a number of accessory proteins, which are not commonly found in other retroviruses. These proteins, which include Vif, Vpr, Vpu and Nef, act as multifunctional adapters capable of recruiting and modulating basic host cell processes to optimize wide-ranging aspects of viral replication. This review describes our current understanding of how the Vpu accessory protein functions to modulate HIV-1 particle release and CD4 receptor expression during HIV-1 infection and underlines the potential opportunities afforded by this viral protein for therapeutic intervention.

Amino Acid Sequence↗

PubMed1991

Seroprevalence of ovine progressive pneumonia virus in various domestic and wild animal species, and species susceptibility to the virus.

Ovine progressive pneumonia is caused by a lentivirus of known infectivity only for sheep and goats. Virus susceptibility of 11 other species of animals was examined. Species included cattle, chickens, deer, dogs, goats, hamsters, horses, mice, pigs, rabbits, and rats. Of these species, only goats and rabbits could be experimentally infected with the virus. The infection in rabbits was acute, and virus did not persist or induce antibody production as it does in sheep and goats. Sera obtained from several people working in close contact with the virus and from several wild species, with unknown exposure history, were tested for antibodies to viral antigens. All results were negative. Knowledge of the host range of this virus is important for scientific studies and for virus eradication programs.

Animals↗

PubMed1987

[Demonstration and organizational structure of the DNA of human papillomaviruses in laryngeal and hypopharyngeal carcinomas].

Thirty biopsy specimens from various histological types of human carcinomas of the larynx and hypopharynx were analysed for the presence of human papillomavirus (HPV) DNA: DNA from the individual specimens were tested for the presence of homologous sequences to HPV genotypes 1, 2, 4, 8, 9, 10, 11, 13, 16 and 18. One squamous cell carcinoma of the hypopharynx (postcricoideal area) contained multiple copies of DNA hybridizing under stringent conditions with HPV 16 DNA. The latter DNA has been found to be frequently associated with human genital cancer. HPV 16 DNA was found mostly episomally as oligomeric circles of 7.9 kbp size, and as larger rear-ranged circular molecules. Integration of the viral DNA in the host cell DNA seems quite likely. Integration and rearrangement of viral DNA into cellular DNA may play a role in the induction and maintenance of the transformed state. The presence of sequences reacting under semistringent conditions with HPV DNA was observed in two additional biopsy specimens of this study. This could suggest that additional laryngeal cancers are associated with papilloma virus infections.

Biopsy↗

PubMed1982

Genetic evidence for separate functional domains on the human adenovirus specified, 72 kd, DNA binding protein.

Seven mutations that affect various activities of the multifunctional DNA binding protein (DBP) encoded by human adenovirus have been physically mapped to different locations within DBP gene by marker rescue experiments. Two of these mutants (Ad5ts107 and Ad5ts125) contain a lesion which, under nonpermissive temperatures, decreases the capacity of the protein to bind single-strand DNA, blocks DNA replication, and prevents normal turn-off of viral early genes. In addition, the efficiency of transformation by the ts viruses compared to wild-type virus is increased at the nonpermissive temperature. Both ts mutations are located in the 3' half of the DBP gene (C-terminal half of DBP). In contrast, the alterations in the five host range mutants (Ad2hr400-Ad2hr403, Ad5hr404) which overcome the block to viral late mRNA synthesis in monkey cells, but have no marked effect on DNA replication or early gene expression map in the 5' half of the DBP gene. These results suggest that the 72 kd DBP of adenovirus contains at least two functionally separable domains.

Adenoviruses, Human↗

PubMed2006

Global impact: elucidating plant responses to viral infection.

Viruses induce a variety of responses in host cells that are mediated by perturbation of different signaling pathways. Advances in our understanding of the functions of viral proteins, plant biology in general, as well as technologies for profiling gene expression have converged in recent years to provide new insight into the events occurring inside susceptible and resistant host cells in response to virus infection. These effects range from nonspecific changes in gene expression due to the general accumulation of viral proteins to those responses that are initiated by the specific interactions between virus and host proteins. Here, we discuss a variety of expression profiling methods and approaches that have been used to study the effects of viruses on host transcriptomes. These studies have identified distinct sets of genes that have altered expression profiles in response to viruses, including stress- and defense-related genes. The activities of viral RNA silencing suppressors and interference with hormone signaling or biogenesis also influence plant gene expression and lead to developmental abnormalities.

Gene Expression Profiling↗

PubMed1981

Host restriction of Friend leukemia virus: gag proteins of host range variants.

The host response to murine ecotropic leukemia viruses is mainly controlled by the mouse Fv-1 gene. This locus controls virus replication at an intracellular stage and prevents provirus integration. Biological studies suggest that the Fv-1 effector molecule recognizes at least one virion structural protein. We have produced host range variants of B-tropic Friend murine leukemia virus in order to study the primary structure of potential viral target proteins. Our results show that conversion of B-tropism to NB-tropism is associated with changes in the primary structure of three gag proteins--p15, p12, and p30. These results suggest that host range conversion is due to a recombinational event, presumably between the parental virus and an endogenous murine virus. They also open the possibility that p12 and p30 may be involved in host range restriction.

Amino Acid Sequence↗