PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Infectious clone”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 901 records · Page 50Linked to original sources

Host range mutants of Minute Virus of Mice with a single VP2 amino acid change require additional silent mutations that regulate NS2 accumulation.

Two host range switch mutants of the immunosuppressive strain of parvovirus Minute Virus of Mice (MVMi) were isolated from plaques on A9 fibroblasts. Both carried a single coding mutation at residue D399 in VP2, to alanine and glycine in hr105 and hr107, respectively, and a second, non-coding, guanine-to-adenine change at nucleotide 1970 in hr105 and 1967 in hr107. These mutations were recreated in a wild type MVMi infectious plasmid clone, both alone and as pairs, in either the original or switched combinations. All single mutants failed to replicate productively in fibroblasts, but the two pairs of changes were functionally equivalent. Single D399 mutations allowed the viruses to initiate infection in fibroblasts, but NS2 expression was severely restricted and correlated with poor accumulation and release of progeny virus. Mutations at 1967 or 1970 enhanced NS2 accumulation, and allowed efficient progeny production and release. Conversely, the D399 mutations destroyed the viruses' ability to infect EL4 lymphocytes. In all productive EL4 infections, NS2 was expressed at high ratios even in the absence of upstream mutations, and progeny accumulation was efficient. However, EL4 cells lack a mechanism for early progeny release, potentially explaining why virus amplification in these cells is slow.

Amino Acid Sequence↗

Serologic marker candidates identified among B-cell linear epitopes of Nsp2 and structural proteins of a North American strain of porcine reproductive and respiratory syndrome virus.

We describe B-cell linear epitopes detected by Pepscan in the Nsp2 and all of the structural proteins of a US PRRSV strain, using sera of 15 experimentally infected pigs. The Nsp2 was found to contain the highest frequency of immunodominant epitopes (n = 18) when compared to structural proteins. Ten of these 18 Nsp2 peptides were reactive with 80 to 100% of the examined sera. In the structural proteins, epitopes consistently recognized by immune sera were located at gp2 (n = 2), gp3 (n = 4), gp5 (n = 3), M (n = 2) and N (n = 2). Overall, the highest degree of immunogenicity and conservation was exhibited by two epitopes identified in the C-terminal end of the M protein (ORF6). The antibodies recognizing the immunodominant epitopes of each protein were detected as early as days 7 to 15 pi and remained detectable until the end of the experiment (day 90 pi). These findings have direct implications for PRRSV differential diagnostics and eventual eradication as the identified epitopes may represent serologic marker candidates for differential (DIVA) PRRSV vaccines, derived from infectious cDNA clones.

Amino Acid Sequence↗

Construction and characterization of CD4-independent infectious recombinant HIV-2 molecular clones.

Human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) differ in their pathogenic mechanisms as evidenced by lower rate of disease progression, lower transmission rates and lower viral load in peripheral blood for HIV-2. One of the many factors that are involved in these characteristics is the interaction between viral glycoproteins and cellular receptors. The study of these interactions in an HIV-2 model could lead to important conclusions regarding pathogenesis and transmission mechanisms of HIV-2 infection. Here we report the design of a method enabling the construction of recombinant proviral HIV-2 DNAs in a moderate copy number plasmid that allows the analysis of env gene structure and functionality. This method constitutes an important tool for the study of HIV-2 env glycoproteins and for the mappings of genetic determinants of HIV-2 coreceptor usage and CD4-independent interaction. Furthermore, this knowledge will help towards the understanding of the different pathogenic mechanisms of HIV-1 and HIV-2.

CD4 Antigens↗

A single amino acid residue of RNA-dependent RNA polymerase in the Potato virus X genome determines the symptoms in Nicotiana plants.

A Potato virus X (PVX) strain, PVX-OS, causes a necrotic mosaic in Nicotiana benthamiana and ring spot mosaic in N. tabacum cv. SamsunNN. By contrast, strain PVX-BS causes a mild mosaic in N. benthamiana and systemic asymptomatic infection in N. tabacum cv. SamsunNN. To investigate the viral determinant of this difference, we produced various infectious cDNA clones chimeric between these PVX genomes and clones with point mutations introduced by site-directed mutagenesis. Inoculation tests with these clones mapped the symptom determinant in Nicotiana plants to the 1422 amino acid residue in the region of the C-terminus of RNA-dependent RNA polymerase (RdRp). Western blot analysis and local lesion assay indicated that virus accumulation in the infected leaves was similar for these PVX strains, suggesting that the symptom difference was not due to virus accumulation.

Amino Acid Substitution↗

Nineteen nucleotides in the variable region of 3' non-translated region are dispensable for the replication of dengue type 1 virus in vitro.

In many flaviruses, first 50-400 nucleotides of 3' non-translated region (3' NTR) exhibit lower conservation level than other regions and are called "variable region". Two dengue type 1 virus (DENV-1) strains, which have 17- and 29-nt deletion in the variable region, were recently isolated from Japanese dengue fever patients. The effect of a small deletion in the 3' NTR was analyzed using two DENV-1 viruses which were prepared from a newly developed infectious cDNA clone. These included a recombinant virus rDENV-1(02-20), without any deletion in 3' NTR, and rDENV-1m10, with 19-nt deletion in the variable region of rDENV-1(02-20). These two viruses were compared for growth kinetics and plaque morphology in Vero, Huh-7 and C6/36 cells. No apparent difference was detected between rDENV-1(02-20) and rDENV-1m10 in replication efficiency and plaque size in these cell lines. The results suggest that the complete variable region of DENV-1 is dispensable for virus replication and propagation in vitro.

3' Untranslated Regions↗

Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence.

Transmissible gastroenteritis coronavirus (TGEV) contains eight overlapping genes that are expressed from a 3'-coterminal nested set of leader-containing mRNAs. To facilitate the genetic manipulation of the viral genome, genes were separated by duplication of transcription regulating sequences (TRSs) and introduction of unique restriction endonuclease sites at the 5' end of each gene using an infectious cDNA clone. The recombinant TGEV (rTGEV) replicated in cell culture with similar efficiency to the wild-type virus and stably maintained the modifications introduced into the genome. In contrast, the rTGEV replication level in the lungs and gut of infected piglets and virulence were significantly reduced. rTGEV in which gene 7 expression was abrogated (rTGEV-delta7) were recovered from cDNA constructs, indicating that TGEV gene 7 was a nonessential gene for virus replication. Interestingly, in vivo infections with rTGEV-delta7 showed an additional reduction in virus replication in the lung and gut, and in virulence, indicating that TGEV gene 7 influences virus pathogenesis.

Animals↗

Convergent evolution of SIV env after independent inoculation of rhesus macaques with infectious proviral DNA.

The env gene of three simian immunodeficiency virus (SIV) variants developed convergent mutations during disease progression in six rhesus macaques. The monkeys had been inoculated with supercoiled plasmids encoding infectious proviruses of SIVmac239 (a pathogenic, wild-type strain), SIVdelta3 (the live attenuated vaccine strain derived from SIVmac239), or SIVdelta3+ (a pathogenic progeny virus that had evolved from SIVdelta3). All six monkeys developed immunodeficiency and progressed to fatal disease. Although many divergent mutations arose in env among the different hosts, three regions consistently mutated in all monkeys studied; these similar mutations developed independently even though the animals had received only a single infectious molecular clone rather than standard viral inocula that contain viral quasispecies. Together, these data indicate that the env genes of SIVmac239, SIVdelta3, and SIVdelta3+, in the context of different proviral backbones, evolve similarly in different hosts during disease progression.

Amino Acid Sequence↗

Functional analysis of the stem-loop structures at the 5' end of the Aichi virus genome.

Aichi virus is a member of the family Picornaviridae. Computer-assisted secondary structure prediction suggested the formation of three stem-loop structures (SL-A, SL-B, and SL-C from the 5' end) within the 5'-end 120 nucleotides of the genome. We have already shown that the most 5'-end stem-loop, SL-A, is critical for viral RNA replication. Here, using an infectious cDNA clone and a replicon harboring a luciferase gene, we revealed that formation of SL-B and SL-C on the positive strand is essential for viral RNA replication. In addition, the specific nucleotide sequence of the loop segment of SL-B was also shown to be critical for viral RNA replication. Mutations of the upper and lower stems of SL-C that do not disrupt the base-pairings hardly affected RNA replication, but decreased the yields of viable viruses significantly compared with for the wild-type. This suggests that SL-C plays a role at some step besides RNA replication during virus infection.

5' Untranslated Regions↗

Early embryonic cells from in vivo-produced goat embryos transmit the caprine arthritis-encephalitis virus (CAEV).

The aim of this study was to investigate whether cells of early goat embryos isolated from in vivo-fertilized goats interact with the caprine arthritis-encephalitis virus (CAEV) in vitro and whether the embryonic zona pellucida (ZP) protects early embryo cells from CAEV infection. ZP-free and ZP-intact 8-16 cell embryos were inoculated for 2 h with CAEVat the 10(4) tissue culture infectious dose 50 (TCID50)/ml. Infected embryos were incubated for 72 h over feeder monolayer containing caprine oviduct epithelial cells (COECs) and CAEV indicator goat synovial membrane (GSM) cells. Noninoculated ZP-free and ZP-intact embryos were submitted to similar treatments and used as controls. Six days postinoculation, infectious virus assay of the wash fluids of inoculated early goat embryos showed typical CAEV-induced cytopathic effects (CPE) on indicator GSM monolayers, with fluids of the first two washes only. The mixed cell monolayer (COEC + GSM) used as feeder cells for CAEV inoculated ZP-free embryos showed CPE. In contrast, none of the feeder monolayers, used for culture of CAEV inoculated ZP-intact embryos or the noninoculated controls, developed any CPE. CAEV exposure apparently did not interfere with development of ZP-free embryos in vitro during the 72 h study period when compared with untreated controls (34.6 and 36% blastocysts, respectively, P > 0.05). From these results one can conclude that the transmission of infectious molecularly cloned CAEV-pBSCA (plasmid binding site CAEV) by embryonic cells from in vivo-produced embryos at the 8-16 cell stages is possible with ZP-free embryos. The absence of interactions between ZP-intact embryos and CAEV in vitro suggests that the ZP is an efficient protective embryo barrier.

Animals↗

Engraftment and tumorigenesis of HTLV-1 transformed T cell lines in SCID/bg and NOD/SCID mice.

Human T cell leukemia/lymphoma virus type-1 (HTLV-1) is recognized as the etiological agent of adult T cell leukemia (ATL). Although HTLV-1 can immortalize human lymphocytes in culture, identification of molecular events leading to tumorigenesis after HTLV-1 infection remain elusive. SCID/bg and NOD/SCID mice have reduced natural killer (NK) cell activity and were inoculated intraperitoneally with HTLV-1 transformed cells to refine and characterize the SCID mouse as a small animal model for investigation of HTLV-1 tumorigenesis. HTLV-1 transformed cell lines originally derived by cocultivation of uninfected peripheral blood mononuclear cells (PBMC) with lethally irradiated leukemic cells from patient samples (SLB-1, MT-2 and HT-1-RV) were lymphomagenic when inoculated into NOD/SCID mice. In contrast, immortalized cell lines generated by transfection PBMC with an infectious molecular clone of HTLV-1 (ACH or ACH.p12) were not tumorigenic. The differing behaviors of HTLV-1 infected cell lines in NOD/SCID mice indicates that viral infection and immortalization of human PBMC for growth in culture is not sufficient for induction of a tumorigenic phenotype. The higher level of engraftment of HTLV-1 transformed cell lines in NOD/SCID mice suggests that this is an effective animal model to investigate molecular determinants of HTLV-1 lymphomagenesis.

Animals↗

Construction of infectious dengue 2 virus cDNA clones using high copy number plasmid.

Procedures for cloning entire dengue serotype 2 virus genome in the multiple cloning site of a commercially available high copy number plasmid are described. The 10.7 kb viral RNA genome was reverse transcribed, amplified as three overlapping DNA fragments and successively ligated into pBluescript II KS, which contains the colE1 origin of replication. When propagated at room temperature (20-25 degrees C) under low level of antibiotic selection, the full-length recombinant plasmid was stable upon serial passages in two common Escherichia coli strains employed. Under the same culture conditions the whole dengue cDNA sequence was transferred successfully to another high copy number plasmid, pGem 3Z. Following in vitro transcription and lipofectin-mediated transfection, capped RNA transcripts derived from the plasmid initiated virus replication in C6/36 mosquito cells and BHK-21 cells within 3-4 days of transfection. Upon subsequent expansion in C6/36 cells, dengue viruses derived from the first- and eighth-plasmid passages achieved similar titers as the parent virus. They were also indistinguishable from the parent virus by the criteria of replication kinetics in mosquito and mammalian cell lines, and size and reactivity of selected viral proteins as detected with polyclonal and monoclonal antibodies. The cloning scheme and resultant recombinant plasmids based on high copy number cloning vectors allows greater flexibility in manipulation of dengue viral genome when compared with previous attempts employing low-copy number counterparts.

Cell Line↗

At least four non-env factors that reside in the LTR, in the 5'-non-coding region, in gag and in part of pol affect neuropathogenicity of PVC-441 murine leukemia virus (MuLV).

PVC-441 murine leukemia virus (MuLV) is neuropathogenic in F344 rats. Recently, an infectious DNA clone was isolated and its nucleotide sequence was determined (J. Virol. 72: 3423-3426. 1998). To identify the viral determinants of neuropathogenicity of the molecularly cloned PVC-441 MuLV, chimeras were constructed between PVC-441 MuLV and F-MuLV clones at appropriate restriction enzyme sites that divide the viral genome approximately in LTR-non-coding, gag-, pol-, and env-gene regions. Results indicated that the LTR-non-coding and the gag-gene regions of PVC-441 MuLV affected independently the neuropathogenicity in combination with the env gene region as evidenced clinically and pathologically. Studies on the distribution of vacuolar degeneration suggested that the pons and cervical spinal cord areas were the primary targets and the large brain was the latest target of PVC-441 MuLV. Further studies with chimeric viruses that were formed in the LTR-non-coding and the gag gene regions revealed that at least four factors affected the neuropathogenicity of PVC-441 MuLV. Two factors were found in the U3, and R-U5-5'-non-coding regions, and at least two factors in the gag gene region that contained the N-terminal part of the pol gene. Among these factors, at least two factors seemed to be 'cis-acting' from each other

5' Untranslated Regions↗

The complete nucleotide sequence and synthesis of infectious RNA of genomic and defective interfering RNAs of TBSV-P.

The complete nucleotide sequences of the genome of the pepper isolate of tomato bushy stunt Tombusvirus (TBSV-P), and its defective interfering (DI) RNAs were determined. The genome of TBSV-P is a linear single-stranded monopartite RNA molecule of positive polarity, 4776 nucleotides long and has an organisation identical to that reported for other tombusviruses. In vitro transcripts of the genome were highly infectious, and it could support replication of the DI RNAs associated with the wild type virus. Two DI RNAs were found in the infected leaves of Nicotiana clevelandii, whose sequences were completely derived from the genomic RNA. The longest DI RNA (DI-5) has 550 nucleotides (nt), while the shorter DI RNA (DI-4) composed of 463 nt, both of them were formed by essentially the same genomic sequence blocks. Since host specificity of TBSV-P and other tombusviruses with available infectious cDNA clones is different, it is feasible to carry out gene exchange studies to determine viral host specificity factors for tombusviruses.

Blotting, Northern↗

Echoviruses 1 and 8 are closely related genetically, and bind to similar determinants within the VLA-2 I domain.

Echoviruses (EV) 1 and 8 were originally considered to be distinct serotypes, but more recently have been considered strains of the same virus. In experiments with chimeric recombinant fusion proteins, both viruses bound to the I domain of the integrin VLA-2, and both required the same receptor residues for attachment. A full-length, infectious cDNA clone encoding EV1 was obtained; its nucleotide sequence was determined, as were the sequences encoding the EV8 capsid. EV1 and 8 show 94% amino acid identity within the capsid region and are more similar to each other than to any other human picornavirus.

Amino Acid Sequence↗

HIV gp120 V(1)/V(2) and C(2)-V(3) domains glycoprotein compatibility is required for viral replication.

The envelope gene, especially the V(3) region, of HIV-1 has been shown to be a principal determinant of cell tropism, replication and cytopathogenicity of the virus. In addition, the V(1)/V(2) region of the envelope gene has been found to be an important factor in cell tropism. We examined the compatibility between the V(1)/V(2) and C(2)-V(3) domains of HIV-1 gp120 in different combinations on viral replication by using envelope recombinants between ME1 and ME46, two infectious molecular clones with diverse biologic activity longitudinally isolated from one seropositive subject. Our data demonstrate that a proper interaction between the regions of V(1)/V(2)and C(2) is essential for viral infection and hence replication. Sequence analysis and subsequent site directed mutagenesis study indicate that the pattern of potential envelope N-glycosylation in the V(1)/V(2) and C(2)-V(3) regions may be the determining factor in such interaction between these two regions. It is possible that improper N-glycosylation sites while not affecting virus assembly, can influence through steric hindrance the conformational change of the V(3) region that is required for the co-receptor attachment and hence the viral infectivity.

Binding Sites↗

Hepatitis C virus core protein inhibits human immunodeficiency virus type 1 replication.

We previously demonstrated that hepatitis C virus (HCV) core protein is a strong repressor of human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) basal transcription. In this study, we have localized the HCV core protein-response domain to a region between nucleotides -65 and +3 within the HIV-LTR. Thus, neither the upstream negative regulatory elements, or binding sites for various transcription factors (e.g. NF-kappa B, USF-1, IL2/IL-2R) nor the downstream TAR regions were involved in HCV core-mediated repression. HCV core protein mediated repression of the basal transcriptional activity of HIV-1 LTR was abrogated by the Tat protein. Furthermore, HeLa-T4 cells expressing HCV core protein showed inhibition of HIV-1 replication after acute infection with cell-free HIV. A similar observation was also noted in CD4+ and CD4-lymphocytic cell lines cotransfected with an infectious molecular clone of HIV-1 and the HCV core protein expression vector. Thus, a repression of basal transcription prior to the accumulation of threshold levels of Tat protein appears to restrict HIV-1 transcription and modulate viral replication.

Anti-HIV Agents↗

Serial passage of human immunodeficiency virus type 1 generates misalignment deletions in non-essential accessory genes.

Human immunodeficiency virus type 1 (HIV-1) derived from an infectious molecular clone pNL432 was extensively passaged in tissue culture by repeated rounds of acute infection. We previously showed the natural occurrence of a nonsense mutation in the vpr gene during continued passage of this virus. In this report, we show that two forms of large deletions (561 and 518 base pairs containing short direct repeats at the deletion junctions) occur after passage 50 in the region that spans the vif and vpr open reading frames. One model to explain the occurrence of these deletion regions is that such mutations result from misalignment of the growing point at a limited number of nucleotide positions. Infection of CD4+ T-cells with a recombinant HIV-1 construct containing the same vif to vpr deletion showed virtually no cytopathogenic phenotype. Thus, misalignment deletions at non-essential accessory genes of HIV-1 might be induced during replication, which result in the generation of virus with a low cytopathogenic potential.

Base Sequence↗

Simian immunodeficiency viruses containing mutations in the long terminal repeat NF-kappa B or Sp1 binding sites replicate efficiently in T cells and PHA-stimulated PBMCs.

The long terminal repeats (LTRs) of primate lentiviruses contain conserved binding sites for the NF-kappa B and Sp1 cellular transcription factors. In order to study the role that these sites play in simian immunodeficiency virus (SIV) replication, we have introduced mutations that disrupt either the NF-kappa B or Sp1 binding sites in the LTR of an infectious molecular clone of SIVmac239. An additional mutation also disrupted the SF3 transcription factor binding site that overlaps the NF-kappa B site. Viruses containing point mutations or deletions of the NF-kappa B, SF3, or Sp1 binding sites retained the ability to replicate efficiently in the CEMx174 and MT4 cell lines, as well as in PHA-stimulated primary rhesus macaque peripheral blood mononuclear cells (PBMCs). Efficient replication of SIVs mutated in either NF-kappa B or Sp1 binding sites suggests that the SIV LTR promoter contains multiple functionally redundant elements capable of supporting sufficient transcription to allow productive viral replication.

Animals↗