Megaprimer-mediated domain swapping for construction of chimeric viruses

Clones that encode viral genomes constructed from two viruses with contrasting biological properties have been widely used in studies of viral-host interactions, particularly when the objective is to determine the identity of the viral component recognized by the host in a resistant response, known as the avirulence factor. This paper presents an efficient method based on megaprimer-mediated domain swapping for the construction of clones encoding chimeric viral genomes as a versatile and widely applicable alternative to conventional restriction enzyme digestion and ligation methods. Potato virus X (PVX)-derived vectors expressing genes encoding fluorescent proteins were used to demonstrate this concept. The cyan fluorescent protein (CFP) gene was cloned into a binary PVX vector and subsequently replaced with the yellow fluorescent protein (YFP) gene using the megaprimer amplification reaction. DNA fragments up to 1480 bp could be replaced efficiently and quickly. Most viral clones showed the expected change in phenotype without altered infectivity. Sequence analysis revealed mutations were not introduced into the four domain-swapped plasmids. This approach will provide a valuable tool for determining which domains of a viral genome are essential for infectivity, avirulence, or otherwise determine biologically significant properties of plant viruses.     

Regulatory effects of matrix protein variations on influenza virus growth

Summary Influenza virus A/WSN/33 forms large plaques (> 3 mm diameter) on MDCK cells whereas A/Aichi/2/68 forms only small plaques (< 1 mm diameter). Fast growing reassortants (AWM), isolated by mixed infection of MDCK cells with these two virus strains in the presence of anti-WSN antibodies, all carried the M gene from WSN. On MDCK cells, these reassortants produced progeny viruses as rapidly as did WSN, and the virus yield was as high as Aichi. The fast-growing reassortants overcame the growth inhibitory effect of lignins. Pulse-labeling experiments at various times after virus infection showed that the reassortant AWM started to synthesize viral proteins earlier than Aichi. Taken together, we conclude that upon infecting MDCK cells, the reassortant viruses advance rapidly into the growth cycle, thereby leading to an elevated level of progeny viruses in the early period of infection. Possible mechanisms of the M gene involvement in the determination of virus growth rate are discussed, in connection with multiple functions of the M proteins.     

LuSIV cells: a reporter cell line for the detection and quantitation of a single cycle of HIV and SIV replication

A single cycle of viral replication is the time required for a virus to enter the host cell, replicate its genome, and produce infectious progeny virions. The primate lentiviruses, human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV), require on average 24 h to complete one cycle of replication. We have now developed and characterized a reporter assay system in CEMx174 cells for the quantitative measurement of HIV/SIV infection within a single replication cycle. The SIV(mac)239 LTR (-225 --> +149) was cloned upstream of the firefly luciferase reporter gene and this reporter plasmid is maintained in CEMx174 cells under stable selection. This cell line, designated LuSIV, is highly sensitive to infection by primary and laboratory strains of HIV/SIV, resulting in Tat-mediated expression of luciferase, which correlates with viral infectivity. Furthermore, manipulation of LuSIV cells for the detection of luciferase activity is easy to perform and requires a minimal amount of time as compared to current HIV/SIV detection systems. The LuSIV system is a powerful tool for the analysis of HIV/SIV infection that provides a unique assay system that can detect virus replication prior to 24 h and does not require virus to spread from cell to cell. Thus these cells can be used for the study of replication-deficient viruses and the high throughput screening of antivirals, or other inhibitors of infection.     

Sequence analysis, viral rescue from infectious clones and generation of recombinant virions of the avian adeno-associated virus

Aiming at the generation of a viral-vectored system for gene delivery and vaccination in poultry, the entire genomes of the VR-865 and DA-1 strains of the avian adeno-associated virus have been cloned and sequenced. Sequence analysis of the clones showed that the genomic distribution of the structural and non-structural protein-coding genes of these viruses is conserved and in agreement with what has been previously described for the primate adeno-associated viruses. Amino acid differences between the avian adeno-associated viruses and the primate adeno-associated viruses are more evident in the genes that code for the non-structural (Rep) proteins of the virus, while the Cap region amino acid sequence was found to be more conserved. Since all the regulatory and coding sequences of the virus were present in the plasmids obtained, complete infectious viral particles were rescued from these clones, and these rescued viral populations were amplified by co-infecting primary embryo liver cells with the rescued virus and the CELO strain of the avian adenovirus type 1. As a proof of concept of the validity of this system for the purpose of gene delivery, recombinant viruses encoding for the LacZ gene as a reporter system were also generated. These recombinant viruses were used to express beta galactosidase activity in primary chicken embryo cell cultures.     

Arenavirus recombination: The formation of recombinants between prototype pichinde and pichinde munchique viruses and evidence that arenavirus S RNA codes for N polypeptide

The ability of arenaviruses to form recombinant viruses by viral RNA segment reassortment has been investigated using a cloned, high-temperature adapted strain of prototype Pichinde virus (PIC), and a cloned, alternate Pichinde virus topotype named Pichinde Munchique (designated MUC). The oligonucleotide fingerprints of the large and small viral RNA segments of the two viruses can be easily distinguished. The virion RNA species of cloned wild-type progeny viruses recovered from dual wild-type PIC and MUC coinfections of BHK-21 cells have been analyzed by oligonucleotide fingerprinting. Other than PIC and MUC genotypes, progeny virus clones were found with PIC/MUC (large/small) RNA segment genotypes, indicating that these recombinant arenaviruses were formed by RNA segment reassortment. Dual infections of BHK-21 cells with a temperature-sensitive (ts), conditional lethal, mutant of MUC and the Group I ts mutants of PIC (but not the PIC Group II ts mutants), have yielded wild-type progeny viruses at high frequency. Genotype analysis of one of these recombinant progeny showed that it had a PIC/MUC genotype. This result indicated that the Group I mutants of PIC have a defective small viral RNA segment, and that the MUC ts mutant (and probably the PIC Group II ts mutants) has a defective large viral RNA segment. Plaque size analyses of the parental wild-type and reassortment viruses have shown that the plaque size of the reassortants was determined by the large viral RNA segment. Tryptic peptide analyses of the nucleocapsid (N) polypeptide of the PIC/MUC recombinant by comparison to similar analyses for PIC and MUC indicate that the recombinant has a MUC N polypeptide, i.e., that the viral S RNA codes for N polypeptide.     

Generation and characterization of HIV-1 clones chimeric for subtypes B and C nef

The impact of human immunodeficiency virus type 1 (HIV-1) Nef on viral infectivity was evaluated by characterization of chimeric clones. Chimera with respect to the nef gene were constructed between subtypes B and C, and monitored for their replication in human peripheral blood mononuclear cells. The parental clones used were pNL432 (subtype B) and pIndie-C1 (Indian subtype C), which show considerable sequence heterogeneity in nef and distinct viral growth phenotype. While an enhancing effect of Nef on viral infectivity was noted, no significant growth difference was observed between the parental and chimeric clones. The difference in growth potential of the two subtype clones was mainly ascribable to viral sequence(s) other than nef. Our results here clearly showed that HIV-1 Nef does not significantly affect the in vitro viral infectivity in natural target cells.     

APOBEC3G-independent reduction in virion infectivity during long-term HIV-1 replication in terminally differentiated macrophages

APOBEC3G (APO3G) is a cellular cytidine deaminase with potent antiviral activity. In the case of HIV, the antiviral activity of APO3G is counteracted by the viral Vif protein. Monocyte-derived macrophages (MDM) are terminally differentiated, non-dividing cells susceptible to HIV infection. Human MDM are known to express APO3G and HIV replication in these cells is dependent on Vif. Here we analyzed the correlation between HIV-1 replication and APO3G expression in MDM. Replication of wild type HIV-1 induced a gradual 4-5-fold reduction in APO3G expression. The efficiency of APO3G downregulation correlated with the efficiency of virus replication. Interestingly, despite downregulation of APO3G, the relative infectivity of viruses rapidly declined during the course of infection and was already reduced ∼ 90% prior to peak virus production. Cell-free virus preparations showed increased levels of a 41 kDa MA-CA processing intermediate. Sequence analysis around the MA-CA cleavage site and the protease and LTR regions did not reveal deaminase-induced hypermutation of the viral genome, suggesting that APO3G activity is not responsible for the incomplete Gag processing. Thus, the loss of infectivity of HIV-1 viruses produced from long-term infected primary macrophages is due to an APO3G-independent mechanism.     

Parainfluenza 3 virus: plaque-type variants lacking neuraminidase activity.

Virus clones lacking detectable neuraminidase activity (SC-YN and M-YN) as well as those possessing it (LT-910N and LT-YN) were isolated from bovine strains of parainfluenza 3 virus. LT-910N and LT-YN viruses produced large turbid plaques in MDBK cells, and SC-YN virus produced small clear plaques. Incorporation of a bacterial neuraminidase in agar overlay medium made SC-YN virus form large turbid plaques, whereas it made M-YN virus form large clear plaques. However, M-YN virus formed only pinhole plaques or no plaques in the absence of neuraminidase. The exogenous neuraminidase had little effect on the plaque formation of LT-910N and LT-YN viruses. M-YN virus induced extensive syncytial formation, and SC-YN virus produced less extensive syncytial formation. The exogenous neuraminidase enhanced replication of SC-YN and M-YN viruses and reduced syncytial formation by these viruses. The enzyme had little effect on replication and cytopathic effect of LT-910N and LT-YN viruses. The reason for these effects of the exogenous neuraminidase is discussed.     

Expression of viral envelope glycoprotein and transformation genes in cells transformed by a defective Kirsten murine sarcoma virus.

Concurrent expression of transformation properties and virion envelope glycoproteins has been observed as a property of several clones of normal rat kidney cells transformed by, but not producing, Kirsten murine sarcoma virus. The present studies were carried out to determine whether a genetic linkage exists between the viral sarcoma and envelope genes in these cells. Several alternative models for the possible structure and origin of the sarcoma and envelope genes were considered. One possibility, that the viral envelope gene was derived from an endogenous rat virus, was studied by characterization of the interference properties of the transformed cells. The sarcoma virus genome of envelope-positive clones was efficiently rescued by woolly monkey and murine xenotropic but not by murine ecotropic viruses. Thus, the interference properties of cells producing the envelope glycoprotein are analogous to those of a cell producing murine ecotropic virus, indicating that the envelope was of murine viral origin. In these experiments it was also found that sarcoma viruses rescued from envelope-positive cells upon superinfection with primate and xenotropic murine viruses could transform host cells for both xenotropic and ecotropic viruses, indicating that these superinfecting viruses became phenotypically mixed with the ecotropic envelope expressed in transformed, envelope-positive cells. Possible linkage between the envelope and transformation genes was analyzed by the frequency of concurrent rescue of sarcoma and envelope genes. Transfer of the Kirsten sarcoma viral genome to uninfected cells upon rescue by superinfection with woolly monkey virus showed a high frequency of apparent segregation of the transformation and envelope genes [from 29 to 57% for (KSV env⁺)NRK-6]. The model supported by the present data is that the transformed, envelope-positive cells were infected with a virus which contained both the envelope and the sarcoma genes.     

Identification and functional analysis of the fowlpox virus homolog of the vaccinia virus p37K major envelope antigen gene.

A fowlpox virus (FPV) gene with homology to the vaccinia virus p37K major envelope antigen gene was identified and sequenced. The predicted product has a molecular weight of 43,018 Da (p43K). The FPV p43K gene has 37.5% identity with its vaccinia counterpart and higher homology with a molluscum contagiosum virus gene (42.6% identity). Based on upstream sequences, p43K appears to be regulated as a late gene. Recombinant FPV were generated in which a large portion of p43K was replaced by the Escherichia coli lacZ gene. These recombinants failed to produce visible plaques under standard conditions. After prolonged incubation the microplaques developed into small macroscopic plaques. Plaques were purified on the basis of lacZ expression. Single-cycle growth curves comparing the p43K-deleted recombinant (designated fJd43Z) with parental FPV showed that the two viruses produce identical amounts of intracellular virions, but that fJd43Z released 20-fold fewer infectious particles into the medium. CsCl gradient centrifugation of [3H]thymidine-labeled virus was employed to examine differences in the production of physical particles. The two viruses produced equivalent levels of intracellular virions, but fJd43Z failed to produce detectable levels of released particles. FPV p43K is therefore involved in the release of virions from infected cells.     

In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication

Molecular clones of infectious bronchitis virus (IBV), derived from the Vero cell adapted Beaudette strain, were constructed, using an in vitro assembly method. In vitro transcribed RNA from a cDNA template that had been constructed from seven cDNA fragments, encompassing the entire genome of IBV, was electroporated into BHK-21 cells. The cells were overlaid onto the susceptible Vero cells and viable virus was recovered from the molecular clone. The molecularly cloned IBV (MIBV) demonstrated growth kinetics, and plaque size and morphology that resembled the parental Beaudette strain IBV. The recombinant virus was further manipulated to express enhanced green fluorescent protein (EGFP) by replacing an open reading frame (ORF) of the group-specific gene, ORF 5a, with the EGFP ORF. The rescued recombinant virus, expressing EGFP (GIBV), replicated to lower viral titers and formed smaller plaques compared to the parental virus and the MIBV. After six passages of GIBV, a minority of plaques were observed that had reverted to the larger plaque size and virus from these plaques no longer expressed EGFP. Direct sequencing of RT-PCR products derived from cells infected with the plaque-purified virus, which had lost expression of EGFP, confirmed loss of the EGFP ORF. The loss of EGFP expression (Delta5a IBV) was also accompanied by reversion to growth kinetics resembling the standard virus and intact recombinant virus. This study demonstrates that the 5a ORF is not essential for viral multiplication in Vero cells.     

A colorimetric assay for viral agents that produce cytopathic effects

Many animal viruses produce cytopathic effects in their host cells during a productive infection. While some virus infections can be assayed by the production of plaques, many viruses, while producing cytotoxicity, do not easily form plaques, or do not form plaques at all. Additionally, viruses within families such as the parvoviruses may have different preferred forms of titration making comparative virology difficult even among related groups. Porcine parvovirus (PPV), canine parvovirus (CPV), and minute virus of mice (MVM) are usually titrated using different infectivity assays. A direct comparison of infectious virus titer between these parvoviruses was sought, and a tetrazolium salt assay, MTT has been applied to measure cytopathic effect produced by viral infection for different members of the parvovirus family. Infectious PPV measured using the MTT and the TCID50 assays exhibited excellent correlation and titers for CPV and MVM were consistently duplicated using the MTT assay. The MTT assay was also applied to an unrelated virus, Sindbis, which is routinely titrated by plaque assay. MTT titration of Sindbis virus mutants was found to be valuable for preliminary screening. This assay can be adapted, by correlation to an accepted titration method, to any viral system which produces measurable cytopathic effect.     

Biological Properties of Two Strains of Simian Virus 40 Isolated from Patients with Progressive Multifocal Leukoencephalopathy

Biological properties of two strains of simian virus 40 (SV40) from brains of two patients with progressive multifocal leukoencephalopathy (PML) have been compared to those of a standard laboratory strain of SV40. Infectivity of both SV40-PML viruses was resistant to treatment with chloroform, low pH, and 50 C for 120 min. African green monkey kidney and BSC-1 cells were the most sensitive for viral replication, and cytopathology in these cultures was indistinguishable from that caused by SV40. Both viruses formed plaques in these cells. but, in African green monkey kidney cells, strain 1 virus produced plaques measuring 2 mm in diameter whereas strain 2 virus produced pleomorphic plaques varying from 1 to 10 mm in diameter. Hamster cells were not permissive for viral replication, and infection resulted only in viral transformation. Inoculation of human fetal glial cells resulted in a permissive lytic infection of one cell type and a persistent infection with only partial expression of the viral genome in the other. No morphological evidence of transformation was evident in the latter cells. Both strains of SV40-PML viruses were neutralized by commercial anti-SV40 serum, but in reciprocal kinetic neutralization tests differences in K values were noted when each was compared to SV40. Both viruses showed oncogenicity for hamsters, producing undifferentiated sarcomas when injected subcutaneously and choroid plexus papillomas after intracerebral inoculation. All hamster tumor cells contained intranuclear immunofluorescent tumor antigen. This was indistinguishable from SV40 T antigen in reciprocal staining reactions using hamster anti-T antibody induced by the two SV40-PML agents and SV40. These two human agents appear therefore to be new variants of simian virus 40.     

The packaging of human immunodeficiency virus type 1 RNA is restricted by overexpression of an RNA helicase DHX30

RNA helicases are a large family of proteins that are able to unwind RNA duplex and remodel the structure of RNA-protein (RNP) complexes using energy derived from hydrolysis of nucleotide triphosphates (NTPs). Every step of cellular RNA metabolism involves the activity of RNA helicases. Not surprisingly, more and more RNA helicases are reported to participate in the replication of viruses including the human immunodeficiency virus type 1 (HIV-1). Here, we provide evidence that overexpression of an RNA helicase named DHX30 enhances HIV-1 gene expression, but leads to the generation of viruses that package significantly low levels of viral RNA and exhibit severely decreased infectivity. These data reveal the complex roles of DHX30 in HIV-1 replication and implicate an inhibitory activity of DHX30 in HIV-1 RNA packaging.