Quantitative determination of the infectivity of the proviral DNA of a retrovirus in vitro: Evaluation of methods for DNA inactivation

All viral vaccines contain contaminating residual DNA derived from the production cell substrate. The potential risk of this DNA, particularly when derived from tumorigenic cells, has been debated for over 40 years. While the major risk has been considered to be the oncogenicity of the DNA, another potential risk is that a genome of an infectious virus is present in this DNA. Such a genome might generate an infectious agent that could establish an infection in vaccine recipients. To determine the quantity of a retroviral provirus in cellular DNA that can establish a productive infection in vitro, we developed a transfection/co-culture system capable of recovering infectious virus from 1 pg of cloned HIV DNA and from 2 μg of cellular DNA from HIV-infected cells. We demonstrate that infectivity can be reduced to below detectable levels either by lowering the median size of the DNA to 350 base pairs or by treatment with β-propiolactone. From the amount of reduction of infectivity, we calculate that clearance values in excess of 10⁷ are attainable with respect to the infectivity associated with residual cell-substrate DNA. Thus, the potential risk associated with DNA can be substantially reduced by degradation or by chemical inactivation.     

Issues associated with residual cell-substrate DNA in viral vaccines

The presence of some residual cellular DNA derived from the production-cell substrate in viral vaccines is inevitable. Whether this DNA represents a safety concern, particularly if the cell substrate is derived from a tumor or is tumorigenic, is unknown. DNA has two biological activities that need to be considered. First, DNA can be oncogenic; second, DNA can be infectious. As part of our studies to assess the risk of residual cell-substrate DNA in viral vaccines, we have established assays that can quantify the biological activities of DNA. From data obtained using these assays, we have estimated the risk of an oncogenic or an infectious event from DNA. Because these estimates were derived from the most sensitive assays identified so far, they likely represent worst-case estimates. In addition, methods that inactivate the biological activities of DNA can be assessed and estimations of risk reduction by these treatments can be made. In this paper, we discuss our approaches to address potential safety issues associated with residual cellular DNA from neoplastic cell substrates in viral vaccines, summarize the development of assays to quantify the oncogenic and infectivity activities of DNA, and discuss methods to reduce the biological activities of DNA.     

Size analysis of residual host cell DNA in cell culture-produced vaccines by capillary gel electrophoresis

Residual host cell DNA poses potential safety concerns for cell culture-derived vaccines or other biological products. In addition to the quantity of residual DNA, the size distribution is an important measure for determination of its associated risk factor. We have developed a new method for residual DNA size analysis, based on capillary gel electrophoresis (CGE) technology with sensitive laser induced fluorescence detection (LIF). The performance of this method was optimized through empirical selection of appropriate testing conditions and optimized conditions are presented. Examples are given to demonstrate the successful employment of this method for residual DNA size analysis of cell culture-produced vaccine samples.     

Introduction of liposome-encapsulated SV40 DNA into cells

DNA, isolated from Simian virus 40 (SV40), has been encapsulated in large (0.4-micrometer diameter) unilamellar phospholipid vesicles. The procedure used for liposome preparation encapsulated the SV40 DNA at high efficiency (30 to 50% entrapment) and did not alter the physical or biological properties of the DNA molecules. The biological activity of the liposome-entrapped viral DNA was determined by plaque assays on a permissive monkey cell line. The infectivity of liposome-entrapped SV40 DNA was enhanced at least 100-fold over that of free naked DNA. Importantly, the infectivity of vesicle-entrapped DNA was resistant to DNase digestion, dependent on the amount of DNA encapsulated per vesicle and on the vesicle lipid composition. Liposomes composed of phosphatidylserine were the most efficient for delivery of DNA to cells (1.8 x 10(3) plaque-forming units/micrograms of DNA). Following the incubation of DNA-containing liposomes with cells, their infectivity could be enhanced an additional 10- to 200-fold by exposing the cells to high concentrations of polyethylene glycol or glycerol. Under these conditions the infectivity of liposome-encapsulated SV40 DNA (3 x 10(5) plaque-forming units/microgram) was comparable with values reported using the calcium phosphate method. In addition to providing a sensitive assay for monitoring and optimizing the delivery of vesicle contents to cells, the liposome-mediated delivery of nucleic acids may have potential for increasing the efficiency of DNA delivery to cells and for extending the number of cell types which can be transformed or transfected.     

Photochemical inactivation of viruses with psoralens: an overview.

In the presence of longwave ultraviolet light, psoralen derivatives photoreact with the nucleic acids within intact viruses and cells. This photoreaction can leave protein antigens and other surface components relatively unmodified, while eliminating the infectivity of a wide range of infectious agents. The kinetics of inactivation differ among RNA and DNA viruses photoreacted with different derivatives of psoralen. The inactivation kinetics are nonlinear as a result of photodegradation of psoralens and the unexplained biphasic inactivation of some viruses. In spite of these complexities, the photoreaction is capable of generating broad safety margins in the disinfection of microbial products under gentle, physiologic conditions. The psoralen photoreaction provides a potential method for inactivating both known and unknown viruses in active blood products. Psoralen-inactivated viruses have already proven useful as noninfectious antigens for use in immunoassays and as successful experimental vaccines.     

Infective Virus Substructure from Vesicular Stomatitis Virus

Treatment of suspensions of vesicular stomatitis virus with Tween-ether results in a rapid and considerable loss of infectivity (ca. 4 logs in 2 min), but the residual infectivity is comparatively stable to further treatment with ether. The infectivity remaining after the short exposure to Tween-ether is not due to virus for the following reasons. (i) It is much less infective for tissue cultures than for mice, whereas the intact virion is equally infective for both hosts. (ii) The residual infectivity is much less stable than virus infectivity in both sucrose and tartrate gradients. (iii) Virus immune serum does not neutralize its activity. (iv) The infectivity is associated with material which sediments further in sucrose gradients and has a greater buoyant density in tartrate gradients than the virion. Experiments with (32)P-labeled virion showed that the infective substructure contains ribonucleic acid with the same sedimentation characteristics as that extracted from the virion. Electron microscopy shows that the infective component has the same overall bullet-like structure as the virion but lacks the outer envelope and fringe structure.     

Real time quantitative PCR as a method to evaluate simian virus 40 removal during pharmaceutical protein purification.

Continuous cell lines used for pharmaceutical protein manufacturing have the potential to be contaminated by viruses. To ensure the safety of pharmaceutical proteins derived from continuous cell lines, validation of the ability of the manufacturing process to clear potential contaminating viruses is required for product registration. In this paper, a real time quantitative PCR method has been applied to the evaluation of simian virus 40 (SV40) removal during chromatography and filtration procedures. This method takes advantage of the 5'-3' exonuclease activity of Taq DNA polymerase and utilizes the PRISM 7700 sequence detection system of PE Applied Biosystems for automated SV40 DNA quantification through a dual-labeled fluorogenic probe. This method provides accurate and reproducible quantification of SV40 DNA. The SV40 clearance during chromatography and filtration procedures determined by this method is highly comparable with that determined by the cell-based infectivity assay. This method offers significant advantages over cell-based infectivity assays, such as higher sensitivity, greater reliability, higher sample throughput and lower cost. This method can be potentially used to evaluate the clearance of all model viruses during chromatography and filtration procedures. This method can be used to substitute cell-based infectivity assays for process validation of viral removal procedures and the availability of this method should greatly facilitate and reduce the cost of viral clearance evaluations required for new biologic product development.     

Transfection of Escherichia coli Spheroplasts II. Relative Infectivity of Native, Denatured, and Renatured Lambda, T7, T5, T4, and P22 Bacteriophage DNAs

The change of infectivity of phage DNAs after heat and alkali denaturation (and renaturation) was measured. T7 phage DNA infectivity increased 4- to 20-fold after denaturation and decreased to the native level after renaturation. Both the heavy and the light single strand of T7 phage DNA were about five times as infective as native T7 DNA. T4 and P22 phage DNA infectivity increased 4- to 20-fold after denaturation and increased another 10- to 20-fold after renaturation. These data, combined with other authors' results on the relative infectivity of various forms of phiX174 and lambda DNAs give the following consistent pattern of relative infectivity. Covalently closed circular double-stranded DNA, nicked circular double-stranded DNA, and double-stranded DNA with cohesive ends are all equally infective and also most highly infectious for Escherichia coli lysozyme-EDTA spheroplasts; linear or circular single-stranded DNAs are about 1/5 to 1/20 as infective; double-stranded DNAs are only 1/100 as infective. Two exceptions to this pattern were noted: lambda phage DNA lost more than 99% of its infectivity after alkaline denaturation; this infectivity could be fully recovered after renaturation. This behavior can be explained by the special role of the cohesive ends of the phage DNA. T5 phage DNA sometimes showed a transient increase in infectivity at temperatures below the completion of the hyperchròmic shift; at higher temperatures, the infectivity was completely destroyed. T5 DNA denatured in alkali lost more than 99.9% of its infectivity; upon renaturation, infectivity was sometimes recovered. This behavior is interpreted in terms of the model of T5 phage DNA structure proposed by Bujard (1969). The results of the denaturation and renaturation experiments show higher efficiencies of transfection for the following phage DNAs (free of single-strand breaks): T4 renatured DNA at 10(-3) instead of 10(-5) for native DNA; renatured P22 DNA at 3 x 10(-7) instead of 3 x 10(-9) for native DNA; and denatured T7 DNA at 3 x 10(-6) instead of 3 x 10(-7) for native DNA.     

Inactivation of human immunodeficiency virus type 1 in blood samples stored as high-salt lysates.

Blood samples to be tested for the presence of parasite DNA by using specific DNA probes are routinely stored in our laboratory as high-salt lysates (HSL). To safeguard against the risk of accidental infection with etiological agents such as the human immunodeficiency virus type 1 (HIV-1) while manipulating large numbers of blood samples in preparation for DNA probing, we determined the residual infectivity of HIV-1 after exposure to HSL components. Both high-titer virus stocks or provirus-carrying cells, suspended either in tissue culture medium or freshly drawn blood, were completely inactivated upon contact with the HSL components. This was verified by the absence of any detectable HIV-1-specific antigen in the supernatants of long-term cultures and the absence of virus-specific DNA fragments after amplification by polymerase chain reaction with DNA from such cultures as target DNA. These results support the conclusion that the virus is in fact completely inactivated by contact with the HSL components, rendering blood specimens stored as HSL noninfectious in regard to HIV-1.     

Inactivation of human immunodeficiency virus type 1 in blood samples stored as high-salt lysates

Blood samples to be tested for the presence of parasite DNA by using specific DNA probes are routinely stored in our laboratory as high-salt lysates (HSL). To safeguard against the risk of accidental infection with etiological agents such as the human immunodeficiency virus type 1 (HIV-1) while manipulating large numbers of blood samples in preparation for DNA probing, we determined the residual infectivity of HIV-1 after exposure to HSL components. Both high-titer virus stocks or provirus-carrying cells, suspended either in tissue culture medium or freshly drawn blood, were completely inactivated upon contact with the HSL components. This was verified by the absence of any detectable HIV-1-specific antigen in the supernatants of long-term cultures and the absence of virus-specific DNA fragments after amplification by polymerase chain reaction with DNA from such cultures as target DNA. These results support the conclusion that the virus is in fact completely inactivated by contact with the HSL components, rendering blood specimens stored as HSL noninfectious in regard to HIV-1.     

地高辛标记探针检测生物制品中残余DNA含量

用地高辛标记探针检测由传代细胞系生产的人用精制狂犬病疫苗,重组（CHO细胞）乙肝疫苗,出血热疫苗及痢疾多糖结合疫苗原液中残余DNA含量。结果表明,该方法特异性强,灵敏度高,可用于上述生物制品中残余DNA含量的检测。     

Delimitation of essential genes of cassava latent virus DNA 2

Insertion and deletion mutagenesis of both extended open reading frames (ORFs) of cassava latent virus DNA 2 destroys infectivity. Infectivity is restored by coinoculating constructs that contain single mutations within different ORFs. Although frequent intermolecular recombination produces dominant parental-type virus, mutants can be retained within the virus population indicating that they are competent for replication and suggesting that rescue can occur by complementation of trans acting gene products. By cloning specific fragments into DNA 1 coat protein deletion vectors we have delimited the DNA 2 coding regions and provide substantive evidence that both are essential for virus infection. Although a DNA 2 component is unique to whitefly-transmitted geminiviruses, the results demonstrate that neither coding region is involved solely in insect transmission. The requirement for a bipartite genome for whitefly-transmitted geminiviruses is discussed.     

Estrogen target cells. Establishment of a cell line derived from the rat pituitary tumor MtT/F4.

Pretreatment of rabbit kidney cells with cytochalasins B and D (CB, CD) enhanced herpes simplex virus type 2 (HSV-2) DNA infectivity 3- to 6-fold over values obtained using the standard CaCl₂ technique. Cells were pretreated with CB for 4–6 h to achieve infectivity enhancement. A lower concentration of CD, and shorter pretreatment periods, resulted in comparable DNA infectivity. Separate exposure of cells to colchicine, colcemid, or vinblastine increased DNA infectivity 7-, 6-, and 5-fold, respectively, over control values. Additional enhancement was obtained when CD was used together with any one of the aforementioned drugs. Maximal enhancement of HSV-2 DNA infectivity was obtained by pretreating recipient cells with a drug mixture containing colchicine, colcemid, and CD. This treatment maximized infectivity levels 20- to 30-fold over CaCl₂ control values.     

Comparison of animal infectivity and excystation as measures of Giardia muris cyst inactivation by chlorine.

In this study, in vitro excystation and mouse infectivity were compared as methods for quantitatively determining the viability of Giardia muris cysts before and after exposure to free residual chlorine. The mouse infectivity results show that very few cysts (1 to 15) constitute an infectious dose. The results of the inactivation studies indicate that in vitro excystation is an adequate indication of G. muris cyst infectivity for the host and can be used to determine the effects of disinfectants on cyst viability.     

Comparison of animal infectivity and excystation as measures of Giardia muris cyst inactivation by chlorine

In this study, in vitro excystation and mouse infectivity were compared as methods for quantitatively determining the viability of Giardia muris cysts before and after exposure to free residual chlorine. The mouse infectivity results show that very few cysts (1 to 15) constitute an infectious dose. The results of the inactivation studies indicate that in vitro excystation is an adequate indication of G. muris cyst infectivity for the host and can be used to determine the effects of disinfectants on cyst viability.     

Influence of Diethylaminoethyl-Dextran on Uptake and Degradation of Polyoma Virus Deoxyribonucleic Acid by Mouse Embryo Cells

The uptake of (32)P-labeled polyoma virus deoxyribonucleic acid (DNA) (I and II + III) by mouse embryo cells was increased from two- to fivefold in the presence of 500 mug of diethylaminoethyl-dextran (DEAE-D) per ml. This concentration of DEAE-D gives maximal enhancement of infectivity; however, the increase is many thousand-fold. As the DEAE-D concentration was increased from 0 mug/ml, uptake and infectivity increased to flat maxima and then decreased in a similar manner, except that at low DEAE-D concentrations uptake was relatively much greater than infectivity. Several other polycations also increased DNA uptake but did not enhance infectivity, and uptake of viral DNA was unaffected by the presence of mouse DNA, although infectivity was reduced. Thus, increased uptake is not the sole basis for the enhancement of infectivity produced by DEAE-D. The possibilities that DNA complexed with DEAE-D penetrates more rapidly or is stabilized against degradation do not completely account for enhancement since complexes formed in mixtures of DNA and DEAE-D, which sedimented heterogeneously from 40 to 60S, were infectious only for monolayers treated with DEAE-D. A more likely factor in enhancement is inhibition of the cellular nuclease activity detected, since virus DNA exposed to cells was much more degraded in the absence than in the presence of DEAE-D. The nuclease activity produced single-strand breaks in double-stranded DNA. Treatment of monolayers with deoxyribonuclease after adsorption of DNA in the presence of DEAE-D reduced cell-associated radioactivity by about 70%, although the number of plaques formed was not affected. In the absence of DEAE-D, 90 to 100% was removed by deoxyribonuclease. Thus, in both cases most of the DNA was adsorbed extracellularly. The greater deoxyribonuclease-resistant fraction in the presence of DEAE-D would be consistent with another possibility: that enhancement results from an increase in DNA penetration rate due to some action of DEAE-D on the cell.     

Rapid clearance of intranasally administered DNA from rat tissues

The cold-adapted (ca) live attenuated influenza vaccine (LAIV) strains are manufactured in embryonated hens' eggs. Recently, a clonal isolate from Madin Darby Canine Kidney (MDCK) cells was derived and characterized to assess its utility as a potential cell substrate for the manufacturing of LAIV [1]. Since MDCK cells are a transformed continuous cell line [2], and low levels of residual cellular components (DNA and protein) are found in the intermediates and final filled vaccine, we sought to characterize the uptake and clearance of MDCK DNA from tissues in order to assess theoretical risks associated with manufacturing LAIV in MDCK cell culture.In order to address this concern, MDCK DNA uptake and clearance studies were performed in Sprague Dawley rats. DNA extracted from MDCK Master Cell Bank (MCB) cells was administered via an intranasal (IN) or intramuscular (IM) route. Tissue distribution and clearance of MDCK DNA were then examined in fourteen selected tissue types at selected time points post-administration using a quantitative PCR assay specific for canine (SINE) DNA.Results from these studies demonstrate that the uptake and clearance of MDCK DNA from tissues vary depending on the route of administration. When DNA was administered intranasally, as compared to intramuscularly, detectable DNA levels were lower at all time points. Thus, the intranasal route of vaccine administration appears to reduce potential risk associated with residual host cell DNA that may be present in cell culture produced final vaccine products.     

Prevention of Contamination by Xenotropic Murine Leukemia Virus-Related Virus: Susceptibility to Alcohol-Based Disinfectants and Environmental Stability

Xenotropic murine leukemia virus-related virus (XMRV) represents a novel γ-retrovirus that is capable of infecting human cells and has been classified as a biosafety level 2 (BSL-2) organism. Hence, XMRV represents a potential risk for personnel in laboratories worldwide. Here, we measured the stability of XMRV and its susceptibility to alcohol-based disinfectants. To this end, we exposed an infectious XMRV reporter virus encoding a secretable luciferase to different temperatures, pH values, and disinfectants and infected XMRV-permissive Raji B cells to measure residual viral infectivity. We found that 1 min treatment of XMRV particles at 60°C is sufficient to reduce infectivity by 99.9%. XMRV infectivity was maximal at a neutral pH but was reduced by 86% at pH 4 and 99.9% at pH 10. The common hand and surface disinfectants ethanol and isopropanol as well as the cell fixation reagent paraformaldehyde abrogated XMRV infectivity entirely, as indicated by a reduction of infectivity exceeding 99.99%. Our findings provide evidence of specific means to inactivate XMRV. Their application will help to prevent unintended XMRV contamination of cell cultures in laboratories and minimize the risk for laboratory personnel and health care workers to become infected with this biosafety level 2 organism.     

Enhanced infectivity of adenovirus type 2 DNA and a DNA-protein complex.

The infectivity of adenovirus type 2 DNA and a DNA-protein complex was studied in 293 cells, a human embryonic kidney cell line transformed by sheared adenovirus type 5 DNA, and in human KB cells. Adenovirus type 2 DNA was more infectious (up to about 40-fold) in 293 cells than in KB cells, whereas a DNA-protein complex (prepared by a rapid procedure) had about the same infectivity in both cell lines. These data may mean that a factor present in 293 cells (perhaps a viral-coded protein) enhances the infectivity of free viral DNA. The infectivity of DNA and the DNA-protein complex was increased up to fivefold by brief treatment of cell monolayers with 25% dimethyl sulfoxide after transfection. Under these conditions, (i) the infectivity of native adenovirus type 2 DNA ranged from 400 to 1,300 PFU/microgram of DNA in 293 cells and from about 9 to 14 PFU/microgram of DNA in KB cells, and (ii) the infectivity of the DNA-protein complex was 6 X 10(3)to 2 X 10(4) PFU/microgram in 293 cells and 1.4 X 10(4) to 1.6 X 10(4) PFU/microgram in KB cells.