Solid phase capture method for the specific amplification of microbial nucleic acids--avoidance of false-positive and false-negative reactions

DNA amplification assays such as the polymerase chain reaction are being developed for the amplification of small quantities of microbial nucleic acids. These assays offer the potential for a great deal of sensitivity. However, the high level of sensitivity increases the likelihood of cross-contamination of amplified products and the generation of false-positive reactions. In addition, substances in body fluids can inhibit the efficient performance of the amplification reactions. We have developed an assay format in which microbial nucleic acids are specifically bound to a solid phase surface. Contaminating DNA and enzyme inhibitors present in the sample are removed by washing prior to the performance of the amplification reaction. We could use this system to amplify and detect small amounts of HIV DNA diluted in whole blood. The assay system could distinguish target DNA from contaminating DNA fragments generated by prior amplification reactions.

Gastrointestinal dysfunction and disaccharide intolerance in children infected with human immunodeficiency virus

Because gastrointestinal dysfunction is a major problem in children with human immunodeficiency virus (HIV) infection, we utilized breath hydrogen measurements to determine the relationship between disaccharide malabsorption and gastrointestinal dysfunction in HIV-infected children. We found a strong association between lactose intolerance and persistent diarrheal disease in this population (p less than 0.007, Mann-Whitney U test). We also found evidence of sucrose malabsorption and persistent diarrheal disease in three of the children. Extensive microbiologic evaluations failed to reveal an etiologic agent related to the occurrence of gastrointestinal symptoms. Our findings indicate that disaccharide intolerance is a common occurrence in HIV-infected children with persistent diarrheal disease. Careful attention to dietary intake may be required to ameliorate clinical symptoms and to maintain adequate nutrition.

Allergenicity of orally administered immunoglobulin preparations in food-allergic children

Passive immunization by the oral administration of immunoglobulin preparations derived from bovine milk, chicken egg, and human sera has been proposed as a method for the prevention and treatment of enteric diseases. However, the allergenic potential of these proteins may be a factor limiting their widespread use for disease prevention. An in vitro study with sera from milk- and egg-allergic children was performed to determine whether these immunoglobulin preparations have allergenic potential. Protein extracts of milk, bovine immunoglobulin, egg white, human immune globulin, and five egg yolk antiviral immunoglobulin preparations were bound to nitrocellulose paper. These preparations were probed for specific IgE binding with sera from milk- and egg-allergic patients. Of 22 milk-hypersensitive patients, 16 had specific IgE binding against the bovine immunoglobulin preparation. Of 28 egg-allergic patients 15 had specific IgE binding against one or more of the egg yolk-derived antiviral chicken immunoglobulins. Control sera were negative against the milk and egg preparations. Western blot analysis confirmed that milk- and egg-allergic patients had IgE-specific antibodies for bovine and chicken immunoglobulin molecules. Therefore, the removal of contaminating proteins from milk and egg antibody preparations would be unlikely to eliminate their allergenic potential. In contrast, sera from milk- and egg-allergic patients displayed no detectable IgE binding to human immunoglobulin preparations. These data indicate that the administration of antibody preparations derived from bovine and chicken sources may lead to severe allergic reactions in milk- or egg-sensitized patients and to sensitization in some nonallergic individuals.(ABSTRACT TRUNCATED AT 250 WORDS)

Humoral immune responses to gag and env proteins from human immunodeficiency virus type 1 in hemophiliac patients

Solid-phase enzyme immunoassays using recombinant gag and env proteins were developed to study humoral immune responses to HIV infection in a cohort of 105 hemophiliac patients. Thirteen patients with ARC or AIDS and 92 asymptomatic patients were studied. A cross-sectional study showed a wide range of antibody responses to gag and env proteins; however, the differences between the ARC/AIDS and asymptomatic patients were statistically significant for both antigens (P less than .0004). In a longitudinal study, antibody levels in sera from 11 asymptomatic patients with gag antibody log units less than or equal to 1.5 were compared to levels in sera from 10 ARC/AIDS patients and 8 asymptomatic patients with gag antibody greater than 1.5. These patient groups were followed for comparable periods of time (67.1-71.7 mo). The asymptomatic patients with low gag antibody and the ARC/AIDS patients showed a similar pattern of antibody response to gag protein overtime. In hemophiliac patients with HIV-1 infection a low titer of antibody to gag protein is not invariably associated with clinical deterioration and is not a useful serologic marker of impending progression to AIDS.

Rotaviruses specifically bind to the neutral glycosphingolipid asialo-GM1

Rotaviruses are the major etiologic agents of severe diarrhea in children. Many rotaviruses encode a hemagglutinin which binds to sialic acids. We report that rotaviruses specifically recognize the neutral glycosphingolipid gangliotetraosylceramide (asialo-GM1 or GA1). GA1 resolved by thin-layer chromatography is bound by rotavirus, and binding is blocked by neutralizing rotavirus antiserum. Similar glycosphingolipid structures, such as globoside, gangliotriaosylceramide, and GA1 oxidized with galactose oxidase are ineffective in binding rotavirus. Other enteric viruses also specifically bind GA1. GA1 adsorbed to polystyrene beads inhibits rotavirus replication in vitro (as do anti-GA1 antibodies). The use of orally administered immobilized GA1 or anti-GA1 antibodies may prove useful in preventing or attenuating rotaviral and other enteric viral infections.

Growth of group A rotaviruses in a human liver cell line

Recent observations in children with rotavirus gastroenteritis and in infant mice given rotavirus vaccine by oral administration suggest that this well-known gastrointestinal pathogen may infect the liver. To examine this possibility, the susceptibility of Hep G2 cells to infection with a variety of rotavirus strains was tested. These cells were used because they are considered to be well differentiated and exhibit many liver-specific functions. The Hep G2 cells supported the growth of the simian strain rhesus rotavirus (MMU 18006), a strain currently being used in vaccine trails, but did not support the growth of any human strain (D, DS1, Price or ST3). The rhesus rotavirus infection was cytopathic and resulted in release of lactate dehydrogenase. Rhesus rotavirus growth in Hep G2 cells displayed trypsin-enhanced infectivity and was inhibited by pretreatment of cells with Arthrobacter ureafaciens neuraminidase but not with neuraminidase from Clostridium perfringens. Hep G2 cells were also permissive for another simian strain (SA11), a bovine strain (UK) and single gene substitution reassortants containing VP7 (the major outer capsid neutralization protein) from a human rotavirus strain and the remaining 10 genes from either rhesus rotavirus or UK. In general, UK and its reassortants produced lower levels of antigen than did rhesus rotavirus and its reassortants. Hep G2 cells and other hepatic cell lines may prove to be useful tools to explore the hepatotropic potential of wild-type rotaviruses and candidate vaccine strains.

Diagnosis of Chlamydia trachomatis cervical infection by detection of amplified DNA with an enzyme immunoassay

A sensitive and specific system for detection of amplified Chlamydia trachomatis DNA from cervical specimens by fluorometric quantitation in an enzyme immunoassay (EIA) format (polymerase chain reaction [PCR]-EIA) is described. The primers selected for PCR-amplified DNA were from the 15 serovars of C. trachomatis and two strains of Chlamydia pneumoniae (TWAR). One strain of Chlamydia psittaci (Borg) was not amplified. One hundred four previously cultured cervical specimens were evaluated. Forty-six culture-positive specimens containing from 1+ to 4+ inclusion bodies were all positive by PCR-EIA. Of 58 culture-negative specimens, 2 were repeatedly positive and were nonreactive with control probes. This assay system represents a sensitive and specific combination of technologies for the quantitative detection of C. trachomatis DNA directly from a body fluid.

Rotavirus

Since their discovery in the 1970s, the human rotaviruses have been recognized as the most important cause of acute infectious gastroenteritis among infants and children worldwide. Rotavirus has been found to infect almost all mammalian and avian species tested, and is primarily a disease of the young. In humans, rotavirus is the most frequent gastrointestinal pathogen in infants and children less than 2 years of age. In developing countries, the attack rate peaks at 6 months of age, whereas in developed areas of the world the virus is most commonly found among children 6-12 months of age. Rotavirus displays a marked seasonality in temperate climates, with the number of cases peaking in the colder winter months. In tropical climates, this seasonality is not as apparent, and infection may occur year round. Symptoms of rotavirus infection are non-specific and include vomiting and diarrhoea, occasionally accompanied by a low grade fever. Dehydration is more common with rotavirus infection than with most bacterial pathogens, and is the most common cause of death related to rotavirus infection. Treatment is non-specific and includes the use of oral rehydration therapy, especially in developing countries where malnutrition is common. Strategies for the prevention of rotavirus infection are dependent on advances in the understanding of the molecular biology of the rotavirus. The genetic structure of the virus has been extensively studied, and a number of the structural proteins have been identified. The neutralization antigens, located on VP4 and VP7, may be important in conferring immunity to rotavirus in vivo. Two animal-derived and several reassortant rotavirus vaccines are currently being evaluated in field studies, and a number of other candidate vaccines are being tested in vitro and in animal studies.

Epidemiology and potential methods for prevention of neonatal intestinal viral infections

Viral infections of the gastrointestinal tract remain a major problem during the neonatal period. In addition to causing acute diarrhea, rotaviruses and other enteric viruses may be involved in the pathogenesis of necrotizing enterocolitis and other neonatal enteric diseases. There are several potential methods for the prevention and treatment of gastrointestinal viral infections. Antiviral immunoglobulins might be used to inhibit intestinal viral replication. Since only small concentrations of serum immunoglobulins are present at mucosal surfaces, oral administration of immunoglobulins might be utilized to maximize antiviral efficacy. Alternatively, inhibitors of specific glycoproteins of virus-cell binding might be used to prevent the productive infection of intestinal epithelial cells. In addition, since many enteric viruses require proteolytic enzymes for protein cleavage, protease inhibitors may prove effective for inhibition of intestinal viral replication. At this time, these methods have proven useful for the inhibition of rotavirus infection in experimental animals. The successful application of these and other methods for the prevention of enteric infections in humans might substantially reduce the morbidity and mortality associated with enteric diseases in high-risk neonates.

SA11 rotavirus is specifically inhibited by an acetylated sialic acid

Bovine salivary mucin (BSM) inhibits rotavirus replication in vitro and in vivo. The inhibitory effect of BSM in vitro is abolished by Arthrobacter ureafaciens neuraminidase but not by Clostridia perfringens neuraminidase; it is abolished by mild base deacetylation but not by influenza C acetylesterase. The data suggest that SA11 rotavirus binds to a specific sialic acid structure on BSM different from the sialic acids recognized by other viruses.

Solution hybridization and enzyme immunoassay for biotinylated DNA-RNA hybrids to detect enteroviral RNA in cell culture

A non-isotopic hybridization assay is described for detection of enteroviral RNA in cell culture. Two biotin-labelled cDNA probes, corresponding to 1 kb from the 5' end and 3.5 kb from the 3' end of the coxsackievirus B3 genome, were hybridized in solution with protease and detergent-treated cell culture suspensions. Labelled DNA-RNA hybrids were captured on microtiter plates coated with anti-biotin antibody and bound hybrids were measured with a beta-galactosidase-labelled monoclonal antibody specific for DNA-RNA hybrids. Coxsackie B3 was detected at a concentration of 500 pfu ml-1. The limit of detection for other enteroviruses ranged from 10(3.3) to 10(5.8) pfu ml-1. The enteroviruses that could be detected included coxsackie B1 and 3, coxsackie A1-6 and 15, poliovirus types 1-3, and enteroviruses 7, 11, and 71. ECHO 22 was the only enterovirus, of those that were tested, that could not be detected. The solution hybridization reaction and enzyme immunoassay for DNA-RNA hybrids does not require the use of radiolabelled probes or extraction of RNA with phenol. The assay yields a quantitative endpoint, which avoids the subjectivity inherent in membrane-based methods. These features would make the assay more adaptable to clinical laboratories than other formats which have been devised for measurement of viral RNA.

Pathology of infectious diarrhea of infant rats (IDIR) induced by an antigenically distinct rotavirus

Suckling rats were inoculated with a group B rotavirus to determine the progression of the morphologic changes induced in the intestine by this virus. Several changes were observed by light microscopy 1 day after viral inoculation: shortening of small intestinal villi, villous epithelial necrosis, and villous epithelial syncytia. The lesions were most often present in the distal small intestine, although other small intestinal segments were affected to a lesser degree. By day 3 post-inoculation, epithelial necrosis, and syncytia were no longer present; however, the villous epithelium was disorganized and irregularly vacuolated, and intestinal crypt epithelium was hyperplastic. Alterations in villous height to crypt depth ratios were present in portions of the small intestine for the remainder of the 12-day study period. Epithelial syncytia appeared to form by the breakdown of the lateral interdigitating membranes of the absorptive villous epithelium. Viral particles, abundant in the syncytia, appeared to form from amorphous or reticular arrays of viral precursor material. Group B rotaviral antigens, as detected by indirect immunofluorescence, were present in large amounts in the small intestinal villous epithelium only on the first day after viral inoculation. These studies show that two important diagnostic features of group B rotaviral infections of rats, epithelial syncytia and viral antigen as determined by immunofluorescence, are present only on the first day of disease. These findings should be taken into consideration when attempting to diagnose disease induced by this agent.

Immunodetection of DNA with biotinylated RNA probes: a study of reactivity of a monoclonal antibody to DNA-RNA hybrids

A quantitative, nonisotopic hybridization assay which measures specific DNA-RNA hybrids is described. A biotinylated RNA probe is reacted in solution with a DNA target and the labeled hybrids are immobilized onto a solid phase surface with an antibiotin antibody. Bound hybrids are detected with a beta-galactosidase-labeled monoclonal antibody against DNA-RNA hybrids and are quantitated with the addition of a fluorogenic substrate. In a model system using pSP65 or pGEM4 plasmids and transcripts, biotinylated RNA probes allowed detection of 5 pg of DNA in 10(6) pg of exogenous nucleic acids in 1000 min. Signals generated in the system depended on input target length. A nucleic acid target of 25 bases was still detectable in the assay. Human immunodeficiency virus type 1 (HIV-1) DNA was amplified in the polymerase chain reaction with Taq polymerase and a set of primers for the pol gene, one of which contained T7 RNA polymerase promoter sequences. A HIV-RNA probe of 326 bases was transcribed with T7 RNA polymerase using polymerase chain reaction (PCR) amplified DNA as a template. The RNA probe of 326 bases performed as well as a RNA probe of 2588 bases for detection of a DNA segment of 355 bp. For detection of dilutions of HIV-1 with PCR, a set of primers (outer set) was used for amplification of HIV-1 DNA. In a separate reaction a set of primers nested between the first set generated through PCR an amplified DNA fragment with the T7 promoter. This fragment was transcribed for the synthesis of a biotinylated RNA probe. This probe could then be reacted with material amplified with the outer set of primers. Ten copies of HIV-DNA could be detected with this procedure.

Nonisotopic detection of RNA in an enzyme immunoassay using a monoclonal antibody against DNA-RNA hybrids

A sensitive nonisotopic solution hybridization assay for detection of RNA is described and characterized using a pSP65 plasmid model system. The assay procedure is based on a hybridization reaction in solution between a biotinylated DNA probe and a target RNA. The biotin-labeled hybrids are captured on a microtiter plate coated with an antibody to biotin. Bound DNA-RNA hybrids are detected by an immunoreaction with an enzyme-labeled monoclonal antibody specifically directed against DNA-RNA heteropolymers and the hybrids are quantitatively measured with the addition of a fluorogenic substrate. Optimal conditions under which to perform the assay were hybridization time, 1000 min; temperature, 75 degrees C; probe concentration, 0.2 microgram/ml; extent of probe biotinylation, 6.7%; buffer stringency, 2x SSC. A bisulfite-modified DNA probe was compared to nick-translated probes synthesized with reporter groups of different lengths (bio-11-dUTP or bio-19-dUTP). All probes could detect 10 pg/ml of target RNA. The presence of nonhomologous DNA or RNA sequences reduced the sensitivity of RNA detection by one half-log to 32 pg/ml (1.6 pg/assay).

Purification and characterization of adult diarrhea rotavirus: identification of viral structural proteins

Adult diarrhea rotavirus (ADRV) is a newly identified strain of noncultivable human group B rotavirus that has been epidemic in the People's Republic of China since 1982. We have used sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western (immuno-) blot analysis to examine the viral proteins present in the outer and inner capsids of ADRV and compared these with the proteins of a group A rotavirus, SA11. EDTA treatment of double-shelled virions removed the outer capsid and resulted in the loss of three polypeptides of 64, 61, and 41, kilodaltons (kDa). Endo-beta-N-acetylglucosaminidase H digestion of double-shelled virions identified the 41-kDa polypeptide as a glycoprotein. CaCl2 treatment of single-shelled particles removed the inner capsid and resulted in the loss of one polypeptide with a molecular mass of 47 kDa. The remaining core particle had two major structural proteins of 136 and 113 kDa. All of the proteins visualized on sodium dodecyl sulfate-polyacrylamide gel electrophoresis were antigenic by Western blot analysis when probed with convalescent-phase human and animal antisera. A 47-kDa polypeptide was most abundant and was strongly immunoreactive with human sera, animal sera raised against ADRV and against other group B animal rotaviruses (infectious diarrhea of infant rat virus, bovine and porcine group B rotavirus, and bovine enteric syncytial virus) and a monoclonal antibody prepared against infectious diarrhea of infant rat virus. This 47-kDa inner capsid polypeptide contains a common group B antigen and is similar to the VP6 of the group A rotaviruses. Human convalescent-phase sera also responded to a 41-kDa polypeptide of the outer capsid that seems similar to the VP7 of group A rotavirus. Other polypeptides have been given tentative designations on the basis of similarities to the control preparation of SA11, including a 136-kDa polypeptide designated VP1, a 113-kDa polypeptide designated VP2, 64- and 61-kDa polypeptides designated VP5 and VP5a, and several proteins in the 110- to 72-kDa range that may be VP3, VP4, or related proteins. The lack of cross-reactivity on Western blots between antisera to group A versus group B rotaviruses confirmed that these viruses are antigenically quite distinct.

Comparison of colorimetric, fluorescent, and enzymatic amplification substrate systems in an enzyme immunoassay for detection of DNA-RNA hybrids

The monoclonal antibody solution hybridization assay is a novel enzyme immunoassay for detection of RNA with a biotinylated DNA probe. To increase the sensitivity of this test, a fluorescent substrate and an enzymatic amplification cycling system were compared with a conventional colorigenic substrate for alkaline phosphatase. The fluorescent, cycling, and colorigenic substrates detected, respectively, 10, 10, and 100 amol of unbound alkaline phosphatase in 2 h. With a prolonged incubation period of 16.6 h, the conventional substrate measured 10 amol of the enzyme. In the immunoassay for RNA detection, the fluorescence and cycling assays were faster than that using the colorigenic substrate and reached an endpoint sensitivity of 3.2 pg/ml (0.16 pg per assay) of cRNA. However, longer incubation periods (16.6 h) for optimal generation of the colorigenic product led to a comparable level of sensitivity for the conventional substrate.

Detection of group B rotavirus in fecal specimens by dot hybridization with a cloned cDNA probe

Cloned cDNA copies were synthesized from the genomic RNA of the IDIR strain of group B rotavirus (GBR) isolated in Baltimore, Md. These clones were screened for hybridization with heterologous GBR to identify cDNA for use in dot hybridization experiments. In multiple screening experiments, cDNA clones derived from gene segment 3 provided the most intense hybridization signals. 32P-labeled probes were produced from one of the gene 3 clones, and these were employed in dot hybridization assays. Purified preparations of bovine GBR were detected in concentrations of greater than or equal to 0.5 ng, and GBR was detected in fecal specimens obtained from five of six infected calves. Four of six human fecal specimens containing the Baltimore strain of GBR were also positive in the hybridization assay, while GBR was identified in only one of the six specimens by means of immunoelectron microscopy. A fecal specimen obtained from a patient infected with the adult diarrhea rotavirus strain of GBR was also positive in the dot hybridization assay. Fecal specimens from uninfected humans, calves, and rats, as well as specimens containing group A rotaviruses, did not hybridize with the cloned cDNA probe.

Monoclonal antibody assay for detection of double-stranded RNA and application for detection of group A and non-group A rotaviruses

Fastidious viruses are generally detected in human body fluids by means of immunoassay or nucleic acid hybridization systems. These approaches can be difficult to apply to the detection of viruses which display variations in antigenic or genetic composition. Rotaviruses are examples of viruses which can display such variations. Recently identified antigenic variants, designated as non-group A rotaviruses, cannot be detected by immunoassays or nucleic acid hybridization assays which utilize reagents directed at group A rotavirus strains. The incomplete understanding of the extent of antigenic and genetic variation has inhibited the development of assay systems for all of the non-group A rotaviruses and has limited the study of their role in human disease. While rotaviruses display genetic variation, they all contain a genome which consists of double-stranded RNA. We utilized a monoclonal antibody to devise a sensitive assay for the measurement of double-stranded RNA and applied it to the detection of a wide range of rotaviruses. We found that the assay could detect double-stranded RNA from as few as 10 PFU of standard strains of group A rotaviruses. The assay system was also capable of detecting double-stranded RNA from several strains of group B rotaviruses isolated from calves, rats, and pigs at levels below those at which viral RNA could be visualized by means of polyacrylamide gel electrophoresis. When applied to the detection of double-stranded RNA in serial stools shed by rotavirus-infected children, the assay system was capable of detecting double-stranded RNA in samples in which antigen could not be detected by immunoassay. The specific nature of the double-stranded RNA detected by this assay system could be determined by the elution of the nucleic acids from the monoclonal antibody and the reaction of the RNA with specific nucleotide probes. The measurement of double-stranded RNA offers a potential method for the sensitive detection of a wide range of rotaviruses and other members of the family Reoviridae.

New prospects for the diagnosis of viral infections

The diagnosis of viral infections is important for the accurate management of patients with infectious diseases and for the monitoring of the course of epidemics in susceptible populations. The utility of traditional viral diagnostic assays is limited by the time, expense, and expertise required for the performance of tissue culture techniques. Similarly, the application of immunoassay techniques has been inhibited by the limited degrees of sensitivity and specificity which can be attained by most immunoassay methods. Recently, techniques for the identification of DNA and RNA have been applied to the detection of viral nucleic acids in clinical samples. Such assays have a number of potential advantages over corresponding immunoassays directed at the detection of viral antigens. In order to be generally applicable to clinical diagnosis, however, formats for the detection of viral nucleic acids have to be devised which allow for the reproducible quantitation of target DNA or RNA in human body fluids. Furthermore, formats need to be devised which allow enhanced assay sensitivity while maintaining high degrees of specificity and reproducibility. The use of non-isotopic labeling, liquid-phase hybridization, and target amplification techniques offers partial solutions to these problems. The development of practical assays for the detection of viral nucleic acids under a broad range of clinical and laboratory conditions would represent a major advance in the ability of physicians to care for patients with suspected infections.

Protease inhibitors suppress the in vitro and in vivo replication of rotavirus

Rotaviruses are major causes of infectious gastroenteritis in humans and other animals. We found that a variety of protease inhibitors suppressed the replication of the SA-11 strain of rotavirus in MA-104 cell cultures. Three of these compounds, leupeptin, pentamidine, and bis (5-amidino-2-benzimidazolyl) methane (BABIM) also restricted the intestinal replication of the murine strain of rotavirus when protease inhibitor and virus were administered simultaneously to suckling mice. Repeated administration of BABIM resulted in significantly reduced levels of intestinal rotaviral antigen even if administration of the compound was begun as late as 48 h after viral inoculation. Additionally, BABIM-treated animals had significantly less intestinal replication of rotavirus than did placebo-treated controls when placed in a heavily rotavirus-contaminated environment. The use of protease inhibitors represents a novel approach to the control of this important gastrointestinal pathogen and is a potential modality for the prevention and treatment of diseases caused by other enteric viruses, for which proteolytic cleavage is necessary for efficient replication.