Detection of Mycobacterium avium subsp. paratuberculosis in tissue samples by single, fluorescent and nested PCR based on the IS900 gene.

The aim of this study was to determine if fluorescent PCR could be used instead of nested PCR, for the detection of Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) in clinical specimens, to improve the sensitivity without increasing the risk for cross-contamination. We investigated and compared the sensitivity of single PCR, fluorescent PCR and nested PCR for the detection of IS900, an insertion sequence specific for M. paratuberculosis. A previously described extraction method for clinical specimens, based on xylene, was evaluated regarding its suitability for routine diagnostic work. The sensitivity of each PCR system was assessed by analysing a serial dilution of M. paratuberculosis DNA. To improve the reliability of the PCR and to facilitate the interpretation of the PCR results, a positive internal control molecule ("mimic") was developed and used for single and fluorescent PCR. In nested PCR, an existing mimic was used. The efficiency of recovering DNA of M. paratuberculosis from clinical specimens by the extraction method and detection of the organism by PCR was studied by analysing spiked ileum mucosa specimens. The final evaluation was performed on seventeen ileum mucosa specimens, previously found positive for M. paratuberculosis by bacterial culture. Twelve of the samples were positive by fluorescent PCR and nested PCR, and 10 samples were positive by single PCR. The use of mimics showed inhibition in specimens harbouring few M. paratuberculosis organisms, illustrating the effect of inhibitory substances in combination with small amounts of M. paratuberculosis DNA. We conclude that the extraction method was not adequate to recover small amounts of M. paratuberculosis and that inhibitory substances were still present in the processed specimens, but that the method is useful for identifying positive samples. Fluorescent PCR was a suitable alternative to both single PCR and nested PCR for the detection of M. paratuberculosis.

Single PCR and nested PCR with a mimic molecule for detection of Mycobacterium avium subsp. paratuberculosis.

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. The current methods for detection of M. avium subsp. paratuberculosis are slow and insensitive. We report the use of a polymerase chain reaction (PCR) based on IS900 to confirm growth of M. avium subsp. paratuberculosis in primary bacterial cultures from bovine tissue and fecal samples. The use of PCR on single colonies reduced the time for analysis by 2 months compared with conventional methods. We also report the development of a nested PCR based on IS900 and the development of a positive internal control molecule, a so-called mimic. The system was tested with spiked tissue samples, and the sensitivity was estimated to 10 CFU per sample. Seventeen tissue samples, previously found M. avium subsp. paratuberculosis positive by microbiological culture, were analyzed by nested PCR and the efficiency of the PCR was checked by co-amplification of the mimic. Absence of the mimic amplicon indicated inhibition of the amplification. Ten of the samples were positive and five were negative, as judged from the presence or absence of the IS900 PCR product. Two negative samples could not be judged because of inhibition revealed by mimic molecules. It was concluded that the nested PCR, together with the mimic, could be a useful tool in screening tissue materials.

An experimental study of a concurrent primary infection with bovine respiratory syncytial virus (BRSV) and bovine viral diarrhoea virus (BVDV) in calves.

Experimental infections with bovine respiratory syncytial virus (BRSV) and bovine viral diarrhoea virus (BVDV) were performed to study the effect of concurrent BRSV and BVDV infections. Twelve seronegative calves, in 3 groups, were inoculated on a single occasion with pure BRSV (group A), BRSV and noncytopathogenic BVDV (group B) or mock infected (group C). Mild respiratory symptoms were recorded 4 to 5 days post inoculation (dpi) in group A and group B calves. One calf in group A was severely affected and required medical treatment. In group B, fever (40.7-41.4 degrees C) was prominent 7 to 8 dpi. Only calves in group B were BVDV positive in purified lymphocytes at 2 to 14 dpi and showed increased serum interferon levels, with a peak at 4 dpi, indicating BVDV to be responsible for inducing the rise. BRSV was detected in lung lavage fluids up to 7 dpi for group A calves, compared to 11 dpi for group B and calves in this group also seroconverted later displaying lower BRSV titers. The time lag before an antibody response and the titers recorded in group B, indicated that the duration of BVDV infection in lymphocytes negatively influenced the capacity to mount a BRSV antibody response.

Detection of challenge virus in fetal tissues by nested PCR as a test of the potency of a porcine parvovirus vaccine.

To estimate the potency of a porcine parvovirus (PPV) vaccine, three vaccinated and three non-vaccinated pregnant gilts were infected with PPV and the distribution of the virus was studied in the tissues of their 51 fetuses. Virus detection was attempted using haemagglutination (HA) and immunofluorescence (IF) assays, as well as by standard (single) and nested polymerase chain reactions (PCR). None of the detection methods yielded positive results when used to test for the presence of virus in suspensions of organs from the fetuses from the vaccinated gilts. However, the virus was detected in the fetuses from non-vaccinated gilts as follows: HA was positive in 14 cases out of 23 (60.8%), IF in 16/23 (69.5%), standard PCR in 12/20 (60%), and the nested PCR in 19/23 (82.6%). Although the correlation among the results of various methods of virus detection was rather close (r < 0.83), the sensitivity of the nested PCR was the highest, both when testing dilutions of PPV and when analysing the fetal organs. The nested PCR therefore provides a reliable approach for studies of virus distribution in fetal organs, with special reference to potency tests on vaccines.

A mimic as internal standard to monitor PCR analysis of food-borne pathogens.

This report describes a method for the construction of a mimic molecule for monitoring PCR. A blue cheese homogenate spiked with Yersinia enterocolitica was used to demonstrate how false-negative PCR results may be avoided using the mimic. Further, the possibility of estimating bacterial numbers using the mimic was illustrated by varying the target concentration.

Newcastle disease outbreaks in recent years in western Europe were caused by an old (VI) and a novel genotype (VII).

Newcastle disease virus (NDV) strains, isolated from outbreaks during epizootics between 1992 and 1996 in Western European countries, were compared by restriction enzyme cleavage site mapping of the fusion (F) protein gene between nucleotides 334 and 1682 and by sequence analysis between nucleotides 47 and 435. Both methods revealed that NDV strains responsible for these epizootics belong to two distinct genotypes. Strains derived from sporadic cases in Denmark, Sweden, Switzerland and Austria were classified into genotype VI [6], the same group which caused outbreaks in the Middle East and Greece in the late 1960's and in Hungary in the early 1980's. In contrast, viruses that caused epizootics in Germany, Belgium, The Netherlands, Spain and Italy could be classified into a novel genotype (provisionally termed VII), hitherto undetected in Europe. It is possible that the genotype VII viruses originated in the Far East because they showed a high genetic similarity (97%) to NDV strains isolated from Indonesia in the late 1980's.

Genetic and antigenic analysis of the G attachment protein of bovine respiratory syncytial virus strains.

Antigenic and genetic studies of bovine respiratory syncytial virus (BRSV) were made on isolates obtained from three continents over 27 years. Antigenic variation between eight isolates was initially determined using protein G-specific monoclonal antibodies. Four distinct reaction patterns were observed, two of which corresponded to the previously established subgroups A and AB. A third pattern was produced by five Scandinavian strains and a fourth was observed from a single Dutch isolate. The genetic diversity of 27 strains of BRSV was investigated by comparative nucleotide sequence analysis of a 731 nucleotide fragment in the G protein gene. Nine of the BRSV strains were analysed by direct sequencing of RT-PCR amplicons whereas sequences of 18 BRSV and three human respiratory syncytial virus (HRSV) strains were obtained from GenBank. The analysis revealed similarities of 88-100% among BRSV strains and 38-41% between BRSV and HRSV. A phylogenetic tree created for BRSV revealed two main branches, one of which divided into five further lineages, each representing a geographic cluster. A correlation was evident between the positions of some strains in the phylogenetic tree and their antigenic pattern. For HRSV strains, a genetic similarity of only 62% allowed the distinction of two antigenic subgroups, A and B, a pattern which was not seen for BRSV. This study showed that genetic analysis was an accurate method for discriminating BRSV strains and that these viruses should be regarded as a single genetic and antigenic group, within which variants can be distinguished.

Rapid identification of Newcastle disease virus vaccine strains LaSota and B-1 by restriction site analysis of their matrix gene.

A region constituting 88% of the matrix gene of Newcastle disease virus vaccine strains LaSota and B-1 was amplified by reverse transcription-polymerase chain reaction. Amplified products of LaSota and B-1 strains derived from vaccine serials of different companies were digested with restriction enzymes MboI and HinfI. Strain characteristic cleavage site maps were obtained that allowed for a reliable and rapid differentiation between strains LaSota and B-1.

Detection of pseudorabies virus genomic sequences in apparently uninfected 'single reactor' pigs.

With a pseudorabies virus (PrV) gB ELISA, performed on 480,000 pigs on 8,900 Swedish farms, approximately 1,300 cases were observed with only one single animal reacting positively. These animals were termed 'single reactors' (SR). In order to find explanations for this peculiar phenomenon, the presence of PrV was investigated in organs of immunosuppressed and non-immunosuppressed SR animals. The virus was not detected by immunohistochemistry, virus isolation or co-cultivation. An in situ DNA hybridization test detected PrV gC gene sequences in the olfactory bulb of one sow. A nested polymerase chain reaction (PCR) assay revealed gB, gE and gD gene sequences of PrV in the tissues of trigeminal ganglia, olfactory bulb, tonsils and brain. The nucleotide sequences of the amplicons revealed 98 to 100% homology with the corresponding sequences of PrV. The large latency transcript (LLT) was not detected in the organs of the SR pigs. Transmission of the SR phenomenon to animals in contact or to the next generation was not observed. Considering the present observations and the facts that (i) PrV vaccination is not applied in Sweden; (ii) the SR animals occur not only in the South, but also in Northern Scandinavia, which has no history of PrV infection and (iii) viral reactivation was not observed under natural conditions or after experimental immunosuppression, it is concluded that the SR phenomenon should hardly be considered as a typical PrV latency. The present findings show that certain herpesviral genomic sequences exist in apparently uninfected individuals.

Phylogenetic analysis of rabbit haemorrhagic disease and European brown hare syndrome viruses by comparison of sequences from the capsid protein gene.

A 398 bp fragment of the capsid protein (VP60) gene of 39 clinical samples of rabbit haemorrhagic disease virus (RHDV) and 17 of European brown hare syndrome virus (EBHSV), collected between 1981 and 1995 from 17 countries, was amplified by PCR and directly sequenced. The alignment of the nucleotide sequences and the subsequently constructed phylogenetic tree clearly separated RHDV from EBHSV as phylogenetic entities. The nucleotide homology rates between the RHDV and EBHSV groups ranged between 52.6% and 60.0%. The homology rates within the groups were much higher, 89.4% to 100% for the RHDV samples, and 89.4% to 100% for the EBHSV specimens. No intermediate viruses were found. Despite the high homology, three main branches could be identified in the phylogenetic tree of the RHDV samples, corresponding to the epizootiological data, while the EBHSV dendrogram did not show such well defined branches. The present results support the classification of RHDV and EBHSV as two distinct members of the Caliciviridae family. Nevertheless, a comparison with previously determined sequences of other caliciviruses shows that RHDV and EBHSV are more closely related to each other than to any other calicivirus.

Genetic heterogeneity of classical swine fever virus in Central Europe.

The aim of this work was to genetically characterize Central European isolates of classical swine fever virus (CSFV) and to evaluate the applicability of molecular analysis in the epizootiology of CSFV infections. Thirty four viruses, derived from Central European pigs or wild boar, were examined. All of these viruses were detected by each of three sets of oligonucleotide primers which had been designed for the specific RT-PCR amplification of different genomic regions. Comparative sequence analysis of the PCR products showed that they were of a genetic type common in Western Europe. Further discrimination of virus isolates was possible, into subgroups that largely coincided with their regions of origin in Poland, Slovakia, Hungary and Estonia. The discriminatory ability of the technique was improved by the analysis of a composite dataset consisting of all of the sequence data from all of the viruses. Using this approach we were able to distinguish between all of the viruses and to group them in a manner that precisely matched their geographical origins, apart from a single Estonian isolate which grouped with viruses from Eastern Poland.

A comparison between a PCR method and a conventional culture method for detecting pathogenic Yersinia enterocolitica in food.

The aim of this study was to develop a polymerase chain reaction (PCR) method for the detection of pathogenic Yersinia enterocolitica and to compare it with an official culture method (NMKL-117). Primers were selected for nested PCR directed at the attachment invasion locus, ail, on the bacterial chromosome, as well as at a sequence on the pathogenic marker plasmid, termed virulence factor, virF. The final results obtained by the two methods were similar. However, while the conventional method yielded contradictory data for some steps the PCR method provided unambiguous results. Considerable advantages, i.e. higher sensitivity and specificity of the PCR method, compared with the conventional method for detecting pathogenic Y. enterocolitica, were demonstrated in this study.

Genetic variability of classical swine fever virus.

The genetic variability of classical swine fever virus was studied by comparative nucleotide sequence analysis of 76 virus isolates, collected during a half century from three continents. Parts of the E2 (gp55) and the polymerase gene coding regions of the viral genome were amplified by RT-PCR and DNA fragments of 254 and 207 bp, respectively, were sequenced. The comparative sequence analysis of the E2 region revealed two main phylogenetic groups of CSFV, indicating that the virus apparently evolved from two ancestor nodes. Group I (represented by Brescia strain) consisted of old and recent American and Asian viruses, as well as old English isolates from the 1950s. This group was subdivided into three subgroups, termed I.A-I.C. Group II (represented by Alfort strain) consisted of relatively recent isolates from Europe, together with strain Osaka, which was isolated in Japan from a pig of European origin. Based on genetic distances the group was divided into subgroups II.A and II.B. Malaysian isolates were branched into both groups, indicating multiple origins for contemporaneous outbreaks in that country. All ten vaccine strains tested were branched in group I, implying a common ancestor. The Japanese Kanagawa strain, isolated in 1974, and the British Congenital Tremor strain from 1964 were the most distinct variants of CSFV in our collection. The comparison of the nucleotide sequences of the polymerase coding region of 32 European strains distinguished subgroups II.A and II.B which were similar to the corresponding subgroups of the E2 phylogenetic tree. Thus, the results revealed that the E2 region and the polymerase coding regions seem to be appropriate for the grouping of CSFV isolates from all over the world, distinguishing two major groups of the virus. The reliability of these regions for phylogenetic analysis is indicated by the similarity of the results obtained from the two separate parts of the CSFV genome.

The use of mimics as internal standards to avoid false negatives in diagnostic PCR.

The PCR laboratories may face not only the frequently documented false positive results, but also unexpected false negatives. The latter are mostly due to inhibitory effects of some ingredients and/ or to pipetting errors. In order to reveal the errors, it is advisable to apply standard molecules as indicators of the efficacy of the reactions. In the present paper a rapid and simple method is presented to create internal standards for two test PCR assays. One of the assays detects proviral DNA of bovine leukemia virus (BLV-PCR), the other assay amplifies cDNA of feline infectious peritonitis virus (FIPV-RT-PCR). The internal standard molecules, termed 'mimics', were constructed to have the same primer-binding nucleotide sequences as the viral nucleic acids, but to flank a heterologous DNA fragment of different size. As heterologous DNA, a part of human beta-acin gene was used for the mimic construction. The identical primer-binding nucleotide sequences allowed co-amplification of the viral nucleic acid and the mimic in the same tube, and simultaneously, the size differences allowed easy discrimination between their PCR products. By running a rapid agarose gel electrophoresis after co-amplification, the presence or absence of the mimic PCR products provided proper information on the efficacy of the PCR in each reaction tube. We came to the conclusion that 5 to 20 mimic molecules, co-amplified with the samples, significantly increased the reliability of the diagnostic PCR assays.

Studies of in vivo distribution of bovine herpesvirus type 4 in the natural host.

The in vivo distribution of bovine herpesvirus type 4 (BHV-4) was examined by testing nasal and conjunctival exudates, peripheral blood leukocytes, and various organs of experimentally infected calves. For virus detection, a nested PCR assay, virus isolation, and immunohistochemistry were applied. The nervous system and the muscles were free of viral DNA. Liver and intestinal lymph nodes contained low amounts of virus (less than two copies per 1 microgram of cellular DNA). Intestinal, tonsil, thymus, and kidney tissues contained more viral DNA copies (5 to 50 copies per 1 microgram of cellular DNA). The highest amounts of BHV-4 DNA (50 to 500 copies per 1 microgram of cellular DNA) were found in the spleen, lungs, trachea, and nasal epithelium. Amplification of DNA from blood lymphocytes through postinoculation (p.i.) day 48 proved that the virus started to replicate in these cells immediately after inoculation of the calves and that intensive virus growth took place during the 7 to 8 weeks of the infection. The number of virus-infected lymphocytes reached the maximum on p.i. days 22 to 26 and slowly declined thereafter. Virus-infected cells were found only in the spleen on p.i. day 48 by immunohistochemistry. Western blotting (immunoblotting) detected signs of an immune response against 9 of the 29 BHV-4 proteins.

Identification and grouping of Newcastle disease virus strains by restriction site analysis of a region from the F gene.

A 75% region of the F gene (between nucleotides 334 and 1682) of Newcastle disease virus (NDV) RNA was amplified by reverse transcription polymerase chain reaction (RT-PCR). PCR products were cleaved by three restriction endonucleases and the positions of thirty cleavage sites were mapped in more than 200 NDV strains. Restrictions site analysis established six major groups of NDV isolates and unique fingerprints of vaccine strains. Group I comprised lentogenic strains isolated mainly from waterfowl with some from chickens. "Old" (prior to 1960s) North American isolates of varying virulence including lentogenic and mesogenic vaccine strains belonged to group II. Group III included two early isolates from the Far East. Early European strains (Herts 33 and Italien) of the first panzootic (starting in the late 1920s) and their descendants with some modifications were placed into group IV. NDV strains isolated during the second panzootic of chickens (starting in the early 1960s) were classified into two groups. Group V included strains originating in imported psittacines and in epizootics of chickens in the early 1970s. Group V1 comprised strains from the Middle East in the late 1960s and later isolates from Asia and Europe. Pigeon paramyxovirus-1 strains that were responsible for the third panzootic formed a distinct subgroup in group V1. Our grouping of NDV strains has confirmed group differences established by monoclonal antibodies. It is concluded that restriction site analysis of F gene PCR amplicons is a relatively fast, simple and reliable method for the differentiation and identification of NDV strains.

Bovine leukaemia virus: rapid detection of proviral DNA by nested PCR in blood and organs of experimentally infected calves.

The early stage of bovine leukaemia virus (BLV) infection was studied in experimentally infected calves in order to assess the diagnostic applicability of a double polymerase chain reaction (PCR). In addition, the kinetics of infection and virus distribution were evaluated. To simulate the natural route of virus transmission, the calves were infected by transferring two different infectious doses of whole blood from a BLV infected cow. The establishment of infection was determined by the double PCR and syncytia formation assay and by indirect serological methods including indirect ELISA, gp51/p24 ELISA, agar gel immunodiffusion (AGID) and Western blotting. BLV antibodies were first detected in ELISA on post infection (p.i.) day 26. Close agreement was found between the results of the various indirect methods. BLV infection was first detected in peripheral blood lymphocytes (PBL) by the PCR on p.i. day 7. No animal became seropositive to BLV prior to direct detection of BLV infection by the PCR. At slaughter, urine and saliva specimens as well as various organs were collected from the calves and tested by the double PCR. Several of the organs yielded positive results: e.g. spleen, uterus, liver, kidney, abomasum, and lymph nodes. Nine out of eleven spleen suspensions were positive by the PCR, including the spleen from one calf, which otherwise remained negative in all tests throughout the experiment. This phenomenon indicates that an animal may be infected without detectable levels of BLV proviral DNA in PBLs and without circulating antibodies, further emphasizing the diagnostic importance of the PCR. The findings indicate that the PCR is the most rapid method for the early detection of BLV infection in cattle and a valuable tool for studying the tropism of the virus.

Development of nested PCR assays for detection of bovine respiratory syncytial virus in clinical samples.

Two nested PCR assays were developed for the detection of bovine respiratory syncytial virus (BRSV). Primers were selected from the gene encoding the F fusion protein (PCR-F) and the gene encoding the G attachment protein (PCR-G). Biotinylated oligonucleotide probes, termed F and G, were selected for the hybridization of the respective PCR products. The sensitivities of the PCR-F and PCR-G assays were similar, both detecting 0.1 tissue culture infective dose of the virus. The PCR-F assay amplified all bovine strains and one human strain (RS32) tested. No cross-reactions were observed with nine heterologous respiratory viruses. PCR-F products of bovine and human RSV strains were discriminated by using endonuclease restriction enzyme ScaI, which specifically cleaved, products of BRSV. Oligonucleotide probe F was also specific for products of BRSV. The PCR-G assay detected all bovine strains and none of the human strains tested. A faint electrophoretic band was also observed with products of Sendai virus. However, probe G did not hybridize with this product, only with products of BRSV. Nasal swabs collected from cattle with no symptoms and cattle in the acute stage of respiratory disease were analyzed for BRSV by the immunofluorescence (IF) method and by the PCR-F and PCR-G assays. The virus was detected by the PCR assays in 31 of 35 (89%) samples tested. Only 23 samples (66%) were positive by the IF method, and these samples were also positive by both the PCR-F and PCR-G assays. The 31 samples detected as positive by PCR originated from cattle presenting clinical signs of acute respiratory disease; the four PCR-negative samples originated from clinically asymptomatic neighboring cattle. All sampled animals subsequently seroconverted and became reactive to BRSV. Thus, the detection of BRSV by PCR correlated with clinical observations and was considerably more sensitive (66 versus 89%) than IF. These results indicate that both nested PCR assays provide rapid and sensitive means for the detection of BRSV infection in cattle. Considering its higher specificity, the PCR-F assay can be recommended as the method of choice in the analysis of clinical specimens of BRSV.

Experiences on the application of the polymerase chain reaction in a diagnostic laboratory.

Double polymerase chain reaction (PCR) assays with nested primers have been applied in a routine laboratory for the diagnosis of herpes-, pesti- and retroviral infections of animals. Various methods and tools have been tested to prevent and to eliminate false positive results as well as to visualize the PCR products (amplicons). The u.v. and DNase treatments proved to be unsuitable for decontamination of PCR mixtures contaminated with amplicons shorter than 380 bp. By constructing special tube-holders and openers, and by applying a simple technique of pipetting, the false-positive PCR results were eliminated. The PCR products were visualized by three simple methods. The solid phase colorimetric method termed 'Detect Immobilized Amplified DNA' (DIANA) has been adapted to microplate. The other method, termed 'Colorimetric Detection Assay on Filter' (CODAF), proved to be very rapid. However, despite these advantages of DIANA and CODAF, henceforward the nucleic acid hybridization methods were found most reliable for safe identification of PCR amplicons. In order to simplify the hybridization, various non-radioactive labelling methods of oligonucleotide probes were compared. Biotinylation at the 5' end by means of oligonucleotide synthesis was the most simple and practical labelling method in this laboratory. The routine applicability of hybridization was further simplified by constructing a robot device, which automatically performs filter-hybridization and subsequently develops the signals derived from the biotinylated hybrids.