Detection of Yersinia enterocolitica in food by PCR amplification.

A polymerase chain reaction (PCR) assay was developed for detection of pathogenic, virulent strains of Yersinia enterocolitica. By using both virulence loci virF and ail as markers for pathogenicity, detection of species with a virulence factor present was possible. DNA preparation in the presence of hexadecyl trimethy ammonium bromide (CTAB) was followed by two 44 cycle amplification reactions, one for each of the markers. As few as 10(2) Y. enterocolitica cells were detected in ground pork in the presence of 10(5)-10(6) bacteria of other species. The described PCR assay provides a sensitive robust assay for the detection of virulent Y. enterocolitica in food.

PCR detection of Listeria monocytogenes in 'gravad' rainbow trout.

'Gravad' rainbow trout artificially contaminated with Listeria monocytogenes was analyzed by use of a 4 h enrichment period followed by extraction of DNA and PCR amplification. This procedure made it possible to detect 10-100 cfu L. monocytogenes per gram 'gravad' rainbow trout, within 12 h. After a prolonged enrichment period of 24 h, numbers as low as 1-10 cfu L. monocytogenes per gram could be detected. The method described may be a useful tool for screening samples of 'gravad' rainbow trout for the presence of L. monocytogenes, since it is sensitive, rapid and simple.

Patterns of viremia in liver transplant recipients with symptomatic cytomegalovirus infection.

Cytomegalovirus (CMV) titer in blood seems to be the principal determinant of clinical symptoms in immunosuppressed patients. We have developed an assay for quantitation of CMV DNA in serum. The assay requires the coamplification by polymerase chain reaction (PCR) of extracted serum DNA with 1000 molecules of mutated internal standard DNA, and then an ELISA detection system. We examined 133 paired buffy coats and sera from 15 patients with symptomatic infection. Sera were examined by quantitative PCR, and buffy coats were examined by qualitative PCR (with a detection threshold of approximately 40 copies per 150,000 cells). Serum viral titers peaked during the seventh week after transplant (median day 40, range 26-58) at about the time of symptom onset. Mean viral titer measured during the seventh week was 1.2 x 10(5) copies per milliliter of serum (standard error 6.5 x 10(4). Buffy-coat PCR results were generally concordant with results of serum PCR (overall concordance 103/133=77.4%). Serum CMV titer fell, as symptoms resolved with reduction of immunosuppression and specific antiviral therapy. High titers and poor response to antiviral therapy were observed in the context of excessive immunosuppression and bacterial sepsis. Measurement of serum CMV titer may be useful for the management of immunosuppressed transplant recipients, and provides a tool for the better understanding of factors that enhance or inhibit viral replication.

Biological phenotype of HIV type 2 isolates correlates with V3 genotype.

The biological phenotype of HIV-2 isolates can be divided into two groups, rapid/high and slow/low, based on the ability to infect CD4+ tumor cell lines. Similar differences in the biological phenotype of HIV-1 isolates are largely determined by the charge of two specific amino acids in the V3 loop of the envelope protein gp120. In this study we have sequenced the V3 loop and flanking regions of 14 HIV-2 isolates from Guinea-Bissau and the Ivory Coast and correlated the results to the biological phenotype of the isolates. The sequences were obtained by PCR amplification of DNA from peripheral blood mononuclear cells infected with the different isolates, followed by direct sequencing of the amplified products. Eleven other HIV-2 isolates with known V3 sequence and biological phenotype were also included. Thirteen of the 14 new isolates were classified as subtype A of HIV-2 and one as subtype B. The V3 loop of rapid/high HIV-2 isolates differed significantly from slow/low isolates in that it was more heterogeneous in sequence and had higher net charge. Mutations at two specific amino acid positions (313 and 314), often to positively charged amino acids, were also significantly associated with the rapid/high phenotype. There were no sequence differences between rapid/high and slow/low isolates in the regions that flank the V3 loop. Our findings indicate that there may be a high degree of similarity in the molecular features that underlie the biological phenotypes of HIV-1 and HIV-2 isolates.

Quantitation of cytomegalovirus in the blood of liver transplant recipients.

An assay for quantitation of cytomegalovirus (CMV) has been developed. The assay combines DNA amplification and enzyme-linked immunosorbent assay (ELISA) detection. In this study, the assay has been used to examine sequential buffy-coats from 32 consecutive liver transplant recipients. In a febrile patient, CMV titres in excess of 10(4) copies per 150,000 cells strongly suggest a diagnosis of symptomatic CMV infection. Antiviral therapy causes a rapid decline in viral titre. Viral titres are seen to rise presymptomatically in some patients. Median peak viral titres differ significantly between symptomatic patients (1.1 x 10(5)), asymptomatic CMV IgM-positive patients (1.7 x 10(3)), and asymptomatic CMV immunoglobulin (Ig)M-negative patients (2.9 x 10(2)). CMV quantitation can be used for diagnosis and surveillance and can also be used to monitor antiviral treatment.

Division of Listeria monocytogenes serovar 4b strains into two groups by PCR and restriction enzyme analysis.

Altogether, 133 strains of Listeria monocytogenes serovar 4b were investigated. A segment of 2,916 bp containing parts of the two genes inlA and inlB in L. monocytogenes was amplified by the PCR technique. The PCR product obtained was cleaved with the restriction enzyme AluI, and the fragments generated were separated by gel electrophoresis, leading to two distinct groups: PCR-restriction enzyme analysis groups I and II, containing 37 and 96 strains, respectively. The PCR-restriction enzyme analysis method described in this paper could be a useful tool for the subtyping of L. monocytogenes serovar 4b strains.

Subtyping of a frequent phagovar of Listeria monocytogenes in Sweden by use of restriction endonuclease analysis.

In Sweden, many Listeria monocytogenes strains belonging to serovar 4b and isolated during the last five years from different sources share the same phagovar--2389:2425:3274:2671:47:108:340. The object of the present study was to investigate if 31 L. monocytogenes serovar 4b strains belonging to this particular phagovar could be differentiated by use of a simple restriction endonuclease analysis (REA). Among the enzymes tested, Xho I was found to be the most useful, since this enzyme could divide the 31 strains into five groups. The profiles of all human clinical isolates were indistinguishable from each other, which indicates that these strains may represent a single clone. The food isolates and the strains of human origin did not share the same profile. This further characterization may be of epidemiological importance as this phagovar of L. monocytogenes has been associated with at least two outbreaks of human listeriosis in Europe.

Autologous neutralizing antibodies to SIVsm in cynomolgus monkeys correlate to prognosis.

Sequential virus isolates from eight cynomolgus monkeys experimentally infected with SIVsm were studied for susceptibility to neutralization by autologous antibodies. The biological and antigenic characteristics of sequential reisolates differed both from the inoculum virus and from each other. Five monkeys developed neutralizing antibodies to the inoculum virus and the 12-day reisolate at 4 months postinfection, while the remaining three monkeys produced very little, if any, neutralizing antibodies. Strikingly, the two long survivor monkeys developed neutralizing antibody response to a second or third autologous reisolate and to 12 reisolates obtained from other monkeys. Thus the neutralizing antibody response of the long survivor monkeys showed a relatively broad specificity, whereas the neutralizing antibody response of the monkeys with early disease, if at all present, was specific for the infecting strain only and lost over time. Our results show that the pattern of virus neutralization in SIVsm-infected monkeys is similar to human immunodeficiency virus type 1-infected humans. In both cases, variant viruses resistant to neutralization by autologous sera emerge during the entire course of infection. In addition, the ability to produce autologous neutralizing antibodies to sequential virus reisolates appeared to correlate with the degree of immunodeficiency in the host.

Identification of group-common linear epitopes in structural and nonstructural proteins of enteroviruses by using synthetic peptides.

Synthetic peptides were employed in enzyme-linked immunosorbent assays to identify group-common linear epitopes in the structural and nonstructural proteins of enteroviruses. Nine linear epitopes were recognized by using sera from patients with heterotypic immunoglobulin G antibody responses to enterovirus infections. The most-reactive peptides were derived from conserved regions of the amino-terminal part of VP1, whereas peptides representing sequences from other conserved regions of VP1, as well as VP2, VP3, and VP4, and from a nonstructural region showed no or poor reactivity. These findings may be useful in the development of serological tests for the diagnosis of infections caused by a broad range of enteroviruses.

Jurkat-tat but not other tat-expressing cell lines support replication of slow/low type HIV.

The Jurkat-tat cell line, carrying the transactivator (tat) gene of HIV-1 IIIB and thus constitutively expressing the tat protein, has the capacity to support replication of HIV isolates obtained from asymptomatic individuals, so called slow/low (s/l) type virus. A major characteristic of the s/l isolates in vitro is their inability to continuously replicate in cells of CD4+ established lines. In contrast, virus isolates designated rapid/high (r/h) obtained from patients in advanced stages of the HIV-infection do not show this restriction in replicative capacity. To analyze whether introduction of the tat protein into certain cell types or an over-expression of the tat protein would render cells permissive for s/l virus replication, the tat gene was transfected into cells of monocytoid and T cell origin. The resulting cell lines were then tested for their susceptibility to infection with s/l and r/h type HIV-1 isolates. The results conclusively show that mere constitutive expression of the tat protein in established CD4+ cell lines will not provide conditions allowing for continuous replication of s/l type virus. Thus, the Jurkat-tat cell line is a unique cell system for long-term propagation of this type of virus. In addition, it is a suitable system to study virus-host cell interactions and control of virus replication.

Identification of a uniquely immunodominant, cross-reacting site in the human immunodeficiency virus endonuclease protein.

One of the features of the life cycle of retroviruses is insertion of the proviral DNA into host chromosomes. A protein encoded by the 3' end of the pol gene of the virus genome has been shown to possess endonuclease activity (D. P. Grandgenett, A. C. Vora, and R. D. Schiff, Virology 89:119-132, 1978), which is necessary for DNA integration. Sera from the majority of human immunodeficiency virus (HIV)-infected individuals react with endonuclease protein p31 in serological tests (J. S. Allan, J. E. Coligan, T.-H. Lee, F. Barin, P. J. Kanki, S. M'Boup, M. F. McLane, J. E. Groopman, and M. Essex, Blood 69:331-333, 1987; E. F. Lillehoj, F. H. R. Salazar, R. J. Mervis, M. G. Raum, H. W. Chan, N. Ahmad, and S. Venkatesan, J. Virol. 62:3053-3058, 1988; K. S. Steimer, K. W. Higgins, M. A. Powers, J. C. Stephans, A. Gyenes, G. George-Nascimento, P. A. Liciw, P. J. Barr, R. A. Hallewell, and R. Sanchez-Pescador, J. Virol. 58:9-16, 1986). It is not known, however, which part of the protein represents the target(s) for antibody response. To study this, we synthesized peptides and used them in an enzyme-linked immunosorbent assay system to map the reactivity of human immunodeficiency virus type 1 (HIV-1) antibody-positive sera to the different regions of the HIV endonuclease. A uniquely antigenic, HIV-1- and HIV-2-cross-reacting site was identified in the central part of this protein from Phe-663 to Trp-670.

Cytomegalovirus DNA detection of an immediate early protein gene with nested primer oligonucleotides.

A rapid and sensitive polymerase chain reaction (PCR) was developed to detect conserved sequences from the immediate early gene of human cytomegalovirus (HCMV). The primers sequences were from EcoRI J fragment of Ad169. The first primer set was selected to amplify a 242 bp fragment and the next primer set was nested within the first and amplified a 146 bp fragment. With the single PCR system it was possible to detect 100 fg HCMV DNA but with double PCR 5-10 fg were detectable. Specific amplification was seen in urines from patients with HCMV infections. 20 urine samples were analysed by single PCR, double PCR and virus cultivation. The double PCR was the most sensitive method. Urines from healthy seropositive persons and cells infected with other members of the herpes virus family were negative with all three methods. This suggests that specific amplification by double PCR is sensitive and can be used for rapid detection of HCMV DNA in cases with activated infection.

Use of synthetic oligodeoxyribonucleotides for type-specific identification of coxsackie B viruses.

Synthetic oligodeoxyribonucleotides were used for type-specific identification of members of the coxsackie B virus group by nucleic acid hybridization. Two pairs of oligonucleotide chains were constructed based on nucleotide sequences in the VP1 regions of coxsackieviruses B3 and B4. Each labelled probe had a length of 24 nucleotides. The results showed that the oligonucleotide hybridized in a type-specific manner when assayed with extracts from cells infected with all different coxsackie B viruses. A method based on similar principles may thus be used for enterovirus typing.

Nucleic acid sequence relationships between enterovirus serotypes.

Forty-eight different enterovirus serotypes were analysed by a nucleic-acid hybridization test using probes derived from the 3' end of coxsackievirus A21 (CA21) and B3 (CB3), poliovirus 3 (P3) and enterovirus 70 (E70). More than 90% of the serotypes could be detected with this collection of reagents. The CB3 probe reacted with all the coxsackie B viruses, with all three poliovirus serotypes, and with almost all of the 30 ECHO virus types tested. In addition some of the coxsackie A viruses and the BrDr 73 strain of enterovirus 71 gave a positive signal with this probe. The P3 probe detected all the poliovirus strains and also some coxsackievirus A isolates but no coxsackie B or ECHO viruses. A similar hybridization pattern as with the P3 probe was obtained when the CA 21 probe was used. The E70 probe appeared to be strain-specific. The results indicate that nucleic-acid hybridization is a useful method for rapid detection and subgrouping of enteroviruses during virus isolation, and that the test could be further developed for typing of the strains.

Genome of coxsackievirus B3.

The entire nucleotide sequence of the coxsackievirus B3 strain Nancy (CB3) genome has been determined from cDNA. The genome is 7396 nucleotides long, and encodes a 2185 amino acid long polyprotein. It exhibits the same gene organization as other enterovirus genomes. A detailed comparison was carried out between the proteins encoded by the CB3 and poliovirus type 1 strain Mahoney (PV1) genomes. The genes encoding the VPg polypeptide and the viral polymerase are the most conserved regions. The structural polypeptides VP1, VP2, and VP3 are less well conserved although proline and tryptophan residues frequently are found in identical positions. The VP1 protein of CB3 shows a particularly limited homology in those regions which have been found to induce neutralizing antibodies against PV1. The 5' noncoding region of CB3 is closely related to that of PV1, with regard to both length and sequence organization, whereas the 3' noncoding region of CB3 exhibits some unique features.

Detection of adenoviruses in stool specimens by nucleic acid spot hybridization.

Nucleic acid hybridization was used for the detection of adenovirus DNA in stool specimens, and the results were compared with those obtained by a radioimmunoassay (RIA) for adenovirus hexon antigen. DNA from 40 specimens, 18 of which were positive by RIA, were spotted onto nitrocellulose filters and analyzed by hybridization using radioactively labeled adenovirus-2 DNA or a cloned DNA fragment from enteric adenovirus-41 as probes. With the adenovirus-2 DNA probe, 15 of the 18 RIA-positive specimens were also positive in the hybridization assay, and one of the RIA negative specimens was also scored as positive. The cloned adenovirus-41 fragment gave a positive signal with five specimens, all of which were also detected with the adenovirus-2 DNA probe. The results show that hybridization is an alternative method for detection of adenovirus in stool specimens. The sensitivity of the assay is comparable to that of the RIA.

Replicase gene of coxsackievirus B3.

A cDNA copy covering two-thirds of the coxsackievirus B3 genome was cloned in the PstI site of the pBR322 vector. A nucleotide sequence containing the gene for the viral replicase and the 3' noncoding region of the coxsackievirus B3 genome was determined. The predicted amino acid sequence of the coxsackievirus B3 replicase was shown to be remarkably similar to that of the poliovirus 1 replicase. The 3' noncoding region, in contrast, was only weakly homologous to the poliovirus 1 sequence but showed a close relationship to the sequence of swine vesicular disease virus, a variant of coxsackievirus B5. A 13-nucleotide-long segment located near the polyadenylic acid junction is conserved in several members of the enterovirus group and may thus serve an important function during replication of viral RNA.

Detection of enteroviruses by spot hybridization.

A cloned partial cDNA copy of the coxsackievirus B3 genome was used for detecting enteroviruses in infected cells by employing a nucleic acid hybridization procedure. Cells infected with coxsackieviruses A and B, echovirus, and poliovirus gave positive hybridization signals, whereas cells infected with nonrelated viruses did not.

Polyadenylic acid addition sites in the adenovirus type 2 major late transcription unit.

The cytoplasmic mRNAs which are transcribed from the major late adenovirus promoter can be arranged into five 3'-coterminal families, L1 to L5. We have defined the polyadenylation sites of the mRNAs that belong to the five families at the nucleotide level. From the results, the following conclusions can be made. (i) The hexanucleotide sequence AAUAAA is present at the 3' end of all late adenovirus type 2 mRNAs and precedes the site of polyadenylation by 12 to 30 nucleotides. (ii) Between one and three A residues are present in the genomic sequence at the polyadenylation site. (iii) A sequence with the composition (T)n (A)p (T)q (n, p, q greater than or equal to 1) is found 4 to 24 nucleotides beyond all the adenovirus-specific polyadenylation sites except the 3'-coterminal family L4. This sequence is also found beyond many cellular polyadenylation sites. (iv) The L1 and L2 polyadenylation sites are very similar in structure. The other polyadenylation sites show no apparent sequence relationship, except for the hexanucleotide sequence.

Structure of three spliced mRNAs from region E3 of adenovirus type 2.

A cDNA library representing early adenovirus type 2 (Ad2) mRNA was constructed. The cDNA copies were inserted into the PstI cleavage site of the pBR322 plasmid, and clones containing sequences from region E3 of the Ad2 genome were identified by colony hybridization. Selected clones were characterized by restriction enzyme cleavage, hybridization, and partial DNA sequence analysis. The precise structure of three spliced mRNAs was established by comparing the results with the DNA sequence of region E3 from Ad2 (Herissé et al., Nucl. Acids Res. 8 (1980) 2173--2191; Herissé and Galibert, Nucl. Acids Res. 9 (1981) 1229--1249). One of the characterized mRNA species encodes the E3/19K glycoprotein, whereas the other two most likely encode the E3/14K protein. The results demonstrate, moreover, that certain splice points which are used to generate the major E3 mRNAs are also used to splice the supplementary leader segments to the fibre mRNA at late times after infection. Two separate poly(A)-addition sites were identified in region E3 by analysis of the cDNA clones; one is preceded by the hexanucleotide sequence AAUAAA, whereas the other is preceded by an altered hexanucleotide, having the sequence AUUAAA.