Virus Nucleic Acid Amplification Research Articles

Restriction fragment length polymorphism analysis of strains of porcine reproductive and respiratory syndrome virus by use of a nested-set reverse transcriptase-polymerase chain reaction

Abstract Objective To increase the timeliness and sensitivity of a procedure that uses viral nucleic acid amplification followed by restriction fragment length polymorphism (RFLP) analysis for identifying strains of porcine reproductive and respiratory syndrome virus (PRRSV). Sample Population 24 strains of PRRSV. Procedure A nested-set reverse transcriptase-polymerase chain reaction (RT-PCR) was developed and compared with a nonnested-set RT-PCR for sensitivity in amplifying known quantities of infective PRRSV. Once reaction conditions were optimized, the nested-set RT-PCR was tested for effectiveness with 24 strains of PRRSV isolated from swine. Results The nested-set RT-PCR was 100- to 1,000- fold more sensitive than the nonnested-set RT-PCR, detecting as little as 1 infective unit of PRRSV/ml of sample. It also was generally as sensitive as the combination of steps, namely virus isolation or propagation and nonnested-set RT-PCR, currently used routinely for amplifying PRRSV prior to RFLP analysis, and it was effective for amplifying all of the 24 strains of PRRSV tested. Using this RT-PCR, all tests were completed within 1.5 days (including RFLP analysis), compared with the > 7 days often required for the currently used method involving virus isolation and propagation. Conclusions The nested-set RT-PCR was generally as sensitive as the combination of methods now used for PRRSV amplification prior to RFLP analysis, and it can markedly reduce the time required for testing. Clinical Relevance Presumptive identification of PRRSV strains can be provided in a more timely manner by use of a nested-set RT-PCR. (Am J Vet Res 1999;60:802–806)

Laboratory diagnostic investigations for bovine viral diarrhoea virus infections in cattle

There are no pathognomonic clinical signs of infection with bovine viral diarrhoea virus (BVDV) in cattle. Diagnostic investigations therefore rely on laboratory-based detection of the virus, or of virus-induced antigens or antibodies in submitted samples. In unvaccinated dairy herds, serological testing of bulk milk is a convenient method for BVDV prevalence screening. Alternatively, serological testing of young stock may indicate if BVDV is present in a herd. In BVDV positive herds, animals persistently infected (PI) with BVDV can be identified by combined use of serological and virological tests for examination of blood samples. ELISAs have been used for rapid detection of both BVDV antibodies and antigens in blood, but should preferably be backed up by other methods such as virus neutralization, virus isolation in cell cultures or amplification of viral nucleic acid. Detailed knowledge of the performance of the diagnostic tests in use, as well as of the epidemiology of bovine virus diarrhoea is essential for identification of viremic animals in affected herds.

Clinical implications of nucleic acid amplification methods for the diagnosis of viral infections of the nervous system.

Amplification of viral nucleic acids from the cerebrospinal fluid (CSF) has considerably improved the diagnosis of several acute, subacute and chronic viral infections of the nervous system. In herpes simplex virus (HSV) encephalitis (HSE) the polymerase chain reaction (PCR) has become the method of choice for the rapid, non invasive diagnosis. Other herpes virus associated diseases which can now be reliably diagnosed are encephalitis, ventriculoencephalitis, polymyeloradiculitis, myelitis and an inflammatory polyradiculoneuropathy caused by cytomegalovirus (CMV), HSV, varicella-zoster virus (VZV) or Epstein-Barr virus (EBV), EBV associated primary B-cell-lymphoma of the brain, acute aseptic meningitis in young adults allied with VZV, and meningoencephalitis with recurrent seizures due to human herpes virus type 6 (HHV-6). In AIDS patients, PCR has helped to differentiate lesions either due to the human immunodeficiency virus (HIV) itself or to opportunistic infections such as progressive multifocal leukoencephalopathy (PML) caused by JC virus (JCV) or CMV related complications. HIV can be detected early in the course of infection in the CSF and the amount of proviral DNA in CSF cells seems to be correlated with the severity and/or progression of neurological signs and symptoms. Acute epidemic aseptic meningitis caused by enterovirus infections can now be reliably diagnosed and typed by reverse transcriptase PCR (RT-PCR). Meningitis cases caused by vaccination with the Jeryl Lynn and Urabe vaccine strain of mumps virus have been identified using RT-PCR and sequencing of the amplified products (amplicon).

Environmental virology: from detection of virus in sewage and water by isolation to identification by molecular biology--a trip of over 50 years.

Environmental virology began with efforts to detect poliovirus in sewage and water more than 50 years ago. Since that time, cell-culture methods useful for detection of enteroviruses have been replaced by molecular biology techniques for detection of pathogens (hepatitis A and E viruses, caliciviruses, rotaviruses, and astroviruses) that do not grow in cell culture or grow with great difficulty. Amplification of viral nucleic acid using the polymerase chain reaction (PCR) is the current preferred method. PCR or RT-PCR (to detect RNA viral genomes) is rapid, sensitive, specific, and quantitative. Method shortcomings include potential inhibition by substances in some environmental samples and an inability of test results to distinguish between infectious and noninfectious virus. Current questions involving use of PCR/RT-PCR tests for public health purposes include: What is the public health significance of a positive test, and should direct tests for viruses replace current public health-monitoring programs?

Analysis of capsid protein gene variation among divergent isolates of feline calicivirus

Genomic variability within the capsid protein gene of feline calicivirus (FCV) was evaluated among different isolates using hybridization analysis and enzymatic viral nucleic acid amplification. Total infected cell RNA was first hybridized with cDNA clones generated to the capsid gene of the FCV isolates CFI/68, 255, LLK, NADC and KCD. Field isolates of FCV were categorized by hybridization with capsid gene cDNA from the reference strains. Isolates that did not hybridize were positive by Western blot using a cross-reactive cat polyclonal FCV CFI/68 capsid protein antiserum. Using previously published sequence information, oligonucleotide primers were generated based on conserved sequences surrounding the hypervariable capsid protein gene regions. Analysis of the FCV capsid protein gene hypervariable regions was completed by sequencing products of FCV nucleic acid amplified by reverse transcription and polymerase chain reaction. From these data, amino acid substitutions in the hypervariable regions of the capsid protein were identified for those isolates that did not hybridize with the original cDNA clones. An association between phylogenetic relationships and serum neutralization was established among FCV isolates examined.

Hepatitis C virus RNA in blood donor sera detected by the polymerase chain reaction: Comparison with supplementary hepatitis C antibody assays

The low specificity of screening ELISAs for antibodies to hepatitis C virus in blood donors has called for confirmatory tests. Two types of supplementary antibody assays are available, recombinant immunoblot assays (RIBA-1 and RIBA-2) and an antibody consumption test referred to as a neutralization assay. Amplification of viral nucleic acid by the polymerase chain reaction (PCR) provides an antibody independent mode of detecting viral infection. We applied reverse transcription-double PCR to detect an HCV 5'-noncoding viral RNA sequence in serum specimens and compared PCR findings with confirmatory antibody tests. This study includes sera from 37 blood donors found positive by the Ortho anti-HCV (C100-3) ELISA out of 14,591 donations. Of the 37 positive sera, 8 were positive by RIBA-1 and 1 further by RIBA-2. Seven of the RIBA positive sera contained HCV RNA by PCR. Among the 8 indeterminate and the 21 negative donor sera by RIBA-1, no PCR positive serum was found. The 37 anti-HCV positive donor sera identified by Ortho ELISA were also tested by Abbott anti-HCV (C100-3) ELISA whereby 22 were positive. Of these 22 sera plus 1 further with ELISA OD just below cutoff, 8 were positive by the "neutralization assay," (Abbott Laboratories, North Chicago, IL, USA) and 6 of these, including the borderline serum, were PCR positive. One of the two neutralizable but PCR negative sera was RIBA positive and the other was indeterminate. However, one ELISA (Abbott Laboratories) positive (OD 1.99) serum was not neutralizable but nevertheless contained HCV RNA by PCR.(ABSTRACT TRUNCATED AT 250 WORDS)