Performance and Cost evaluation of one commercial and six in-house conventional and real-time reverse transcription-pcr assays for detection of severe acute respiratory syndrome coronavirus

Amplification- and Enzyme-Free Magnetic Diagnostics Circuit for Whole-Genome Detection of SARS-CoV-2 RNA

Polymerase chain reaction (PCR) requires thermal cycling and enzymatic reactions for sequence amplification, hampering their applications in point-of-care (POC) settings. Magnetic bioassays based on magnetic particle spectroscopy (MPS) and magnetic nanoparticles (MNPs) are isothermal, wash-free, and can be quantitative. Realizing them amplification- and enzyme-free on a benchtop device, they will become irreplaceable for POC applications. Here we demonstrate a first-in-class magnetic signal amplification circuit (MAC) that enables detection of whole genome of SARS-CoV-2 by combining the specificity of toehold-mediated DNA strand displacement with the magnetic response of MNPs to declustering processes. Using MAC, we detect the N gene of SARS-CoV-2 samples at a concentration of 104 RNA copies/μl as determined by droplet digital PCR. Further, we demonstrate that MAC can reliably distinguish between SARS-CoV-2 and other human coronaviruses. Being a wash-, amplification- and enzyme-free biosensing concept and working at isothermal conditions (25 °C) on a low-cost benchtop MPS device, our MAC biosensing concept offers several indispensable features for translating nucleic acid detection to POC applications.

Ultrasensitive qPCR platform for rapid detection of bacterial contamination of raw biological samples at the point of care

Contamination of cell cultures can result in a significant loss of precious biological material, particularly in long-term processes including amplification of chimeric antigen receptors (CAR)-T cells and differentiation of patient-derived stem cells, for therapeutic purposes. Bacterial contamination can also lead to more complex conditions such as sepsis which can cause morbidity and mortality, despite strict controls and good laboratory/manufacturing practices in the manipulation of complex biological samples such as blood used in autologous and allogeneic stem cells transplantation. The current standard method to identify biological risk is the set-up of microbial cultures, which can be time consuming with the likelihood of wasting large amounts of reagents in the event of contamination. Real-Time Polymerase Chain Reaction (qPCR) is a molecular method able to detect biological agents in a highly sensitive and specific way and in a short time. However, qPCR assays require complex DNA/RNA purification steps and expensive benchtop instruments, which may not always be available. This paper reports an extraction-free and low-volume protocol for qPCR in a standard instrument, which has been demonstrated to be effective on both Gram-positive (Gram+) and Gram-negative (Gram-) bacteria. Detection has been obtained from spiked cell culture samples, reaching a limit of detection (LOD) of 1 colony forming unit (CFU)/ml. To demonstrate the high potential of this optimized procedure, the same samples were also tested on a Point-Of-Care platform, which includes a cartridge with micro-chambers and a compact instrument, capable of performing qPCR with the same efficiency. Staphylococcus aureus (Gram+) was selected as the target for a proof of concept, achieving a LOD of 1 CFU/ml also on the portable device. The availability of these results paves the way for a simplified protocol for DNA extraction and amplification.

Progress and Challenges of Point-of-Need Photonic Biosensors for the Diagnosis of COVID-19 Infections and Immunity

The new coronavirus disease, COVID-19, caused by SARS-CoV-2, continues to affect the world and after more than two years of the pandemic, approximately half a billion people are reported to have been infected. Due to its high contagiousness, our life has changed dramatically, with consequences that remain to be seen. To prevent the transmission of the virus, it is crucial to diagnose COVID-19 accurately, such that the infected cases can be rapidly identified and managed. Currently, the gold standard of testing is polymerase chain reaction (PCR), which provides the highest accuracy. However, the reliance on centralized rapid testing modalities throughout the COVID-19 pandemic has made access to timely diagnosis inconsistent and inefficient. Recent advancements in photonic biosensors with respect to cost-effectiveness, analytical performance, and portability have shown the potential for such platforms to enable the delivery of preventative and diagnostic care beyond clinics and into point-of-need (PON) settings. Herein, we review photonic technologies that have become commercially relevant throughout the COVID-19 pandemic, as well as emerging research in the field of photonic biosensors, shedding light on prospective technologies for responding to future health outbreaks. Therefore, in this article, we provide a review of recent progress and challenges of photonic biosensors that are developed for the testing of COVID-19, consisting of their working fundamentals and implementation for COVID-19 testing in practice with emphasis on the challenges that are faced in different development stages towards commercialization. In addition, we also present the characteristics of a biosensor both from technical and clinical perspectives. We present an estimate of the impact of testing on disease burden (in terms of Disability-Adjusted Life Years (DALYs), Quality Adjusted Life Years (QALYs), and Quality-Adjusted Life Days (QALDs)) and how improvements in cost can lower the economic impact and lead to reduced or averted DALYs. While COVID19 is the main focus of these technologies, similar concepts and approaches can be used and developed for future outbreaks of other infectious diseases.

Preprocedural Pool Testing Strategy for Dentistry during the COVID-19 Pandemic

INTRODUCTION

Aerosol-generating procedures (AGPs) put the dental health care professionals (DHCPs) at a greater risk for acquiring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In late June 2020, the Centers for Disease Control and Prevention advised elective dental procedures provision to asymptomatic patients while mandating strict infection control protocol and suggested the use of preprocedural testing as an adjunct. A cost-effective method for mass preprocedural testing is pool testing, which has specificity and sensitivity similar to polymerase chain reaction. This article aims to assess the outcomes and utility of incorporating preprocedural testing protocol for SARS-CoV-2 in dental clinics before providing AGPs.

METHOD

The patients who were recommended AGPs where rubber dam placement was not possible were advised to undergo preprocedural testing for SARS-CoV-2. Pool testing strategy was employed, and patients were asked to get tested 48 h before the day of the procedure.

RESULTS

Out of a total of 1,000 patients, who presented from June 2020 to late July 2020, 464 were recommended dental procedures. In 194 of 464, AGPs could not be performed under rubber dam isolation; therefore, the patients were advised to get a preprocedural pool test. In total, 111 patients deferred the procedure and testing. Out of 83 who got tested, 7 were positive for SARS-CoV-2, 5 of whom were tested in early June 2020 and 2 in late July 2020.

CONCLUSION

Pool testing within its limitations can be a useful preprocedure test in asymptomatic low-risk patients for AGP in dentistry, especially when the disease prevalence is low or moderate (<10%). It has the potential of reducing testing costs significantly while conserving reagent and other resources. Preprocedure testing, however, also gives rise to certain ethical concerns that also need to be addressed.

KNOWLEDGE TRANSFER STATEMENT

The results of this study can be used by clinicians when deciding which preprocedure testing approach they wish to use when performing aerosol-generating procedures in asymptomatic patients with consideration of cost sensitivity and specificity values.

SARS-CoV, MERS-CoV and SARS-CoV-2: A Diagnostic Challenge

The highly pathogenic MERS-CoV, SARS-CoV and SARS-CoV-2 cause acute respiratory syndrome and are often fatal. These new viruses pose major problems to global health in general and primarily to infection control and public health services. Accurate and selective assessment of MERS-CoV, SARS-CoV and SARS-CoV-2 would assist in the effective diagnosis of infected individual, offer clinical guidance and aid in assessing clinical outcomes. In this mini-review, we review the literature on various aspects, including the history and diversity of SARS-CoV-2, SARS-CoV and MERS-CoV, their detection methods in effective clinical diagnosis, clinical assessment of COVID-19, safety guidelines recommended by World Health Organization and legal regulations. This review article also deals with existing challenges and difficulties in the clinical diagnosis of SARS-CoV-2. Developing alternative diagnostic platforms by spotting the shortcomings of the existing point-of-care diagnostic devices would be useful in preventing future outbreaks.

Developments of Riboswitches and Toehold Switches for Molecular Detection-Biosensing and Molecular Diagnostics

Riboswitches and toehold switches are considered to have potential for implementation in various fields, i.e., biosensing, metabolic engineering, and molecular diagnostics. The specific binding, programmability, and manipulability of these RNA-based molecules enable their intensive deployments in molecular detection as biosensors for regulating gene expressions, tracking metabolites, or detecting RNA sequences of pathogenic microorganisms. In this review, we will focus on the development of riboswitches and toehold switches in biosensing and molecular diagnostics. This review introduces the operating principles and the notable design features of riboswitches as well as toehold switches. Moreover, we will describe the advances and future directions of riboswitches and toehold switches in biosensing and molecular diagnostics.

Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review

Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus (2019-nCoV) outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus (MERS-CoV) and severe acute respiratory syndrome (SARS)-CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases (PubMed, Embase and Cochrane Library) to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction (RT-PCR) have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.

Find the right sample: A study on the versatility of saliva and urine samples for the diagnosis of emerging viruses

BACKGROUND

The emergence of different viral infections during the last decades like dengue, West Nile, SARS, chikungunya, MERS-CoV, Ebola, Zika and Yellow Fever raised some questions on quickness and reliability of laboratory diagnostic tests for verification of suspected cases. Since sampling of blood requires medically trained personal and comprises some risks for the patient as well as for the health care personal, the sampling by non-invasive methods (e.g. saliva and/ or urine) might be a very valuable alternative for investigating a diseased patient.

MAIN BODY

To analyse the usefulness of alternative non-invasive samples for the diagnosis of emerging infectious viral diseases, a literature search was performed on PubMed for alternative sampling for these viral infections. In total, 711 papers of potential relevance were found, of which we have included 128 in this review.

CONCLUSIONS

Considering the experience using non-invasive sampling for the diagnostic of emerging viral diseases, it seems important to perform an investigation using alternative samples for routine diagnostics. Moreover, during an outbreak situation, evaluation of appropriate sampling and further processing for laboratory analysis on various diagnostic platforms are very crucial. This will help to achieve optimal diagnostic results for a good and reliable case identification.

Basic overview of method validation in the clinical virology laboratory

Diagnostic virology laboratories are an essential part of the health system and are often relied upon to provide information to clinicians that will inform clinical decision making. It is therefore imperative that diagnostic results produced in the laboratory are reliable. One way of ensuring quality results is by ensuring that all tests are either validated (for tests developed in-house) or verified (for commercial assays that are FDA-approved or CE-labeled). In the diagnostic virology laboratory, these processes can be complex as both qualitative and quantitative measurements for serological and molecular tests are routinely offered. While there are numerous guidelines governing quality assurance in the virology laboratory, all accrediting agencies would insist on tests being validated or verified prior to implementation without providing explicit guidance to the process. As there is no universal guideline on the optimal way to perform validation/verification experiments, this review will provide a basic overview of method validation/verification, specific for clinical virology laboratories, and includes explanation of statistical analysis and acceptance/rejection criteria.

Comparison of three DNA extraction methods for feed products and four amplification methods for the 5'-junction fragment of Roundup Ready soybean

Three methods of DNA extraction from feed products and four detection methods for the 5'-junction fragment of genetically modified (GM) Roundup Ready soybean (RRS) were compared and evaluated. The DNA extraction methods, including cetyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), and guanidine hydrochloride (Kit), were assessed for their yields and purity of DNA, extraction time, and reagent cost. The DNA yields of CTAB, SDS, and Kit were 52-694, 164-1750 and 23-105 ng/mg sample, and their extraction time was 2.5-3, 2-2.5, and 1.5-2 h with reagent cost about US dollar 0.24, 0.13, and 1.9 per extraction, respectively. The SDS method was generally well suited to all kinds of feed matrices tested. The limits of detection for the four amplification protocols, including loop-mediated isothermal amplification (LAMP), hyperbranched rolling circle amplification (HRCA), conventional polymerase chain reaction (PCR), and real-time PCR, were 48.5, 4.85, 485, and 9 copies of the pTLH10 plasmid, respectively. The ranked results of the four detection methods were based on multiattribute utility theory as follows (from best to worse): HRCA, LAMP, PCR, and real-time PCR. This comparative evaluation was specifically useful for selection of a highly efficient DNA extraction or amplification method for detecting different GM ingredients.

Development of a molecular-beacon-based multi-allelic real-time RT-PCR assay for the detection of human coronavirus causing severe acute respiratory syndrome (SARS-CoV): a general methodology for detecting rapidly mutating viruses

Emerging infectious diseases have caused a global effort for development of fast and accurate detection techniques. The rapidly mutating nature of viruses presents a major difficulty, highlighting the need for specific detection of genetically diverse strains. One such infectious agent is SARS-associated coronavirus (SARS-CoV), which emerged in 2003. This study aimed to develop a real-time RT-PCR detection assay specific for SARS-CoV, taking into account its intrinsic polymorphic nature due to genetic drift and recombination and the possibility of continuous and multiple introductions of genetically non-identical strains into the human population, by using mismatch-tolerant molecular beacons designed to specifically detect the SARS-CoV S, E, M and N genes. These were applied in simple, reproducible duplex and multiplex real-time PCR assays on 25 post-mortem samples and constructed RNA controls, and they demonstrated high target detection ability and specificity. This assay can readily be adapted for detection of other emerging and rapidly mutating pathogens.

Development and field evaluation of a nested RT-PCR kit for detecting Japanese encephalitis virus in mosquitoes

A novel nested reverse transcription-polymerase chain reaction (RT-PCR)-based kit is described for detecting Japanese encephalitis virus (JEV), especially for genotype 1 and 3 strains. The assay consists of a first round RT-PCR and a subsequent nested PCR amplification. It has unique features such as the use of a premix system in which all reagents are lyophilized in reaction tubes and the inclusion of control RNA in each reaction to monitor false negative results. In addition, an automatic tissue homogenizer and a RNA extraction system are used concurrently for assay standardization and increasing throughput. The assay using the kit proved specific for JEV with no amplification of other JEV-related flaviviruses. The detection limits were approximately 0.1 PFU/ml and 1 PFU/ml for JEV genotypes 1 and 3, respectively. The assay protocol has been validated in large-scale field trials in South Korea during the 2008-2009 surveillance seasons. Nineteen of 1136 pools of mosquitoes (54,583 mosquitoes total) were identified as JEV positive. This nested RT-PCR kit combined with control RNA and an automatic RNA extraction system should be suitable for routine JEV surveillance programs.

Validation of laboratory-developed molecular assays for infectious diseases

Molecular technology has changed the way that clinical laboratories diagnose and manage many infectious diseases. Excellent sensitivity, specificity, and speed have made molecular assays an attractive alternative to culture or enzyme immunoassay methods. Many molecular assays are commercially available and FDA approved. Others, especially those that test for less common analytes, are often laboratory developed. Laboratories also often modify FDA-approved assays to include different extraction systems or additional specimen types. The Clinical Laboratory Improvement Amendments (CLIA) federal regulatory standards require clinical laboratories to establish and document their own performance specifications for laboratory-developed tests to ensure accurate and precise results prior to implementation of the test. The performance characteristics that must be established include accuracy, precision, reportable range, reference interval, analytical sensitivity, and analytical specificity. Clinical laboratories are challenged to understand the requirements and determine the types of experiments and analyses necessary to meet the requirements. A variety of protocols and guidelines are available in various texts and documents. Many of the guidelines are general and more appropriate for assays in chemistry sections of the laboratory but are applied in principle to molecular assays. This review presents information that laboratories may consider in their efforts to meet regulatory requirements.

Molecular targets for diagnostics and therapeutics of severe acute respiratory syndrome (SARS-CoV)

PURPOSE

The large number of deaths in a short period of time due to the spread of severe acute respiratory syndrome (SARS) infection led to the unparalleled collaborative efforts world wide to determine and characterize the new coronavirus (SARS-CoV). The full genome sequence was determined within weeks of the first outbreak by the Canadian group with international collaboration. As per the World Health Organization (WHO), the continual lack of a rapid laboratory test to aid the early diagnosis of suspected cases of SARS makes this area a priority for future research. To prevent deaths in the future, early diagnosis and therapy of this infectious disease is of paramount importance.

METHODS

This review describes the specific molecular targets for diagnostics and therapeutics of viral infection.

RESULTS

The three major diagnostic methods available for SARS includes viral RNA detection by reverse transcription polymerase chain reaction (RT-PCR), virus induced antibodies by immunofluorescence assay (IFA) or by enzyme linked immunosorbant assay (ELISA) of nucleocapsid protein (NP). The spike glycoprotein of SARS-CoV is the major inducer of neutralizing antibodies. The receptor binding domain (RBD) in the S1 region of the spike glycoprotein contains multiple conformational epitopes that induces highly potent neutralizing antibodies. The genetically engineered attenuated form of the virus or viral vector vaccine encoding for the SARS-CoV spike glycoprotein has been shown to elicit protective immunity in vaccinated animals.

CONCLUSION

NP is the preferred target for routine detection of SARS-CoV infection by ELISA which is an economical method compared to other methods. The RBD of the spike glycoprotein is both a functional domain for cell receptor binding and also a major neutralizing determinant of SARS-CoV. The progress in evaluating a therapeutic or vaccine would depend on the avail ability of clinically relevant animal model.

Currently used nucleic acid amplification tests for the detection of viruses and atypicals in acute respiratory infections

For the detection of respiratory viruses conventional culture techniques are still considered as the gold standard. However, results are mostly available too late to have an impact on patient management. The latest developments include appropriate DNA- and RNA-based amplification techniques (both NASBA and PCR) for the detection of an extended number of agents responsible for LRTI. Real time amplification, the latest technical progress, produces, within a considerable shorter time, results with a lower risk of false positives. As results can be obtained within the same day, patient management with appropriate therapy or reduction of unnecessary antibiotic therapy in LRTI will be possible. A number of technical aspects of these amplification assays, and their advantages are discussed.

The availability and use of these new diagnostic tools in virology has contributed to a better understanding of the role of respiratory viruses in LRTI. The increasing importance of the viral agents, Mycoplasma pneumoniae and Chlamydophila pneumoniae in ARI is illustrated. A great proportion of ARI are caused by viruses, but their relative importance depends on the spectrum of agents covered by the diagnostic techniques and on the populations studied, the geographical location and the season. The discovery of new viruses is ongoing; examples are the hMPV and the increasing number of coronaviruses. Indications for the use of these rapid techniques in different clinical situations are discussed. Depending on the possibilities, the laboratory could optimize its diagnostic strategy by applying a combination of immunofluorescence for the detection of RSV an IFL, and a combination of real-time amplification tests for other respiratory viruses and the atypical agents. When implementing a strategy, a compromise between sensitivity, clinical utility, turn around time and cost will have to be found.

Evaluation of a multiplexed PCR assay for detection of respiratory viral pathogens in a public health laboratory setting

There are numerous viral and bacterial causes of respiratory disease. To enable rapid and sensitive detection of even the most prevalent causes, there is a need for more-simplified testing systems that enable researchers and clinicians to perform multiplexed molecular diagnostics quickly and easily. To this end, a new multiplexed molecular test called the MultiCode-PLx respiratory virus panel (PLx-RVP) was developed and then implemented in a public health laboratory setting. A total of 687 respiratory samples were analyzed for the presence of 17 viruses that commonly cause respiratory disease. As a comparator, the samples were also tested using a standard testing algorithm that included the use of a real-time influenza virus A and B reverse transcription-PCR test and routine viral culture identification. The standard testing algorithm identified 503 (73%) samples as positive and 184 as negative. Analyzing the same 687 samples, the PLx-RVP assay detected one or more targets in 528 (77%) samples and found 159 samples negative for all targets. There were 25 discordant results between the two systems; 14 samples were positive for viruses not routinely tested for by the Wisconsin State Laboratory of Hygiene, and 13 of these were confirmed by real-time PCR. When the results of the standard testing algorithm were considered "true positives," the PLx-RVP assay showed an overall sensitivity of 99% and an overall specificity of 87%. In total, the PLx-RVP assay detected an additional 40 viral infections, of which 11 were mixed infections.

Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV)

Background

Severe acute respiratory syndrome (SARS) caused a large outbreak of pneumonia in Beijing, China, in 2003. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect and quantify SARS-CoV in 934 sera and self-collected throat washes and fecal samples from 271 patients with laboratory-confirmed SARS managed at a single institution.

Results

SARS-CoV detection rates in sera were highest in the first 9 days of illness, whereas detection was highest in throat washes 5–14 days after onset of symptoms. The highest SARS-CoV RT-PCR rates (70.4–86.3%) and viral loads (log₁₀ 4.5–6.1) were seen in fecal samples collected 2–4 weeks after the onset of clinical illness. Fecal samples were frequently SARS-CoV RT-PCR positive beyond 40 days, and occasional sera still had SARS-CoV detected after 3 weeks of illness.

Conclusion

In the context of an extensive outbreak with major pressure on hospital resources, patient self-collected samples are an alternative to nasopharyngeal aspirates for laboratory confirmation of SARS-CoV infection.

Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens

The emergence of a novel coronavirus (CoV) as the cause of severe acute respiratory syndrome (SARS) catalyzed the development of rapid diagnostic tests. Stool samples have been shown to be appropriate for diagnostic testing for SARS CoV, although it has been recognized to be a heterogeneous and difficult sample that contains amplification inhibitors. Limited information on the efficiency of extraction methods for the purification and concentration of SARS CoV RNA from stool samples is available. Our study objectives were to determine the optimal extraction method for SARS CoV RNA detection and to examine the effect of increased specimen volume for the detection of SARS CoV RNA in stool specimens. We conducted a multicenter evaluation of four automated and four manual extraction methods using dilutions of viral lysate in replicate mock stool samples, followed by quantitation of SARS CoV RNA using real-time reverse transcriptase PCR. The sensitivities of the manual methods ranged from 50% to 100%, with the Cortex Biochem Magazorb method, a magnetic bead isolation method, allowing detection of all 12 positive samples. The sensitivities of the automated methods ranged from 75% to 100%. The bioMérieux NucliSens automated extractor and miniMag extraction methods each had a sensitivity of 100%. Examination of the copy numbers detected and the generation of 10-fold dilutions of the extracted material indicated that a number of extraction methods retained inhibitory substances that prevented optimal amplification. Increasing the volume of sample input did improve detection. This information could be useful for the extraction of other RNA viruses from stool samples and demonstrates the need to evaluate extraction methods for different specimen types.

Detection of severe acute respiratory syndrome coronavirus in stool specimens by commercially available real-time reverse transcriptase PCR assays

Three commercially available real-time reverse transcriptase PCR assays (the Artus RealArt HPA coronavirus LightCycler, the Artus RealArt HPA coronavirus Rotor-Gene, and the EraGen severe acute respiratory syndrome coronavirus POL assay) and three RNA extraction methodologies were evaluated for the detection of severe acute respiratory syndrome coronavirus RNA from 91 stool specimens. The assays' sensitivities were highest (58% to 75%) for specimens obtained 8 to 21 days after symptom onset. The assays were less sensitive when specimens were obtained less than 8 days or more than 21 days after the onset of symptoms. All assays were 100% specific.

SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses

Coronaviruses are etiologic agents of respiratory and enteric diseases in humans and in animals. In this study, a one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay based on SYBR Green chemistry and degenerate primers was developed for the generic detection of coronaviruses. The primers, designed in the open reading frame 1b, enabled the detection of 32 animal coronaviruses including strains of canine coronavirus, feline coronavirus, transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), murine hepatitis virus (MHV) and infectious bronchitis virus (IBV). A specific amplification was also observed with the human coronaviruses (HCoV) HCoV-NL63, HCoV-OC43, HCoV-229E and severe acute respiratory syndrome coronavirus (SARS-CoV). The real-time RT-PCR detected down to 10 cRNA copies from TGEV, BCoV, SARS-CoV and IBV. In addition, the assay exhibited a high sensitivity and specificity on clinical samples from different animal species. The developed assay represents a potential tool for laboratory diagnostics and for detecting still uncharacterized coronaviruses.

A simple method for preparing synthetic controls for conventional and real-time PCR for the identification of endemic and exotic disease agents

Medical and veterinary diagnostic and public health laboratories world-wide are increasingly being called upon to introduce molecular diagnostic tests for both endemic and exotic diseases. This demand has accelerated following increasing terrorism fears. Ironically these same concerns have lead to tightening of both import and export controls preventing many laboratories, particularly those outside of the United States, from gaining access to positive control material. This in turn has prevented many laboratories from introducing much needed molecular diagnostic tests. We describe here a generic approach for preparing synthetic DNA or RNA control material for use in either TaqMan or conventional PCR assays. The production of synthetic controls using this approach does not require cloning or special equipment or facilities beyond that found in any laboratory performing molecular diagnostics. The approach significantly reduces the possibility of contamination or erroneously reporting false-positive reactions due to contamination from positive control material. Synthetic controls produced using this approach have been employed in all molecular diagnostic tests performed in our laboratory and are used irrespective of whether we possess the organism or not.

Detection and monitoring of virus infections by real-time PCR

The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.

Detection and monitoring of virus infections by real-time PCR

The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.

Real-time NASBA detection of SARS-associated coronavirus and comparison with real-time reverse transcription-PCR

Severe acute respiratory syndrome (SARS) exhibits a high mortality rate and the potential for rapid epidemic spread. Additionally, it has a poorly defined clinical presentation, and no known treatment or prevention methods. Collectively, these factors underscore the need for early diagnosis. Molecular tests have been developed to detect SARS coronavirus (SARS-CoV) RNA using real time reverse transcription polymerase chain reaction (RT-PCR) with varying levels of sensitivity. However, RNA amplification methods have been demonstrated to be more sensitive for the detection of some RNA viruses. We therefore developed a real-time nucleic acid sequence-based amplification (NASBA) test for SARS-CoV. A number of primer/beacon sets were designed to target different regions of the SARS-CoV genome, and were tested for sensitivity and specificity. The performance of the assays was compared with RT-PCR assays. A multi-target real-time NASBA application was developed for detection of SARS-CoV polymerase (Pol) and nucleocapsid (N) genes. The N targets were found to be consistently more sensitive than the Pol targets, and the real-time NASBA assay demonstrates equivalent sensitivity when compared to testing by real-time RT-PCR. A multi-target real-time NASBA assay has been successfully developed for the sensitive detection of SARS-CoV.

Real-time PCR in clinical microbiology: applications for routine laboratory testing

Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

Molecular diagnosis of severe acute respiratory syndrome: the state of the art

Severe acute respiratory syndrome (SARS) first appeared in Guangdong Province, China, in November 2002. Although virus isolation and serology were useful early in the SARS outbreak for diagnosing new cases, these tests are not generally useful because virus culture requires a BSL-3 laboratory and seroconversion is often delayed until 2 to 3 weeks after infection. The first qualitative reverse transcriptase-polymerase chain reaction tests for SARS-coronavirus (CoV) were sensitive and capable of detecting 1 to 10 genome equivalents. These assays were quickly supplemented with quantitative real-time assays that helped elucidate the natural history of SARS, particularly the initial presence of low viral loads in the upper respiratory tract and high viral loads in the lower respiratory tract. The unique natural history of SARS-CoV infection dictates the testing of both respiratory and nonrespiratory specimens, the testing of multiple specimens from the same patient, and sending out positives to be confirmed by a reference laboratory. Commercially available reverse transcriptase-polymerase chain reaction tests for SARS have recently appeared; however, meaningful evaluations of these assays have not yet been performed and their true performance has not been determined. These and other issues related to diagnosis of SARS-CoV infection are discussed in this review.

Performance of single-step gel-based reverse transcription-PCR (RT-PCR) assays equivalent to that of real-time RT-PCR assays for detection of the severe acute respiratory syndrome-associated coronavirus

Simple gel-based one-step reverse transcription-PCR (RT-PCR) assays, used to investigate patients during the 2003 severe acute respiratory syndrome (SARS) outbreak in Singapore, were found to be as sensitive as commercial and in-house real-time RT-PCR assays. The detection limit was approximately 1 genome equivalent (GE) per 5 microl PCR mixture. One PFU of SARS coronavirus was estimated to be 258 +/- 46 GE.

Amotosalen photochemical inactivation of severe acute respiratory syndrome coronavirus in human platelet concentrates

A novel human coronavirus causing severe acute respiratory syndrome (SARS) emerged in epidemic form in early 2003 in China and spread worldwide in a few months. Every newly emerging human pathogen is of concern for the safety of the blood supply during and after an epidemic crisis. For this purpose, we have evaluated the inactivation of SARS-coronavirus (CoV) in platelet concentrates using an approved pathogen inactivation device, the INTERCEPT Blood System. Apheresis platelet concentrates (APCs) were inoculated with approximately 10(6) pfu mL(-1) of either Urbani or HSR1 isolates of SARS-CoV. The inoculated units were mixed with 150 microm amotosalen and illuminated with 3 J cm(-2) UV-A light. The viral titres were determined by plaque formation in Vero E6 cells. Mixing SARS-CoV with APC in the absence of any treatment decreased viral infectivity by approximately 0.5-1 log10. Following photochemical treatment, SARS-CoV was consistently inactivated to the limit of detection in seven independent APC units. No infectious virus was detected after treatment when up to one-third of the APC unit was assayed, demonstrating a mean log10-reduction of >6.2. Potent inactivation of SARS-CoV therefore extends the capability of the INTERCEPT Blood System in inactivating a broad spectrum of human pathogens including recently emerging respiratory viruses.

Immunofluorescence assay for detection of the nucleocapsid antigen of the severe acute respiratory syndrome (SARS)-associated coronavirus in cells derived from throat wash samples of patients with SARS

An antigen detection assay for severe acute respiratory syndrome (SARS) coronavirus was established in this study by an indirect immunofluorescence test, which utilized cells derived from throat wash samples of patients with SARS and a rabbit serum that recognized the nucleocapsid protein of SARS-associated coronavirus (SARS-CoV) but not that of other human coronavirus tested. It detected SARS-CoV in 11 of 17 (65%) samples from SARS patients as early as day 2 of illness but in none of the 10 samples from healthy controls. Compared with other diagnostic modalities for detecting SARS-CoV, this assay is simpler, more convenient, and economical. It could be an alternative for early and rapid diagnosis, should SARS return in the future.

Persistent shedding of viable SARS-CoV in urine and stool of SARS patients during the convalescent phase

In order to further the present knowledge of the emerging severe acute respiratory syndrome-associated coronavirus (SARS-CoV), 486 different specimens from 54 patients with a clinical diagnosis of SARS were investigated for the presence of viral RNA, and 314 plasma specimens of 73 patients were examined for IgM and IgG antibodies specific against SARS-CoV using an indirect ELISA. Viral RNA was detectable in 28 of the 54 patients tested. Cumulative data showed that 67 of the 73 SARS patients demonstrated seroconversion by week 5 of illness. In contrast, only 1 of 278 healthy subjects enrolled in the study was found to be positive for the IgG antibody. Coexistence of viral RNA in plasma and specific antibodies was simultaneously observed over three consecutive weeks in two critical cases. In three convalescent patients in particular, cultivable SARS-CoV was detected in stool or urine specimens for longer than 4 weeks (29-36 days). These findings suggest that SARS-CoV may remain viable in the excretions of convalescent patients.

Multiplex real-time reverse transcription-polymerase chain reaction for the detection of three viruses associated with poult enteritis complex: turkey astrovirus, turkey coronavirus, and turkey reovirus

Poult enteritis complex (PEC) is an economically important disease of young turkeys characterized by diarrhea, poor weight gain, and, in some cases, high mortality. Although PEC is considered to be a polymicrobial disease, numerous viruses, including turkey coronavirus (TCV), turkey astrovirus type 2 (TAstV-2), and avian reoviruses (ARVs), have been associated with PEC-like disease. Real-time reverse transcription-polymerase chain reaction (RRT-PCR), a highly sensitive and specific detection method for viral RNA, was developed in a multiplex format for the simultaneous detection of TAstV-2 and TCV and for the detection of two genetic types of ARV. Assay sensitivity was determined using in vitro transcribed RNA and varied by target between 150 gene copies for TAstV-2 alone and 2200 gene copies for TCV when multiplexed. Virus detection was evaluated with samples collected from poults inoculated at 1 day of age with each of the viruses. Cloacal swabs and intestinal samples were obtained at 1, 2, 3, 4, 6, 9, 14, 17, and 21 days after inoculation, processed, and tested for virus detection by RRT-PCR Cloacal swabs from TAstV-2- and TCV-infected poults were shown to have sensitivity for virus detection similar to that of intestinal samples when compared directly. ARV detection by RRT-PCR was compared with virus isolation and had similar sensitivity.

Using autoregressive integrated moving average (ARIMA) models to predict and monitor the number of beds occupied during a SARS outbreak in a tertiary hospital in Singapore

Background

The main objective of this study is to apply autoregressive integrated moving average (ARIMA) models to make real-time predictions on the number of beds occupied in Tan Tock Seng Hospital, during the recent SARS outbreak.

Methods

This is a retrospective study design. Hospital admission and occupancy data for isolation beds was collected from Tan Tock Seng hospital for the period 14^th March 2003 to 31^st May 2003. The main outcome measure was daily number of isolation beds occupied by SARS patients. Among the covariates considered were daily number of people screened, daily number of people admitted (including observation, suspect and probable cases) and days from the most recent significant event discovery. We utilized the following strategy for the analysis. Firstly, we split the outbreak data into two. Data from 14^th March to 21^st April 2003 was used for model development. We used structural ARIMA models in an attempt to model the number of beds occupied. Estimation is via the maximum likelihood method using the Kalman filter. For the ARIMA model parameters, we considered the simplest parsimonious lowest order model.

Results

We found that the ARIMA (1,0,3) model was able to describe and predict the number of beds occupied during the SARS outbreak well. The mean absolute percentage error (MAPE) for the training set and validation set were 5.7% and 8.6% respectively, which we found was reasonable for use in the hospital setting. Furthermore, the model also provided three-day forecasts of the number of beds required. Total number of admissions and probable cases admitted on the previous day were also found to be independent prognostic factors of bed occupancy.

Conclusion

ARIMA models provide useful tools for administrators and clinicians in planning for real-time bed capacity during an outbreak of an infectious disease such as SARS. The model could well be used in planning for bed-capacity during outbreaks of other infectious diseases as well.

Inactivation of viruses in platelet concentrates by photochemical treatment with amotosalen and long-wavelength ultraviolet light

BACKGROUND

Viral contamination of platelet (PLT) concentrates can result in transfusion-transmitted diseases. A photochemical treatment (PCT) process with amotosalen-HCl and long-wavelength ultraviolet light (UVA), which cross-links nucleic acids, was developed to inactivate viruses and other pathogens in PLT concentrates.

STUDY DESIGN AND METHODS

High titers of pathogenic or blood-borne viruses, representing 10 different families, were added to single-donor PLT concentrates containing 3.0 x 10(11) to 6.0 x 10(11) PLTs in approximately 300 mL of 35 percent plasma and 65 percent PLT additive solution (InterSol). After PCT with 150 micromol per L amotosalen and 3 J per cm(2) UVA, residual viral infectivity was assayed by sensitive cell culture or animal systems.

RESULTS

Enveloped viruses were uniformly sensitive to inactivation by PCT whereas nonenveloped viruses demonstrated variable inactivation. Log reduction of enveloped viruses for cell-free HIV-1 was >6.2; for cell-associated HIV-1, >6.1; for clinical isolate HIV-1, >3.4; for clinical isolate HIV-2, >2.5; for HBV, >5.5; for HCV, >4.5; for DHBV, >6.2; for BVDV, >6.0; for HTLV-I, 4.2; for HTLV-II, 4.6; for CMV, >5.9; for WNV, >5.5; for SARS-HCoV, >5.8; and for vaccinia virus, >4.7. Log reduction of nonenveloped viruses for human adenovirus 5 was >5.2; for parvovirus B19, 3.5->5.0; for bluetongue virus, 5.6-5.9; for feline conjunctivitis virus, 1.7-2.4; and for simian adenovirus 15, 0.7-2.3.

CONCLUSION

PCT inactivates a broad spectrum of pathogenic, blood-borne viruses. Inactivation of viruses in PLT concentrates with amotosalen and UVA offers the potential to prospectively prevent the majority of PLT transfusion-associated viral diseases.

Molecular genetic methods in the diagnosis of lower respiratory tract infections

Molecular diagnostic techniques, such as PCR, have become useful tools for the rapid etiological diagnosis of lower respiratory tract infections. Nucleic acid amplification tests (NAATs) have been evaluated for detecting most respiratory pathogens, and commercial assays are available for some pathogens. However, standardized protocols are needed before these assays are introduced into routine diagnostic use. For pneumonia, NAATs offer advantages over conventional tests for the detection of Mycoplasma pneumoniae, Legionella spp. and Chlamydia pneumoniae. For pneumococcal pneumonia in adults, PCR adds little to existing diagnostic tests, and is unable to distinguish pneumococcal colonization from infection when testing respiratory samples. Although less sensitive than culture-based methods, several commercial molecular diagnostic assays have been developed for tuberculosis and are useful rapid tests for selected patients. PCR can now be considered the rapid diagnostic test of choice for pertussis and some respiratory virus infections. Further work is required to better characterize the role of molecular diagnostic tests for diagnosing lower respiratory tract infections, and to develop standard assays that can be readily adopted by routine diagnostic laboratories.

Quantitation of adenovirus genome during acute infection in normal children

BACKGROUND

Adenovirus infection causes a wide range of clinical illness in normal children. New molecular techniques allow quantitation of viral genome to study the natural history of adenovirus infection and viral load in normal children.

METHODS

Clinical samples were collected from 38 previously healthy, febrile children, and viral cultures were performed. Quantitative polymerase chain reaction (PCR) was used to detect adenovirus genome and to determine viral load. Adenovirus isolates were genotyped with a PCR-based assay.

RESULTS

Adenovirus culture was positive in 6 children who were diagnosed with acute adenovirus infection. Throat swabs contained high copy numbers of adenovirus genome (1.6 x 10(6)-6 x 10(7) copies/swab) from 4 of 4 adenovirus culture-positive children. Only 2 of 32 adenovirus culture-negative children had detectable adenovirus genome from throat swabs, but with a lower copy number (8 x 10(2) copies/swab). Adenovirus genome was not detected in blood samples from 5 of 6 adenovirus culture-positive children with uncomplicated upper respiratory tract infection and from all adenovirus culture-negative children. High level viremia (1.8 x 10(8)/ml) was detected in an adenovirus culture-positive 6-month-old infant with fever, pneumonia, conjunctivitis and hepatitis. Subsequent reduction in viral load paralleled her clinical recovery. Adenovirus viruria (1 x 10(9) copies/ml) with normal urinanalysis was detected in another adenovirus culture-positive child. All 6 adenovirus isolates were genotyped as adenovirus type 7h.

CONCLUSION

Viral load assessment in clinical samples determined by quantitative PCR can be useful in the diagnosis of adenovirus infection in immunocompetent, febrile children.

The laboratory diagnosis of severe acute respiratory syndrome: emerging laboratory tests for an emerging pathogen

The 2003 pandemic of Severe Acute Respiratory Syndrome (SARS) profiled the ability of modern diagnostic microbiology and molecular biology to identify, isolate and characterize, within weeks, a previously unknown viral infectious pathogen. The culprit, SARS coronavirus (SARS-CoV), was detected in patient specimens by traditional cell culture using an unusual cell line for respiratory viruses, Vero E6, and by reverse transcriptase polymerase chain reaction (RT-PCR) targeting the polymerase 1 B region of the genome. In addition, serologic assays were rapidly developed, and the genome of this large virus was sequenced within one month of its spread to North America. At the present time, diagnostics have progressed to the point that RT-PCR has a sensitivity approaching 80% within the first few days of onset of illness, while serology has a sensitivity close to 100% on convalescent sera taken >21 days after illness onset. Viral culture remains a method confined to biosafety level III laboratories. The specificity of RT-PCR and serology remains to be conclusively defined, but in most studies to date seems to be >90%. Serologic cross-reactivity with human coronaviruses causing the common cold may be a problem with some serologic assays. The early development of SARS-CoV diagnostics is now being replaced by refinement and optimization of these assays. Although at the present time we do not have a test that will definitively rule in or rule out SARS at the time of initial presentation of a patient with a respiratory infection, modifications of existing assays will hopefully result in our ability to make this diagnosis with a high degree of accuracy in the future.