Influenza virus types and subtypes detection by single step single tube multiplex reverse transcription-polymerase chain reaction (RT-PCR) and agarose gel electrophoresis

RT-LAMP is a potential future molecular diagnostic tool for influenza A virus

Aim: Influenza A virus (IAV) causes serious illness and is responsible for significant morbidity and mortality. To diagnose IAV infection in its early stages, a quick, sensitive, precise detection method is needed for effective clinical management. Materials & methods: In-house hydroxylnaphthol blue (HNB)-based RT-LAMP assay for early detection of IAV using the HA gene was compared with RT-PCR/multiplex-RT-PCR. Results: For the reference strains of IAV, (H1N1 (A/Texas/50/2012) and H3N2 (A/Malaysia/2089302/2009)) RT-LAMP and RT-PCR/M-RT-PCR exhibited a limit of detection (LOD) of 10 and 100 fg/ml, respectively. Conclusion: HNB-based RT-LAMP is a rapid, sensitive, cost-effective diagnostic tool, and could be a point-of-care test for IAV patients during outbreaks.

PCR Techniques and Their Clinical Applications

Kary B. Mullis developed a revolutionary method name polymerase chain reaction (PCR) in 1983, which can synthesize new strand of DNA complementary to the template strand of DNA and produce billions of copies of a DNA fragment only in few hours. Denaturation, annealing, and extension are the three primary steps involved in the PCR process, which generally requires thermocyclers, DNA template, a pair of primers, Taq polymerase, nucleotides, buffers, etc. With the development of PCR, from traditional PCR, quantitative PCR, to next digital PCR, PCR has become a powerful tool in life sciences and medicine. Applications of PCR techniques for infectious diseases include specific or broad-spectrum pathogen detection, assessment and surveillance of emerging infections, early detection of biological threat agents, and antimicrobial resistance analysis. Applications of PCR techniques for genetic diseases include prenatal diagnosis and screening of neonatal genetic diseases. Applications of PCR techniques for cancer research include tumor-related gene detection. This chapter aimed to discuss about the different types of PCR techniques, including traditional PCR, quantitative PCR, digital PCR, etc., and their applications for rapid detection, mutation screen or diagnosis in infectious diseases, inherited diseases, cancer, and other diseases.

Point-of-care COVID-19 testing: colorimetric diagnosis using rapid and ultra-sensitive ramified rolling circle amplification

In this paper, we report a molecular diagnostic system—combining a colorimetric probe (RHthio-CuSO₄) for pyrophosphate sensing and isothermal gene amplification (ramified rolling circle amplification)—that operates with high selectivity and sensitivity for clinical point-of-care diagnosis of SARS-CoV-2. During the polymerase phase of the DNA amplification process, pyrophosphate was released from the nucleotide triphosphate as a side product, which was then sensed by our RHthio-CuSO₄ probe with a visible color change. This simple colorimetric diagnostic system allowed highly sensitive (1.13 copies/reaction) detection of clinical SARS-CoV-2 within 1 h, while also displaying high selectivity, as evidenced by its discrimination of two respiratory viral genomes (human rhino virus and respiratory syncytial virus) from that of SARS-CoV-2. All of the reactions in this system were performed at a single temperature, with positive identification being made by the naked eye, without requiring any instrumentation. The high sensitivity and selectivity, short detection time (1 h), simple treatment (one-pot reaction), isothermal amplification, and colorimetric detection together satisfy the requirements for clinical point-of-care detection of SARS-CoV-2. Therefore, we believe that this combination of a colorimetric probe and isothermal amplification will be useful for point-of-care testing to prevent the propagation of COVID-19.

Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures

The entire H5N1 highly pathogenic avian influenza viral genomes were identified in the frozen autopsy specimens: the trachea, lung, colon, and intestinal feces from a patient who died of the disease in 2006. Phylogenetic analysis of the viral genomes showed that these viruses belonged to clade 1 and were the reassortants generated from the reassortment of the viruses within the same clade. The sequencing data from the autopsy specimens revealed at least 8 quasispecies of the H5N1 viruses across all 4 specimen types. These sequences were compared to those derived from the virus isolates grown in Madin Darby canine kidney (MDCK) cells. The virus isolates from the trachea, lung, and fecal specimens showed 27 nucleotide substitutions, leading to the changes of 18 amino acid residues. However, there was no change in the amino acid residues that determined the viral virulence. The changes were more commonly observed in the lung, particularly in the HA and NA genes. Our study suggested that the adaptation changes for the viral fitness to survive in a new host species (MDCK cells) might involve many genes, for example, the amino acid substitution 177G or 177W adjacent to the receptor-binding residues in the HA1 globular head and the substitution M315I in PB2. However, a mutation changes near the receptor binding domain may play an important role in determining the cell tropism and is needed to be further explored.

Rapid diagnosis of two marine viruses, red sea bream iridovirus and viral hemorrhagic septicemia virus by PCR combined with lateral flow assay

Red sea bream iridovirus (RSIV) and Viral hemorrhagic septicemia virus (VHSV) are the most important viral marine pathogens in South Korea because RSIV and VHSV infect and cause high mortality rates in major fish species such as Paralichthys olivaceus and Sebastes schlegelii. These viruses can be transmitted both vertically and horizontally, and early diagnosis is imperative. In this research, RSIV and VHSV viral genomes are detected by PCR-lateral flow assay (LFA). PCR-LFA is sensitive, capable of detecting a viral genome at a concentration of 2-200 fg/µL. Development of this detection method is very meaningful because LFA is simple, requiring a minimum of personnel training to perform. Additionally, LFA requires less time than other detection methods and can be an immediate detection tool that is indispensable in preventing rapid viral spread.

Highlights in Mesoporous Silica Nanoparticles as a Multifunctional Controlled Drug Delivery Nanoplatform for Infectious Diseases Treatment

Infectious diseases are a major global concern being responsible for high morbidity and mortality mainly due to the development and enhancement of multidrug-resistant microorganisms exposing the fragility of medicines and vaccines commonly used to these treatments. Taking into account the scarcity of effective formulation to treat infectious diseases, nanotechnology offers a vast possibility of ground-breaking platforms to design new treatment through smart nanostructures for drug delivery purposes. Among the available nanosystems, mesoporous silica nanoparticles (MSNs) stand out due their multifunctionality, biocompatibility and tunable properties make them emerging and actual nanocarriers for specific and controlled drug release. Considering the high demand for diseases prevention and treatment, this review exploits the MSNs fabrication and their behavior in biological media besides highlighting the most of strategies to explore the wide MSNs functionality as engineered, smart and effective controlled drug release nanovehicles for infectious diseases treatment. Graphical Abstract Schematic representation of multifunctional MSNs-based nanoplatforms for infectious diseases treatment.

An epidemiological investigation of porcine circovirus type 2 and porcine circovirus type 3 infections in Tianjin, North China

Novel porcine circovirus type 3 (PCV3), first identified in the United States, has been detected in many other countries. Porcine circovirus is associated with postweaning multisystemic wasting syndrome, reproductive failure, congenital tremors, and other clinical symptoms. In this study, we established a double polymerase chain reaction assay for detecting both porcine circovirus type 2 (PCV2) and PCV3. This is the first study to detect and characterize the PCV3 genome in the Tianjin region of North China. We collected a total of 169 tissue samples from seven farms between 2016 and 2018. The PCV3-positive rate of all tissue samples was 37.3% (63/169) and the rate of PCV2 and PCV3 coinfection was 14.8% (25/169). PCV2 and PCV3 coinfections with more serious clinical symptoms were found in only three farms. We sequenced three PCV3 strains selected from tissue samples that were positively identified. The complete genome sequences of the three strains shared 97.6-99.4% nucleotide identities with the PCV3 strains in GenBank. Our results showed the extent of PCV3's spread in Tianjin, and the need to further study PCV3's pathobiology, epidemiology, isolation, and coinfection.

A Molecular Immunoproteomics Approach to Assess the Viral Antigenicity of Influenza

New surveillance methods employing mass spectrometry (MS) have been developed to characterize the influenza virus and, by extension, other biopathogens at the molecular level. The structure and antigenicity of protein antigens on the surface of the viral capsid are screened in a single step employing the immunoproteomics MS-based approach. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) coupled to gel electrophoresis is used both to identify viral antigens and screen their antigenicity. Evidence that antigen-antibody complexes, and protein complexes more generally, can survive on conventional MALDI targets has allowed both the primary structure and antigenicity of viral strains to be rapidly screened and protein epitopes to be identified with molecular precision. The approach should aid in future screening of the virus and assist in the development of immunogenic peptide constructs as alternative treatments to vaccination over the whole inactivated virus. The assay adds to the repertoire of mass spectrometric approaches for examining antigen-antibody interactions, in particular, and protein complexes, in general, without the need to immobilize, tag, or recover either component.

Molecular Evidence of Transmission of Influenza A/H1N1 2009 on a University Campus

Background

In the recent years, the data on the molecular epidemiology of influenza viruses have expanded enormously because of the availability of cutting-edge sequencing technologies. However, much of the information is from the temperate regions with few studies from tropical regions such as South-east Asia. Despite the fact that influenza has been known to transmit rapidly within semi-closed communities, such as military camps and educational institutions, data are limited from these communities.

Objectives

To determine the phylogeography of influenza viruses on a university campus, we examined the spatial distribution of influenza virus on the National University of Singapore (NUS) campus.

Methods

Consenting students from the NUS who sought medical attention at the UHC provided two nasopharyngeal swabs and demographic data. PCR was used for detection of influenza viruses. 34 full-genomes of pH1N1/09 viruses were successfully sequenced by Sanger method and concatenated using Geneious R7. Phylogenetic analysis was conducted using these 34 sequences and 1518 global sequences. Phylogeographic analysis was done using BaTS software and Association index and Fitch parsimony scores were determined.

Results

Integrating whole genome sequencing data with epidemiological data, we found strong evidence of influenza transmission on campus as isolates from students residing on-campus were highly similar to each other (AI, P value = 0.009; PS, P value = 0.04). There was also evidence of multiple introductions from the community.

Conclusions

Such data are useful in formulating pandemic preparedness plans which can use these communities as sentinel sites for detection and monitoring of emerging respiratory viral infections.

Comparison of multiplex RT-PCR with virus isolation for detection, typing and sub-typing of influenza virus from influenza-like illness cases

PURPOSE

Influenza epidemics and periodic pandemics occur worldwide resulting in significant mortality, morbidity and economic loss. There is need for a sensitive, rapid and cost-effective assay to detect, type and sub-type influenza viruses, as cell culture has a long turnaround time.

MATERIALS AND METHODS

Nasopharyngeal swabs were collected from patients presenting with influenza-like illness (ILI) at AIIMS OPD and Primary Health Centre Ballabhgarh (Haryana). From June 2007 to January 2009 and then from September to November 2009, of 1567 specimens collected, 544 were randomly selected and were tested by virus culture using Madin-Darby Canine Kidney (MDCK) cells and by reverse transcription polymerase chain reaction (RT-PCR) for influenza A using primers for matrix gene and for influenza B using non-structural gene (NS) primers. All influenza A positives were sub-typed using primers for HA and NA genes of A/H1, A/H3. A separate multiplex RT-PCR having primers from matrix and HA genes of pandemic A (H1N1) pdm09 viruses was carried out on samples collected after September 2009.

RESULTS

Of the 544 samples, 136 (25%) were positive for influenza by RT-PCR. Further typing analysis revealed 86 (63.2%) were typed as influenza A and 47 (34.5%) as influenza B viruses and 3 (2%) samples showed dual infection with influenza A and B. Of the 86 influenza A positive samples 48 (55.8%) were identified as seasonal influenza A/H1N1, 22 (25.6%) as A (H1N1) pdm09 and 16 (18.6%) as A/H3N2. Comparison of influenza positivity using virus culture revealed that only 97/136 (71.3%) were influenza positive. Sensitivity of viral detection was lowest for seasonal A/H1 (26/48; 54%), followed by H3N2 (11/16; 68.7%) and influenza B (38/47; 80.8%); all influenza A/H1N1pdm09 viruses were detected by both methods.

CONCLUSION

RT-PCR is a sensitive, low cost and rapid screening test for diagnosing influenza infection during epidemics and pandemics. mRT-PCR increased the detection rates for influenza by 28.6% as compared with virus isolation and thus is a useful assay in both diagnostic and epidemiological settings in resource poor countries.

Application of RT-Bst to enhance detection of pathogenic viruses of the respiratory tract

Inefficiency of RT-PCR can be associated with the suboptimal process of reverse transcription as only 40-80% of RNA is converted to cDNA. We employed a novel method, RT-Bst, to enrich the concentration of cDNA for subsequent multiplex PCR detection of selected RNA viruses. The RT-Bst method amplifies cDNA through reverse transcription of viral RNA using reverse transcriptase and amplification of cDNA using Bst DNA polymerase. Viral RNA was extracted from 25 nasopharyngeal samples for detection of influenza A, B and C; parainfluenza 1-4; human coronaviruses 229E and OC43; respiratory syncytial virus (RSV) and rhinovirus. Both multiplex one-step RT-PCR and RT-Bst PCR were used to compare their performances for detection of virus sequences. These findings were compared with routine laboratory detection. When using RT-Bst PCR, 28% of samples yielded a viral pathogen compared to 20% with RT-PCR and 12% using routine diagnostic tests. RT-Bst PCR was shown to have particular utility in the detection of RSV RNA as this was present in 20% of the samples studied compared to 8% when using RT-PCR. For one patient, RT-Bst PCR was able to detect RSV five days earlier than conventional hospital diagnostic testing. RT-Bst and RT-Bst PCR can be used as alternative approaches to reverse transcription and one-step RT-PCR, respectively, for sequence-independent amplification of RNA virus sequences and a larger scale analysis of this new diagnostic approach is warranted.

Prospective surveillance and molecular characterization of seasonal influenza in a university cohort in Singapore

BACKGROUND

Southeast Asia is believed to be a potential locus for the emergence of novel influenza strains, and therefore accurate sentinel surveillance in the region is critical. Limited information exists on sentinel surveillance of influenza-like illness (ILI) in young adults in Singapore in a University campus setting. The objective of the present study was to determine the proportion of ILI caused by influenza A and B viruses in a university cohort in Singapore.

METHODOLOGY/PRINCIPAL FINDINGS

We conducted a prospective surveillance study from May through October 2007, at the National University of Singapore (NUS). Basic demographic information and nasopharyngeal swabs were collected from students and staff with ILI. Reverse-transcriptase PCR (RT-PCR) and viral isolation were employed to detect influenza viruses. Sequencing of hemagglutinin (HA) and neuraminidase (NA) genes of some representative isolates was also performed. Overall proportions of influenza A and B virus infections were 47/266 (18%) and 9/266 (3%) respectively. The predominant subtype was A/H3N2 (55%) and the rest were A/H1N1 (45%). The overall sensitivity difference for detection of influenza A viruses using RT-PCR and viral isolation was 53%. Phylogenetic analyses of HA and NA gene sequences of Singapore strains showed identities higher than 98% within both the genes. The strains were more similar to strains included in the WHO vaccine recommendation for the following year (2008). Genetic markers of oseltamivir resistance were not detected in any of the sequenced Singapore isolates.

CONCLUSIONS/SIGNIFICANCE

HA and NA gene sequences of Singapore strains were similar to vaccine strains for the upcoming influenza season. No drug resistance was found. Sentinel surveillance on university campuses should make use of molecular methods to better detect emerging and re-emerging influenza viral threats.

An immunoproteomics approach to screen the antigenicity of the influenza virus

The structure and antigenicity of protein antigens of the influenza virus are screened in a single step employing an immunoproteomics approach. Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) coupled to gel electrophoresis is used both to identify viral antigens and screen their antigenicity. Earlier evidence that antigen-antibody complexes can survive on MALDI targets has allowed both the primary structure and antigenicity of viral strains to be rapidly screened with the specific localization of protein epitopes. The approach is anticipated to have a greater role in the future surveillance of the virus and should also aid in the development of immunogenic peptide constructs as alternatives to whole virus for vaccination.

A multiplex reverse transcription-PCR assay for the detection of influenza A virus and differentiation of the H1, H3, H5 and H9 subtypes

A multiplex reverse transcription-PCR (mRT-PCR) assay was developed for the rapid detection of influenza A viruses. The assay simultaneously differentiated H1, H3, H5 and H9 hemagglutinin subtypes in a single reaction mixture. Five sets of specific primers targeted to the M, H1, H3, H5 and H9 genes were used in this assay. The amplified products were visualized by agarose gel electrophoresis. The sizes of the PCR amplified fragments were 612 bp for H1, 187 bp for H3, 338 bp for H5, 289 bp for H9 and 239 bp for M. The detection limit of the viral RNA template was 1 ng for the H1, H3 and H5 subtypes and 0.1 ng for the H9 subtype. Nonspecific product bands from RNAs of other viral pathogens were not amplified. The sensitivity analysis demonstrated that the mRT-PCR assay is as sensitive as conventional RT-PCR and 10 times less sensitive than SYBR Green real-time RT-PCR. In conclusion, the mRT-PCR assay developed in this study was able to type influenza A viruses and simultaneously differentiate H1, H3, H5 and H9 subtypes in both human and avian clinical specimens, and thus, the mRT-PCR assay could be a rapid, convenient and relatively inexpensive molecular diagnostic tool for large-scale screening of clinical samples.

Management, breeding, and health records from a captive colony of pekin robins (Leiothrix lutea), 2001 - 2010

Pekin robins (Leiothrix lutea) were once the most widely kept softbills in captivity. As a result of the Convention on the International Trade of Endangered Species of Fauna and Flora (CITES-1997), the worldwide trade of wild-caught pekin robins has been prohibited due to the depletion of native populations of this species. In Brazil, as in other countries, pekin robins imported prior to the enactment of the CITES have disappeared from aviaries because the end of the birds' natural life span has passed, and only very few captive-bred pekin robins now exist. While captive propagation fails to address the primary causes of wild bird population decline, it might help the recovery of populations of this species. This article presents records made over a 10-yr period of a captive colony of pekin robins. Emphasis is placed on the management of the flock, the ailments affecting the birds, and the findings associated with bird losses. The main causes of bird losses included rearing management failures and age-related disorders.

HPAI 9G DNAChip: discrimination of highly pathogenic influenza virus genes

The HPAI 9G DNAChip discriminates the single nucleotide polymorphism of H5N1, H5N1 (K), and H5N3 in a 60:1 ratio. It allows the simultaneous detection of highly pathogenic avian influenza viruses with a signal to background ratio of 200 and 100% target-specific hybridization in 30 min at 25 °C.

Comparison of two real-time RT-PCR-based systems for the detection and typing of the pandemic influenza A virus, 2009

During the 2009 pandemic the Virology Laboratory of L. Spallanzani, Rome, Italy, adopted a real-time RT-PCR developed by the Centers for Disease Control and Prevention (CDC), Atlanta, Georgia to diagnose pandemic influenza A/H1N1 (H1N1pdm). A new multiplex real-time RT-PCR distributed by Astra Diagnostics, coupled with the extraction system developed and commercialized by Siemens Healthcare Diagnostics (referred to as the RealStar system), was tested for the ability to detect and type influenza A in clinical samples, with particular emphasis on influenza A-positive samples untyped by the CDC method. Seventy-six nasopharyngeal swabs, resulting by the CDC method H1N1pdm (n=7), H3N2 (n=3), and not subtyped (n=66), were re-analysed with the RealStar system. All H3N2 and H1N1pdm-positive samples were correctly identified; among the untyped samples, the RealStar system detected 24/66 (36.4%) H1N1pdm and 1/66 (1.5%) seasonal influenza A. In conclusion, the RealStar system confirmed the results of all the influenza A-positive samples subtyped by the CDC method, and was able to type 37.9% of samples untyped by the CDC method. However, 62.1% of samples, detected as influenza A-positive but not subtyped by the CDC method, were found to be negative by the RealStar system. Further investigation is needed to explain this latter, unexpected, finding.

Co-infection with influenza A/H1N1 and A/H3N2 viruses in a patient with influenza-like illness during the winter/spring of 2008 in Shanghai, China

Co-infection with different influenza viruses occurs naturally and plays an important role in epidemiology and pathogenicity. To monitor the prevalence of influenza viruses in humans during seasonal influenza epidemics in Shanghai, China, and to analyze the genetic characteristics of the viruses, 365 nasopharyngeal swabs collected from patients with influenza-like illness between January and April 2008, were tested by a colloidal gold assay, viral isolation in Madin-Darby canine kidney (MDCK) cells, direct immunofluorescence assay and multiplex RT-PCR. The genetic characteristics of the viruses were analyzed by full-length PCR amplification of the HA segment. One case of co-infection with influenza A/H1N1 and A/H3N2 viruses was detected among the 7 cases of A/H1N1, 84 cases of A/H3N2 and 48 cases of influenza B virus during the winter/spring of 2008. All influenza A/H1N1 and A/H3N2 isolates were similar, including the co-infecting isolates. The present study demonstrates the possibility of natural co-infection with different types of influenza viruses in humans, which could provide the opportunity for the occurrence of viral genetic reassortment within the human respiratory tract.

Fatal case of Reye's syndrome associated with H3N2 influenza virus infection and salicylate intake in a 12-year-old patient

We describe a fatal case of Reye's syndrome in a 12-year-old male patient during an influenza A (H3N2) infection for which he received salicylates. In the current situation of the novel A/H1N1 virus pandemic, we believe that it is of high importance to emphasize the risks associated with salicylate intake to avoid the reappearance of Reye's syndrome.

Reduction of seasonal influenza transmission among healthcare workers in an intensive care unit: a 4-year intervention study in Thailand

OBJECTIVE

To evaluate the feasibility and effectiveness of an influenza control bundle to minimize healthcare-associated seasonal influenza transmission among healthcare workers (HCWs) in an intensive care unit (ICU) equipped with central air conditioning.

METHODS

A quasi-experimental study was conducted in a 500-bed tertiary care center in Thailand from July 1, 2005, through June 30,2009. The medical ICU (MICU) implemented an influenza control bundle including healthcare worker (HCW) education, influenza screening of adult community-acquired pneumonia patients, antiviral treatment of patients and ill HCWs who tested positive for influenza, promotion of influenza vaccination among HCWs, and reinforcement of standard infection control policies. The surgical ICU (SICU) and coronary care unit (CCU) received no intervention.

RESULTS

The numbers of influenza infections among HCWs during the pre- and postintervention periods were 18 cases in 5,294 HCW days and 0 cases in 5,336 HCW-days in the MICU (3.4 vs 0 cases per 1,000 HCW-days; P ! .001), 19 cases in 4,318 HCW-days and 20 cases in 4,348 HCW-days in the SICU (4.4 vs 4.6 cases per 1,000 HCW-days; Pp.80), and 18 cases in 5,000 HCW-days and 18 cases in 5,143 HCW-days in the CCU (3.6 vs 3.5 cases per 1,000 HCW-days; Pp.92), respectively. Outbreak-related influenza occurred in 7 MICUHCWs, 6 SICU HCWs, and 4 CCU HCWs before intervention and 0 MICU HCWs, 9 SICU HCWs, and 8 CCU HCWs after intervention.Before and after intervention, 25 (71%) and 35 (100%) of 35 MICU HCWs were vaccinated, respectively (P ! .001); HCW vaccination coverage did not change significantly in the SICU (21 [70%] of 30 vs 24 [80%] of 30; Pp.89) and CCU (19 [68%] of 28 vs 21 [75%]of 28; Pp.83). The estimated costs of US $6,471 per unit for postintervention outbreak investigations exceeded the intervention costs of US $4,969.

CONCLUSION

A sustained influenza intervention bundle was associated with clinical and economic benefits to a Thai hospital.

Control of Streptococcus pneumoniae serotype 5 epidemic of severe pneumonia among young army recruits by mass antibiotic treatment and vaccination

During an outbreak of severe pneumonia among new army recruits, an epidemiological investigation combined with repeated nasopharyngeal/oropharyngeal cultures from sick and healthy contacts subjects was conducted. Fifteen pneumonia cases and 19 influenza-like illness cases occurred among 596 recruits over a 4-week period in December 2005. Pneumonia attack rates reached up to 5.5%. A single pneumococcus serotype 5 clone was isolated from blood or sputum cultures in 4 patients and 30/124 (24.1%) contacts. Immunization with 23-valent polysaccharide vaccine supplemented with a 2-dose azithromycin mass treatment rapidly terminated the outbreak. Carriage rates dropped to <1%, 24 and 45 days after intervention.

Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay

BACKGROUND

For more than a decade there has been increasing interest in the use of nanotechnology and microarray platforms for diagnostic applications. In this report, we describe a rapid and simple gold nanoparticle (NP)-based genomic microarray assay for specific identification of avian influenza virus H5N1 and its discrimination from other major influenza A virus strains (H1N1, H3N2).

RESULTS

Capture and intermediate oligonucleotides were designed based on the consensus sequences of the matrix (M) gene of H1N1, H3N2 and H5N1 viruses, and sequences specific for the hemaglutinin (HA) and neuraminidase (NA) genes of the H5N1 virus. Viral RNA was detected within 2.5 hours using capture-target-intermediate oligonucleotide hybridization and gold NP-mediated silver staining in the absence of RNA fragmentation, target amplification, and enzymatic reactions. The lower limit of detection (LOD) of the assay was less than 100 fM for purified PCR fragments and 103 TCID50 units for H5N1 viral RNA.

CONCLUSIONS

The NP-based microarray assay was able to detect and distinguish H5N1 sequences from those of major influenza A viruses (H1N1, H3N2). The new method described here may be useful for simultaneous detection and subtyping of major influenza A viruses.

Frequency of detection of upper respiratory tract viruses in patients tested for pandemic H1N1/09 viral infection

Molecular testing of 270 consecutive nasopharyngeal swab samples taken in May and June 2009 and 274 samples from patients hospitalized between July and December 2009 showed similar findings of respiratory viruses, with influenza A pandemic virus H1N1/09 being the most represented, followed by human parainfluenza virus type 3 and rhinoviruses. Statistical analyses suggested virus cocirculation in the absence of viral interference.

Development and implementation of influenza a virus subtyping and detection of genotypic resistance to neuraminidase inhibitors

Influenza virus hemagglutinin and neuraminidase, surface glycoproteins with an essential role in viral pathogenesis, are important antigen determinants and essential markers for epidemiological surveillance. Neuraminidase is also a suitable target for designing antiviral drugs. The introduction into clinical practice of neuraminidase inhibitors and the development of random point mutations have increased the emergence of drug-resistant viruses. A universal RT nested PCR-based system has been developed for subtyping H1, H3, N1 and N2, in influenza A viruses of human or animal origin. The subsequent sequencing and analysis of the hemagglutinin and neuraminidase templates reveal antigenic and receptor binding changes in the HA1 subunit and mutations of clinical relevance concerning resistance to neuraminidase inhibitors. The specificity and sensitivity of the method were evaluated using 113 influenza A isolates, 105 influenza A positive respiratory samples obtained from patients and 29 prototype strains of both human and animal origin. The resulting analytical sensitivity of the subtyping techniques is one to at least 100 molecules of cloned DNA product in a final reaction volume of 50 microl. In the course of implementing the method, two H1N1 isolates with the H274Y mutation in the neuraminidase segment have been detected and their molecular features analyzed. The emergence of influenza virus resistance makes the neuraminidase genetic characterization and surveillance activities to detect antiviral resistance necessary.

Differences in clinical predictors of influenza in adults and children with influenza-like illness

Influenza contributes significantly to morbidity and mortality in the winter season. The aim of the study was to identify clinical signs and symptoms most predictive of influenza infection in children and adults with influenza-like illness. A prospective systematic sampling analysis of clinical data collected through sentinel surveillance system for influenza in 32 primary care centers and one tertiary care hospital in Slovenia during two consecutive influenza seasons (2004/2005 and 2005/2006) was carried out. Children and adults who had influenza-like illness, defined as febrille illness with sudden onset, prostration and weakness, muscle and joint pain and at least (cough, sore throat, coryza) were included and tested for influenza A and B virus, adenovirus, respiratory syncytial virus and enterovirus by RT-PCR. Clinical data were evaluated in statistical models to identify the best predictors for the confirmation of influenza for children (under age of 15) and adults. Of 1,286 patients with influenza-like symptoms in both seasons 211 were confirmed to have influenza A or B alone and compared to 780 influenza-negative patients. A fever over 38°C, chills, headache, malaise and sore eyes revealed a significant association with positive RT-PCR test for influenza virus in children. In adults, only three symptoms were significantly related to PCR-confirmed influenza infection: fever, cough and abnormal breath sounds. The stepwise logistic regression analysis showed that four symptoms predicted influenza in children: fever (38°C or more) (p=0.010), headache (p=0.030), cough (p=0.044) and absence of abnormal breathing sounds (p=0.015) with sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of 5.1%, 98.1%, 57.1% and 80.1%, respectively. For adults, the strongest impact on influenza positivity was found for fever (p=0.008) and cough (p=0.085). The model for adults had less favorable characteristics, with sensitivity, specificity, PPV and NPV of 0%, 100%, 0% and 76.4%, respectively. Differences in clinical predictors of influenza in children compared to adults were found. The model for adults was acceptable but not a good one. The model for children was found to be more reliable than the prediction model for adults.

Severe pneumonia associated with pandemic (H1N1) 2009 outbreak, San Luis Potosí, Mexico

Severe pneumonia developed in young adults who had no identifiable risk factors.

We describe the clinical characteristics and outcomes of adults hospitalized with pneumonia during the pandemic (H1N1) 2009 outbreak. Patients admitted to a general hospital in San Luis Potosí, Mexico, from April 10 through May 11, 2009, suspected to have influenza virus–associated pneumonia were evaluated. We identified 50 patients with suspected influenza pneumonia; the presence of influenza virus was confirmed in 18: 11 with pandemic (H1N1) 2009 virus, 5 with unsubtypeable influenza A virus, 1 with seasonal influenza A virus (H3N2), and 1 in whom assay results for seasonal and pandemic (H1N1) 2009 viruses were positive. Eighteen patients were treated in the intensive care unit, and 10 died. During the pandemic (H1N1) 2009 outbreak, severe pneumonia developed in young adults who had no identifiable risk factors; early diagnosis and treatment of influenza virus infections may have a determinant role in outcome.

Genotyping and screening of reassortant live-attenuated influenza B vaccine strain

Live-attenuated influenza virus vaccines can be generated by reassortment of gene segments between an attenuated donor strain and a virulent wild-type virus. The annual production schedule for the seasonal influenza vaccine necessitates rapid and efficient genotyping of the reassorted progeny to identify the desired vaccine strains. This study describes a multiplex RT-PCR system capable of identifying each gene segment from the cold-adapted attenuated donor virus, B/Lee/40ca. The specificity of the amplification system was optimized by testing various wild-type influenza B viruses. The resulting RT-PCR method is sensitive and efficient enough for routine identification of reassortant clones to identify the desired gene constellation, consisting of six segments from the attenuated donor virus and the H and N genes from the wild-type virus. By providing a more rapid and efficient means of genotyping the candidate reassortant strains, this method could be implemented to expedite the generation of each component strain and allow more time to culture and process the final seasonal influenza vaccine.

Porcine circovirus 2 (PCV2) induces a procoagulant state in naturally infected swine and in cultured endothelial cells

Porcine circovirus 2 (PCV2) is the primary causative agent of porcine circovirus disease (PCVD). PCVD is an emerging disease that has been reported worldwide, associated with wasting, lymphoid depletion, enteritis, pneumonia, vasculitis, ischemic lesions, and necrotizing dermatitis. Although PCVD causes considerable economic losses, the pathogenesis of PCV2 has not been fully understood. The aim of the present work was to study the participation of hemostatic system and of vascular endothelium in PCV2 infection, as well as their possible role in PCVD pathogenesis. Our results showed that naturally PCV2-infected swine displayed a prothrombotic state in vivo, since a diminished coagulation time (recalcification time, activated partial thromboplastin time and prothrombin time), a higher platelet aggregation ability (despite a diminished platelet blood count), and an increased thrombin plasma activity (associated with a reduced fibrinogen level) were observed. The PCV2-infected animals showed vasculitis and positive staining for PCV2 antigen in capillary vessels. Furthermore, PCV2-infected endothelial cells displayed an activated phenotype, characterized by an increase in cell surface procoagulant activity. Moreover, the PCV2-infected endothelial cells pre-treated with exogenous thrombin displayed an increased viral load. This work reports, for the first time, the role of the hemostatic system and of endothelium in the pathogenesis and infectivity of PCV2. The study reinforces the importance of the phenomena which occur during PCV2 infection, and affords a better knowledge of the mechanisms behind the pathophysiology of PCVD.

The detection of influenza A and B viruses in clinical specimens using a quartz crystal microbalance

Current methods for the accurate diagnosis of influenza based on culture of the virus or PCR are highly sensitive and specific but require specialised laboratory facilities and highly trained personnel and, in the case of viral culture, can take up to 14 days to obtain a definitive result. In this study, a quartz crystal microbalance-based immunosensor (QCM) has been developed and its potential evaluated for the rapid and sensitive detection of both influenza A and B viruses in laboratory-cultured preparations and clinical samples. The effective limit for detection by QCM for stock preparations of both A/PR/8/34 and B/Lee/40 viruses was 1 × 10⁴ pfu/mL, associated with observed frequency shifts of 30 (±5) and 37 (±6.5) Hz, respectively. Conjugation of 13 nm gold nanoparticles to the detecting antibody improved the mass sensitivity of the immunosensor, resulting in a 10-fold increase in sensitivity and a detection limit of 1 × 10³ pfu/mL for both preparations, with resulting frequency shifts of 102 (±11) and 115 (±5) Hz, respectively. Detection of virus in nasal washes with this technique was achieved by overnight passage in MDCK cultures prior to analysis. A comparison of results obtained from 67 clinical samples using existing RT-PCR, shell vial, cell culture and ELISA methods showed that QCM techniques were comparable in sensitivity and specificity to cell culture methods.

The inactivation of avian influenza virus subtype H5N1 isolated from chickens in Thailand by chemical and physical treatments

The objectives of this study were to determine the survival of avian influenza virus (AIV) subtype H5N1 under various physical and chemical treatments, including disinfectants, temperature and pH. The highly pathogenic AIVs subtype H5N1 were isolated from internal organs of suspected chickens and were characterized by the inoculation into chicken embryonated eggs (CEEs), hemagglutination (HA) test, hemagglutination inhibition (HI) test, reverse transcriptase polymerase chain reaction (RT-PCR) and nucleotide sequencing of hemagglutinin (H) and neuraminidase (N) genes. Three H5N1 isolates, at the concentration of 10(9) 50% embryo lethal dose (ELD(50))/ml, were used for the determination of the survival of the virus under different chemical and physical treatments. The chemical treatments were performed by incubating the viruses with various types of disinfectants including glutaraldehyde (Glu), hydrogen peroxide, quaternary ammonium compounds (QAC), Glu+QAC, iodine, chlorine, formalin and phenol, at 25 and 37 degrees C, for 0, 5, 7, and 14 days. The physical treatments included incubation of the viruses at 55, 60, 65, 70 and 75 degrees C for 10, 15, 30, 45 and 60 min or pH 3, 5, 7, 9 and 12. The results revealed that AIV H5N1 reference viruses, 2004.1, CUK-2/04 and 2004.2, showed low or no resistance against Glu+QAC, chlorine and phenol at both tested temperatures. Incubations at 70 degrees C for 60 min or at least 75 degrees C for at least 45 min could effectively inactivate all of the isolates, whereas all ranges of pH could not inactivate any of them. In this study, CUK-2/04 was more resistant to the disinfectants, temperatures, and pH compared to the other isolates.

Real-time RT-PCR assays for type and subtype detection of influenza A and B viruses

Influenza viruses type A (H3N2 and H1N1 subtypes) and B are the most prevalently circulating human influenza viruses. However, an increase in several confirmed cases of high pathogenic H5N1 in humans has raised concerns of a potential pandemic underscoring the need for rapid, point of contact detection. In this report, we describe development and evaluation of ‘type,’ i.e., influenza virus A and B, and ‘subtype,’ i.e., H1, H3, and H5, specific, single‐step/reaction vessel format, real‐time RT‐PCR assays using total RNA from archived reference strains, shell‐vial cultured and uncultured primary (throat swab/nasal wash) clinical samples. The type A and B specific assays detected all 16 influenza type A viruses and both currently circulating influenza B lineages (Yamagata and Victoria), respectively. ‘Type’ and ‘subtype’ specific assays utilize one common set of thermocycling conditions, are specific and highly sensitive (detection threshold of approximately 100 target template molecules). All clinical specimens and samples were evaluated using both the unconventional portable Ruggedized Advanced Pathogen Identification Device (RAPID) and standard laboratory bench LightCycler instruments. These potentially field‐deployable assays could offer significant utility for rapid, point of care screening needs arising from a pandemic influenza outbreak.

Molecular characterization of low pathogenic avian influenza viruses, isolated from food products imported into Singapore

We have completed the genetic characterization of all eight gene segments for four low pathogenic avian influenza (LPAI) viruses. The objective of this study was to detect the presence of novel signatures that may serve as early warning indicators of the conversion of LPAI viruses to high pathogenic avian influenza (HPAI) viruses. This study included three H5N2 and one H5N3 viruses that were isolated from live poultry imported into Singapore as part of the national avian influenza virus (AIV) surveillance program. Based on the molecular criterion of the World Organisation for Animal Health (OIE), sequence analysis with the translated amino acid (aa) sequence of the hemagglutinin (HA) gene revealed the absence of multibasic aa at the HA cleavage site, identifying all four virus isolates as LPAI. Detailed phylogenetic tree analyses using the HA and neuraminidase (NA) genes clustered these isolates in the Eurasian H5 lineage, but away from the HPAI H5 subtypes. This analysis further revealed that the internal genes clustered to different avian and swine subtypes, suggesting that the four isolates may possibly share their ancestry with these different influenza subtypes. Our results suggest that the four LPAI isolates in this study contained mainly avian signatures, and the phylogenetic tree for the internal genes further suggests the potential for reassortment with other different circulating avian subtypes. This is the first comprehensive report on the genetic characterization of LPAI H5N2/3 viruses isolated in South-East Asia.

Verification of the Combimatrix influenza detection assay for the detection of influenza A subtype during the 2007-2008 influenza season in Toronto, Canada

The increase in adamantine resistance in influenza A (H3N2) and the emergence of oseltamivir resistance in influenza A (H1N1) has necessitated the use of rapid methodologies to detect influenza subtype. The purpose of this study was to evaluate the CombiMatrix influenza detection system compared to the FDA approved Luminex Respiratory virus panel (RVP) assay for influenza A subtyping. Verification of the CombiMatrix influenza detection system was carried out using the Luminex RVP assay as a reference method. A limit of detection (LOD) series was performed using the Luminex and CombiMatrix systems with both influenza A H3N2 and H1N1 viruses. Seventy-five clinical specimens were used in the study. Of these, 16 were influenza A (H3N2) positive and five were influenza A (H1N1) positive. Fifty-four specimens were influenza A negative or "no call" (inconclusive) or could not be subtyped. The LOD of the Luminex RVP assay was found to be 0.3 TCID₅₀s/mL for influenza A (H3N2) and 16 TCID₅₀s/mL for influenza A (H1N1). The LOD of the CombiMatrix influenza detection system was 200 TCID₅₀s/mL for influenza A (H3N2) and 16 000 TCID₅₀s/mL for influenza A (H1N1). The sensitivity of the CombiMatrix influenza detection system was 95.2% and the specificity was 100%. The CombiMatrix influenza detection system is an effective methodology for influenza A subtype analysis, specifically in laboratories with a constrained budget or limited molecular capabilities.

[Application of molecular methods in the diagnosis and epidemiological study of viral respiratory infections]

Hasta la fecha se han identificado más de 200 virus pertenecientes a 6 familias taxonómicas diferentes asociados con la infección del tracto respiratorio humano. La utilización generalizada de métodos moleculares en los laboratorios de microbiología clínica no sólo ha aportado grandes ventajas al diagnóstico de estas infecciones, sino también está permitiendo profundizar en el conocimiento de la enfermedad y el comportamiento epidemiológico de los virus causantes. Esta tecnología incrementa de manera notable el rendimiento de detección de virus en las muestras respiratorias, debido a su elevada sensibilidad en comparación con las técnicas clásicas y a la posibilidad de identificar virus no cultivables o de crecimiento fastidioso en las líneas celulares habituales, lo que permite realizar el diagnóstico etiológico con mayor rapidez. Sin embargo, también comporta algunos inconvenientes, como son detectar virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas, o en secreciones de pacientes que ya se han recuperado de una infección pasada, a consecuencia de excreción prolongada de éstos. La secuenciación de los productos obtenidos en la reacción de amplificación genómica permite caracterizar de forma adicional los virus detectados mediante su genotipado, realizar estudios de epidemiología molecular e identificar resistencias a determinados antivirales, por citar sólo algunos ejemplos.

Detection of H5, H7 and H9 subtypes of avian influenza viruses by multiplex reverse transcription-polymerase chain reaction

Subtype-specific multiplex reverse transcription-polymerase chain reaction (RT-PCR) was developed to simultaneously detect three subtypes (H5, H7 and H9) of avian influenza virus (AIV) type A. The sensitivity of the multiplex RT-PCR was evaluated and compared to that of RT-PCR-enzyme-linked immunosorbent assay (ELISA) and conventional RT-PCR. While the sensitivity of the multiplex RT-PCR is as sensitive as the conventional RT-PCR, it is 10 times less sensitive than RT-PCR-ELISA. The multiplex RT-PCR is also as sensitive as the virus isolation method in detecting H9N2 from tracheal samples collected at day 3 and 5 post inoculation. Hence, the developed multiplex RT-PCR assay is a rapid, sensitive and specific assay for detecting of AIV subtypes.

A reverse transcription-PCR for subtyping of the neuraminidase of avian influenza viruses

To date, nine neuraminidase (NA) subtypes of avian influenza viruses have been identified. In order to differentiate the NA of avian influenza viruses rapidly, a reverse transcription PCR (RT-PCR) was developed. Nine pairs of NA-specific primers for the RT-PCR were designed based on the analysis of 509 complete NA sequences in GenBank. The primers were designed to amplify partial NA genes and each pair is unique to a single NA subtype (N1-N9). By nine RT-PCRs simultaneously in a set of separate tubes, the subtype of NA was determined by subsequent agarose gel electrophoresis and ethidium bromide staining, since only one of the nine RT-PCRs would give a product of expected size for each virus strain. In comparison with the established method of sequence analysis of 101 reference strains or isolates of avian influenza viruses, the RT-PCR method had a sensitivity of 97.3% and a specificity of 91.1% in subtyping avian influenza viruses. These results indicate that the RT-PCR method described below provides a specific and sensitive alternative to conventional NA-subtyping methods.

Detection of respiratory viruses by molecular methods

SUMMARY

Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.

Detection of influenza virus types A and B and type A subtypes (H1, H3, and H5) by multiplex polymerase chain reaction

Infections with influenza virus type A and B present serious public health problems on a global scale. However, only influenza A virus has been reported to cause fatal pandemic in many species. To provide suitable clinical management and prevent further virus transmission, efficient and effective clinical diagnosis is essential. Therefore, we developed multiplex PCR assays for detecting influenza types A and B and the subtypes of influenza A virus (H1, H3 and H5). Upon performing multiplex PCR assays with type-specific primer sets, the clearly distinguishable products representing influenza A and B virus were separated by agarose gel electrophoresis. In addition, the subtypes of influenza A virus (H1, H3 and H5), which are most common in humans, can be readily distinguished by PCR with subtype-specific primer sets, yielding PCR products of different sizes depending on which subtype has been amplified. This method was tested on 46 influenza virus positive specimens of avian and mammalian (dog and human) origins collected between 2006 and 2008. The sensitivity of this method, tested against known concentrations of each type and subtype specific plasmid, was established to detect 10(3) copies/microl. The method's specificity was determined by testing against other subtypes of influenza A virus (H2, H4 and H6-H15) and respiratory pathogens commonly found in humans. None of them could be amplified, thus excluding cross reactivity. In conclusion, the multiplex PCR assays developed are advantageous as to rapidity, specificity, and cost effectiveness.

Simultaneous detection of different respiratory virus by a multiplex reverse transcription polymerase chain reaction combined with flow-through reverse dot blotting assay

Cell culture and immunofluorescence (IF) assays have been traditionally used for the laboratory diagnosis of respiratory viral infections, but these assays have a low sensitivity and are time consuming. We developed a multiplex reverse transcription polymerase chain reaction combined with flow-through reverse dot blotting (mRT-PCR-FT-RDB) assay for the simultaneous detection of influenza virus type A including H5 subtype and H9 subtype, influenza virus type B, parainfluenza virus types 1 and 3, respiratory syncytial virus, human rhinovirus, and human coxsackievirus. In comparison with viral culture and IF assay as the gold standard method, the mRT-PCR-FT-RDB assay gave a sensitivity and a specificity of 100% and 98%. The high sensitivity and specificity, the rapid result turnaround time, and the reduced expense of the mRT-PCR-FT-RDB assay compared with viral culture and IF assay suggest that this assay would be a significant improvement over traditional ones for the detection of respiratory viruses in a clinical laboratory.

A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus

BACKGROUND

The emergence of high pathogenicity strains of Influenza A virus in a variety of human and animal hosts, with wide geographic distribution, has highlighted the importance of rapid identification and subtyping of the virus for outbreak management and treatment. Type A virus can be classified into subtypes according to the viral envelope glycoproteins, hemagglutinin and neuraminidase. Here we review the existing specificity and amplification of published primers to subtype neuraminidase genes and describe a new broad spectrum primer pair that can detect all 9 neuraminidase subtypes.

RESULTS

Bioinformatic analysis of 3,337 full-length influenza A neuraminidase segments in the NCBI database revealed semi-conserved regions not previously targeted by primers. Two degenerate primers with M13 tags, NA8F-M13 and NA10R-M13 were designed from these regions and used to generate a 253 bp cDNA product. One-step RT-PCR testing was successful in 31/32 (97%) cases using a touchdown protocol with RNA from over 32 different cultured influenza A virus strains representing the 9 neuraminidase subtypes. Frozen blinded clinical nasopharyngeal aspirates were also assayed and were mostly of subtype N2. The region amplified was direct sequenced and then used in database searches to confirm the identity of the template RNA. The RT-PCR fragment generated includes one of the mutation sites related to oseltamivir resistance, H274Y.

CONCLUSION

Our one-step RT-PCR assay followed by sequencing is a rapid, accurate, and specific method for detection and subtyping of different neuraminidase subtypes from a range of host species and from different geographical locations.

Detection and identification of the H5 hemagglutinin subtype by real-time RT-PCR

Serological methods, gene sequencing, and RT-PCR-based methods have all been used for the identification of influenza virus hemagglutinin (HA) subtypes. Compared to serological methods and gene sequencing, RT-PCR is fast, sensitive, and relatively inexpensive. However, since RT-PCR generally lacks the specificity of sequencing or serology, the most practical application of RT-PCR methods for subtype identification is either to target a few of the most important subtypes such as H5 and H7 or to use it in situations where a specific strain is being targeted, such as during an outbreak or with experimental samples. Since identification of viruses from the Asian-origin H5N1 highly pathogenic avian influenza virus lineage is a high priority worldwide, the procedure for real-time RT-PCR (rRT-PCR) identification of the H5 H subtype is presented here. This assay can identify the H5 hemagglutinin of any genetic lineage (North American or Asian) and either pathotype (highly pathogenic or low pathogenic), but does not differentiate between subtypes or pathotypes.

Development of a multiplex real-time polymerase chain reaction for the detection of influenza virus type A including H5 and H9 subtypes

Avian influenza viruses (AIVs) are endemic in wild birds and, if transmitted to poultry, can cause serious economic losses. The aim of this study was to develop a multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) for rapid detection of influenza virus type A, including H5 and H9 subtypes. The selected primers and various labeled TaqMan reporter probes corresponding to matrix, H5, and H9 genes were used in a multiplex real-time RT-PCR to simultaneously detect triple fluorescent signals. The results showed that the multiplex real-time RT-PCR assay can be applied to detect RNA of influenza virus type A including H5 and H9 subtypes with a high specificity and a sensitivity of 10 copies per reaction. As a result of its short turnaround times and a high specificity and sensitivity, the assay is very suitable for large-scale screening during AIV outbreaks.

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.