Design and validation of real-time reverse transcription-PCR assays for detection of pandemic (H1N1) 2009 virus

End-point RT-PCR based on a conservation landscape for SARS-COV-2 detection

End-point RT-PCR is a suitable alternative diagnostic technique since it is cheaper than RT-qPCR tests and can be implemented on a massive scale in low- and middle-income countries. In this work, a bioinformatic approach to guide the design of PCR primers was developed, and an alternative diagnostic test based on end-point PCR was designed. End-point PCR primers were designed through conservation analysis based on kmer frequency in SARS-CoV-2 and human respiratory pathogen genomes. Highly conserved regions were identified for primer design, and the resulting PCR primers were used to amplify 871 nasopharyngeal human samples with a previous RT-qPCR based SARS-CoV-2 diagnosis. The diagnostic test showed high accuracy in identifying SARS-CoV-2-positive samples including B.1.1.7, P.1, B.1.427/B.1.429 and B.1.617.2/ AY samples with a detection limit of 7.2 viral copies/µL. In addition, this test could discern SARS-CoV-2 infection from other viral infections with COVID-19-like symptomatology. The designed end-point PCR diagnostic test to detect SARS-CoV-2 is a suitable alternative to RT-qPCR. Since the proposed bioinformatic approach can be easily applied in thousands of viral genomes and over highly divergent strains, it can be used as a PCR design tool as new SARS-CoV-2 variants emerge. Therefore, this end-point PCR test could be employed in epidemiological surveillance to detect new SARS-CoV-2 variants as they emerge and propagate.

CovDif, a Tool to Visualize the Conservation between SARS-CoV-2 Genomes and Variants

The spread of the newly emerged severe acute respiratory syndrome (SARS-CoV-2) virus has led to more than 430 million confirmed cases, including more than 5.9 million deaths, reported worldwide as of 24 February 2022. Conservation of viral genomes is important for pathogen identification and diagnosis, therapeutics development and epidemiological surveillance to detect the emergence of new viral variants. An intense surveillance of virus variants has led to the identification of Variants of Interest and Variants of Concern. Although these classifications dynamically change as the pandemic evolves, they have been useful to guide public health efforts on containment and mitigation. In this work, we present CovDif, a tool to detect conserved regions between groups of viral genomes. CovDif creates a conservation landscape for each group of genomes of interest and a differential landscape able to highlight differences in the conservation level between groups. CovDif is able to identify loss in conservation due to point mutations, deletions, inversions and chromosomal rearrangements. In this work, we applied CovDif to SARS-CoV-2 clades (G, GH, GR, GV, L, O, S and G) and variants. We identified all regions for any defining SNPs. We also applied CovDif to a group of population genomes and evaluated the conservation of primer regions for current SARS-CoV-2 detection and diagnostic protocols. We found that some of these protocols should be applied with caution as few of the primer-template regions are no longer conserved in some SARS-CoV-2 variants. We conclude that CovDif is a tool that could be widely applied to study the conservation of any group of viral genomes as long as whole genomes exist.

Standardization of a high-performance RT-qPCR for viral load absolute quantification of influenza A

Influenza is an acute viral infectious respiratory disease worldwide, presenting in different clinical forms, from influenza-like illness (ILI) to severe acute respiratory infection (SARI). Although real-time quantitative polymerase chain reaction (qPCR) is already an important tool for both diagnosis and treatment monitoring of several viral infections, the correlation between the clinical aspects and the viral load of influenza is still unclear. This lack of clarity is primarily due to the low accuracy and reproducibility of the methodologies developed to quantify the influenza virus. Thus, this study aimed to develop and standardize a universal absolute quantification for influenza A by reverse transcription-quantitative PCR (RT-qPCR), using a plasmid DNA. The assay showed efficiency (Eff%) 98.6, determination coefficient (R₂⁾ 0.998, linear range 10^¹ to 10^¹⁰, limit of detection (LOD) 6.77, limit of quantification (LOQ) 20.52 copies/reaction. No inter and intra assay variability was shown, and neither was the matrix effect observed. Serial measurements of clinical samples collected at a 72h interval showed no change in viral load. By contrast, immunocompetent patients have a significantly lower viral load than immunosuppressed ones. Absolute quantification in clinical samples showed some predictors associated with increased viral load: (H1N1)pdm09 (0.045); women (p = 0.049) and asthmatics (p = 0.035). The high efficiency, precision, and previous performance in clinical samples suggest the assay can be used as an accurate universal viral load quantification of influenza A. Its applicability in predicting severity and response to antivirals needs to be evaluated.

A Recent Update on Advanced Molecular Diagnostic Techniques for COVID-19 Pandemic: An Overview

Coronavirus disease 2019 (COVID-19), which started out as an outbreak of pneumonia, has now turned into a pandemic due to its rapid transmission. Besides developing a vaccine, rapid, accurate, and cost-effective diagnosis is essential for monitoring and combating the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its related variants on time with precision and accuracy. Currently, the gold standard for detection of SARS-CoV-2 is Reverse Transcription Polymerase Chain Reaction (RT-PCR), but it lacks accuracy, is time-consuming and cumbersome, and fails to detect multi-variant forms of the virus. Herein, we have summarized conventional diagnostic methods such as Chest-CT (Computed Tomography), RT-PCR, Loop Mediated Isothermal Amplification (LAMP), Reverse Transcription-LAMP (RT-LAMP), as well new modern diagnostics such as CRISPR-Cas-based assays, Surface Enhanced Raman Spectroscopy (SERS), Lateral Flow Assays (LFA), Graphene-Field Effect Transistor (GraFET), electrochemical sensors, immunosensors, antisense oligonucleotides (ASOs)-based assays, and microarrays for SARS-CoV-2 detection. This review will also provide an insight into an ongoing research and the possibility of developing more economical tools to tackle the COVID-19 pandemic.

COVID-19 diagnosis -A review of current methods

A fast and accurate self-testing tool for COVID-19 diagnosis has become a prerequisite to comprehend the exact number of cases worldwide and to take medical and governmental actions accordingly. SARS-CoV-2 (formerly, 2019-nCoV) infection was first reported in Wuhan (China) in December 2019, and then it has rapidly spread around the world, causing ~14 million active cases with ~582,000 deaths as of July 2020. The diagnosis tools available so far have been based on a) viral gene detection, b) human antibody detection, and c) viral antigen detection, among which the viral gene detection by RT-PCR has been found as the most reliable technique. In this report, the current SARS-CoV-2 detection kits, exclusively the ones that were issued an "Emergency Use Authorization" from the U.S. Food and Drug Administration, were discussed. The key structural components of the virus were presented to provide the audience with an understanding of the scientific principles behind the testing tools. The methods that are still in the early research state were also reviewed in a subsection based on the reports available so far.

Characterization of Swine Influenza A(H1N2) Variant, Alberta, Canada, 2020

Influenza strains circulating among swine populations can cause outbreaks in humans. In October 2020, we detected a variant influenza A subtype H1N2 of swine origin in a person in Alberta, Canada. We initiated a public health, veterinary, and laboratory investigation to identify the source of the infection and determine whether it had spread. We identified the probable source as a local pig farm where a household contact of the index patient worked. Phylogenetic analysis revealed that the isolate closely resembled strains found at that farm in 2017. Retrospective and prospective surveillance using molecular testing did not identify any secondary cases among 1,532 persons tested in the surrounding area. Quick collaboration between human and veterinary public health practitioners in this case enabled a rapid response to a potential outbreak.

Influenza virus detection in the stool of children with acute gastroenteritis

OBJECTIVES

To determine if the clinical characteristics of children with gastroenteritis and influenza identified in their stool differ from those whose stool was influenza-negative.

METHODS

Children <18-years with gastroenteritis whose stool tested negative for enteropathogen were tested for influenza in stool. The clinical features between influenza-positive and influenza-negative gastroenteritis cases were compared. Stools from controls without infection were also tested for influenza.

RESULTS

Among the 440 gastroenteritis cases, those who were influenza test-positive were older [median age 4.0 (IQR: 2.3, 5.5) vs. 1.5 (IQR: 0.5, 4.0) years; P = 0.008], more likely to present in fall or winter (92.3 % vs. 48.0 %; P = 0.001), be febrile (84.6 % vs. 30.6 %; P < 0.001), have respiratory symptoms (91.7 % vs. 44.8 %; P = 0.002), have dehydration [median Clinical Dehydration Scale score: 4 (IQR: 1.5, 4.5) vs. 2 (IQR: 0, 3); P = 0.034], and have higher Modified Vesikari Scale scores [median: 13 (IQR: 10.5, 14.0) vs. 10 (IQR: 9.0, 13.0); P = 0.044], than those who tested negative. Thirteen gastroenteritis cases (13/440; 3.0 %) including one child without respiratory symptoms vs. one control (1/250; 0.4 %) were influenza stool positive.

CONCLUSIONS

Fever, respiratory symptoms, more severe illness, and older age were more common in children with gastroenteritis with influenza detected in stool, compared to those tested negative.

Using population-wide administrative and laboratory data to estimate type- and subtype-specific influenza vaccine effectiveness: a surveillance protocol

INTRODUCTION

The appropriateness of using routinely collected laboratory data combined with administrative data for estimating influenza vaccine effectiveness (VE) is still being explored. This paper outlines a protocol to estimate influenza VE using linked laboratory and administrative data which could act as a companion to estimates derived from other methods.

METHODS AND ANALYSIS

We will use the test-negative design to estimate VE for each influenza type/subtype and season. Province-wide individual-level records of positive and negative influenza tests at the Provincial Laboratory for Public Health in Alberta will be linked, by unique personal health numbers, to administrative databases and vaccination records held at the Ministry of Health in Alberta to determine covariates and influenza vaccination status, respectively. Covariates of interests include age, sex, immunocompromising chronic conditions and healthcare setting. Cases will be defined based on an individual's first positive influenza test during the season, and potential controls will be defined based on an individual's first negative influenza test during the season. One control for each case will be randomly selected based on the week the specimen was collected. We will estimate VE using multivariable logistic regression.

ETHICS AND DISSEMINATION

Ethics approval was obtained from the University of Alberta's Health Research Ethics Board-Health Panel under study ID Pro00075997. Results will be disseminated by public health officials in Alberta.

Effectiveness of Live Attenuated vs Inactivated Influenza Vaccines in Children During the 2012-2013 Through 2015-2016 Influenza Seasons in Alberta, Canada: A Canadian Immunization Research Network (CIRN) Study

IMPORTANCE

Recent observational studies report conflicting results regarding the effectiveness of live attenuated influenza vaccine (LAIV), particularly against influenza A(H1N1)pdm09.

OBJECTIVE

To compare the effectiveness of LAIV and inactivated influenza vaccine (IIV) against laboratory-confirmed influenza.

DESIGN, SETTING, AND PARTICIPANTS

A test-negative study to estimate influenza vaccine effectiveness (VE) using population-based, linked, individual-level laboratory, health administrative, and immunization data. Data were obtained from 10 169 children and adolescents aged 2 to 17 years (children) who were tested for influenza in inpatient or outpatient settings during periods when influenza was circulating based on a threshold level of 5% weekly test positivity for the province during the 4 influenza seasons spanning from November 11, 2012, to April 30, 2016, in Alberta, Canada. Logistic regression was used to estimate VE by vaccine type, influenza season, and influenza type and subtype. The relative effectiveness of each vaccine type was assessed by comparing the odds of laboratory-confirmed influenza infection for LAIV recipients with that for IIV recipients.

EXPOSURES

The primary exposure was receipt of LAIV or IIV before testing for influenza.

MAIN OUTCOMES AND MEASURES

The primary outcome was influenza case status as determined by reverse-transcriptase polymerase chain reaction testing.

RESULTS

A total of 10 779 respiratory specimens (from 10 169 children) collected and tested for influenza during the 4 influenza seasons were included, with 53.4% from males; the mean (SD) age was 7.0 (4.6) years. Across the 4 influenza seasons, 3161 children tested positive for influenza. Combining the 4 influenza seasons, the adjusted VE against influenza A(H1N1)pdm09 was 69% (95% CI, 56%-78%) for LAIV compared with 79% (95% CI, 70%-86%) for IIV. Vaccine effectiveness against influenza A(H3N2) was 36% (95% CI, 14%-53%) for LAIV and 43% (95% CI, 22%-59%) for IIV. Against influenza B, VE was 74% (95% CI, 62%-82%) for LAIV and 56% (95% CI, 41%-66%) for IIV. There were no significant differences in the odds of influenza infection for LAIV recipients compared with IIV recipients except for influenza B during the 2015-2016 season, when LAIV recipients had lower odds of infection than IIV recipients (odds ratio, 0.36; 95% CI, 0.17-0.76).

CONCLUSIONS AND RELEVANCE

There was no evidence to support the lack of effectiveness of LAIV against influenza A(H1N1)pdm09. These results support administration of either vaccine type in this age group.

Could urine be useful for the diagnosis of Chlamydia trachomatis pneumonia in infancy?

A 9-week-old infant presented with respiratory distress. The presumptive diagnosis of Chlamydia trachomatis pneumonia was ultimately made in a novel manner by a positive nucleic acid amplification test on a urine sample.

Microdroplet sandwich real-time rt-PCR for detection of pandemic and seasonal influenza subtypes

As demonstrated by the recent 2012/2013 flu epidemic, the continual emergence of new viral strains highlights the need for accurate medical diagnostics in multiple community settings. If rapid, robust, and sensitive diagnostics for influenza subtyping were available, it would help identify epidemics, facilitate appropriate antiviral usage, decrease inappropriate antibiotic usage, and eliminate the extra cost of unnecessary laboratory testing and treatment. Here, we describe a droplet sandwich platform that can detect influenza subtypes using real-time reverse-transcription polymerase chain reaction (rtRT-PCR). Using clinical samples collected during the 2010/11 season, we effectively differentiate between H1N1p (swine pandemic), H1N1s (seasonal), and H3N2 with an overall assay sensitivity was 96%, with 100% specificity for each subtype. Additionally, we demonstrate the ability to detect viral loads as low as 10⁴ copies/mL, which is two orders of magnitude lower than viral loads in typical infected patients. This platform performs diagnostics in a miniaturized format without sacrificing any sensitivity, and can thus be easily developed into devices which are ideal for small clinics and pharmacies.

Detection of the pandemic H1N1/2009 influenza A virus by a highly sensitive quantitative real-time reverse-transcription polymerase chain reaction assay

A quantitative real time reverse-transcription polymerase chain reaction (qRT-PCR) assay with specific primers recommended by the World Health Organization (WHO) has been widely used successfully for detection and monitoring of the pandemic H1N1/2009 influenza A virus. In this study, we report the design and characterization of a novel set of primers to be used in a qRT-PCR assay for detecting the pandemic H1N1/2009 virus. The newly designed primers target three regions that are highly conserved among the hemagglutinin (HA) genes of the pandemic H1N1/2009 viruses and are different from those targeted by the WHO-recommended primers. The qRT-PCR assays with the newly designed primers are highly specific, and as specific as the WHO-recommended primers for detecting pandemic H1N1/2009 viruses and other influenza viruses including influenza B viruses and influenza A viruses of human, swine, and raccoon dog origin. Furthermore, the qRT-PCR assays with the newly designed primers appeared to be at least 10-fold more sensitive than those with the WHO-recommended primers as the detection limits of the assays with our primers and the WHO-recommended primers were 2.5 and 25 copies of target RNA per reaction, respectively. When tested with 83 clinical samples, 32 were detected to be positive using the qRT-PCR assays with our designed primers, while only 25 were positive by the assays with the WHO-recommended primers. These results suggest that the qRT-PCR system with the newly designed primers represent a highly sensitive assay for diagnosis of the pandemic H1N1/2009 virus infection.

Polymeric LabChip real-time PCR as a point-of-care-potential diagnostic tool for rapid detection of influenza A/H1N1 virus in human clinical specimens

It is clinically important to be able to detect influenza A/H1N1 virus using a fast, portable, and accurate system that has high specificity and sensitivity. To achieve this goal, it is necessary to develop a highly specific primer set that recognizes only influenza A viral genes and a rapid real-time PCR system that can detect even a single copy of the viral gene. In this study, we developed and validated a novel fluidic chip-type real-time PCR (LabChip real-time PCR) system that is sensitive and specific for the detection of influenza A/H1N1, including the pandemic influenza strain A/H1N1 of 2009. This LabChip real-time PCR system has several remarkable features: (1) It allows rapid quantitative analysis, requiring only 15 min to perform 30 cycles of real-time PCR. (2) It is portable, with a weight of only 5.5 kg. (3) The reaction cost is low, since it uses disposable plastic chips. (4) Its high efficiency is equivalent to that of commercially available tube-type real-time PCR systems. The developed disposable LabChip is an economic, heat-transferable, light-transparent, and easy-to-fabricate polymeric chip compared to conventional silicon- or glass-based labchip. In addition, our LabChip has large surface-to-volume ratios in micro channels that are required for overcoming time consumed for temperature control during real-time PCR. The efficiency of the LabChip real-time PCR system was confirmed using novel primer sets specifically targeted to the hemagglutinin (HA) gene of influenza A/H1N1 and clinical specimens. Eighty-five human clinical swab samples were tested using the LabChip real-time PCR. The results demonstrated 100% sensitivity and specificity, showing 72 positive and 13 negative cases. These results were identical to those from a tube-type real-time PCR system. This indicates that the novel LabChip real-time PCR may be an ultra-fast, quantitative, point-of-care-potential diagnostic tool for influenza A/H1N1 with a high sensitivity and specificity.

Update on influenza diagnostics: lessons from the novel H1N1 influenza A pandemic

The menu of diagnostic tools that can be utilized to establish a diagnosis of influenza is extensive and includes classic virology techniques as well as new and emerging methods. This review of how the various existing diagnostic methods have been utilized, first in the context of a rapidly evolving outbreak of novel influenza virus and then during the different subsequent phases and waves of the pandemic, demonstrates the unique roles, advantages, and limitations of each of these methods. Rapid antigen tests were used extensively throughout the pandemic. Recognition of the low negative predictive values of these tests is important. Private laboratories with preexisting expertise, infrastructure, and resources for rapid development, validation, and implementation of laboratory-developed assays played an unprecedented role in helping to meet the diagnostic demands during the pandemic. FDA-cleared assays remain an important element of the diagnostic armamentarium during a pandemic, and a process must be developed with the FDA to allow manufacturers to modify these assays for detection of novel strains in a timely fashion. The need and role for subtyping of influenza viruses and antiviral susceptibility testing will likely depend on qualitative (circulating subtypes and their resistance patterns) and quantitative (relative prevalence) characterization of influenza viruses circulating during future epidemics and pandemics.

Comparison of the Roche RealTime ready Influenza A/H1N1 Detection Set with CDC A/H1N1pdm09 RT-PCR on samples from three hospitals in Ho Chi Minh City, Vietnam

Real-time polymerase chain reaction (PCR) can be considered the gold standard for detection of influenza viruses due to its high sensitivity and specificity. Roche has developed the RealTime ready Influenza A/H1N1 Detection Set, consisting of a generic influenza virus A PCR targeting the M2 gene (M2 PCR) and a specific PCR targeting the hemagglutinin (HA) of A/H1N1-pdm09 (HA PCR, 2009 H1N1), with the intention to make a reliable, rapid, and simple test to detect and quantify 2009 H1N1 in clinical samples. We evaluated this kit against the US Centers for Disease Control and Prevention (USCDC)/World Health Organization real-time PCR for influenza virus using 419 nose and throat swabs from 210 patients collected in 3 large hospitals in Ho Chi Minh City, Vietnam. In the per-patient analysis, when compared to CDC PCR, the sensitivity and specificity of the M2 PCR were 85.8% and 97.6%, respectively; the sensitivity and specificity of HA PCR were 88.2% and 100%, respectively. In the per-sample analysis, the sensitivity and specificity in nose swabs were higher than those in throat swabs for both M2 and HA PCRs. The viral loads as determined with the M2 and HA PCRs correlated well with the Ct values of the CDC PCR. Compared with the CDC PCR, the kit has a reasonable sensitivity and very good specificity for the detection and quantification of influenza A virus and A/H1N1-pdm09. However, given the current status of 2009 H1N1, a kit that can detect all circulating seasonal influenza viruses would be preferable.

Two years after pandemic influenza A/2009/H1N1: what have we learned?

The world had been anticipating another influenza pandemic since the last one in 1968. The pandemic influenza A H1N1 2009 virus (A/2009/H1N1) finally arrived, causing the first pandemic influenza of the new millennium, which has affected over 214 countries and caused over 18,449 deaths. Because of the persistent threat from the A/H5N1 virus since 1997 and the outbreak of the severe acute respiratory syndrome (SARS) coronavirus in 2003, medical and scientific communities have been more prepared in mindset and infrastructure. This preparedness has allowed for rapid and effective research on the epidemiological, clinical, pathological, immunological, virological, and other basic scientific aspects of the disease, with impacts on its control. A PubMed search using the keywords "pandemic influenza virus H1N1 2009" yielded over 2,500 publications, which markedly exceeded the number published on previous pandemics. Only representative works with relevance to clinical microbiology and infectious diseases are reviewed in this article. A significant increase in the understanding of this virus and the disease within such a short amount of time has allowed for the timely development of diagnostic tests, treatments, and preventive measures. These findings could prove useful for future randomized controlled clinical trials and the epidemiological control of future pandemics.

Improving influenza virus detection

INTRODUCTION

Influenza virus infections cause significant morbidity, and the unique ability of these viruses to undergo antigenic drift and shift means that it is critical for current laboratory assays to keep pace with these changes for accurate diagnosis. New subtypes have the potential to evolve into pandemics hence accurate virus subtyping is also essential.

AREAS COVERED

In this article, the authors review the current techniques available to detect influenza virus.

EXPERT OPINION

The biggest gains in improving on influenza diagnostics may lie in reappraising our current approach and optimizing all existing steps in influenza detection: pre-analytical, analytical, post-analytical. In addition, we must foster close collaboration between governments, surveillance networks and frontline diagnostic laboratories, and utilize advances in information technology to facilitate these interactions and to disseminate crucial information.

Rethinking approaches to improve the utilization of nucleic acid amplification tests for detection and characterization of influenza A in diagnostic and reference laboratories

Influenza A virus (IFVA) is a significant cause of respiratory infections worldwide and was also responsible for a recent pandemic in 2009. Laboratory identification of IFVA can guide antiviral therapy, assist in cohorting of patients and prevent antibiotic use. Characterization of the virus can track the emergence of novel strains, identify resistance and determine how circulating strains match with vaccine components. The gold standard for detection and characterization of IFVA is nucleic acid amplification technology (e.g., reverse transcriptase PCR [RT-PCR]), which must contend with a constantly evolving viral genome. Although molecular technology has been available for over two decades, there is still an operational gap between assay design and utilization of these tests for the diagnosis and characterization of IFVA. This review will discuss issues surrounding the implementation and use of RT-PCR for the identification and characterization of IFVA, and speculate on why RT-PCR has not been used more widely in clinical laboratories or moved closer to the patient. Newer, less widely used technologies that may change our laboratory practices will be identified and the authors will close with an attempt to identify some future applications of RT-PCR-based technologies for the detection and characterization of IFVA.

High success and low mortality rates with non-invasive ventilation in influenza A H1N1 patients in a tertiary hospital

Background

In 2009, an outbreak of respiratory illness caused by influenza A H1N1 virus occurred worldwide. Some patients required Intensive Care Unit (ICU) admission. The use of non-invasive ventilation (NIV) in these patients is controversial, as the aerosol dispersion may contaminate the environment and health-care co-workers.

Methods

Describe the respiratory profile, the mortality rate, and the benefit of using NIV in patients with confirmed diagnosis of influenza AH1N1 who were admitted in the ICU during the year 2009.

Results

A total of 1, 401 cases of influenza A H1N1 were confirmed in our hospital by real-time RT-PCR in 2009, and 20 patients were admitted to the ICU. The patients' ages ranged from 18 to 74 years (median of 42). Acute Respiratory Failure (ARF) was present in 70% of patients. The median Acute Physiology and Chronic Health Evaluation II score was 7 (range 7 to 25). Of the 14 patients who developed ARF, 85.7% needed NIV and 14% needed invasive MV at admission. Our success rate (41.6%) with NIV was higher than that described by others. The hospital mortality rate was 2.1%. When influenza A H1N1 arrived in Brazil, the disease was already on endemic alert in other countries. The population was already aware of the symptoms and the health-care system of the treatment. This allowed patients to be properly and promptly treated for influenza A H1N1, while health-care workers took protective measures to avoid contamination.

Conclusion

In our study we found a high success and low mortality rates with non-invasive ventilation in patients with influenza A H1N1.

Single-step multiplex reverse transcription polymerase chain reaction assay for detection and differentiation of the 2009 H1N1 Influenza A virus pandemic in Thai swine populations

A recently emerged H1N1 Influenza A virus (pandemic H1N1 (pH1N1)) with a Swine influenza virus (SIV) genetic background spread globally from human-to-human causing the first influenza virus pandemic of the 21st century. In a short period, reverse zoonotic cases in pigs followed by a widespread of the virus in the pig population were documented. The implementation of effective control strategies, rapid diagnosis, and differentiation of such virus from endemically circulating SIV in the various swine populations of the world is needed. To address the problem, a multiplex reverse transcription polymerase chain reaction assay utilizing a combination of the PB1, H1, and N1 primers that can rapidly and simultaneously subtype and screen for the presence of pH1N1 virus infection in Thai pigs was developed. The assay had 100% specificity and did not amplify genetic material from other subtypes of SIV, seasonal H1N1 human influenza (huH1N1) virus, highly pathogenic influenza H5N1 virus, and other important swine respiratory viral pathogens. The assay was able to both detect and subtype pH1N1 virus as low as 0.1-50% tissue culture infective doses/ml (TCID(50)/ml). The assay was used to screen 175 clinical samples obtained from SIV suspected cases, of which 6 samples were pH1N1 positive and were confirmed through virus isolation and whole genome sequencing. The results of the study suggested that the assay would be useful for the rapid diagnosis of pH1N1 in suspected Thai swineherds, where genetics of the endemically circulating SIV differ from the strains circulating in North American and European herds.

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.

A validation study comparing the sensitivity and specificity of the new Dr. KSU H1N1 RT-PCR kit with real-time RT-PCR for diagnosing influenza A (H1N1)

BACKGROUND AND OBJECTIVES

A new test (Dr. KSU H1N1 RT-PCR kit) was recently developed to provide a less expensive alternative to real-time reverse transcriptase-polymerase chain reaction (RT-PCR). We report the findings of a validation study designed to assess the diagnostic accuracy, including sensitivity and specificity, of the new kit, as compared to real-time RT-PCR.

DESIGN AND SETTING

Cross-sectional validation study conducted from 18-22 November 2009 at a primary care clinic for H1N1 at a tertiary care teaching hospital in Riyadh.

PATIENTS AND METHODS

Nasopharyngeal swab samples and data on socio-demographic characteristics and symptoms were collected from 186 patients. Swab samples were sent to the laboratory for testing with both real-time RT-PCR and the new Dr. KSU H1N1 RT-PCR kit. We measured the sensitivity and specificity of the new test across the entire sample size and investigated how these values were affected by patient socio-demographic characteristics and symptoms.

RESULTS

The outcomes of the two tests were highly correlated (kappa=0.85; P<.0001). The sensitivity and specificity of the new test were 99.11% and 83.78%, respectively. The sensitivity of the new test was affected only minimally (96%-100%) by patient characteristics and number of symptoms. On the other hand, the specificity of the new test varied depending on how soon patients were tested after onset of symptoms (100% specificity when swabs were taken on the first day of the symptoms, decreasing to 75% when swabs were taken on or after the third day). The specificity of the new test also increased with increasing body temperature.

CONCLUSION

The new test seems to provide a cost-effective alternative to real-time RT-PCR for diagnosing H1N1 influenza. However, further testing may be needed to verify the efficacy of the test in different settings and communities.

Salivary Detection of H1N1 Virus: A Clinical Feasibility Investigation

The fast and efficient transportation among continents will continue to play a role in the spread of airborne pandemics. The objective of this study was to detect H1N1 virus in the saliva of individuals who visited the emergency department and were diagnosed as having H1N1 influenza. Nasopharyngeal swabs and saliva samples from those who presented to the emergency department with flu-like symptoms were sent to the laboratory. RNA was extracted from both samples. Real-time RT-PCR tests were performed, and the saliva and nasopharyngeal swab tests were compared. Samples were drawn from 26 individuals. A positive nasopharyngeal swab test and salivary test was found in 14 persons, and negative tests were found in 12 persons. Saliva sampling for H1N1 has excellent predictive value, is highly accurate and reliable, and is more convenient than the nasopharyngeal swab. Clinical trial with the Helsinki Committee at Rambam Health Care Campus, registration number 036309-RMB.

Comparison of a singleplex real-time RT-PCR assay and multiplex respiratory viral panel assay for detection of influenza "A" in respiratory specimens

BACKGROUND

Evaluation of different molecular tests for the detection of pandemic (H1N1) 2009 virus is important before the next wave of the pandemic.

OBJECTIVES

To compare a hydrolysis probe-based real-time RTPCR assay recommended by the CDC to the xTAG respiratory viral panel (RVP) (Luminex Molecular Diagnostics) for the detection of influenza A.

METHODS

Eleven thousand eight hundred and ninety-eight respiratory specimens were tested by the real-time RT-PCR and RVP assays for the detection of influenza A. The distribution of seasonal H1, H3 and pandemic H1N1 subtypes in these specimens was compared.

RESULTS

The RVP assay was generally unable to identify influenza A–positive samples with a low viral load, whereas the real-time RT-PCR assay detected most of these samples resulting in a subset of specimens that could not be confirmed as either seasonal or pandemic influenza A subtypes.

CONCLUSIONS

When the prevalence of influenza A is high, the CDC recommended real-time RT-PCR has significant advantages as a frontline assay, namely higher sensitivity and shorter time to reporting a result. Anticipated scenarios would be during the peaks of the pandemic and episodes of seasonal influenza. Furthermore, the better sensitivity of the RT-PCR makes it the preferred assay to detect influenza in patients with severe respiratory disease tested late in their clinical course. If pandemic (H1N1) 2009 virus is not the dominant virus and there is a high proportion of other respiratory viruses circulating, laboratories will be faced with the decision to use the RVP assay for the detection of pandemic (H1N1) 2009 virus.

Determination of the relative economic impact of different molecular-based laboratory algorithms for respiratory viral pathogen detection, including Pandemic (H1N1), using a secure web based platform

Background

During period of crisis, laboratory planners may be faced with a need to make operational and clinical decisions in the face of limited information. To avoid this dilemma, our laboratory utilizes a secure web based platform, Data Integration for Alberta Laboratories (DIAL) to make near real-time decisions.

This manuscript utilizes the data collected by DIAL as well as laboratory test cost modeling to identify the relative economic impact of four proposed scenarios of testing for Pandemic H1N1 (2009) and other respiratory viral pathogens.

Methods

Historical data was collected from the two waves of the pandemic using DIAL. Four proposed molecular testing scenarios were generated: A) Luminex respiratory virus panel (RVP) first with/without US centers for Disease Control Influenza A Matrix gene assay (CDC-M), B) CDC-M first with/without RVP, C) RVP only, and D) CDC-M only. Relative cost estimates of different testing algorithm were generated from a review of historical costs in the lab and were based on 2009 Canadian dollars.

Results

Scenarios A and B had similar costs when the rate of influenza A was low (< 10%) with higher relative cost in Scenario A with increasing incidence. Scenario A provided more information about mixed respiratory virus infection as compared with Scenario B.

Conclusions

No one approach is applicable to all conditions. Testing costs will vary depending on the test volume, prevalence of influenza A strains, as well as other circulating viruses and a more costly algorithm involving a combination of different tests may be chosen to ensure that tests results are returned to the clinician in a quicker manner. Costing should not be the only consideration for determination of laboratory algorithms.

Swine outbreak of pandemic influenza A virus on a Canadian research farm supports human-to-swine transmission

BACKGROUND

Swine outbreaks of pandemic influenza A (pH1N1) suggest human introduction of the virus into herds. This study investigates a pH1N1 outbreak occurring on a swine research farm with 37 humans and 1300 swine in Alberta, Canada, from 12 June through 4 July 2009.

METHODS

The staff was surveyed about symptoms, vaccinations, and livestock exposures. Clinical findings were recorded, and viral testing and molecular characterization of isolates from humans and swine were performed. Human serological testing and performance of the human influenza-like illness (ILI) case definition were also studied.

RESULTS

Humans were infected before swine. Seven of 37 humans developed ILI, and 2 (including the index case) were positive for pH1N1 by reverse-transcriptase polymerase chain reaction (RT-PCR). Swine were positive for pH1N1 by RT-PCR 6 days after contact with the human index case and developed symptoms within 24 h of their positive viral test results. Molecular characterization of the entire viral genomes from both species showed minor nucleotide heterogeneity, with 1 amino acid change each in the hemagglutinin and nucleoprotein genes. Sixty-seven percent of humans with positive serological test results and 94% of swine with positive swab specimens had few or no symptoms. Compared with serological testing, the human ILI case definition had a specificity of 100% and sensitivity of 33.3%. The only factor associated with seropositivity was working in the swine nursery.

CONCLUSIONS

Epidemiologic data support human-to-swine transmission, and molecular characterization confirms that virtually identical viruses infected humans and swine in this outbreak. Both species had mild illness and recovered without sequelae.

Clinical performance of three rapid diagnostic tests for influenza virus in nasopharyngeal specimens to detect novel swine-origin influenza viruses

BACKGROUND

Influenza is an important public health problem. The aim of this study was to evaluate and compare the sensitivity and specificity of three rapid diagnostic tests (SEKISUI, QuickVue Influenza A + B, and SD BIOLINE) for novel swine-origin influenza viruses (S-OIV) and seasonal influenza.

MATERIALS AND METHODS

A total of 210 nasopharyngeal swabs from unique clinical specimens were previously tested by real-time reverse transcription polymerase chain reaction (RT-PCR) assay and tested again in this study.

RESULTS AND DISCUSSION

Of these, 164 (78%) were influenza A-positive and 46 (22%) were influenza A-negative by RT-PCR. From 115 positive swabs, 80 (69.6%), 66 (57.4%), and 46 (40.0%) showed S-OIV by SEKISUI, QuickVue Influenza A + B, and SD BIOLINE, respectively. Specific positive and negative predictive values of these three commercial rapid tests were all 100%. Therefore, positive rapid influenza virus diagnosis does not require an RT-PCR confirmatory test. Conversely, only negative rapid influenza virus diagnosis should be evaluated. The SEKISUI test would be a useful diagnostic tool for screening clinical samples for influenza. Concerning the various specimen types, among 25 patients with RT-PCR-proven S-OIV infection, influenza was identified in sputum (21/25; 84.0%) and nasopharyngeal swab (15/25; 60.0%) specimens, but in only 36.0% (9/25) of throat swab specimens. Sputum and nasopharyngeal swab specimens were the most predictive of influenza virus infection, while throat swab specimens were the least predictive of influenza virus infection.

Comparison of the Luminex xTAG respiratory viral panel with xTAG respiratory viral panel fast for diagnosis of respiratory virus infections

Nucleic acid tests are sensitive and specific and provide a rapid diagnosis, making them invaluable for patient and outbreak management. Multiplex PCR assays have additional advantages in providing an economical and comprehensive panel for many common respiratory viruses. Previous reports have shown the utility of the xTAG respiratory viral panel (RVP) assay manufactured by Luminex Molecular Diagnostics for this purpose. A newer generation of this kit, released in Canada in early 2010, is designed to simplify the procedure and reduce the turnaround time by about 24 h. The assay methodology and targets included in this version of the kit are different; consequently, the objective of this study was to compare the detection of a panel of respiratory viral targets using the older Luminex xTAG RVP (RVP Classic) assay with that using the newer xTAG RVP Fast assay. This study included 334 respiratory specimens that had been characterized for a variety of respiratory viral targets; all samples were tested by both versions of the RVP assay in parallel. Overall, the RVP Classic assay was more sensitive than the RVP Fast assay (88.6% and 77.5% sensitivities, respectively) for all the viral targets combined. Targets not detected by the RVP Fast assay included primarily influenza B virus, parainfluenza virus type 2, and human coronavirus 229E. A small number of samples positive for influenza A virus, respiratory syncytial virus B, human metapneumovirus, and parainfluenza virus type 1 were not detected by the RVP Classic assay and in general had low viral loads.

Evaluation of reverse transcription loop-mediated isothermal amplification assays for rapid diagnosis of pandemic influenza A/H1N1 2009 virus

Two genetic diagnosis systems using reverse transcription-loop-mediated isothermal amplification (RT-LAMP) technology were evaluated: one for detecting the HA gene of the pandemic influenza A/H1N1 2009 virus (H1pdm RT-LAMP) and the other for detecting the matrix gene of the influenza A virus (TypeA RT-LAMP). The competence of these two RT-LAMP assay kits for the diagnosis of the pandemic influenza A/H1N1 2009 virus was compared using real-time RT-PCR assays developed recently on viruses isolated and clinical specimens collected from patients with suspected infection. TypeA RT-LAMP and H1pdm RT-LAMP showed almost the same sensitivity as real-time RT-PCR for viruses isolated. The sensitivity and specificity of TypeA RT-LAMP and H1pdm RT-LAMP were 96.3% and 88.9%, respectively, for clinical specimens. Considering that the ability of the two RT-LAMP assay kits for detection of the pandemic influenza A/H1N1 2009 virus was comparable to that of the real-time RT-PCR assays, and that the assays were completed within 1 hr and did not require any expensive equipment, these two RT-LAMP assays are promising rapid diagnostic tests for the pandemic influenza A/H1N1 2009 virus at the hospital bedside.

Facial protective equipment, personnel, and pandemics: impact of the pandemic (H1N1) 2009 virus on personnel and use of facial protective equipment

BACKGROUND

Before the emergence of the pandemic (H1N1) 2009 virus, estimates of the stockpiles of facial protective equipment (FPE) and the impact that information had on personnel during a pandemic varied.

OBJECTIVE

To describe the impact of H1N1 on FPE use and hospital employee absenteeism. Setting. One tertiary care hospital and 2 community hospitals in the Vancouver Coastal Health (VCH) region, Vancouver, Canada. Patients. All persons with influenza-like illness admitted to the 3 VCH facilities during the period from June 28 through December 19, 2009.

METHODS

Data on patients and on FPE use were recorded prospectively. Data on salaried employee absenteeism were recorded during the period from August 1 through December 19, 2009.

RESULTS

During the study period, 865 patients with influenza-like illness were admitted to the 3 VCH facilities. Of these patients, 149 (17.2%) had laboratory-confirmed H1N1 influenza infection. The mean duration of hospital stay for these patients was 8.9 days, and the mean duration of intensive care unit stay was 9.2 days. A total of 134,281 masks and 173,145 N95 respirators (hereafter referred to as respirators) were used during the 24-week epidemic, double the weekly use of both items, compared with the previous influenza season. A ratio of 3 masks to 4 respirators was observed. Use of disposable eyewear doubled. Absenteeism mirrored the community epidemiologic curve, with a 260% increase in sick calls at the epidemic peak, compared with the nadir.

CONCLUSION

Overall, FPE use more than doubled, compared with the previous influenza season, with respirator use exceeding literature estimates. A significant proportion of FPE resources were used while managing suspected cases. Planners should prepare for at least a doubling in mask and respirator use, and a 3.6-fold increase in staff sick calls.

Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes

Resistance to oseltamivir in pandemic (H1N1) 2009 influenza A virus is linked to an amino acid change from histidine (H) to tyrosine (Y) at position 275 in the neuraminidase protein (NA). A real-time one step RT-PCR assay using single nucleotide polymorphism (SNP) probes was developed to detect this mutation in respiratory specimens. The limit of detection was 47.6 copies/reaction for wild-type H275 RNA and 52.9 copies/reaction for the mutant H275Y RNA. The assay did not cross-react with other respiratory pathogens. The clinical sensitivity and specificity of the assay was compared to the gold standard Sanger sequencing method using 25 sensitive, 15 resistant and 20 negative samples. The sensitivity and specificity was 88.0% and 100% respectively with the SOIV_Osel_SEN probe designed to detect the H275 allele and 100% for the SOIV_Osel_RES probe detecting the 275Y allele. The sensitivity of the assay using nine admixtures of sensitive and resistant alleles was 88.9% and 77.8% with the SOIV_Osel_SEN probe and SOIV_Osel_RES probe respectively. The presence of mixed sensitive and resistant alleles in patient samples and mixtures of in vitro RNA were detected reproducibly. This assay can be used for screening of original samples for oseltamivir resistance without the need for culture and phenotypic testing.

Transcriptomics and proteomics in the study of H1N1 2009

Influenza A virus (H1N1) 2009, a new swine-origin influenza A virus, has been spread worldwidely and caused great public fear. High-throughput transcriptomics and proteomics methods are now being used to identify H1N1 and H1N1-host interaction. This article reviews recent transcriptomics and proteomics research in H1N1 diagnosis, treatment, and H1N1 virus-host interaction, to offer some help for further understanding the infection mechanism and controlling H1N1 transmission.

Evaluation of twelve real-time reverse transcriptase PCR primer-probe sets for detection of pandemic influenza A/H1N1 2009 virus

Real-time reverse transcriptase PCR (rRT-PCR) assays have greatly contributed to the detection, control, and prevention of the pandemic influenza A/H1N1 2009 virus. To improve the rRT-PCR assays for detection of pandemic influenza A/H1N1 2009 virus, we evaluated the sensitivity, specificity, and performance of 12 rRT-PCR primer-probe sets [SW (a) to SW (l)] using a panel of virus strains and clinical specimens. These primer-probe sets were derived from published work and designed for detecting the hemagglutinin (HA) or the neuraminidase (NA) gene of the pandemic influenza A/H1N1 2009 virus. A primer-probe set, SW (CDC), developed by the Centers for Disease Control and Prevention (U.S. CDC) to target the HA gene of pandemic influenza A/H1N1 2009 virus, was used as a referee method. Our results demonstrated that although all primer-probe sets in this study had as high as 98.4 to 100% in silico coverage, some of the primer-probe sets had better specificity, sensitivity, and amplification efficiency than others. Two primer-probe sets, SW (h) and SW (l), which target the NA gene of pandemic influenza A/H1N1 2009 virus, were highly sensitive (10(4) copies/reaction), had high detection rates (56/60, P = 0.134, and 59/60, P = 1.000), and showed ideal specificity compared with SW (CDC). In addition, a cocktail of primer-probe sets targeted to the HA and NA genes displayed higher detection sensitivity than primer-probe sets targeting HA or NA alone, indicating that for practical applications, a combination of primer-probes targeting HA and NA genes is the best option for the detection of pandemic influenza A/H1N1 2009 virus.

Development and evaluation of reverse transcription loop-mediated isothermal amplification assay for rapid and real-time detection of the swine-origin influenza A H1N1 virus

The recent emergence of the swine-origin influenza A H1N1 virus (S-OIV) poses a serious global health threat. Rapid detection and differentiation of S-OIV from seasonal influenza is crucial for patient management and control of the epidemics. A one-step, single-tube accelerated and quantitative S-OIV-specific H1 reverse transcription loop-mediated isothermal amplification (RTLAMP) assay for clinical diagnosis of S-OIV by targeting the H1 gene is reported in this article. A comparative evaluation of the H1-specific RTLAMP assay vis-à-vis the World Health Organization-approved real-time polymerase chain reaction (RTPCR), involving 239 acute-phase throat swab samples, demonstrated exceptionally higher sensitivity by picking up all of the 116 H1N1-positive cases and 36 additional positive cases among the negatives that were sequence-confirmed as S-OIV H1N1. None of the real-time RTPCR-positive samples were missed by the RTLAMP system. The comparative analysis revealed that S-OIV RTLAMP was up to tenfold more sensitive than the World Health Organization real-time RTPCR; it had a detection limit of 0.1 tissue culture infectious dosage of (50)/ml. One of the most attractive features of this isothermal gene amplification assay is that it seems to have an advantage in monitoring gene amplification by means of SYBR Green I dye-mediated naked-eye visualization within 30 minutes compared to 2 to 3 hours for a real-time reverse transcription polymerase chain reaction. This suggests that the RTLAMP assay is a valuable tool for rapid, real-time detection and quantification of S-OIV in acute-phase throat swab samples without requiring sophisticated equipment.

Development and characterization of a highly specific and sensitive SYBR green reverse transcriptase PCR assay for detection of the 2009 pandemic H1N1 influenza virus on the basis of sequence signatures

The emergence and rapid spread of the 2009 H1N1 pandemic influenza virus showed that many diagnostic tests were unsuitable for detecting the novel virus isolates. In most countries the probe-based TaqMan assay developed by the U.S. Centers for Disease Control and Prevention was used for diagnostic purposes. The substantial sequence data that became available during the course of the pandemic created the opportunity to utilize bioinformatics tools to evaluate the unique sequence properties of this virus for the development of diagnostic tests. We used a comprehensive computational approach to examine conserved 2009 H1N1 sequence signatures that are at least 20 nucleotides long and contain at least two mismatches compared to any other known H1N1 genome. We found that the hemagglutinin (HA) and neuraminidase (NA) genes contained sequence signatures that are highly conserved among 2009 H1N1 isolates. Based on the NA gene signatures, we used Visual-OMP to design primers with optimal hybridization affinity and we used ThermoBLAST to minimize amplification artifacts. This procedure resulted in a highly sensitive and discriminatory 2009 H1N1 detection assay. Importantly, we found that the primer set can be used reliably in both a conventional TaqMan and a SYBR green reverse transcriptase (RT)-PCR assay with no loss of specificity or sensitivity. We validated the diagnostic accuracy of the NA SYBR green assay with 125 clinical specimens obtained between May and August 2009 in Chile, and we showed diagnostic efficacy comparable to the CDC assay. Our approach highlights the use of systematic computational approaches to develop robust diagnostic tests during a viral pandemic.

Surveillance of autopsy cases for D222G substitutions in haemagglutinin of the pandemic (H1N1) 2009 virus in Alberta, Canada

Pandemic (H1N1) 2009 virus-positive specimens were collected from autopsy patients and matched to pandemic (H1N1) 2009 virus-positive nasopharyngeal specimens from community control patients and pandemic (H1N1) 2009 virus-positive specimens from intensive-care unit (ICU) patients. Specimens were analysed for polymorphisms at amino acid 222 of the haemagglutinin (HA) glycoprotein. Whereas some specimens from autopsy patients were positive for D222N, none was positive for D222G. All control patient specimens were wild-type D222. D222G polymorphisms were also identified in a subset of ICU patients with admixtures of D222G and D222 and of D222N, D222G and D222 present. The relevance of D222N and D222G to influenza pathogenesis and transmissibility currently remains unclear.

One-step real-time reverse transcription-PCR assays for detecting and subtyping pandemic influenza A/H1N1 2009, seasonal influenza A/H1N1, and seasonal influenza A/H3N2 viruses

Pandemic influenza A/H1N1 2009 (A/H1N1pdm) virus has caused significant outbreaks worldwide. A previous one-step real-time reverse transcription-PCR (rRT-PCR) assay for detecting A/H1N1pdm virus (H1pdm rRT-PCR assay) was improved since the former probe had a low melting temperature and low tolerance to viral mutation. To help with the screening of the A/H1N1pdm virus, rRT-PCR assays were also developed for detecting human seasonal A/H1N1 (H1 rRT-PCR assay) and A/H3N2 influenza viruses (H3 rRT-PCR assay). H1pdm, H1, and H3 rRT-PCR assays were evaluated using in vitro-transcribed control RNA, isolated viruses, and other respiratory pathogenic viruses, and were shown to have high sensitivity, good linearity (R(2)=0.99), and high specificity. In addition, the improved H1pdm rRT-PCR assay could detect two viral strains of A/H1N1pdm, namely, A/Aichi/472/2009 (H1N1)pdm and A/Sakai/89/2009 (H1N1)pdm, which have mutation(s) in the probe-binding region of the hemagglutinin gene, without loss of sensitivity. Using the three rRT-PCR assays developed, 90 clinical specimens collected between May and October 2009 were then tested. Of these, 26, 20, and 2 samples were identified as positive for A/H1pdm, A/H3, and A/H1, respectively, while 42 samples were negative for influenza A viruses. The present results suggest that these highly sensitive and specific H1pdm, H1, and H3 rRT-PCR assays are useful not only for diagnosing influenza viruses, but also for the surveillance of influenza viruses.

A matrix gene-based multiplex real-time RT-PCR for detection and differentiation of 2009 pandemic H1N1 and other influenza A viruses in North America

Please cite this paper as: Harmon et al. (2010) A matrix gene–based multiplex real‐time RT‐PCR for detection and differentiation of 2009 pandemic H1N1 and other influenza A viruses in North America. Influenza and Other Respiratory Viruses 4(6), 405–410.

Background  The emergence in humans of pandemic (H1N1) 2009 (pH1N1) with similarities to swine influenza viruses (SIVs) caused much concern for both human and animal health as potential for interspecies transmission was initially unknown.

Objectives  The goal of this study was to develop a real‐time RT‐PCR test for the detection and differentiation of 2009 pH1N1 and endemic influenza A viruses in North America.

Methods  Matrix (M) gene sequences from U.S. human pH1N1 cases and U.S. SIVs were aligned to determine a suitable region for an assay target. Primers were selected to amplify all influenza A. Two probes were designed to differentiate pH1N1 (EA matrix) from endemic (NA matrix) SIVs. The assay was validated using the first U.S. pH1N1 strain, 10 human pH1N1‐positive specimens and nine U.S. SIV isolates, then evaluated on 165 specimens of swine and other animal origin submitted to the Iowa State University Veterinary Diagnostic Laboratory. Results were compared to other influenza A PCR assays. Sequences from additional pH1N1 strains and contemporary H1N1 SIVs were used to assess robustness of the selected primers and probes for the intended purpose.

Results  The new assay’s results from clinical specimens concurred with confirmatory PCR testing. The additional probe designed from sequence analysis improved detection of the NA matrix subtype when added to the reaction mixture.

Conclusion  This assay detects and differentiates pH1N1 and US influenza A viruses in various sample matrices and species. Good bioinformatics support is critical when designing RT‐PCR assays and monitoring their performance.

Evaluation of a rapid diagnostic test, NanoSign® Influenza A/B Antigen, for detection of the 2009 pandemic influenza A/H1N1 viruses

Background

This study evaluated the clinical accuracy and analytical sensitivity of the NanoSign^® Influenza A/B antigen kit in detecting 2009 pandemic influenza A/H1N1 viruses. The kit is one of the most popular rapid diagnostic tests for detecting influenza in Republic of Korea.

Results

The NanoSign^® Influenza A/B kit resulted in 79.4% sensitivity and 97.2% specificity compared to RT-PCR in the detection of the viruses from 1,023 specimens. In addition, the kit was able to detect two strains of novel influenza viruses, Influenza A/California/12/2009(H1N1) and clinically isolated wild-type novel influenza A/H1N1, both of which are spreading epidemically throughout the world. In addition, the correlation between NanoSign^® Influenza A/B test and conventional RT-PCR was approximately 94%, indicating a high concordance rate. Analytical sensitivity of the kit was approximately 73 ± 3.65 ng/mL of the purified viral proteins and 1.13 ± 0.11 hemagglutination units for the cultured virus.

Conclusions

As the NanoSign^® Influenza A/B kit showed relatively high sensitivity and specificity and the good correlation with RT-PCR, it will be very useful in the early control of influenza infection and in helping physicians in making early treatment decisions.

Development of a novel bead-based multiplex PCR assay for combined subtyping and oseltamivir resistance genotyping (H275Y) of seasonal and pandemic H1N1 influenza A viruses

BACKGROUND

The identification of influenza A virus subtypes in clinical specimens is becoming increasingly important for clinical laboratories since seasonal H1N1, H3N2 and pandemic H1N1 influenza A viruses can have defined antiviral resistance patterns and subtyping can be used as a surrogate for antiviral resistance testing.

OBJECTIVES

To develop a novel multiplex PCR (M-PCR) assay for the combined identification of influenza A subtype and oseltamivir resistance (H275Y) genotype in a combined assay format using Luminex xMAP™ technology.

STUDY DESIGN

The M-PCR assay employed five degenerate primers to amplify the hemagglutinin (HA) and neuraminidase (NA) genes and eight tagged primers in a target specific primer extension reaction (TSPE). Products were analysed using xTAG™ beads containing specific anti-tag oligonucleotides.

RESULTS

M-PCR correctly identified the subtype for 54/54 specimens that were influenza A positive, including 13/13 seasonal H3N2, 17/17 seasonal H1N1 and 24/24 pandemic H1N1 for both HA and NA genes. For oseltamivir resistance the M-PCR assay correctly identified 41/41 H1N1 viruses as oseltamivir sensitive (H275) or resistant (H275Y). Analysis of sequential specimens from two immunocompromised patients revealed the appearance of the H275Y allele at earlier time points after infection compared with Sanger sequencing.

CONCLUSIONS

The combined M-PCR assay correctly subtyped seasonal and pandemic influenza A viruses and accurately detected the H275Y oseltamivir resistance allele. This assay should provide useful information to clinicians for appropriate patient management.

Evaluation of three influenza A and B real-time reverse transcription-PCR assays and a new 2009 H1N1 assay for detection of influenza viruses

The performance characteristics of three real-time influenza A/B virus reverse transcription-PCR (RT-PCR) assays and two real-time 2009 H1N1 RT-PCR assays were evaluated using previously characterized clinical specimens. A total of 150 respiratory specimens from children (30 influenza A/H1 virus-, 30 influenza A/H3 virus-, 30 2009 H1N1-, and 30 influenza B virus-positive specimens and 30 influenza virus-negative specimens) were tested with the CDC influenza A/B PCR (CDC), ProFlu(+) multiplex real-time RT-PCR assay (ProFlu(+)), and MGB Alert Influenza A/B & RSV RUO (MGB) assays. A second set of 157 respiratory specimens (100 2009 H1N1-, 22 seasonal influenza A/H1-, and 15 seasonal influenza A/H3-positive specimens and 20 influenza-negative specimens) were tested with a new laboratory-developed 2009 H1N1 RT-PCR and the CDC 2009 H1N1 assay. The overall sensitivities of the CDC, ProFlu(+), and MGB assays for detection of influenza A and B viruses were 100%, 98.3%, and 94%, respectively. The ProFlu(+) assay failed to detect one influenza A/H1 virus-positive specimen and yielded one unresolved result with another influenza A/H1 virus-positive specimen. The MGB assay detected 84/87 (96.5%) of influenza A and B viruses and 26/30 (86.6%) of 2009 H1N1 viruses. The new laboratory-developed 2009 H1N1 RT-PCR assay detected 100/100 (100%) 2009 H1N1 virus-positive specimens, while the CDC SW Inf A and SW H1 PCR assays failed to detect one and three low-positive 2009 H1N1-positive specimens, respectively. The CDC influenza A/B virus assay and the newly developed 2009 H1N1 RT-PCR assay with an internal control can be set up in two separate reactions in the same assay for routine clinical testing to detect influenza A and B viruses and to specifically identify the 2009 H1N1 influenza virus.

[Evaluation of the efficacies of rapid antigen test, multiplex PCR, and real-time PCR for the detection of a novel influenza A (H1N1) virus]

BACKGROUND

In April 2009, a novel influenza A (H1N1) virus was detected in the US, and at the time of conducting this study, H1N1 infection had reached pandemic proportions. In Korea, rapid antigen tests and PCR assays have been developed to detect the H1N1 virus. We evaluated the efficacies of rapid antigen test, multiplex PCR, and real-time PCR for detecting the H1N1 virus.

METHODS

From August to September 2009, we tested 734 samples obtained from nasopharyngeal swab or nasal swab using rapid antigen test (SD Influenza Antigen, Standard Diagnostics, Inc., Korea) and multiplex PCR (Seeplex FluA ACE Subtyping, Seegene, Korea). We also tested 224 samples using the AdvanSure real-time PCR (LG Life Sciences, Korea) to compare the results obtained using real-time PCR with those obtained using multiplex PCR. Furthermore, 99 samples were tested using the AdvanSure real-time PCR and the AccuPower real-time PCR (Bioneer, Korea).

RESULTS

In comparison with the results of multiplex PCR, the sensitivity and specificity of the rapid antigen test were 48.0% and 99.8%, respectively. The concordance rate for multiplex PCR and the AdvanSure real-time PCR was 99.6% (kappa=0.991, P=0.000), and that for the AdvanSure real-time PCR and the AccuPower real-time PCR was 97.0% (kappa=0.936, P=0.000).

CONCLUSIONS

The rapid antigen test is significantly less sensitive than PCR assay; therefore, it is not useful for H1N1 detection; however multiplex PCR, the AdvanSure real-time PCR, and the Accu-Power real-time PCR can be useful for H1N1 detection.