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

Transmission of pandemic influenza A (H1N1) 2009 within households: Edmonton, Canada

BACKGROUND

In April 2009, a novel influenza A, subtype H1N1, now referred to as the Pandemic (H1N1) 2009 virus (pH1N1), began circulating in countries around the world. Describing the transmission characteristics of this novel influenza A virus is important to predict current, and future, disease spread. The Public Health response to the first wave of pH1N1 in Alberta focused on the identification and management of secondary cases within households.

OBJECTIVES

The purpose of this study was to describe transmission characteristics of pH1N1 in households in Edmonton, the capital city of Alberta, during the first wave, and to identify the serial interval and secondary attack rate (SAR) in this setting.

STUDY DESIGN

This is a prospective analysis of pH1N1 household transmission within 87 urban Canadian households between April 30 and June 9, 2009; with each household having at least one laboratory-confirmed case. The secondary attack rate was calculated in the 262 household contacts using a weighted average by number of susceptible individuals in each household. The serial interval, or time to illness in secondary cases, was analyzed using survival analysis with a Weibull model.

RESULTS

Within the 87 households, 42 (48.3%) had no secondary cases develop; 25 (28.7%) had one secondary case develop; and 20 (22.9%) had more than one secondary case develop. The secondary attack rate did not decrease with increasing household size and households with two members exhibited the lowest secondary attack rate at 14.1%. Children under the age of 19, and individuals with an underlying medical condition, were at increased risk (p<0.05) of becoming a secondary case. The overall secondary attack rate among the 262 susceptible household contacts was 30.2% (95% CI: 12.6-52.2). The median serial interval for pH1N1 transmission was 3.4 days (95% CI: 2.9-3.9).

CONCLUSIONS

The identified transmission characteristics of pH1N1 among Canadian households differ slightly from other previously reported North American estimates, but are in keeping with historical transmission rates of pandemic influenza viruses.

H1N1 Influenza Pandemic of 2009 Compared With Other Influenza Pandemics: Epidemiology, Diagnosis, Management, Pulmonary Complications, and Outcomes

Influenza pandemics are complex events that have occurred frequently throughout human history, three during the past century alone. Now the world is facing the first 21st century pandemic, and the comparison among them is essential to identify common epidemiologic patterns, clinical characteristics, and outcomes. The evolution of medicine, including diagnostic and treatment options, the critical care advances, and global responses are new interventions that could modify the general outcome of the pandemic. Learning from past and current events could lead to a plan for prompt and efficient response in future pandemics and may be help us to predict the unpredictable.

Laboratory diagnosis of 2009 H1N1 influenza A virus

The emergence of 2009 pandemic influenza H1N1 has necessarily led to the rapid evolution of sensitive, specific, and high-throughput molecular diagnostic assays for this virus at the same time that clinical laboratories attempt to cope with increasing demands in the setting of resource limitations. This situation has given rise to testing algorithms focusing on priority, clinical relevance, and appropriate surveillance. We describe the current state of understanding around diagnostic testing and laboratory detection of 2009 H1N1 influenza A virus.

Diagnostic approach for the differentiation of the pandemic influenza A(H1N1)v virus from recent human influenza viruses by real-time PCR

Background

The current spread of pandemic influenza A(H1N1)v virus necessitates an intensified surveillance of influenza virus infections worldwide. So far, in many laboratories routine diagnostics were limited to generic influenza virus detection only. To provide interested laboratories with real-time PCR assays for type and subtype identification, we present a bundle of PCR assays with which any human influenza A and B virus can be easily identified, including assays for the detection of the pandemic A(H1N1)v virus.

Principal Findings

The assays show optimal performance characteristics in their validation on plasmids containing the respective assay target sequences. All assays have furthermore been applied to several thousand clinical samples since 2007 (assays for seasonal influenza) and April 2009 (pandemic influenza assays), respectively, and showed excellent results also on clinical material.

Conclusions

We consider the presented assays to be well suited for the detection and subtyping of circulating influenza viruses.

Development of a multiplex real-time RT-PCR assay for detection of influenza A, influenza B, RSV and typing of the 2009-H1N1 influenza virus

A high-throughput real-time RT-PCR assay was developed to amplify and detect a conserved region of the hemagglutinin gene of the 2009-H1N1 influenza A virus using a minor groove binder-conjugated hybridization probe. The assay was paired with a separate triplex real-time assay that detects influenza A via the matrix gene, influenza B and RSV in a multiplex format and compared with the Centers for Disease Control and Prevention (CDC) rRT-PCR assay using 143 samples. The 2009-H1N1 portion of the multiplex assay had 100% correlation with the CDC assay, while the triplex assay had a 99% agreement. An additional 105 samples collected from October to November 2009 were also tested using both the individual 2009-H1N1 and triplex assays. Of these 105 samples, eight were positive for the hemagglutinin target in the H1N1 assay and negative for the matrix target in the triplex assay. Discrepant analysis revealed single nucleotide polymorphisms within the matrix gene of 2009-H1N1 virus-positive samples. The limit of detection for the 2009-H1N1 assay was between 750 and 1,500 copies/reaction and no cross-reactivity with other respiratory pathogens was observed. Overall, this multiplexed format proved to be sensitive, robust and easy to use and serves as a useful tool for pandemic testing.

Simultaneous typing and HA/NA subtyping of influenza A and B viruses including the pandemic influenza A/H1N1 2009 by multiplex real-time RT-PCR

Pandemic influenza A/H1N1 2009 and seasonal influenza viruses are currently co-circulating worldwide. A rapid, sensitive, and specific assay for distinguishing pandemic influenza A/H1N1 2009 from seasonal influenza viruses and for subtyping seasonal influenza A viruses could aid in the surveillance and control of these viral infections. Here, such a multiplex real-time RT-PCR (rRT-PCR) assay for typing influenza A and B viruses and the pandemic influenza A/H1N1 2009 is developed. This assay can also subtype seasonal influenza A viruses simultaneously. The analytical sensitivity is 10–10⁴ copies/reaction. The coefficients of variation of inter-assay and intra-assay are 0.04–0.45% and 0.08–0.97%, respectively. The new multiplex rRT-PCR assay is more sensitive in subtyping seasonal influenza viruses than the conventional PCR techniques. Results obtained with this assay for the detection of pandemic influenza A/H1N1 2009 are highly consistent (96.88%) with those achieved using the US CDC's rRT-PCR protocol. A sample identified as “pandemic influenza A/H1N1 2009 positive” by the US CDC's rRT-PCR was reclassified correctly as subtype H3N2 using this assay. Taken together, this new multiplex rRT-PCR protocol could be an important tool for improving diagnosis and management of the pandemic influenza A/H1N1 2009 and seasonal influenza viruses.

Duplex real-time reverse transcriptase PCR assays for rapid detection and identification of pandemic (H1N1) 2009 and seasonal influenza A/H1, A/H3, and B viruses

Reports of a novel influenza virus type A (H1N1), now designated by the World Health Organization as pandemic (H1N1) 2009, emerged from the United States and Mexico in April 2009. The management of the pandemic in Australia required rapid and reliable testing of large numbers of specimens for the novel influenza strain and differentiation from seasonal influenza strains. A real-time reverse transcriptase PCR (RT-PCR) assay for the detection of pandemic (H1N1) 2009 was designed and used with existing real-time RT-PCR assays for seasonal influenza viruses A and B. MS2 coliphage was added to all samples and amplified as a quality control. Three duplex RT-PCR assays, each containing two primer pairs and corresponding 5' nuclease probes, were initially evaluated on control material and stored samples and showed high sensitivity and specificity. More than 11,000 clinical samples were then tested for influenza A and B matrix gene targets and specific hemagglutinin gene targets for seasonal influenza A/H1, A/H3, and pandemic A (H1N1) 2009. Minimum sensitivities and specificities were 98.8% and 100%, respectively, for pandemic (H1N1) 2009, 81.5% and 98.9% for seasonal A/H1, and 96.3% and 99.6% for A/H3. Automated sample extraction facilitated the rapid processing of samples so that the assays allowed accurate, rapid, and cost-effective screening of large numbers of clinical samples.