Collection and Testing of Respiratory Samples

Each year the morbidity and mortality associated with acute respiratory tract infections
fluctuates seasonally. This rise and fall is associated with the changing prevalence of
respiratory viruses in the population. Myriad respiratory viruses are responsible for these
infections. For example, Influenza Virus, Respiratory Syncytial Virus (RSV), Parainfluenza
Virus, Human Metapneumovirus, Rhinovirus, and Adenovirus have all been identified as causing
such acute infections. Numerous pathogenic subtypes have been identified within most of
these viral groups. The outbreak of Severe Acute Respiratory Syndrome (SARS) in 2003 was
eventually identified as a Coronavirus; the mortality of SARS among the elderly can be as
high as 50%. More recently, Human Bocavirus (HBoV) has also been identified as causing
acute respiratory tract infections. In 2005 the HBoV was identified by molecular testing
and was found to be the only virus identified in a subpopulation of patients suffering from
respiratory tract infections. Apart from supportive measure (e.g., bed rest, hydration,
etc.), there are no effective treatments for many of these viral infections; however,
antiviral agents (e.g., the neuraminidase inhibitors oseltamivir or zanamivir) can be used
to alleviate the severity of flu-like symptoms. Identification of a respiratory virus as
the causative agent is important because it eliminates the need for treatment with
antibiotics; physicians typically wait 7-10 days for symptoms to alleviate before
prescribing antibiotics due to risks associated with exacerbating bacterial antibiotic
resistance.

Each year the virus population fluctuates, and with it the antigenic presentation of the
dominant strains that circulate through the population. Epidemics arise when larger and
larger portions of the population do not have innate or acquired immunological resistance to
such strain(s) in a given season. The World Health Organization (WHO) maintains a separate
website dedicated to tracking outbreaks of influenza, especially avian influenza
(https://www.who.int/fluvirus_tracker). These zoonotic transmissions that further adapt to
enable human-to-human transmission are of the greatest concern because it is predicted that
virtually all humans will be immunologically naïve. Zoonotic transmissions in the human
population are monitored in the hope that a pandemic similar to the Spanish Flu of 1918 can
be avoided; it is estimated that well over 25 million people died from the Spanish Flu. The
United States government also maintains a separate website with resources regarding the flu
and pandemic related information (http://www.pandemicflu.gov/). On June 11, 2009 the WHO
raised the pandemic threat level to 6 in response to the global appearance of a new strain
of swine Influenza A (subtype H1N1). The rapidity with which the H1N1 virus has spread
exemplifies the notion that quickly and accurately identifying a viral pathogen associated
with an outbreak is critical to global public health.

In addition to the threat of an influenza outbreak, the expansion in the number of viruses
that cause acute respiratory tract infections compounds the difficulty in correctly and
rapidly identifying the primary pathogen; each new virus or subtype increases the complexity
of testing. Molecular diagnostic assays are ideally suited to address this complexity.
Assays based on the polymerase chain reaction (PCR) can incorporate multiple primers and
probes (e.g., multiplexed) in a single reaction to deal with this complexity.4 Such assays
are extremely sensitive, have a high degree of specificity, and can be performed very
quickly. The artus Influenza A/B RT-PCR test is a real-time PCR assay for the detection and
identification of Influenza A and B, while the QIAGEN ResPlex II Advanced Panel test is a
nucleic acid amplification-based assay for the detection and identification of a broad range
of some of the most common respiratory viruses associated with acute respiratory tract
infections. In the present study respiratory specimens will be prospectively collected and
tested using the artus Influenza A/B RT-PCR test and the QIAGEN ResPlex II Advanced Panel
test.