Molecular diagnosis of respiratory virus infections

Abstract

The appearance of eight new respiratory viruses, including the SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009, in the human population in the past nine years has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid based amplification tests (NATs) for respiratory viruses were first introduced two decades ago and today are utilized for the detection of both conventional and emerging viruses. These tests are more sensitive than other diagnostic approaches, including virus isolation in cell culture, shell vial culture (SVC), antigen detection by direct fluorescent antibody (DFA) staining, and rapid enzyme immunoassay (EIA), and now form the backbone of clinical virology laboratory testing around the world. NATs not only provide fast, accurate and sensitive detection of respiratory viruses in clinical specimens but also have increased our understanding of the epidemiology of both new emerging viruses such as the pandemic H1N1 influenza virus of 2009, and conventional viruses such as the common cold viruses, including rhinovirus and coronavirus. Multiplex polymerase chain reaction (PCR) assays introduced in the last five years detect up to 19 different viruses in a single test. Several multiplex PCR tests are now commercially available and tests are working their way into clinical laboratories. The final chapter in the evolution of respiratory virus diagnostics has been the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance. These assays are now being multiplexed with primary detection and subtyping assays, especially in the case of influenza virus. These resistance assays, together with viral load assays, will enable clinical laboratories to provide physicians with new and important information for optimal treatment of respiratory virus infections.

Keywords::

• Virus detection
• nucleic acid amplification
• multiplex PCR
• assay performance

Acknowledgments

The authors gratefully acknowledge the secretarial assistance of Sarah Grimes and Joanne Warner. We apologize to those authors whose work has not been cited due to space limitations.

Declaration of interest

JBM has received speaking honoraria and consulting fees from Luminex Molecular Diagnostics and EraGen Biosciences. He has been a scientific advisor for Luminex Molecular Diagnostics, Chemicon Corporation (now Millipore), and EraGen Biosciences. He received a research grant from TmBiosciences Corporation (now Luminex Molecular Diagnostics) to assist with the development of the xTAG^™ RVP test and is co-holder of a patent on this product. MS has an investigator initiated grant from Copan Italia for quality assessment of specimen collection. AP has no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. No writing assistance was utilized in the production of this manuscript.