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.

Determination of the Frequency of Human Bocavirus and Other Respiratory Viruses Among 0-2 Years Age Group Children Diagnosed as Acute Bronchiolitis

“…Buna karşın, tek bir örnekten DNA ve RNA viruslarının tespitinde multipleks RT-PCR yöntemi duyarlı, özgül ve hızlı bir metottur 8 . Diğer yandan, bu çalışmada kullandığımız mikroarray teknolojisi ile birleştirilmiş multipleks PCR (M-PCR) tekniğinin performans özellikleri ile ilgili sınırlı çalışma olsa da, bu testin kültür ve RT-PCR ile karşılaştırıldığında oldukça duyarlı bulunduğu ve çok sayıda virusun tespitine olanak sağladığı belirtilmektedir 18,19 .…”

“…Farklı solunum viruslarıyla enfekte hastalar benzer klinik sendromlara sahip olduğundan, etiyolojik etkenin özgül olarak tanımlanması ancak laboratuvar çalışmalarıyla mümkündür. Günümüzde polimeraz zincir reaksiyonu (PCR) temelli testler, solunum yolu viruslarının tanımlanmasında, konvansiyonel yöntemlerden (virus izolasyonu ve antijen testleri) daha hızlı ve duyarlı sonuç vermektedir [6][7][8] . Özellikle çok sayıdaki solunum virusunu tek bir örnekte aynı anda tespit edebilen multipleks PCR/mikroarray yöntemlerinin kullanıma girmesi, gerek viral koenfeksiyonların prevalansının belirlenmesinde, gerekse doğru ve etkili antiviral tedaviye karar verilmesinde büyük yarar sağlamıştır 4,[8][9][10] .…”

Human Metapneumovirus Circulation in the United States, 2008 to 2014

“…A study conducted in 3 U.S. sites identified HMPV circulation in winter and spring months; 6 however, it remains unclear if this pattern reflects trends in national HMPV circulation. The increased availability and use of molecular diagnostic assays to detect respiratory viruses 11 in recent years has highlighted several HMPV-associated outbreaks throughout the United States 12 and has enhanced the opportunity to evaluate national trends in HMPV circulation.…”

Detection of Enterovirus D68 in Canadian Laboratories

“…While NAATs have become the method of choice for the detection of respiratory viruses, there is evidence that assays vary in their performance characteristics, including analytical sensitivity (9)(10)(11). Given the diversity of laboratory tests utilized, it is important to verify the ability of laboratory-developed tests (LDTs) and commercially available NAATs to accurately detect emerging pathogens (9)(10)(11)(12)(13)(14).…”