Methods for molecular surveillance of influenza

Abstract

Molecular-based techniques for detecting influenza viruses have become an integral component of human and animal surveillance programs in the last two decades. The recent pandemic of the swineorigin influenza A virus (H1N1) and the continuing circulation of highly pathogenic avian influenza A virus (H5N1) further stress the need for rapid and accurate identification and subtyping of influenza viruses for surveillance, outbreak management, diagnosis and treatment. There has been remarkable progress on the detection and molecular characterization of influenza virus infections in clinical, mammalian, domestic poultry and wild bird samples in recent years. The application of these techniques, including reverse transcriptase-PCR, real-time PCR, microarrays and other nucleic acid sequencing-based amplifications, have greatly enhanced the capability for surveillance and characterization of influenza viruses.

Mapping of H3N2 influenza antigenic evolution in China reveals a strategy for vaccine strain recommendation

“…Moreover, compared with HI data, sequence data is very reliable and will not vary from one lab to another. Largescale sequencing is now widely used in influenza surveillance 28,29 .…”

Nucleic acid-based detection of influenza A virus subtypes H7 and N9 with a special emphasis on the avian H7N9 virus

“…With the availability of RT-PCR, numerous assays for the subtyping of influenza viruses have been developed, and multiplex approaches have frequently been proposed [17]. Continuous progress is achieved regarding the signal detection of the PCR products, e. g. by PCR-ELISAs [18,19] and in particular by RT-qPCR technologies.…”

Diagnostic Methods of Influenza a From Clinical Specimens: A Critical Review of Literature

“…Because influenza A subtypes are defined by their surface HA and NA proteins, primers that specifically amplify the corresponding genes are effective for determining the subtype of influenza A viruses (WHO, 2011). The conventional RT-PCR has the advantage of being relatively sensitive and specific and allows further sequence analysis, but it is not easily quantitative, and not ideal for high-throughput (Wang & Taubenberger 2010). As long as the time to get test results can be as little as 3 hours, routine surveillance samples are most often processed within 24 hours (Chauhan et al 2013).…”

“…Probe-based real time PCR (TaqMan) shows high sensitivity and specificity, what is ideal for quantitative and multiplex detection, as well as it can be high-throughput. Notwithstanding, the high-cost probe, special equipment required and further sequence analysis is not generally possible (Wang & Taubenberger 2010).…”

“…This assay is especially important when negative results are found for HA or neuroaminidase (NA) detection. Generally of high sensitivity and specificity, TaqMan probes required for each PCR target are relatively expensive for largescale screening and surveillance in many applications (Wang & Taubenberger 2010). During the procedures of the Real Time PCR protocols for Influenza detection, the CDC highlights that for each RT-PCR run the RNA extract´ s sample must be tested by separate primer/ probe sets: InfA, Universal swine(swFluA), Swine H1 (swH1) and RNaseP.…”