PCR for detection of respiratory viruses: seasonal variations of virus infections

Figures & data

Figure 1. Schematic overview of respiratory virus seasonality.

Intensity of color represents number of positive detections. Blue: temperate regions, Northern Hemisphere. Green: temperate regions, Southern Hemisphere. Red: tropical regions.

AdV: Adenoviruses; HCoV: Human coronaviruses; HMPV: Human metapneumovirus; IFA: Influenza virus A; RSV: Respiratory syncytial virus.

See section ‘Seasonal distribution of respiratory viruses’ for references.

Table 1. PCR methods used in laboratory diagnosis of respiratory viruses.

Method	Description	Comments
Conventional PCR	Usually evaluated by colorometry or agarose gel electrophoresis	No quantitationHigh risk of cross-contamination, especially when using nested formatObsolete
Real-time PCR	PCR products evaluated in real time during each PCR cycleEvaluation either by colorometry or by specific, light-emitting probes (e.g., hydrolysis or FRET probes)	Suitable for limited multiplexingPermits quantitation or semiquantitation of virusHighly specific provided that specific probes are usedVery low risk for cross-contaminationExcellent for in-house tests, resulting in an affordable analysis for the clinic
Multiplex PCR linked with liquid array (Luminex^®; Luminex Corporation); commercial systems:X-TAG^® RVP (Abbott)ResPlex^® (Qiagen)MultiCode^®-PLx (EraGen Biosciences)	Traditional PCR designed to affix amplicons to specific beads in a highly multiplexed format	Excellent multiplexingSeveral commercial tests availableNo quantification optionExogenous handling of amplified materials results in risks for cross-contaminationNeed for commercial systems not cost-compatible
NASBA; LAMP	Isothermal cyclic amplification involving DNA (LAMP) or RNA/DNA (NASBA) intermediates	No need for thermal cyclerNo reverse transcriptase step for RNA viruses^†High sensitivitySuitable for in-house tests, resulting in an affordable analysis for the clinicQuantitation cumbersome
Rapid diagnostic PCR instruments:Xpert^® (Cepheid)FilmArray^® (Idaho)Jaguar^® (BD diagnostics)Infiniti^® (AutoGenomics)	Integrated extraction and PCR run in preloaded reaction cassettes, requiring a minimum of hands-on time	No specimen batching neededSuitable for point-of-care testingLocked to commercial assays linked to the instrumentRelatively expensive

^†Nucleic acid sequence-based amplification only.

For references, see section ‘Procedures for molecular diagnosis of respiratory viruses’ in text.

FRET: Fluorescence resonance energy transfer; LAMP: Loop-mediated isothermal amplification; NASBA: Nucleic acid sequence-based amplification.