**6. Laboratory testing**

Laboratory diagnosis of viral pneumonia has relied on detection of virus or viral antigen in upper-respiratory specimens (e.g., nasopharyngeal aspirates) and lower respiratory samples (e.g., induced sputum) by culture or immunofluorescence microscopy.

Traditional microbiological methods for detection of respiratory tract pathogens are relatively slow, often are not sensitive and are influenced by previous antibiotic therapy. Molecular diagnostics on the other hand hold much potential for detection of both common and atypical pathogens causing CAP. Analysis can be completed in hours, rather than days, for detection of typical pathogens and weeks for detection of atypical pathogens [68].

There are >200 known respiratory viruses, but accurate data on how many are etiological agents in CAP are lacking. The discovery of 6 new respiratory viruses since 2000—including metapneumovirus (hMPV), the severe acute respiratory syndrome coronavirus, influenza virus strain H5N1, coronavirus strains NL63 and Hku1, and human bocavirus—has presented new challenges for comprehensive viral diagnostics [69]. The significance of respiratory viral infections in patients with sepsis is underestimated. During the winter season, viral such as coronavirus, influenza A virus, human metapneumovirus, and respiratory syncytial virus are clinically underdiagnosed in 70% of patients detected by the multiplex PCR assay [70].

Quantitative multiplex PCR testing of respiratory secretions is recognized as a highly sensitive method for the diagnosis with the ability to detect viral pathogens and atypical bacterial pathogens. An acute viral infection can be confirmed with detection of influenza virus, parainfluenza virus, RSV, or hMPV. The presence of nucleic acid from adenoviruses, bocaviruses, coronaviruses or rhinoviruses is often found in asymptomatic persons. In the future the study of the virus concentration over time will contribute to distinguishing acute infections from protracted nucleic acid excretion [71].
