ABSTRACT
The respiratory tract can be directly sampled by nasal or throat swabs, nasal washings, nasal aspirates, nasopharyngeal aspirates, sputum, transtracheal aspirates, bronchoalveolar lavage, or biopsy. The method used to collect the specimen is chosen on the technique to be used to identify the virus. A nasal swab is usually taken from the inferior turbinates for maximum virus recovery but usually involves some discomfort to the patient. Similarly, nasal washings [requiring solutions such as phosphate-buffered saline (PBS)] may also be uncomfortable for the patient. Compared to nasal and throat swabs, nasal washings are a more reliable method of recovering virus but are less convenient for both operator and patient. Both methods are suitable for virus culture. Nasopharyngeal aspirates (NPAs) are particularly suitable for virus culture, antigen detection, and PCR and are collected using a mucus extractor using disposable suction catheters that are commercially available (Vygon Laboratories, Ecouen, France). In the authors' experience, the diagnosis of common cold viruses can be made using nasal aspirates (NAs) in preference to NPAs, particularly as acute infections are accompanied by rhinorrhea, the same equipment can be used with less discomfort, and are more suitable for use in infants, children, and neonates. Sputum is rarely used for respiratory viruses because the clinical syndrome of viral pneumonia is usually accompanied by upper and lower respiratory tract symptoms and the diagnosis can be made on either a NA or NPA. In terms of diagnosis in severely ill patients, whether intubated or not, or for research purposes, the diagnosis can be made using bronchoalveolar lavage (BAL) samples (6,7) or in biopsy specimens (8,9), which reduce the risk of contamination by respiratory pathogens in the upper airways.
