Specimen Sources
Specimen sources should be thought of as the very first, absolutely crucial step in getting accurate results. If we don’t start with the right specimen, collected correctly, everything else we do in the lab is compromised. This section will cover the key principles, different specimen types, and what viruses we typically look for in each
General Principles
- The Right Specimen for the Right Test: This is the golden rule. Different viruses replicate in different areas of the body. To detect a specific virus, you must collect a specimen from the site where that virus is likely to be present and actively replicating
- Timing Matters: Viral load changes throughout the course of an infection. Specimen collection should ideally occur as early as possible in the acute phase of the illness, when viral shedding is typically highest. However, some tests, like serology, rely on the presence of antibodies, which develop later in the infection
- Collection Technique: Proper collection is essential to maintain the integrity of the specimen. Use the correct swabs, collection devices, and transport media as specified by the laboratory and test manufacturer. A poorly collected specimen may yield false-negative results
- Transport and Storage: Viruses are fragile! Rapid transport to the lab is crucial. If immediate testing isn’t possible, follow specific storage instructions (e.g., refrigeration, freezing) to preserve viral viability and nucleic acid integrity
- Universal Precautions: Always treat specimens as potentially infectious and adhere to strict safety protocols
Specimen Types and Associated Viruses
Respiratory Specimens
These are essential for diagnosing respiratory viral infections
-
Nasopharyngeal Swabs/Aspirates: Gold standard for many respiratory viruses. Detects:
- Influenza viruses (A & B)
- Respiratory Syncytial Virus (RSV)
- Parainfluenza viruses (1-4)
- Adenoviruses
- Rhinoviruses
- Human metapneumovirus (hMPV)
- SARS-CoV-2 (COVID-19)
-
Nasal Swabs: A more comfortable option than nasopharyngeal swabs, but may be slightly less sensitive. Good for:
- Influenza
- SARS-CoV-2
-
Throat Swabs: Useful for some respiratory viruses, but less sensitive than nasopharyngeal swabs for many. Detects:
- Adenovirus
- Herpes Simplex Virus (HSV) (in cases of pharyngitis)
-
Bronchoalveolar Lavage (BAL) / Tracheal Aspirates: Collected from the lower respiratory tract. Used for severe respiratory infections or in immunocompromised patients. Detects:
- CMV
- Influenza
- Adenovirus
- Pneumocystis jirovecii (a fungus, but often tested for in conjunction with respiratory viruses)
-
Sputum: Less commonly used for viral detection due to the presence of bacteria and other contaminants. Can be used for:
- Influenza (in some cases)
- RSV (in infants)
Blood Specimens
Used for detecting systemic viral infections or monitoring viral load * Whole Blood * CMV (in newborns, immunocompromised) * Plasma/Serum * HIV (viral load monitoring) * Hepatitis viruses (HAV, HBV, HCV) * West Nile Virus * Dengue Virus * Zika Virus * EBV * Parvovirus B19
Cerebrospinal Fluid (CSF)
Collected via lumbar puncture. Used to diagnose viral meningitis or encephalitis * Enteroviruses * Herpes Simplex Virus (HSV) * Varicella-Zoster Virus (VZV) * West Nile Virus
Stool Specimens
Used to diagnose viral gastroenteritis * Norovirus * Rotavirus * Adenoviruses (especially types 40 and 41) * Astrovirus
Urine Specimens
Useful for detecting certain viruses, especially in immunocompromised patients * Cytomegalovirus (CMV) * BK Virus * JC Virus * Mumps
Swabs from Vesicles/Lesions
Used to diagnose localized viral infections * Genital, Oral, or Skin Lesions * Herpes Simplex Virus (HSV-1 and HSV-2) * Varicella-Zoster Virus (VZV)
Key Considerations for Specific Viruses
- HIV: EDTA plasma is the preferred specimen for viral load testing
- Hepatitis Viruses: Serum or plasma are used for serological testing (detecting antibodies) and viral load testing (detecting viral RNA or DNA)
- CMV: Specimen choice depends on the patient population (e.g., urine or blood for congenital CMV, BAL for pneumonia in immunocompromised)
- HSV/VZV: Swabs from lesions are preferred. CSF is used for encephalitis
- Respiratory Viruses: Nasopharyngeal swabs or aspirates are generally the best choice
Important Notes
- Always consult the laboratory’s specific guidelines for specimen collection and handling.: These guidelines will provide detailed instructions on the correct procedures and acceptable transport media
- Proper labeling is crucial.: Include patient name, date of birth, specimen type, date and time of collection, and the test(s) requested
- Document any relevant clinical information: on the requisition form, such as symptoms, travel history, and immune status. This information can help the laboratory interpret the results
Key Terms
- Specimen: A sample of body fluid or tissue taken for testing
- Viral Load: The quantity of virus present in a specific amount of a patient’s body fluid (e.g., copies/mL)
- Nasopharyngeal: Relating to the nasal passages and pharynx (the back of the throat)
- Aspirate: Fluid or other substance withdrawn (aspirated) from the body
- Bronchoalveolar Lavage (BAL): A procedure where fluid is introduced and then collected from the lungs for analysis
- Cerebrospinal Fluid (CSF): The fluid that surrounds the brain and spinal cord
- Lesion: An area of damaged tissue or skin
- Transport Medium: A liquid or gel designed to preserve the viability of microorganisms during transport to the laboratory
- Serology: The study of blood serum, especially with regard to the response of the immune system to pathogens
- Etiology: The cause or origin of a disease or condition