May. 13, 2024
This article is made available via the PMC Open Access Subset for unrestricted noncommercial re-use and secondary analysis in any form or by any means with acknowledgment of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
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Given the ongoing COVID-19 pandemic, the demand for SARS-CoV-2 testing has surged globally, leading to severe shortages of established specimen collection devices for respiratory viral testing in diagnostic microbiology laboratories. Consequently, there is a pressing need to validate unverified collection devices from non-registered manufacturers to ensure the continuity of testing processes.
Due to these shortages, clinical laboratories, which do not regularly perform quality control on established collection devices, must adopt a systematic and thorough approach to evaluate alternative unregistered swabs and viral transport media (VTM). This evaluation must consider several critical aspects, including device integrity, the sterility of swabs and VTM, in vitro performance, VTM stability, and the clinical performance of the device. These criteria were applied in a frontline medical microbiology laboratory to evaluate swabs and VTM from an unregistered manufacturer, which yielded suboptimal results and could not be implemented. As the pandemic continues, it is essential for diagnostic laboratories to maintain a flexible and efficient strategy to ensure a steady supply of testing reagents and materials.
The proper collection, storage, and transport of specimens are crucial for the accurate diagnosis of viral infections by nucleic acid amplification testing (NAAT) methods like real-time reverse transcriptase PCR (RT-PCR). Flocked nylon swabs (FLOQSwab; Copan Diagnostics) are often regarded as the gold standard for the collection of nasopharyngeal specimens for the detection of respiratory viruses due to their superior performance compared to other swab types. Many different transport media that adequately preserve virus viability and viral nucleic acid recovery can be employed, including viral transport media (VTM) or saline. Among these, VTM is widely used for the transport of specimens for downstream respiratory testing.
Since the World Health Organization (WHO) declared a pandemic of novel coronavirus disease 2019 (COVID-19) in March 2020, testing for the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become the cornerstone of pandemic management. Consequently, COVID-19 testing has increased exponentially worldwide. SARS-CoV-2 detection is typically swab-based, collected from the nasopharynx (NP), oropharynx (OP), or nose (N). This has led to a continued depletion of the global supply chain for established specimen collection devices for respiratory viral testing. Diagnostic microbiology laboratories can consider using preexisting commercial swabs not initially intended for respiratory viral testing or unregistered respiratory testing swabs. Some studies have also explored using phosphate-buffered saline (PBS) or saline instead of VTM with good results. This protocol focuses on commercially produced VTM but could also be applicable to PBS or saline. Swabs and specimen collection kits containing swabs are regulated as medical devices, and manufacturers must comply with regulatory requirements to import or sell these kits. According to the Clinical and Laboratory Standards Institute (CLSI) guidelines on quality control of microbiological transport systems, manufacturers must ensure collection devices meet quality standards. Recent national acquisition of collection devices in Canada showed swabs that were visibly contaminated, emphasizing the importance of thorough quality assessment of this preanalytical device. The quality and performance of any collection swab and VTM from unregistered manufacturers must be confirmed before clinical use in patient specimen collection.
Our frontline clinical microbiology laboratory was required to evaluate new collection devices that were not listed as a registered medical device, often with limited sampling size available. We describe a detailed protocol for the extensive quality and performance evaluation of such new collection devices for the detection of SARS-CoV-2 and other respiratory viruses. As the pandemic progresses into the influenza season, the protocol also includes influenza A, influenza B, and respiratory syncytial virus (RSV). The method outlined below can be completed with a small number of paired swabs and VTM.
This assessment comprises four phases: overall inspection of the collection kit, evaluation of the swabs, evaluation of the VTM, and, if the device is deemed suitable, a clinical performance assessment. A viral specimen collection device previously validated by the laboratory should be used as the reference standard for the assessment of new collection devices. In our case, this is Copan's universal transport medium (UTM) and FLOQSwab (Copan Diagnostics, Brescia, Italy).
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| Phase | Description | Protocol outline | Acceptance criterion |
|---|---|---|---|
| 1 | Visual inspection | VTM: leakage, vol, discoloration, turbidity, or visible contamination Swabs: size, flexibility, breakage |
No significant leakage or visibly compromised VTM tubes No breakage outside designated breakpoints, flexibility and size comparable with reference swab |
| 2 | Evaluation of swabs | Sterility In vitro performance |
No bacterial or fungal growth; no contamination detectable by PCR Results comparable with reference swab (CT difference of <2) |
| 3 | Evaluation of UTM | Sterility Recovery of viral nucleic acids Stability at different storage conditions |
No bacterial or fungal growth; no contamination detectable by PCR Results comparable with reference swab (categorical agreement) Results comparable with reference swab at different time points (CT difference of <2) |
| 4 | Clinical performance | Performance on patients or volunteers | Results between reference swab and test swab in categorical agreement; tolerable comfort reported by patients |
Unroofing or aspiration of lesions (or otherwise using sharp instruments for mpox testing) is not necessary, nor recommended, due to the risk for sharps injury.
All recommended PPE should be worn when collecting a specimen from a person with suspected or confirmed mpox.
Only sterile, synthetic swabs (including but not limited to polyester, nylon, or Dacron) with plastic, wood, or thin aluminum (wire) shafts should be used to collect suspected or confirmed mpox specimens for diagnostic testing. Do not use cotton swabs.
Skin lesion material, including swabs of lesion surface, exudate, or lesion crusts, are the recommended specimen types for laboratory testing of mpox virus specimens. Procedures and materials used for collecting specimens may vary depending on the phase of the rash (e.g., swabs from lesion surface or crust from healing lesion). Collect two swabs from each lesion, preferably from different locations on the body or from lesions that differ in appearance (e.g., a pair of swabs for each lesion with a total of 2-3 lesions). Vigorously swab each lesion, avoiding contamination of gloved hands, to ensure adequate viral DNA is collected. Unroofing or aspiration of lesions (or otherwise using sharp instruments for mpox testing) before swabbing is not necessary, nor recommended due to the risk for sharps injury. Place swabs from lesions, crusts, and exudate in separate tubes.
The type of acceptable specimen (dry swab or wet swab in transport media) for diagnostic testing may vary depending on the laboratory. Contact the appropriate laboratory facility to determine the specimen types accepted. At CDC, only dry swabs or swabs in viral transport media (VTM) from lesions, or lesion crusts are currently accepted for testing. Swabs in media designated for bacterial preservation may cause PCR inhibition and are not recommended.
Insert each swab into a sterile container such as a sterile tube or urine container. Glass containers are not recommended. Carefully bend to break the swab’s shaft to fit inside the sterile container (if applicable, or place the entire swab into the container). After completely securing the lid, wipe the container with an EPA-approved disinfectant for emerging viral pathogens. Placing parafilm around the lid of the container is recommended for additional leak-proof protection, but not required. Remove gloves, wash your hands (hand hygiene), and don a new pair of gloves.
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