Table 1 Summary of challenges for establishment of the IGI SARS-CoV-2 testing laboratory
Category | Nature of challenge | Solution | Supporting documentation |
|---|---|---|---|
Regulatory (CLIA) | A CLIA certificate and license for a diagnostic testing facility is required | Extend CLIA license from UC Berkeley University Health Services to the IGI testing lab | “Useful Links” on Figshare |
CLIA regulations require testing personnel to be licensed CLS | Regulations are temporarily revised, allowing non-CLS scientists to act as testing personnel with revised training requirements. IGI created an accelerated in-house CLIA training program. | “Useful Links” and “Regulatory Compliance” on Figshare | |
Testing personnel must be proficiency tested | Test blinded contrived specimens provided by the American Proficiency Institute | ||
Regulatory (FDA/CLIA) | Validation study must be performed to determine LOD of LDT | Test contrived specimens with synthetic viral RNA in collection medium (semi-automated) and in clinical matrix (automated) | “Useful Links,” “Limit of Detection Validation and Clinical Sample Evaluation in Semi-Automated Method” and “Limit of Detection and Clinical Sample Validation in Automated Method” on Figshare |
Clinical validation of LDT must be performed | Test panel of specimens resulted as negative and positive by a CLIA-certified laboratory with an issued EUA for a SARS-CoV-2 test. If specimens unavailable, use contrived ones in clinical matrix. | “Useful Links,” “Limit of Detection Validation and Clinical Sample Evaluation in Semi-Automated Method” and “Limit of Detection and Clinical Sample Validation in Automated Method” on Figshare | |
An initial batch of negative and positive specimens tested by the LDT must be tested by a third party | Submit the first 5 negative and 5 positive specimens tested under the LDT to a CLIA laboratory with an issued EUA for a SARS-CoV-2 LDT | “Useful Links” on Figshare | |
Regulatory (HIPAA) | Privacy and security of PHI must be consistently maintained during data handling | Develop and implement a LIMS that meets HIPAA standards for PHI privacy and security; restrict access to PHI within the LIMS to authorized personnel | “Test, LIMS and Physician Interface Development” and “Video—Semi-Automated Method LIMS Interface” on Figshare |
Testing lab and other personnel must comply with HIPAA regulations | Ensure all personnel complete an online HIPAA training class and pass the end-of-class assessment, with certificate of training placed on permanent record | The IGI team used the online HIPAA training available from Thompson Reuters | |
Biosafety | Specimens must be processed in a manner that complies with institutional biosafety regulations | Obtain a BUA from the university CLEB that defines how specimens are to be processed safely and what PPE the testing personnel must wear | “Regulatory Compliance” on Figshare |
Measures must be taken to reduce the possibility of SARS-CoV-2 transmission between testing team members | Require all personnel to take a self-assessment questionnaire daily before entering the building where the diagnostic lab is located | “Personnel Training and Biosafety” on Figshare | |
Concerns about bringing samples with live virus on site | Develop a customized sample collection kit that uses a deactivating sample transport medium (DNA/RNA Shield) | “Sample Collection Kit—Preparation, Patient Sample, Collection and Transport” on Figshare | |
Healthcare partners | Challenges of serving non-campus patients | Build a physician portal into the LIMS that can be accessed by non-UC Berkeley physicians. Partner with local healthcare providers to perform swabbing of community members. | “IGI Interface with UC and Non-UC Health Partners” and “Test, LIMS and Physician Interface Development” on Figshare |
Testing kits must be made available to UHS and to third-party clinicians | Establish a kit assembly SOP. Employ a dedicated kit assembly team to generate sufficient kits on a weekly basis. Use a professional courier service to deliver the kits to the testing sites. Establish a kit use SOP and provide it to the clinicians. Establish diagnostic specimen return SOPs for every partner site. | “Sample Collection Kit—Preparation, Patient Sample, Collection and Transport” on Figshare | |
The physicians requisitioning the test must receive the results in a CLIA- and HIPAA-compliant manner | As per State of California regulations, CLS report all positive results within 24 h to the requisitioning physician via a direct phone call. All test results are subsequently accessible through our CLIA- and HIPAA-compliant clinician portal. | “Test, LIMS and Physician Interface Development” on Figshare | |
Supply chain | A sustained supply of specimen collection components is necessary | Identify a tube and swab manufacturer with sufficient supply, and configure the LDT SOPs around it | Main text; “Test, LIMS and Physician Interface Development” on Figshare |
A sustained supply of diagnostic testing reagents and disposables is necessary | Identify a supplier (Thermo Fisher) with robust reagent production capacity; develop an LDT that uses half-reactions |
