Making Life in COVID-19 Diagnostic Labs Easier: A COVID LIMS for Managing Data and Automating Workflows


On July 16, 2020, the World Health Organization (WHO) reported a total of 13,378,853 global COVID-19 cases. A total of 226,181 of these global cases were reported within the past 24 hours. These numbers emphasize the importance of implementing appropriate workflows for rapid diagnostic testing of COVID-19 specimens. Rapid and accurate testing is essential for diagnosing and quarantining COVID-19 positive individuals, in order to limit the overall spread of coronavirus. A major challenge faced by all diagnostic laboratories is the influx of symptomatic and asymptomatic patients in need of rapid diagnostic testing.

Improving Workflows

Maintaining Quality Assurance (QA) by improving the workflows is critical for all COVID-19 diagnostic testing laboratories and helps prevent false positives and negatives. This can be done by implementing a Laboratory Information Management System (LIMS), which is an essential data management tool for maintaining quality assurance among all global laboratories. A LIMS improves processes by automating workflows among the laboratory personnel, maintaining the location of each stored specimen, and by saving the data associated with each stored specimen. As a result, this improves productivity by streamlining laboratory processes, which in turn can increase profitability. A LIMS also helps in managing results of Quality Control (QC) samples and their test results, and in validating actual test results by comparing them with the QC test results. Furthermore, it helps in analyzing trends across a set of QC results to identify anomalies in test results. Due to the urgency involved with the COVID-19 pandemic, a LIMS should be utilized among laboratories across the globe because it enables them to effectively collaborate, manage specimens, anonymize sensitive patient data, record tests and test results, and analyze the data associated with each specimen. A LIMS is essential in generating data reports associated with each specimen as per FDA and CDC guidelines.

Laboratory management must train new and existing staff on how to effectively utilize a LIMS. All incoming staff must be able to capture the needed data via the patient’s electronic medical record and then properly enter the data into a LIMS. In regards to capturing data needed for LIMS, management will need an efficient workflow that includes the following: 1) how to obtain data associated with the specimens, 2) where to locate needed data within the electronic medical records, 3) how to enter the data into a LIMS, and 4) process in place for data checking. This workflow will enhance accurate, efficient data reporting.

Diagnostic Testing & Specimen Storage

The Centers for Disease Control and Prevention (CDC) does not recommend using an antibody test as the sole basis for diagnosis and antibody tests are not authorized by the U.S. Food and Drug Administration (FDA) for diagnostic purposes. Diagnostic laboratories must check for COVID-19 by conducting a Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) test that is used to detect the virus’s RNA in collected upper and lower respiratory tract specimens. SARS CoV-2 diagnostic tests should always be performed in a clean room and the instruments being utilized be calibrated per the manufacturer’s instructions or laboratory’s own Standard Operating Procedures (SOPs). Aside from LIMS capturing data, it will provide alerts associated with instrument calibration and maintenance, which is essential in producing accurate diagnostic testing results. A LIMS can also be integrated with analytical instruments for data transfer, thereby ensuring data integrity, eliminating transcription errors, and minimizing turnaround time. Per the CDC guidelines, once these specimens have been collected, they should be shipped at 2-8oC with ice packs. If the specimens are frozen, it is important to immediately ship overnight on dry ice. The primary receptacle and the secondary packaging should maintain specimen integrity at the temperature of the refrigerant used as well as the temperatures and the pressures.

When handling and shipping specimens for packaging and transporting, the laboratory must follow the written guidelines per the International Air Transport Association (IATA) Dangerous Goods Regulations (DGR), which provides instructions on the packaging and how to transport specimens for diagnosis and investigation. Suspected or confirmed COVID-19 specimens, cultures or isolates must be packed as UN 3373 Biological Substance, Category B. This is very important since COVID-19 specimens are infectious. Standard Operating Procedures (SOP) are needed on the proper steps needed for collecting and handling specimens. The CDC recommends when working with COVID-19 specimens, laboratory staff should use Personal Protective Equipment (PPE), eye protection, face shields, masks, gloves, and gown.


All laboratory staff members must be trained on the Health Insurance Portability and Accountability Act (HIPAA), Clinical Laboratory Improvement Amendments (CLIA), and ISO 15189:2012. HIPAA guidelines remind staff members of the importance of guaranteeing the security and privacy of each patient’s health information. CLIA provides quality standards for laboratory testing performed on all human samples. CLIA is important because it provides guidance related to facilities performing COVID-19 tests. For example, COVID-19 diagnostic testing facilities must be CLIA certified with a certified laboratory director. ISO 15189:2012 is the international standard that provides laboratories with quality management system requirements and technical specifications.

Concluding Remarks

The laboratory manager or laboratory director must ensure that each staff member has received appropriate training and follows Standard Operating Procedures (SOPs) for specimen handling, testing workflows, instrument calibration, disposal and so on. Management must ensure diagnostic laboratories have the needed supplies to stay safe, in order to collect, store and analyze COVID-19 specimens. Management must ensure adequate supplies of sterile testing kits, PPE, and other laboratory supplies are always plentiful. Laboratories will overcome many challenges if the steps mentioned within this blog are carried out effectively. A COVID LIMS aids in creating productive, efficient diagnostic laboratories with very quick turnaround time, and at the same time assuring quality, which is needed to curb the pandemic.