Helping Missouri labs through the pandemic

Jan. 21, 2021

Will you describe what type of SARS-CoV-2 testing the Missouri State Public Health Laboratory (MSPHL) is doing?

The MSPHL offers rapid PCR testing utilizing assays from the Centers for Disease Control and Prevention (CDC) and TaqPath. The CDC assay was the first test used. We also offer serology testing for COVID antibodies, but the demand for that test within our laboratory has not been robust.

What are your daily testing totals and turnaround times?

In February and early March our daily specimen load was very low – typically in the single digits, but that steadily increased through the summer months to 200 per day. By the fall of 2020, our lab was testing as many as 800 specimens per day. Throughout these times, however, our turnaround time (TAT) has been 24 hours. We have maintained this TAT by acquiring additional high-throughput extraction devices and PCR instrumentation. We were also fortunate to be able to hire additional staff to accession specimens and test those specimens.

What steps has the MSPHL taken to help clinical labs throughout the state access equipment, supplies and other resources to facilitate testing for SARS-CoV-2?

We have been working with the Missouri labs, including those not on a state contract, to ascertain how to best accommodate their supply needs. Working with our state’s emergency management agency, we utilize a website where labs enter an order for supplies and the support unit at the MSPHL fulfills and ships those orders the same day. To date, the MSPHL has shipped out nearly 500,000 tubes of media and 400,000 swabs to laboratories in Missouri. In addition, the lab has shipped out to hospitals and local public health agencies 9,500 vials of Remdesivir (mainly after hours to hospitals) and nearly 75,000 COVID test cartridges for the Abbott ID NOW rapid instrument.

The MSPHL laboratory director also has direct access to the regional resource representative at the Department of Health and Human Services. When a commercial or hospital laboratory finds itself in need of supplies or equipment that are back-ordered, the laboratory reaches out to me as the MSPHL laboratory director for assistance. I, in turn, receive the purchase order from the lab and send it on to the HHS representative and ask that the order be pushed up in the queue. That can be accomplished if the state is in what is termed a “red zone,” or is in a state of high case counts or hospitalizations. More often than not, the back-ordered supplies or equipment will be received earlier using this method. Recently, plastics, like pipette tips, are in such short supply that this method has not achieved total success for orders with those supplies.

What lessons did MSPHL officials learn during the first wave of the pandemic and how are they applying those lessons going forward, particularly with the added complexity of flu season?

We should be ordering our supplies as a standing order, meaning we should receive supplies on a regular basis. We often do not receive as much as we order, but we do get some supplies, which allows us to get by.

In our lab we have numerous assays to consider with a multiplex flu/COVID, CDC COVID-only and then the assays for specific flu strains. Depending on what the clinicians request and what the health programs and the epidemiologists desire, it can present a confusing picture of which test should be run on a specimen. Adding to this picture is the continued shortage of plastic consumables. We can’t just run a number of tests on each specimen anymore. We all have to have thoughtful use of our supplies.

Let us turn now to the role of the Association of Public Health Laboratories (APHL). What does the association see as its role during the COVID-19 pandemic and how is it fulfilling that role?

We have been working diligently to support our member laboratories throughout the pandemic response. This includes developing and sharing guidance, closely coordinating activities among federal, state, local and industry partners, advocating for greater investment to expand laboratory testing capacity and much more.

Will you briefly describe the Sara Alert system and COVID-19 data lake and how APHL and public health organizations are using these electronic tools to monitor and manage the COVID-19 pandemic?

Sara Alert is a real-time COVID-19 monitoring and reporting tool. It enables public health officials to enroll people who are ill or who are at risk of developing COVID-19. Those who enroll can enter their symptoms, which provides officials with real-time insights into the spread of disease and allows them to quickly and efficiently identify people requiring care, or for those who have developed COVID-19, alert them when it is safe to discontinue isolation. Sara Alert is hosted on the APHL Informatics Messaging Services (AIMS) platform, a secure, cloud-based environment.

APHL also has built and maintains a data lake on AIMS to help paint a comprehensive picture of the nation’s testing landscape and needs. APHL originally developed the data lake for monitoring cases of antibiotic resistance, but with the emergence of COVID-19, APHL quickly reconfigured its data lake. It now holds nearly all the nation’s COVID-19 testing data from public health departments.