By Allison Proffitt
June 15, 2020 | The Association for Molecular Pathology (AMP) surveyed laboratory professionals offering molecular diagnostic tests for clinical diagnosis of SARS-CoV-2 infection. They released the first findings and recommendations based on that survey last week.
AMP launched the survey, “in order to obtain a real-world view of the experience of laboratories during this unprecedented time and to gain insight into the current testing infrastructure in the U.S.,” said Karen Weck, AMP President and Professor of Pathology and Laboratory Medicine, Professor of Genetics and Director of Molecular Genetics and Pharmacogenomics at University of North Carolina Chapel Hill, during a virtual town hall last week.
As a result of the survey, AMP recommended that testing labs reassess the type and location of SARS-CoV-2 testing, reprioritize supply allocations based on clinical testing needs, increase transparency between labs and suppliers, coordinate among labs to manage capacity, and finally standardize reporting.
Different Labs, Different Challenges
The AMP survey was sent to both Association members and non-members from April 23 to May 5 at labs around the world who are conducting SARS-CoV-2 testing. AMP is still analyzing the results; the first set of public findings are limited to 118 US-based testing labs that completed the full 67-question survey and does not include any international or partial responses. Responses came from 45 academic medical centers, 33 community hospitals or health systems, and 40 commercial reference labs in 38 states plus Washington, D.C.
In breaking down the survey findings, AMP noted that responses often varied by lab type. For example, on average, academic medical centers began offering tests on March 21. Commercial labs and health systems’ average testing start date was April 2. About half the labs use commercial testing kits under FDA’s Emergency Use Authorization, 10% used laboratory-developed tests (LDTs), and 38% use both types.
Across the lab type, respondents reported that supply chain disruptions either delayed and/or decreased testing. Academic medical centers and community hospital labs report the most barriers to increasing testing including limited supply of testing kits and reagents. Of all of the supplies that AMP asked about, swabs were most commonly in shortage.
These shortages can be attributed to different causes. About half of the labs reported that they had been informed by a manufacturer or supplier that they cannot purchase testing kits or reagents due to government restrictions and/or allocations for these products. Pediatric hospitals were told that supplies needed to be saved for adult hospitals. Some smaller labs saw their shipments diverted to hotspots or larger laboratories.
Weck highlighted this possible preference for larger commercial labs as a particular challenge for community response. “The survey showed that many of the supplies are going to large, commercial reference laboratories over the huge network of local academic, hospital and community labs that are really essential for rapid and front-line testing,” she said during the virtual event.
Karen Kaul, former AMP President and Chairman of Department of Pathology at NorthShore Research Institute, challenged the community: “We need to try to find data driven ways to demonstrate the impact of having a local test available in a few hours or a day rather than something that takes a few days to return.”
Several of AMP’s recommendations address the problems of supply chain disruptions. AMP recommends that supply allocations be prioritized based on clinical testing needs. “The need for testing supplies designed for acute care, surveillance, high-throughput, and other clinical needs should be monitored widely to provide real-time feedback to agencies to support data-driven supply allocations,” the Association suggests in its report. “Ideally these monitoring systems would be proactively established, rapidly activated following novel pathogen identification, and maintained throughout the course of response.”
AMP also called for increased transparency and communication about resource delays and their causes between labs, suppliers, and any government entities acting on the supply chain.
Capacity Management
To keep up with testing demand and deal with uncertainties in the supply chain, most labs used multiple tests. Reference labs used one or two different tests, while academic medical centers and community hospital labs used four or more testing methods. LDTs along with the Roche cobas SARS-CoV-2 test, Abbott’s RealTime SARS-CoV-2 assay, Cephieid’s Xpert Xpress SARS-CoV-2 test, and Hologic Panther Fusion SARS-CoV-2 test were the top five tests labs mentioned. Commercial reference labs preferred their own LDTs. Academic medical centers favored the Abbott and Roche tests along with LDTs. Community hospitals use commercial tests from these four companies as well as tests from Thermo Fisher, Quidel, and DiaSoren.
In general, the mix of tests has allowed labs to meet their testing needs. About half the labs surveyed report that demand is currently lower than testing capacity, though many expect demand will increase with phased opening particularly resuming of surgical and additional medical procedures. But 1/3 of the labs of each type (commercial labs, academic medical centers, community hospital or health system) report that demand is higher than capacity.
AMP believes there may be an opportunity to coordinate testing regionally to best use excess test capacity. The Association proposes, for example, a dashboard consisting of laboratories, manufacturers, and government representatives that would facilitate real-time supply chain understanding and help to prevent communication and resource bottlenecks.
Tests—when you can get them—are fairly quick: 90% of labs are returning test results in less than 24 hours; 44% are returning results in less than 12 hours.
Reporting and Public Health Responsibilities
Labs were split on whether or not public health reporting was troublesome. 90% of labs report at least to their state’s health department; only 18% are reporting results to CDC. 57% of the survey respondents said that multiple public health reporting requirements were not burdensome, but other respondents called reporting to multiple groups time consuming and challenging because data are required in different formats.
AMP addressed that issue in its recommendations as well, calling for standardized agency reporting formats and processes for reportable infectious diseases during any future pandemic.
In the future, AMP recommended, the public health laboratory community, clinical laboratories, and CDC should collaborate to:
- Define minimal required data elements for supporting public health contact tracing
- Establish standardized reporting format that Electronic Health Records (EHR) / Laboratory Information Systems (LIS) vendors could adopt
- Establish a standardized and centralized reporting agency / process that minimizes delays in return of results and eliminates need for laboratories to duplicate reporting to multiple agencies
- Provide logistical support for laboratories to provide reportable infectious disease data electronically.
Next Steps
In addition to further data releases from the current survey—including analysis of partial surveys and the international responses—AMP is planning future surveys to explore supply chain problems over time, watch for shifts in primary diagnostic test methodologies, track testing capacity, and look at how patient demographics change.
AMP is also sharing the survey results widely. Weck said that the survey results have been presented in a Congressional briefing and there are plans to present them to CDC. “We are very hopeful that we can continue to get the word out about the importance of being prepared,” she said.
But although there were challenges, the molecular diagnostics community has risen to meet them. “Even though I’ve been in laboratory medicine for over 20 years,” Weck said, “I have been so impressed by the ability of the laboratory community to respond to this pandemic despite multiple external pressures.”