key: cord-307702-n74wvika
authors: Durant, Thomas J S; Peaper, David R; Ferguson, David; Schulz, Wade L
title: Impact of COVID-19 Pandemic on Laboratory Utilization
date: 2020-07-14
journal: J Appl Lab Med
DOI: 10.1093/jalm/jfaa121
sha: 
doc_id: 307702
cord_uid: n74wvika

BACKGROUND: Coronavirus Disease 2019 (COVID-19) was formally characterized as a pandemic on March 11, 2020. Since that time, the COVID-19 pandemic has led to unprecedented demand for healthcare resources. The purpose of this study was to identify changes in laboratory test utilization in the setting of increasing local incidence of COVID-19. METHODS: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Data were extracted from the laboratory information system database over a 10-week period, spanning the primordial inflection of COVID-19 incidence in our region. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. RESULTS: Between February 2, 2020 and April 11, 2020, there were 873,397 tests ordered and final verified. The in-house SARS-CoV-2 PCR positivity rate for admitted patients in the last week of the observation period was 30.8%. Significant increases in workload were observed in the send-out laboratory section and for COVID-19 diagnosis (PCR) and management-related testing. Otherwise, there was a net decrease in overall demand across nearly all laboratory sections. Increases in testing were noted for tests related to COVID-19 management. Viral transport media and citrated blue top containers demonstrated increases in utilization. CONCLUSION: Increasing local incidence of COVID-19 had a profound impact on laboratory operations. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. During events such as COVID-19, monitoring of such patterns can help inform laboratory management, staffing, and test stewardship recommendations for managing resource and supply availability.

Background: Coronavirus Disease 2019 (COVID- 19) was formally characterized as a pandemic on March 11, 2020. Since that time, the COVID-19 pandemic has led to unprecedented demand for healthcare resources. The purpose of this study was to identify changes in laboratory test utilization in the setting of increasing local incidence of COVID-19.

We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Data were extracted from the laboratory information system database over a 10-week period, spanning the primordial inflection of COVID-19 incidence in our region. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods.

Results: Between February 2, 2020 and April 11, 2020, there were 873,397 tests ordered and final verified. The in-house SARS-CoV-2 PCR positivity rate for admitted patients in the last week of the observation period was 30.8%. Significant increases in workload were observed in the send-out laboratory section and for COVID-19 diagnosis (PCR) and management-related testing. Otherwise, there was a net decrease in overall demand across nearly all laboratory sections. Increases in testing were noted for tests related to COVID-19 management. Viral transport media and citrated blue top containers demonstrated increases in utilization.

Increasing local incidence of COVID-19 had a profound impact on laboratory operations. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. During events such as COVID-19, monitoring of such patterns can help inform laboratory management, staffing, and test stewardship recommendations for managing resource and supply availability.

In this report, we characterize observed changes in the demand for laboratory testing following the COVID-19 outbreak at a tertiary care clinical laboratory near one of the US epicenters of the pandemic.

• These data provide an overview of utilization changes laboratories may anticipate in response to increasing COVID-19 incidence in their region and may provide guidance on how these changes may impact operational decision making.

• We found an overall decrease in laboratory test volume, but there were striking increases in demand for COVID-19-related testing. In addition to tests for SARS-CoV-2 itself, increases were seen for tests related to COVID-19 management, including those associated with coagulopathy, myocardial stress/injury, host immune dysregulation, and prognostic indicators in the setting of multiorgan dysfunction and sepsis.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has resulted in an 

Retrospective laboratory test order and result data were extracted from our laboratory information system (LIS)(Beaker; Epic, Madison, WI). Record-level data consisted of test orders that had a final verified result. Additional metadata included procedure name, procedure code, ordering department, laboratory resulting section, and specimen received time. Default collection containers were extracted from the LIS for analysis of specimen container type utilization. All laboratory tests were performed at a single, urban tertiary care medical center, which consists of 1,541 licensed beds on two campuses. This work was part of an IRB-approved project within our department (IRB Protocol ID: 2000027747).

Frequency of laboratory test orders were collated into weekly buckets based on the date the specimen was received to reduce the typical variation seen in testing volumes on different days of the week.

Absolute and percent change in number of test orders and container types were analyzed prior to (February 2 nd to April 11 th ) and after the time SARS-CoV-2 PCR testing becoming available on March 8 th , 2020. Total testing volumes were calculated during the first and last two-weeks of the observation period. These totals were used to calculate the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge period. Orders were collated into groups based on the laboratory section performing the related assay -e.g., hematology, chemistry, microbiology, etc. Of note, our laboratory has separate sections for virology and microbiology, so PCR testing for COVID-19 is reflected in counts for the virology section, rather than microbiology. Orders were also organized by patient status (inpatient, outpatient, and emergency department) based on the collecting department.

Custom Python (version 3.7.4) scripts were used to obtain counts of container types by linking laboratory test orders to the 'default' container type defined in the LIS. Following the initial decrease in test volumes, test volume remained lower in all laboratory sections relative to the pre-pandemic state. The most notable exception was the increase send-out test volume which, following an initial decrease of 18.3% during the week of March 15 th , was ultimately observed to experience a 65.6% increase relative to the pre-pandemic baseline ( Figure 2 ).

Laboratory section-level data indicated that overall order volumes had sustained decreases in all sections except for the send-out laboratory and tests performed on blood gas analyzers, the latter of which includes both point of care (POC) and central laboratory testing. As shown in Figure 2 , molecular diagnostics (-76.3%), immunology (-66.5%), and flow cytometry (-60.7%) experienced the largest declines in order volumes.

Absolute and relative differences between the total number of orders in the first two and last two weeks of the observation period were used to assess overall change (Table 1) . We found an overall decrease in laboratory test volume by 14.8%, but notable increases were observed among biomarkers used to monitor host immune response, cardiovascular status, and hemostatic abnormalities. We also analyzed tests that are commonly ordered in the setting of respiratory tract infections. Of these, procalcitonin, arterial blood gases, Influenza A/B PCR, PCR for methicillin resistant Staphylococcus aureus (MRSA), and antigen testing for Streptococcus pneumoniae (S. pneumoniae) and Legionella were all observed to have an increased inpatient volume (Table 2) . Of note, the number of orders for blood cultures was observed to decrease by approximately 40% across all patient settings.

Of the containers associated with the test orders in this dataset, viral transport media (VTM) and citrated blue top containers were the only two with a marked increase in use over the last two weeks compared to the first two weeks in the analysis period (Table 3) .

Light green top tubes and blood spots showed operationally equivocal differences in use. The other container types showed a decrease in overall utilization (Table 3 ). Of note, use of blood gas syringes were shown to decrease by 21.7% while ordering of 'blood gas' tests were increased by 16.7%.

The COVID-19 pandemic has resulted in unprecedented demand for healthcare resources. Notably, container utilization data indicated a decrease in blood gas syringe usage relative to the pre-pandemic state. However, tests performed in the blood gas laboratory increased as did order volume for arterial blood gases among admitted patients. The discrepancy is likely due to the default container type of 'blood gas syringe' being mapped with other POC-tests such as activated clotting time, troponin I, and GEM 4000 blood gases, all of which had a decrease in order frequency (data not presented). This increase in blood gas testing however, did lead to low supplies of these consumables.

At our institution, blood gas syringes are purchased and distributed throughout the hospital by central supply chain services and rely on each floor, unit, or crash cart manager to request more syringes when supplies are low. At the time of this writing, we are currently working closely with supply chain as our preferred and backup heparinized blood gas syringes are on allocation or backorder, and there has been a resulting shortage on specific units in our hospital. This is likely due to a multitude of factors including unit-specific usage rates and global supply chain issues, the former of which is poorly captured with hospital-level data exports using default container type as the surrogate data element.

Among ordering trends for respiratory pathogen testing, we observed a decrease in influenza A/B PCR, group A Streptococcus (GAS) PCR, and respiratory viral panel (RVP) orders. These declines likely reflect operational changes which were made in light of CDC recommendations that respiratory specimens from PUIs be processed in class-II biosafety cabinets. (29) Because of this, all respiratory specimens processed in the clinical laboratories were treated as though they were collected from a patient suspected to be infected with SARS-CoV-2. Further, upper respiratory sampling was discontinued at outpatient practices. Future studies should assess for changes in clinical management (e.g. greater use of empiric antibiotics for GAS pharyngitis) related to a reduced laboratory formulary because of such changes in specimen collection and laboratory practice.

The reported incidence of COVID-19 is, in part, influenced by not only the availability of SARS- Institutional guidelines changed frequently and eventually recommended less restrictive testing practices. Early in the pandemic, the limited availability of testing capacity contributed to more restrictive ordering practices and these practices may have continued out of habit even after guidelines called for more wide-spread testing. Currently, all patients admitted through the ED receive a SARS-CoV-2 PCR test, regardless of clinical suspicion, but this was not implemented until after the study period.

Lastly, there are a variety of clinical scenarios which require a negative SARS-CoV-2 PCR test prior to advancement such as, any procedure with the potential for aerosolization of respiratory secretions. But, in all cases, inpatient and outpatient testing within our system is the decision of the patient's primary provider.

The clinical virology section had an overall decrease in testing volume; however, significant changes in personnel management and testing strategies were required to respond to the demands of COVID-19. In response to the increase in demand for rapid TAT SARS-CoV-2 PCR, the virology laboratory transitioned from covering two shifts, 7 days per week, to a three-shift schedule which resulted in more consistent and shorter TATs. The virology laboratory also discontinued viral culture methods and DFA testing for viral respiratory pathogens based on CDC and WHO recommendations. (30, 31) The volume of batch testing for viral load, serology, and antigen assays for other pathogens was also decreased. These changes and the elimination of highly manual tests allowed for the redistribution of staff within the virology laboratory to accommodate needs for SARS-CoV-2 PCR testing.

Cross-coverage throughout the laboratory has also been a common point of discussion throughout the COVID-19 outbreak. We conducted a skills assessment of all laboratory staff in anticipation of the need to reassign staff to other laboratory sections to accommodate possible surges in viral molecular testing or to address COVID-19 related staff shortages. Staff who required minimal crosstraining for appropriate competency to perform virology testing were trained during gaps in their schedule in case immediate reassignment was needed. The molecular diagnostics laboratory, which had a marked decline in order volume, was able to provide much needed assistance to the testing efforts in virology, particularly those related to SARS-CoV-2 PCR. Decreases in overall laboratory test volumes also allowed us to re-allocate staff across laboratory sections, but as we prepare to reopen clinical operations, normal laboratory demand will return and possibly increase, at least over the short term, with the likelihood that we will experience ongoing and likely increasing needs for COVID-19 testing, both NAAT and serologic. We anticipate new staffing models will be implemented to accommodate these shifting demands.

Local treatment protocols may include testing recommendations for the management of patients with COVID-19 and may significantly influence laboratory test utilization. At our institution, the initial recommendations for admitted adults with COVID-19 included CBC with differential, and dramatically increasing testing capacity to meet institutional and public health needs. It is likely that COVID-19 incidence will experience at least some rebound as society reopens, and the laboratory will face continued demand for rapid and accurate diagnostic tests for COVID-19 along with more typical testing needs. Finally, it is possible that active COVID-19 transmission will occur during the traditional influenza season, further exacerbating the demands for rapid respiratory viral testing. Thus, the shifting demands on the clinical laboratory are likely to persist for the near future. : Changes in laboratory test order trends relative to pre-and pandemic state, collated into groups designated by resulting laboratory section. X-axis represents the percent difference between the total number of final verified test orders during the first and last two-weeks of the observation period.

Abbreviations: Dx = Diagnostics.

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