Research Article| Volume 27, ISSUE 5, P302-311, October 2022

# Buildout and integration of an automated high-throughput CLIA laboratory for SARS-CoV-2 testing on a large urban campus

Open AccessPublished:June 16, 2022

## Abstract

In 2019, the first cases of SARS-CoV-2 were detected in Wuhan, China, and by early 2020 the first cases were identified in the United States. SARS-CoV-2 infections increased in the US causing many states to implement stay-at-home orders and additional safety precautions to mitigate potential outbreaks. As policies changed throughout the pandemic and restrictions lifted, there was an increase in demand for COVID-19 testing which was costly, difficult to obtain, or had long turn-around times. Some academic institutions, including Boston University (BU), created an on-campus COVID-19 screening protocol as part of a plan for the safe return of students, faculty, and staff to campus with the option for in-person classes. At BU, we put together an automated high-throughput clinical testing laboratory with the capacity to run 45,000 individual tests weekly by Fall of 2020, with a purpose-built clinical testing laboratory, a multiplexed reverse transcription PCR (RT-qPCR) test, robotic instrumentation, and trained staff. There were many challenges including supply chain issues for personal protective equipment and testing materials in addition to equipment that were in high demand. The BU Clinical Testing Laboratory (CTL) was operational at the start of Fall 2020 and performed over 1 million SARS-CoV-2 PCR tests during the 2020-2021 academic year.

## Introduction

### Impact of COVID-19 in Boston and Boston University

In late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus, was first reported in Wuhan, China [
• Astuti I.
• Ysrafil
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response.
,
• Huang C.
• et al.
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.
, ]. Cases in the United States were documented in Washington State on January 20, 2020, and shortly after the World Health Organization (WHO) declared the Coronavirus disease 2019 (COVID-19) pandemic in March of 2020 [
• Holshue M.L.
• et al.
First Case of 2019 Novel Coronavirus in the United States.
,
• Cucinotta D.
• Vanelli M.
WHO declares COVID-19 a pandemic.
]. At the height of the SARS-CoV-2 pandemic, individuals of all occupations were taking additional precautions during stay-at-home orders to ensure public safety and health. As the demand for testing increased in parallel with state restrictions lifting and increasing cases in the US, COVID-19 screening was either unavailable, costly, or had test-to-result times that were too long to work as an effective screening tool [

Organization, W. H.Laboratory testing strategy recommendations for COVID-19: interim guidance, 21 March 2020. 6 p. (2020).

]. As part of the initial shutdowns in March 2020, Boston University (BU) pivoted to remote learning and finished the remainder of the semester with online course work. At that time, we began to plan for the return of students in August 2020 which included the construction of a new high-throughput testing laboratory to maintain a testing cadence and turnaround time sufficient to minimize viral spread on campus [
• Hamer D.H.
• et al.
Assessment of a COVID-19 Control Plan on an Urban University Campus During a Second Wave of the Pandemic.
].
For BU, SARS-CoV-2 screening testing was part of a multi-faceted strategy to permit the return to a residential campus and in person teaching in the Fall of 2020. There were examples of newly formed testing facilities with the same purpose, one of the first and most notable was a team at University of California Berkeley that provided a detailed blueprint for converting the Innovative Genomics Institute to test for SARS-CoV-2 at the university and in the local community [
• Amen A.M.
• et al.
Blueprint for a pop-up SARS-CoV-2 testing lab.
]. In Europe, the Francis Crick Institute developed the Crick COVID-19 Consortium with publicly available standard operating procedures (SOP) [
• Aitken J.
• et al.
Scalable and robust SARS-CoV-2 testing in an academic center.
] for other organizations to follow. At Boston Medical Center, the Center for Regenerative Medicine extended the capacity of the BMC Department of Pathology and Laboratory Medicine to perform real-time reverse transcription polymerase chain reaction (RT-qPCR) COVID-19 testing with a 24-hour turn-around time [
• Vanuytsel K.
• et al.
Rapid Implementation of a SARS-CoV-2 Diagnostic Quantitative Real-Time PCR Test with Emergency Use Authorization at a Large Academic Safety Net Hospital.
,
BMC-CReM
BMC-CReM COVID-19 Test.
]. These successes led us to explore doing the same for our entire campus, including 45,000 faculty, students, and staff [
• et al.
qRT-PCR Platforms for Diagnosing and Reporting SARS-CoV-2 Infection in Human Samples.
]. A team was quickly assembled to stand up an on-site high-throughput clinical laboratory from the ground up. The goal was to enable faculty, staff, and students to safely return with an option for in-person or remote classes, a program known as BU's Learn from Anywhere [
• Hamer D.H.
• et al.
Assessment of a COVID-19 Control Plan on an Urban University Campus During a Second Wave of the Pandemic.
] during the 2020-2021 academic year. Across the US, many institutions were making similar plans and it is also important to credit the plethora of online collaboration and communication platforms like Slack where scientists from academic, government, and industry came together to assist each other in these endeavors.
By Fall of 2020, BU implemented a multi-stage plan to perform screening testing of approximately 45,000 students, faculty, and staff for COVID-19. The BU campus comprises three locations in Boston and Brookline, MA. The largest location is the Charles River Campus (CRC), which is approximately three miles from the next largest Boston University Medical Campus, followed by the smaller, Fenway Campus. The proposed plan included an on-site testing facility, collection sites, and contact tracing [
• Hamer D.H.
• et al.
Assessment of a COVID-19 Control Plan on an Urban University Campus During a Second Wave of the Pandemic.
]. Instrumental to the plan was building a clinical testing facility with the capacity to test students, staff, and faculty weekly. The development of the Boston University Clinical Testing Laboratory (BU CTL) was a collaborative effort between the BU Office of Research, the Precision Diagnostics Center (PDC), and the Design, Automation, Manufacturing, and Prototyping (DAMP) Laboratory. Specifically, the development and implementation of the facility required a combination of automation, assay development and systems engineering and management. In addition, the new BU CTL would have to meet regulatory and legal requirements set forth under the Clinical Laboratory Improvements Amendments (CLIA) and Massachusetts state law as well as apply for a Food and Drug Administration (FDA) Emergency Use Authorization (EUA) for a laboratory developed test for COVID-19 [].

### Major decision points

The BU CTL stands out as a technically advanced, purpose built, high throughput automated testing facility. We implemented a high sensitivity RT-qPCR test, integrated automation to support the required throughput, and developed a customized Laboratory Information Management System (LIMS) infrastructure. The sample preparation and RT-qPCR assay were developed to meet both EUA [
] and CLIA [
,
CLIA Regulations and Federal Register Documents.
] requirements which are detailed in publicly available documentation (Fig. 1).
After reviewing various predictive models of SARS-CoV-2 transmission on campus, BU decided to test undergraduate students twice a week and all others based on an assigned testing category with routine asymptomatic screening testing [
• Hamer D.H.
• et al.
Assessment of a COVID-19 Control Plan on an Urban University Campus During a Second Wave of the Pandemic.
]. This resulted in a projected test load of 5,000 tests/day with a required next day turnaround time. Building the physical and digital infrastructure required a university-wide team to source materials, equipment, and human resources to plan and build the space. The team comprised of Sourcing and Procurement, Office of Research, Legal, Medical Advisory Board, Marketing and Communications, is shown in Fig. 2a. The project was driven by the following design requirements: adequate laboratory space, safe and approved sample collection and transportation, efficient RNA purification, assay development, automation, sample lineage tracking, CLIA, EUA, and staffing. An ongoing challenge was equipment, material, and personal protective equipment (PPE) supply chain issues caused by the global pandemic [
• Chowdhury P.
• Paul S.K.
• Kaisar S.
COVID-19 pandemic related supply chain studies: A systematic review.
]. Availability of resources and equipment was a major driving factor in the decisions (Fig. 1) made to build the high throughput clinical laboratory.

## Materials and methods

### Identifying a space for CTL for high throughput automated testing

Identifying a dedicated space on BU's CRC was critical. It needed to house sample receiving, automation robots, qPCR machines, and all auxiliary equipment with the appropriate laboratory footprint. A laboratory space was identified within the Rajen Kilachand Center for Integrated Life Sciences & Engineering. The space was initially designed to house yet to be purchased automation equipment for the Design Automation Manufacturing Prototyping Laboratory, so many of the basic infrastructure needs were in place.
Although the space had some of the required infrastructure, additional renovations were necessary to convert the space into a clinical testing laboratory. The CTL layout required separated stations to mitigate contamination, maintain order, and follow the streamlined workflow illustrated in Fig. 2b. Samples follow a defined workflow upon arrival in the CTL to maintain sample lineage and tracking with each station defined by the process performed. Electrical work included installing additional emergency power outlets to support critical instrument, refrigeration, and freezer units. Additional ceiling support was added for uninterrupted power supplies as backup for the critical robotics and qPCR machines. The space was physically modified with doors to include separated entrances for gowning and to close off the initially open, shared space; all doors were secured by key or swipe access only. This included an additional adjacent space incorporated to house refrigeration, freezers, and the maintain small existing CLIA testing facility. Images of the equipment and space (Supplemental Figures).

### On campus sample collection sites

Anterior nares (lower nostril) samples were self-collected under observation. BU set up five sample collection sites: four on the CRC campus and one on the Boston University Medical Campus. Remote observed collections are also performed for individuals in campus quarantine [
• Hamer D.H.
• et al.
Assessment of a COVID-19 Control Plan on an Urban University Campus During a Second Wave of the Pandemic.
]. All students, faculty and staff were required to complete a daily symptom attestation before coming to campus. Asymptomatic individuals received an electronic clearance badge that they had to present upon entering the collection site. After check-in, individuals would sanitize their hands and approach a check-in station. Everyone was handed a sample tube with a unique barcode and directed to a swabbing station. The observer provides the swab at the swabbing station. Observed swabbing occurs in large, windowed cubicles to allow for social distancing and a physical barrier while the individual removed their mask to swab. A time study showed that the entire process of arriving at the site, checking in, and swabbing required less than 5 minutes for almost all users.
All sample collection sites had windowed check-in and self-collection booths, clear labeled signs, directional arrows on the floor spaced for social distancing, and sanitizer dispensers available between stations. To ensure a clean, sterile surface between collections, a sealed single swab was placed on top of a sheet of parchment. During sample collection the tube cap was placed upside down on the parchment paper while the uncapped tube was placed in a small metal cup to hold the sample tube and prevent spilling. The parchment paper, swab wrapper, and broken off end of swab were disposed of in trash receptacles. A Health Insurance Portability and Accountability Act (HIPAA), Hazardous Material Regulations, and Occupational Safety and Health Administration certified courier transferred samples on a scheduled basis to the CTL. To ensure the safe transport of the samples and compliance with biosafety requirements samples were packaged in Test n’ Toss Disposable Test Tube Racks (Whitney Medical Solutions, Niles, IL) that were contained in a sealed bag. The sealed containers were transported in customized corrugated cardboard boxes labeled with biohazard information, return address, and delivery address.

### Ideation and development of assay and sample testing process flow

In early 2020, the gold standard testing strategy recommended by the Center for Disease Control and Prevention (CDC) was testing the nucleocapsid (N) gene in 3 target regions as a singleplex RT-qPCR [

Organization, W. H.Laboratory testing strategy recommendations for COVID-19: interim guidance, 21 March 2020. 6 p. (2020).

,]. The CDC introduced the first EUA primer and probe set[
• Lu X.
• et al.
US CDC real-time reverse transcription PCR panel for detection of severe acute respiratory syndrome Coronavirus 2.
]. At the time the CTL was establishing an assay protocol, two targets (N1 and N2 with RNase P (RP) as the human material control) were required to identify positive cases. There were also limited multiplex RT-qPCR options with EUAs for clinical use. An example of a widely available option was the TaqPath COVID-19 combo kit [
FDA
] (Thermo Fisher, Waltham, MA) that targeted the S (spike), ORF1ab, N regions and included a spiked in internal control ms2phage. However, the kit at the time did not contain a human specific control and was costly even at scale for our application [
FDA
].

### SARS-CoV-2 research emerging from the BU CTL and the research community

The robust high-throughput automated system in combination with on campus contact tracing enabled the BU research community to have access to data-rich deidentified information during the pandemic [
• Hamer D.H.
• et al.
Assessment of a COVID-19 Control Plan on an Urban University Campus During a Second Wave of the Pandemic.
]. As an example, a multi-university effort that included BU discovered and determined that amplicon residue contamination caused false positive PCR results in researchers working with amplified SARS-CoV-2 materials [
• Davidi D.
• et al.
Amplicon residues in research laboratories masquerade as COVID-19 in surveillance tests.
]. The large complete dataset enabled a large study on cycle threshold values correlated symptoms with SARS-CoV-2 positive and negative tests [
• Landaverde L.
• et al.
]. The rapid emergence of the omicron variant was documented at BU and on other local university campuses [
• Petros B.A.
• et al.
]. A study on matched anterior nares swabs tested with both RT-PCR and Abbott BinaxNOWTM (Abbott Laboratories, Chicago, IL) was critical during the omicron surge as the demand for rapid diagnostic tests increased [
• Landaverde L.
• et al.
]. Data from the BU CTL, contact tracing, and sequencing data provided insight on vaccine efficacy [
• Landsberg H.E.
• et al.
Efficacy of Pfizer-BioNTech in SARS-CoV-2 Delta cluster.
], transmission of SARS-CoV-2 in classrooms [
• Kuhfeldt K.
• et al.
], post-quarantine transmission and quarantine length [
• Liu A.B.
• et al.
Association of COVID-19 Quarantine Duration and Postquarantine Transmission Risk in 4 University Cohorts.
], and isolation release after infection [
• Bouton T.C.
• et al.
Viral dynamics of Omicron and Delta SARS-CoV-2 variants with implications for timing of release from isolation: a longitudinal cohort study.
].

### Considerations and future research opportunities

BU has successfully implemented a screening testing program for the 2020-2021 academic school year with the plan to continue to allow for students, staff, and faculty to safely return to campus. The rapid scale-up of the BU CTL has provided critical insights on materials, space, legal, and personnel required to effectively build an automated high-throughput system in a short period of time leading to a model that can be referenced for future disease outbreaks and pandemics. With over 1 million tests completed this academic year, the university has the unique opportunity to conduct research to contribute to the global SARS-CoV-2 knowledgebase. The university has a controlled data diverse set of de-identified samples that could provide further insight into SARS-CoV-2 and its impacts on public health.

## Author contributions

L.L., D.M., J.R., D.F., L.O., R.C., S.M.D.O., and A.F. built and tested the laboratory and biological assays. S.C, D.C., S.H., C.K., T.L.M., E.M., M.M., and T.S. contributed to the database and software support for the BU CTL. A.B., S.P.B., S.C., D.C., L.D., K.G., D.H.H., L.H., C.L., D.L., K.L., C.M., C.M., R.M., J.P., L.R., J.R., D.R.T., A.Z., R.A.B., G.W., D.D., and C.M.K. contributed to the development of the BU CTL, BU Healthway, and Learn from Anywhere. L.L. and C.M.K. wrote the manuscript. All authors reviewed and approved the final manuscript.

## Declaration of interests

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

## Acknowledgements

Figures were drawn by the Authors of this paper. Photos are taken by authors of the paper. Images are stock from ThermoFisher, Hamilton, and Boston University. The authors of the paper would like to thank our collaborators from across the country including the Broad Institute, University of California Berkeley, and University of California San Diego. Thank you to Sandra Smole and Massachusetts Department of Public Health for their continued support. Thank you to Marcia Eisenberg and LabCorp, Inc. for technical assistance and advice. Thank you to Amy Peace Brewer and Genova Diagnostics for technical assistance and advice. Thank you to the support of Rajen Kilachand and the Rajen Kilachand Center for Integrated Life Sciences & Engineering for the support to develop the BU CTL. Thank you to the technicians, technologists, and Lab Managers of the BU CTL. The authors would like to thank the BU Facilities Management and Operations.

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