1

A Public Health Laboratory Response to the COVID-19 Pandemic 1

2

Kanti Pabbarajua#

, Anita A. Wonga, Mark Douesnard

a, Raymond Ma

a, Kara Gill

a, Paul Dieu

a, 3

Kevin Fonsecaa,b

, Nathan Zelyas c,d

, Graham A. Tipples c,d,e

4

aAlberta Precision Laboratories, Public Health Laboratory, Calgary, Alberta, Canada 5

bDepartment of Microbiology, Immunology and Infectious Diseases, University of Calgary, 6

Alberta, Canada 7

cAlberta Precision Laboratories, Public Health Laboratory, Edmonton, Alberta, Canada 8

dDepartment of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, 9

Canada 10

eLi Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada 11

# Corresponding author. 12

Mailing address: 13

Provincial Laboratory for Public Health, 14

3030 Hospital Drive, Calgary, Alberta, Canada T2N 4W4. 15

Phone: (403) 944-8621. 16

Fax: (403) 283-0142. 17

Email:kanti.pabbaraju@albertaprecisionlabs.ca 18

JCM Accepted Manuscript Posted Online 8 June 2020J. Clin. Microbiol. doi:10.1128/JCM.01110-20Copyright © 2020 American Society for Microbiology. All Rights Reserved.

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Number of words in the Abstract: 237 19

Abstract 20

An outbreak of coronavirus disease 2019 (COVID-19) caused by the 2019 novel coronavirus 21

(SARS-CoV-2) began in Wuhan, Hubei, China, in December 2019, and spread rapidly 22

worldwide. The response by the Alberta Precision Laboratories, Public Health Laboratory 23

(ProvLab), Alberta, Canada, included the development and implementation of nucleic acid 24

detection based assays and dynamic changes in testing protocols for the identification of cases as 25

the epidemic curve increased exponentially. This rapid response was essential to slow down and 26

contain transmission and provide valuable time to the local health authorities to prepare 27

appropriate response strategies. As of May 24, 2020, 236,077 specimens were tested with 6475 28

(2.74%) positives detected in the province of Alberta, Canada. Several commercial assays are 29

now available; however, the response from commercial vendors to develop and market validated 30

tests is a time-consuming process. In addition, the massive global demand made it difficult to 31

secure a reliable commercial supply of testing kits and reagents. 32

A public health laboratory serves a unique and important role in the delivery of health 33

care. One of its functions is to anticipate and prepare for novel emerging pathogens with a plan 34

for pandemic preparedness. Here we outline the response that involved the development and 35

deployment of testing methodologies that evolved as SARS-CoV-2 spread world-wide, the 36

challenges encountered, and mitigation strategies. We also provide insight into the organizational 37

structure of how a public health response is coordinated in Alberta and its benefits. 38

Commentary. 39

Coronaviruses (CoVs) can accumulate mutations that allow them to adapt to new hosts and 40

ecological niches (1). The epidemic and pandemic potential of novel coronaviruses has been 41

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highlighted with the emergence and spread of severe acute respiratory syndrome coronavirus 42

(SARS-CoV) in 2003 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 43

(2). In early December 2019, following the reports of cases with pneumonia of unknown origin 44

from Wuhan, Hubei, China (3, 4), a Betacoronavirus named severe acute respiratory syndrome 45

virus-2 (SARS-CoV-2) was identified as the responsible pathogen (5) (6). On March 11, 2020 46

the World Health Organization declared the outbreak of coronavirus disease (COVID-19) caused 47

by SARS-CoV-2 as a pandemic. Since the first Canadian case of COVID-19 was reported in 48

Ontario, Canada, on January 22, 2020, all provinces and territories (except Nunavut) have seen a 49

steep rise in the number of confirmed cases. Despite mild to moderate disease severity and 50

mortality of 1 to 2%, primarily in the elderly and those with co-morbidities (7), the lack of global 51

immunity to this novel virus is resulting in large numbers of individuals developing significant 52

respiratory sequelae that is threatening to overwhelm the current health system. SARS-CoV-2 is 53

an emerging pathogen and in the absence of antivirals, therapeutics, or vaccines, sensitive and 54

specific tests for the early detection and isolation of cases is the first critical step in the public 55

health response. 56

The Alberta Precision Laboratories, Public Health Laboratory (ProvLab), is based at two 57

sites, Edmonton and Calgary, Alberta, Canada and serves a provincial population of 4.37 million 58

people spread over an area of approximately 660,000 km2, and provides testing support for the 59

Northwest Territories. In addition to providing services such as surveillance, research, education, 60

and training, the ProvLab performs a wide range of specialized tests with a public health impact, 61

water testing, and supports the acute care microbiology testing at the University of Alberta 62

Hospital. The ProvLab tests approximately 2 million patient samples annually. One of the key 63

mandates of the ProvLab is to respond to threats of emerging pathogens by providing the 64

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diagnostic arm for case detection in order to assist public health authorities with contact tracing 65

and outbreak control measures. 66

Following the SARS outbreak in 2003, the role of public health laboratories in rapidly 67

responding to newly emerging diseases was recognized in Canada (https://www.phac-68

aspc.gc.ca/publicat/sars-sras/pdf/sars-e.pdf). The formation of the Canadian Public Health 69

Laboratory Network (CPHLN), of which the ProvLab is a member, occurred in the early 2000s 70

and this established the basis for a well-coordinated network for public health laboratories in 71

Canada. The CPHLN works collaboratively to share protocols and samples thus facilitating the 72

rapid development and validation of tests across the country for emerging diseases such as 73

pandemic H1N1, Zika virus, and Ebola virus outbreaks in the past, and for the current response 74

to SARS-CoV-2. Both the CPHLN and National Microbiology Laboratory (the national 75

reference laboratory of Canada), work closely to facilitate the nationwide sharing of samples as 76

access to positive controls and validation panel samples are a challenge for newly emerging 77

diseases. Similar to our collaboration with other provincial laboratories through the CPHLN, the 78

ProvLab works closely with other clinical laboratories in Alberta within Alberta Precision 79

Laboratories for the sharing of protocols and samples to enhance capacity for efficient testing 80

over a large geographical area. SARS-CoV-2 testing in Alberta was initially implemented at the 81

ProvLab where personnel with training and expertise in development, validation, and 82

implementation of molecular diagnostics were available. Once the testing was operationalized, 83

controls were established and more positive and negative samples were available, efforts to de-84

centralize testing were initiated although the ProvLab continues to support the bulk of the 85

testing. Based on the equipment and expertise available in the different clinical labs, ProvLab 86

provided protocols, controls and validation materials for the implementation of commercial 87

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assays, adaptation of the lab-developed test on commercial platforms or point-of-care tests as 88

appropriate. 89

Within Alberta, the delivery of health care is the responsibility of a single health 90

authority (Alberta Health Services). A single laboratory organization (Alberta Precision 91

Laboratories) is a wholly owned subsidiary of the health authority and is responsible for all 92

clinical diagnostic testing in the province including the work done by the ProvLab. While still a 93

work in progress, there is a move to transition to a single clinical information system and 94

laboratory information system within Alberta. The Chief Medical Officer of Health (CMOH) 95

within the Ministry of Health (Alberta Health) is the most senior public health leader for the 96

pandemic response in Alberta. The close working relationships between the CMOH, the Alberta 97

Health Services Medical Officers of Health (MOHs), the single health authority, the single 98

laboratory organization and the public health laboratory with close ties to the national network of 99

public health laboratories have all been absolutely essential to the ability of ProvLab and its 100

partners to rapidly and effectively respond to COVID-19. 101

Since the genome sequence of SARS-CoV-2 was available early in the pandemic, as a 102

rapid response to this global health emergency, two polymerase chain reaction (PCR) based 103

molecular assays were developed for diagnostic testing. Both assays targeted the RNA dependent 104

RNA polymerase (RdRp) gene; one set of primers was designed for the detection of all alpha, 105

beta, and gamma coronaviruses, and another set was designed for the specific detection of 106

SARS-CoV-2. These were designed as gel-based assays for rapid deployment with the intent that 107

all amplified products would be sequenced for confirmation. These assays were implemented on 108

January 21 and used for the detection of SARS-CoV-2 in January and early February 2020, with 109

about ten samples being tested per week. Real-time reverse transcriptase PCR (rtRT-PCR) assays 110

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were simultaneously developed to increase throughput. Two rtRT-PCR assays, one targeting the 111

envelope (E) gene (8) and one targeting the RdRp gene (in-house), were validated and 112

implemented on February 14. With the implementation of these assays, our testing capacity 113

increased to over 1,000 samples a day and the first positive case in Alberta was detected on 114

March 5. To further increase testing efficiency and throughput, these rtRT-PCR assays were 115

multiplexed and the detection of MS2 (9) as an internal, extraction and inhibition control was 116

also incorporated in the test. This assay was implemented on March 16 and allowed for the 117

testing of over 30,000 samples per week. Rapid assay development and multiplexing allowed the 118

ramp up of capacity to address the growing demand for testing in Alberta. In the early stages of 119

the pandemic when positive specimens were not available, initial validation was performed using 120

in-vitro transcribed quantitated RNA. Different negative specimen matrices were spiked with this 121

RNA to mimic positive patient samples. Blind validation panels provided by the National 122

Microbiology Lab and College of American Pathologists are tested on an on-going basis for 123

assay validation. As commercial assays became available, these assays were verified and 124

implemented for patient testing; the commercial assays currently in use in different clinical 125

laboratories across the province include the cobas®

SARS-CoV-2 Test (Roche Diagnostics), 126

AllplexTM

2019-nCoV Assay (Seegene), Simplexa COVID-19 Direct assay (Diasorin 127

Molecular), and Xpert Xpress SARS-CoV-2 Test (Cepheid). The time line for the evolution of 128

the pandemic and the ProvLab responses are outlined in Figure 1. Specimens submitted from 129

January 20 to May 24, 2020 to the Alberta Precision Laboratories for the investigation of 130

COVID-19 are shown in Figure 2. A total of 236,077 samples were tested during this time period 131

and 6475 (2.74%) samples tested positive. Public health labs cannot depend on the availability of 132

validated commercial kits with a quick response time because of regulatory requirements and 133

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manufacturing processes. Thus, individuals with the expertise and experience in assay 134

development and validation using high quality standards, such as guidelines provided by the 135

College of American Pathologists, are valuable for rapid test development. ProvLab is working 136

with partners within Alberta and nationally to evaluate commercial serology tests and to 137

implement appropriate serological testing for SARS-CoV-2. It is clearly recognized that serology 138

is not appropriate for early acute diagnostics, with the focus being on the serologic surveys to 139

determine the extent of the spread of SARS-CoV-2 in the population over time. 140

This pandemic presented unique challenges, including a rapid increase in the numbers of 141

samples that needed to be tested (initially dozens of tests to several thousand per day), variations 142

in test volumes because of alternating expansion/narrowing of testing criteria defined by the 143

public health authorities, and supply chain issues. The connection between development and 144

deployment was key to the rapid response provided by ProvLab. Teams working concurrently, 145

including decision-making authorities, individuals with the skill set to rapidly design, develop 146

and validate tests, expert technical staff capable of rapid implementation and scale up as the 147

demand of testing increased, were the key features of the successful response. Several changes in 148

workflow and streamlining of testing protocols were made to accommodate the requirements for 149

increased testing and quicker turn-around-time in order to provide a timely diagnoses. Decisions 150

for new equipment purchases such as extractors and analyzers were rapidly made and equipment 151

was borrowed from other laboratories when possible to ensure that capacity was immediately 152

available for a response. Trained technical staff from within the organization and other 153

laboratories were redeployed to the ProvLab as staffing and laboratory operational hours were 154

increased. At time of writing, redeployment and training of staff continues in an effort to 155

optimize workforce for current and future workload surges. 156

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Due to the rapid spread of SARS-CoV-2 and the demand for increasing test volumes, the 157

laboratory’s respiratory testing algorithm underwent several changes during this time period as 158

summarized in Figure 3. Prior to the COVID-19 outbreak, specimens from community patients 159

were tested for only influenza A and B, while hospitalized/emergency room (ER) patients and 160

patients included in outbreaks with a respiratory etiology were tested for all respiratory viruses 161

included on the Respiratory Pathogen Panel (RPP; Luminex, Ontario, Canada), or only influenza 162

A and B. The viral targets included on the RPP are influenza A and B, respiratory syncytial 163

virus, parainfluenza viruses 1-4, seasonal coronaviruses (CoV-229E, CoV-NL63, CoV-OC43, 164

and CoV-HKU1), human metapneumovirus, enterovirus/rhinovirus, and adenovirus. Between 165

January 17 and March 6, the algorithm was updated to include testing of SARS-CoV-2 for 166

patients approved by MOHs and/or at the discretion of the virologist-on-call with an appropriate 167

exposure history, usually travel related. During March 7-13, the need for MOH approval was 168

lifted and community patients were tested for influenza A and B and/or SARS-CoV-2 upon 169

physician request. Hospitalized and ER patients were tested by RPP and for SARS-CoV-2, while 170

respiratory outbreak patients were tested for SARS-CoV-2, with or without RPP, depending on 171

what was requested. From March 13 to the date of writing, all community patients and those 172

presenting at the COVID-19 assessment centers are being tested for SARS-CoV-2 only. All 173

hospitalized and ER patients continue to be tested by the RPP assay and for SARS-CoV-2, and 174

respiratory outbreak patients are tested for either SARS-CoV-2 or by the RPP assay depending 175

on Public Health request. 176

The unprecedented pace at which the pandemic evolved presented several technical and 177

supply chain management issues. Some of the challenges encountered were the shortage of 178

collection swabs, transport media and reagents. To address the shortage of nasopharyngeal 179

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flocked swabs and universal transport media, collection kits used for other specimen types were 180

rapidly validated for their utility to collect and transport respiratory samples. ProvLab and 181

Alberta Health Services procurement teams explored the availability of these supplies worldwide 182

to remove bottlenecks and broaden the supply chain. When new suppliers were identified, all of 183

the non-traditional transport media and swabs were investigated for the stability of the SARS-184

CoV-2 virus at different temperatures, time periods and viral loads (data not shown). Swabs and 185

media with promising results were deployed in the field for the collection of patient samples. A 186

local company that could manufacture universal transport medium was identified and protocols 187

for production were developed. The validity of buffers prepared in-house was concurrently 188

investigated for use as transport media. In addition to the investigation of the utility of a variety 189

of swabs for specimen collection, attempts at 3D printing of swabs are ongoing. Securing a local 190

supplier is predicted to alleviate supply chain issues in the coming months. Similarly, shortages 191

in extraction reagents were addressed by exploring options from other manufacturers and 192

adapting these to instrumentation on hand as well as extensively sourcing alternative reagents 193

from additional local, national and international manufacturers. Attempts to make reagents in-194

house with expert advice from academicians in the different relevant faculties is ongoing. Similar 195

efforts are ongoing for the in-house production of amplification reagents. 196

Brainstorming and experimentation are ongoing to improve efficiency using strategies 197

such as detection directly from specimen without extraction (10, 11) or by pooling multiple 198

samples and screening out negative pools. Patient samples from pools that test positive can be 199

individually tested. Decentralization of testing using point-of-care assays or rapid testing 200

platforms and diversification of testing protocols by validating high throughput commercial 201

testing kits and platforms have helped to scale up the capacity and numbers of samples tested in 202

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Alberta. A comparison of the inter-provincial testing rates based on population has consistently 203

shown that Alberta is able to test at a higher rate as a result of all the strategies mentioned above. 204

The ongoing challenge of emerging infectious agents highlights the role of public health 205

laboratories for pandemic preparedness. Several valuable lessons learned include the importance 206

of a close relationship between public health labs across the country in developing and validating 207

testing protocols by sharing knowledge and materials, a single health authority and laboratory 208

system and a close working relationship between the different laboratories within the province. 209

Other key lessons learned have been the importance of maintaining rapid clinical validation 210

capacity, a strong supply chain management team and proactively establishing multiple supply 211

chains with redundancy for reagents. 212

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Figure 1. Timeline for the evolution of the pandemic and Provlab response 213

World health Organization (WHO), Global Initiative on Sharing All Influenza Data 214

(GISAID), Envelope (E), RNA dependent RNA polymerase (RdRp), Reverse-transcriptase 215

polymerase chain reaction (RT-PCR), Severe acute respiratory syndrome coronavirus-2 216

(SARS-CoV-2) 217 218

219

Figure 2. Samples tested for SARS-CoV-2 and positives detected 220 Total number of samples tested and positives detected from Jan 20 to Apr 12, 2020 are shown as 221

bars. The percent positives are shown by a line graph on the secondary axis. 222

223

Figure 3. Timeline for changes in the laboratory testing algorithm. 224

Emergency room (ER), Respiratory pathogen pane (RPP), Severe acute respiratory 225

syndrome coronavirus-2 (SARS-CoV-2), coronavirus disease-10 (COVID-19). 226 227

228

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Acknowledgements: The authors would like to thank Alahna Gwynn (Technologist III), all 229

technologists from the Molecular Diagnostics and Virology departments and staff at Alberta 230

Precision Laboratories, Public Health Laboratory, Calgary and Edmonton, Alberta, Canada for 231

their hard work and dedication. This response would not been possible without their relentless 232

efforts and excellent technical help in adapting to the changing situation as the pandemic 233

evolved. 234

Conflict of interest: 235 Funding: None 236

Competing interests: None declared 237

Ethical approval: Not required 238

239

Funding: This work did not receive any specific grant from funding agencies in the public, 240

commercial, or not-for-profit sectors. 241

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Dec 8, 2019

Dec 31, 2019

Jan 1, 2020

Jan 12, 2020

Jan 10, 2020

Jan 9, 2020

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Before Jan 17, 2020 Mar 13 to date

Mar 7 to Mar 13 Jan 17 to Mar 6

Community: influenza A/B

Hospitalized, ER, outbreaks: RPP

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First positive detected

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