Saliva Specimen Collection Kit - lucence.com€¦ · Saliva sampling is easy, painless and non-invasive Increased accuracy compared to nasopharyngeal (NP) swabs1 Less risky sampling

Saliva Specimen Collection KitStabilization of Viral Ribonucleic Acid (RNA) in Saliva Specimens

LC-003-SG-EN-01 SAFER™ White Paper

2


– a saliva specimen collection system for SARS-CoV-2 PCR diagnostics with superior accuracy, safety, convenience and cost savings

✓ Saliva sampling is easy, painless and non-invasive

✓ Increased accuracy compared to nasopharyngeal (NP) swabs1

✓ Less risky sampling and processing

✓ Saves costs from cold-chain transport and storage

✓ Suitable for mass testing travelers, healthcare workers, children and the elderly

✓ ISO13485 certified manufacturing in Singapore

✓

3


01. Saliva samples collected with SAFER™ are more accurate than the existing gold standard of nasopharyngeal swabs.• 36% more positives were detected using SAFERTM

02. SAFER™ is safer than existing methods.• Inactivates SARS-CoV-2 in 45 seconds

• Guanidine-free and does not generate cyanide when in contact with disinfectants unlike other preservation reagents, and therefore suitable for use at home, airports, and borders

03. SAFERTM is stable at room temperature, and can be self administered.

04. Process improvements lead to cost savings.

• Labor cost savings: trained workers are not needed for saliva collection

• Transport cost savings: cold-chain transport is not required

• Laboratory savings » Eliminates re-testing due to degraded specimens » Refrigerator space is not required for specimen storage

05. Automation friendly.• Proven compatibility with laboratory automation platforms for

mass testing

IntroducingKey features

Accuracy

Safety

Convenience

Cost savings

Scalable

4


01. Persons being tested• Non-invasive, painless, fearless procedure

• Self-administer test in comfort of home/office

• Eliminate need to queue in close proximity with other potentially COVID-19-positive persons at testing centre

02. Payors of the test (Public Health, Insurance)• More accurate test results

• Reduce costs of re-testing due to sample degradation

• Cheaper as cold-chain transport costs eliminated, lower labor costs as trained healthcare workers for swabbing reduced, particularly for home testing.

03. Healthcare workers• Reduce risk of infection through aerosols during swab collection

as close contact with persons being tested can be avoided using saliva collection.

04. Medical technicians and Laboratory• Specimen is inactivated, so biohazard risks associated with

spills are eliminated

• Weekly rest day possible, as samples will not degrade if delivery to the lab is deferred.

• No risk of cyanide production when used in conjunction with popular automated laboratory molecular diagnostics systems.

• Easy storage of specimens at room temperature, without need for scarce refrigerator space.

Benefits of SAFERTM to

stakeholders

5


The need for scaling up mass

testing

The COVID-19 pandemic has led to an unprecedented global economy shutdown. As countries start re-opening, it is necessary to deploy SARS- CoV-2 diagnostics tests at scale to facilitate mass testing to identify infected persons before a new wave of infections arise2-4. Companies with facilities which employ large numbers of people working in close quarters are also considering systematic re-testing of their employees to ensure their well-being5,6. While laboratory automation has made it possible to rapidly scale up the systematic processing of specimens, there are obstacles at the start of the process when specimens are collected from the individual being tested7.

01 Background and Current Practices

Current practices in mass testing

The gold standard requires the use of nasopharyngeal swabs to collect the specimen for analysis using PCR7. To facilitate mass testing of targeted groups of people, mobile teams of healthcare workers are deployed to collect specimens outside the usual clinical/laboratory settings. In many examples, these collection sites are outdoors, under makeshift tentages, or mobile labs8,9. As both specimen collection reagents and samples are temperature-sensitive, ice boxes or refrigerators are needed on site to maintain the integrity of the reagents, and to preserve the collected specimens.

The healthcare worker must insert the swab deep into the nostril of the patient, traversing a distance equivalent from the nostril to the outer opening of the ear. Even the most experienced staff would cause some discomfort to the patient during this process10, and bleeding occurs for about 5% of cases11. The swab is placed into a tube containing transport media or saline, which is in turn placed in a clean secondary container. In Singapore, biosafety rules require triple-bagging of the specimen. Often, a second healthcare worker is required to assist in this process to ensure that the secondary container is not contaminated. The specimen must be transported to the testing laboratory at 2-8 °C, and arrive within 72 hours to prevent degradation12.

6


01. Accuracy

False negative results are quite common in current COVID-19 tests using nasopharyngeal and nasal swabs. The sensitivity of the tests is estimated to be around 70%13. As many persons with COVID-19 are asymptomatic, a person receiving the false negative result would unknowingly go on to infect others, thus perpetuating the pandemic. A more accurate and sensitive method is required.

02. Safety

Since the virus is still viable in the collection media, there is a risk of infection if any spillage were to occur during transit. The medical technicians must work within the confines of a biosafety cabinet, in full PPE gear to clean each layer of protective bagging as they unpack the samples.

03. Refrigerator Space

Currently, most laboratories keep primary specimens for about 1 week before discarding them, to facilitate repeat tests if required. This takes up precious refrigeration space with the increased test cases. Room temperature storage would solve this problem.

04. Sample degradation

The clinical laboratory must remain open to receive these specimens every day, including Sundays and public holidays, as the specimens would degrade if not processed. 1 week stability is required.

Challenges faced with the current

gold standard

7


Rapid viral inactivation

and prolonged stabilization

To address these needs, Lucence has launched SAFER™ -- our line of saliva collection products. Each SAFER™ kit comprises of a tube of SAFER™ Stabilization Fluid and a funnel with collection tube.

The proprietary SAFER™ Stabilization Fluid stabilizes nucleic acids and has specialized chemistry to inactivate viruses. In June 2020, the US FDA issued a warning letter about the dangers of guanidine thiocyanate which is found in several common commercial transport media14. Cyanide gas is produced when they come into contact with bleach, rendering the transport media incompatible with some popular laboratory testing systems. In keeping with these guidelines, SAFER™ is guanidine-free. Together with scientists at the Duke-NUS Medical School, with support from the Diagnostics Development Hub, A*STAR, it was demonstrated that following incubation of SAFER™ Stabilization Fluid with SARS-CoV-2 virus cultured in a Biosafety Level 3 (BSL3) laboratory, the virus was no longer viable after 45 seconds (Table 1). This reduces the risk of transmission to people involved in transporting the samples, as well as to medical technicians processing the samples in the laboratory. It also saves time from handling of inactivated samples.

SAFER™ Stabilization Fluid has been found to stabilize viral specimens for at least 7 days (Figure 1). Clinical specimens stored at room temperature over 7 days showed similar Ct values for the detection of SARS-CoV-2 (Figure 2). This means that long transit times (<1 week) between sample collection and delivery to the testing laboratory would not affect test performance.

02 New Paradigm -

Virus Titre (Log TCID50/mL)45 secs (n = 3) 5 mins (n = 1) 1 hour (n = 4)

Control 1.5 x 105 ± 0 1.5 x 105 ± 0 1.6 x 105 ± 6.9 x 104

SAFER™ Undetectable Undetectable Undetectable

Table 1. SAFER™ Sample Stabilization Fluid demonstrated virucidal activity (>4 log reduction of viral titre) against SARS-CoV-2 within 45 seconds. The efficacy of SAFER™ Sample Stabilization Fluid against SARS-CoV-2 was tested in a suspension assay. Briefly, 100 µl of SARS-CoV-2 was added to each tube and incubated for the specified time (45 secs, 5 mins and 1 hour) at room temperature. 10-fold serial dilutions from 107 log TC ID50/mL were made and plated in replicates to 96-well plates containing Vero-E6 cells. Cells were incubated at 37°C for 4 days. Cytopathic effect (CPE) was observed and virus titre calculated.

8


Figure 1. Graphical representation of Ct values of the samples over 8 days at room temperature. The Ct values were consistent (<3 ∆Ct) for SAFER™ Sample Stabilization Fluid (Batch 1, 2 and 3) showing that the SAFER™ Sample Stabilization Fluid can preserve the integrity of the RNA up to 7-day period.

Figure 2. Stability of clinical specimens during transit in summer and winter. 95% confidence intervals are represented by error bars. SARS-CoV-2 PCR Ct levels at both baseline (day 0) and day 8 timepoints were similar, demonstrating that delayed processing of specimens for up to 7 days in either summer or winter conditions does not affect the diagnostic performance of the SARS-CoV-2 test.

30292827262524232221

SAFER is stable for >7 days in both summer and winter conditions

LowHigh

Viral load

Abbo

tt m

2000

SAR

S-Co

V-2

CN V

alue

Baselin

eSum

mer

Winte

rBase

line

Summ

erWin

ter

Effective stabilization of viral RNAby SAFER kits

SAFER Batch 1

30

28

26

24

22

20

Ct v

alue

Incubation time at 25ºC (Days)

SAFER Batch 2 SAFER Batch 3

0 3 8

9


To make the specimen collection more convenient and non-invasive, saliva as a specimen for SARS-CoV-2 testing is used by Hong Kong SAR and Japan governments, including testing all passengers arriving at the airport15. The feasibility of saliva as a suitable diagnostic specimen for SARS-CoV-2 has also been demonstrated16-19. Similarly in the USA, Rutgers University has developed a saliva method and obtained FDA Emergency Use Authorization for this test20.

Lucence advises a supervised naso-oropharyngeal (NOP) saliva collection for optimal yield, and is able to share with clinical customers additional optimized approaches for saliva collection. Internal company data has demonstrated that the detection sensitivity and accuracy for SARS-CoV-2 on patient NOP saliva specimens collected using SAFER™ is highly accurate compared against nasopharyngeal swabs (in press)21.

These features make SAFER™ especially suitable for use in home-based settings, schools, at airports and borders, and mass surveillance testing.

Saliva as a feasible diagnostic

specimen

10


A key challenge with saliva samples is the variable viscosity of the specimens. This can sometimes present a challenge especially for automated laboratory systems for DNA/RNA extraction and subsequent molecular analysis22. Lucence has developed validated workflows to optimize saliva solubilization in SAFER™ and increase the concentration of viral RNA extracted.

Overcoming challenges

in specimen handling

03 Specimen Handling in the Laboratory

04 Performance of

To evaluate the performance of SAFER™, we collected paired nasopharyngeal and NOP saliva samples from >100 persons, who presented themselves for COVID-19 testing as part of an active COVID-19 surveillance exercise. The samples were processed according to the Lucence workflow, and analyzed using 3 platforms, including Lucence’s lab-developed test with primers from CDC, USA and 2 commercially available COVID-19 test kits (Table 2). For each platform, results from the nasopharyngeal swabs was used as the gold-standard comparator.

NP SAFERTM

Sensitivity 56.72% 92.54%Specificity 100.00% 100.00%No. of samples 120 120

Table 2. Performance of NOP saliva (SAFER) vs NP swabs across 3 platforms. Overall there were 67 positive samples and 53 negative samples.

Naso-oropharyngeal (NOP) saliva is highly

sensitive

Figure 3. NOP saliva specimens have higher diagnostic utility than other specimen types. 120 matched patient specimens were tested using 2 different PCR kits. The number of positive diagnoses for each specimen type are shown in the Venn diagrams.21

CDCNP Swab

NasalNOP

Saliva421

0

4

130

7

FortitudeNP Swab

Nasal117

0

1

028

1

NOPSaliva

Higher diagnostic utility with Saliva:

36% more positives detected

11


While PCR kits vary in their performance, we observed that we received a higher diagnostic rate using saliva specimens (Figure 3). This could be due to the observation that SARS-CoV-2 titres are higher in saliva than in NP swabs16. Clinicians in USA, China, Japan, Singapore and Malaysia have reported that saliva samples are more accurate than nasopharyngeal swabs1,19,21,23,24,25.

Lucence, together with our partners, have validated SAFER™ for a variety of COVID-19 test kits and instrumentation (Table 3-5).

05 Compatible Test Kits and Instrumentation

Name of Instrument Manufacturer, Country

CFX96 Touch Real-Time PCR Detection System Biorad, USA

Table 3. Nucleic acid extraction and PCR kits which have been tested using clinical samples.

Category Name of Kit Manufacturer, Country

Nucleic Acid Extraction Kit Virus DNA/RNA Extraction Kit II VR300 Geneaid, Taiwan

Nucleic Acid Extraction KitQIAsymphony DSP Virus/Pathogen Midi Kit

Qiagen, Germany

SARS-CoV-2 qPCR kit Fortitude ver. 2.1 MiRXES, Singapore

SARS-CoV-2 qPCR kit Abbott Realtime SARS-CoV-2 Abbott, USA

SARS-CoV-2 qPCR kit Luna universal One-Step RT-qPCR kit NEB, USA

Nucleic acid extraction and

PCR kits

qPCR machine

Name of Automated Platform Manufacturer, Country

M2000 RealTime System Abbott, USA

QiaSymphony Qiagen, Germany

QIAstat-Dx Qiagen, Germany

GeneXpert Cepheid, USA

Automated platforms

Table 4. Automated platforms which have been tested using clinical samples.

Table 5. Lab instrumentation which have been tested using clinical samples.

12


SAFER™ provides an accurate, safe, painless, non-invasive method to collect specimens for SARS-CoV-2 testing. NOP saliva collected in SAFER™ is proven to be more accurate than the gold standard nasopharyngeal swabs by 36%.

Its virucidal properties allow the specimen to be safely transported over long distance to a central laboratory for testing. Temperature and nucleic acid stability will reduce the number of false negatives due to reagent failure. Health authorities and payors will also enjoy cost savings in labor, logistics, and storage. It is thus highly suited for use in mass surveillance for COVID-19.

07 Conclusion

A SAFER way to test for COVID-19

Lucence Diagnostics places a high emphasis in product and service quality. It has achieved ISO 13485:2016 certification for the manufacturing of in vitro medical devices. SAFER™ Products are manufactured according to ISO 13485:2016 and GMP (Good Manufacturing Practices) wholly in Singapore.

SAFER™ products are registered as Class A Medical Device with the Health Sciences Authority (HSA), Singapore. The Lucence clinical laboratory has achieved College of American Pathologists (CAP) and CLIA certifications, providing SARS-CoV-2 and cancer testing services.

06 Quality Management System

Our certifications

13


Ordering

Please complete the enquiry form at https://forms.gle/h6SWb6zmMpdRqhR99More information is available on the Lucence website:https://www.lucence.com/safer-sample

Ordering Information

Technical Support

International Physicians (Outside Singapore): SAFERTM is developed, designed, and sold exclusively for research use only. It is not a test for any disease. Collection and processing of saliva samples for any purpose shall be in accordance with local healthcare regulations. Lucence Diagnostics Pte. Ltd. is not responsible for any injury, loss or damages arising from use outside the intended use. Refer to www.lucence.com/terms-for-sale for Terms for Sale. © 2021 Lucence Diagnostics Pte. Ltd. All Rights Reserved.

SingaporeTel: +65 6909 0390Fax: +65 6725 0590

Hong KongTel: +852 5801 2340Fax: +852 3012 9866

Palo AltoTel: 888-LUCENCE (+1 888 582 3623)Fax: +1 650 618 8501

SuzhouTel: +86 150 5018 3364

Support is available from 9.00a.m. - 5.00p.m. (local), from Monday to Friday.

SAFERTM Products

Product Line Components

SAFER™ Total Saliva Specimen Collection Kit for Home-use (Cat. No.:SAFER-SAL-01-B)

2mL SAFER™ Stabilization Fluid /vial, a Funnel Collection Tube, and a Top Cap in a Clamshell Protective Case. Includes necessary packaging for triple bag protocol that keeps sample upright.

SAFER™ Clinic Saliva Specimen Collection Kit(Cat. No.: SAFER-SAL-01-P)

2mL SAFER™ Stabilization Fluid /vial, with a Funnel Collection Tube, and a Top Cap in a sealed pouch.

SAFER™ VTM Viral Transport Medium for use with NP/ OP swabs(Cat.No.: SAFER-VTM-01)

3mL SAFER™ Stabilization Fluid /vial only.

Our proprietary SAFERTM Stabilization Fluid is packaged into the following product lines:

14


08 About the Authors

Min-Han (Han) is the Founding CEO and Medical director of Lucence Diagnostics. He is also a visiting consultant at the Division of Medical Oncology, National Cancer Centre Singapore (NCCS), and a visiting scholar at the Faculty of Engineering, Waseda University, Japan. A trained medical oncologist and clinical cancer geneticist, Han obtained his MBBS and PhD from National University of Singapore. He completed his cancer specialist training at NCCS. In 2011, he joined the Agency of Science, Technology and Research (A*STAR) in Singapore to lead the Laboratory of Systems Medicine. Han started Lucence in 2016 to commercialise the liquid biopsy technology his lab developed at A*STAR. Han has published over 100 original research publications and filed 13 patents. He was elected Fellow of the Royal College of Physicians Edinburgh in 2015 and received the A*STAR Outstanding Scientist-Entrepreneur Award in 2018.

Dr. Min-Han TanCEO and Medical Director

[email protected]

Dr. Christopher WongVice President,

Medical Affairs (Asia Pacific)[email protected]

Dr Christopher Wong was a founding scientist of the Genome Institute of Singapore from 2001-2017 where he held many roles. As Chief Operating Officer of POLARIS (GIS), he set up the clinical infrastructure for NGS in Singapore. He was the founder of PathGEN Dx, which commercialised the pathogen chip invented at his GIS laboratory and developed PathSeq for pathogen detection using NGS. Prior to joining Lucence, he was Chief Executive Officer for Macrogen Asia Pacific, a genomics services company.

Dr Wong has a PhD (cancer pathology) from the University of Pennsylvania USA, B.S. (Music and Molecular Biology) from Beloit College, USA, and MBA (A*STAR scholarship) from Singapore Management University. Since 2017, he is also a molecular pathology inspector for the College of American Pathologists (CAP).

15


09 References

1. Yang Y, Yang M, Shen C, et al. Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of

2019-nCoV infections. medRxiv. 2020:2020.2002.2011.20021493.

2. Mangan D. The US economy can’t reopen without widespread coronavirus testing. Getting there will take a lot of work and money. CNBC. https://www.

cnbc.com/2020/04/16/coronavirus-testing-needs-to-be-widely-done-before-economy-reopens.html. Published 2020. Updated 16 Apr, 2020. Accessed 29

May, 2020.

3. Petersen E, Wasserman S, Lee SS, et al. COVID-19-We urgently need to start developing an exit strategy. Int J Infect Dis. 2020;96:233-239.

4. Peto J, Alwan NA, Godfrey KM, et al. Universal weekly testing as the UK COVID-19 lockdown exit strategy. Lancet. 2020;395(10234):1420-1421.

5. Farr C, Palmer A. Amazon is planning to build diagnostic labs as it ramps up Covid-19 testing for warehouse workers. CNBC. https://www.cnbc.

com/2020/06/09/amazons-plan-to-provide-covid-19-tests-to-warehouse-workers.html. Published 2020 Accessed Jun 13, 2020.

6. Gurman M. Apple Offering Covid-19 Testing to Staff Returning to Offices. Bloomberg. https://www.bloomberg.com/news/articles/2020-06-04/apple-

offering-covid-19-testing-to-staff-returning-to-offices. Published 2020. Updated Jun 13, 2020. Accessed.

7. Esbin MN, Whitney ON, Chong S, Maurer A, Darzacq X, Tjian R. Overcoming the bottleneck to widespread testing: A rapid review of nucleic acid testing

approaches for COVID-19 detection. RNA. 2020.

8. Lee D, Lee J. Testing on the Move South Korea’s rapid response to the COVID-19 pandemic. Transportation Research Interdisciplinary Perspectives.

2020:100111.

9. McCurry J. Test, trace, contain: how South Korea flattened its coronavirus curve. Guardian News & Media Limited. The Guardian Web site. https://www.

theguardian.com/world/2020/apr/23/test-trace-contain-how-south-korea-flattened-its-coronavirus-curve. Published 2020. Updated 23 Apr 2020.

Accessed.

10. Marty FM, Chen K, Verrill KA. How to Obtain a Nasopharyngeal Swab Specimen. N Engl J Med. 2020;382(22):e76.

11. Wai AKC, Kwok WO, Chan MS, Graham CA, Rainer TH. Patients’ perceptions of nasopharyngeal aspiration in the emergency department of a teaching

hospital in Hong Kong. Emergency medicine journal : EMJ. 2007;24(1):35-36.

12. Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens for COVID-19. National Center for Immunization and Respiratory Diseases

(NCIRD) , Division of Viral Diseases. https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html. Published 2020. Accessed May

28, 2020.

13. Woloshin S, Patel N, Kesselheim AS. False Negative Tests for SARS-CoV-2 Infection — Challenges and Implications. New England Journal of Medicine. 2020.

14. Administration UFaD. Transport Media Safety Risk - Use Compatible Transport Media with SARS-CoV-2 Tests that Use Bleach - Letter to Clinical Laboratory

Staff and Health Care Providers. https://www.fda.gov/medical-devices/letters-health-care-providers/transport-media-safety-risk-use-compatible-

transport-media-sars-cov-2-tests-use-bleach-letter. Published 2020. Accessed July 1, 2020, 2020.

15. Lee D. Coronavirus: Hong Kong’s screening system for airport arrivals holds lessons for travel industry in post-pandemic world. South China Morning

Post Publishers Ltd. South China Morning Post Web site. https://www.scmp.com/news/hong-kong/transport/article/3080088/coronavirus-hong-kongs-

screening-regime-airport-arrivals. Published 2020. Updated 15 April, 2020. Accessed.

16. Pan Y, Zhang D, Yang P, Poon LLM, Wang Q. Viral load of SARS-CoV-2 in clinical samples. The Lancet Infectious diseases. 2020;20(4):411-412.

17. To KK, Tsang OT, Chik-Yan Yip C, et al. Consistent detection of 2019 novel coronavirus in saliva. Clin Infect Dis. 2020.

18. To KK, Tsang OT, Leung WS, et al. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection

by SARS-CoV-2: an observational cohort study. Lancet Infect Dis. 2020;20(5):565-574.

19. Cheuk S, WONG Y, TSE H, et al. Posterior oropharyngeal saliva for the detection of SARS-CoV-2. Clinical Infectious Diseases. 2020.

20. Coronavirus (COVID-19) Update: FDA Authorizes First Diagnostic Test Using At-Home Collection of Saliva Specimens [press release]. US Food & Drug

Administration. May 16, 2020.

21. Teo AKJ, Choudhury Y, Tan IB, et al. Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19

infection. Scientific Reports, In Press.

22. Yu F, Qiu T, Zeng Y, et al. Comparative Evaluation of Three Preprocessing Methods for Extraction and Detection of Influenza A Virus Nucleic Acids from

Sputum. Frontiers in medicine. 2018;5:56-56.

23. Wyllie AL, Fournier J, Casanovas-Massana A, et al. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs.

medRxiv. 2020:2020.2004.2016.2006783.

24. Yokota I, Shane PY, Okada K, et al. Mass screening of asymptomatic persons for SARS-CoV-2 using saliva. medRxiv. 2020:2020.2008.2013.20174078.25.

25. Rao M, Rashid FA, Sabri FSAH, et al. Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2. Clin Infect Dis. 2020.

Lucence Diagnostics Pte LtdSingapore211 Henderson Road,#04-02, Henderson Industrial ParkSingapore 159552

Tel: +65 6592 5102Email: [email protected]

Publication Date: January, 2021LC-003-SG-EN-01 SAFER™ White Paper

Documents

Saliva Specimen Collection Kit - lucence.com€¦ · Saliva sampling is easy, painless and non-invasive Increased accuracy compared to nasopharyngeal (NP) swabs1 Less risky sampling