DIAGNOSTICS & SURVEILLANCE

 

Is there any new data with regards to SARS-CoV-2 transmission between asymptomatic individuals? (Previously discussed April 10, 2020.)

Answered in May 10, 2020 Newsletter

  • Previously, mathematical modelling studies from the Diamond Princess cruise ship (February 2020) demonstrated that 51.7% of all cases were pre-symptomatic and only 17.9% would never develop symptoms.(1)

  • Similarly, a study of obstetric cases in New York City demonstrated 87.9% (29/33) of cases were presymptomatic or asymptomatic.(2) Outbreaks at a long-term care skilled nursing facility(3) and a homeless shelter,(4) as well as testing of international arrivals,(5) have also demonstrated presymptomatic states accounting for a large proportion of positive cases.

  • The preponderance of these cases expose possible limitations of symptom-based surveillance, as case series have described both presymptomatic(6,7,8) and asymptomatic(9) transmission. Evidence modelled from transmission pairs suggests that 44% of secondary cases were infected during the presymptomatic phase of illnesses from index cases.(10) As a result, substantial presymptomatic transmission might also mean that current estimates of R0 are inaccurate.(11)

  • It has become clearer that transmission of SARS-CoV-2 does occur during the presymptomatic phase, but the extent of transmission by people who are never symptomatic remains unclear.

  1. Mizumoto K, Kagaya K, Zarebski A, Chowell G. Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020. Euro Surveill. 2020 Mar;25(10):2000180.  

  2. Sutton D, Fuchs K, D’Alton M, Goffman D. Universal Screening for SARS-CoV-2 in Women Admitted for Delivery. N Engl J Med. 2020 Apr 13. 

  3. Kimball A, Hatfield KM, Arons M, et al. Asymptomatic and Presymptomatic SARS-CoV-2 Infections in Residents of a Long-Term Care Skilled Nursing Facility –King County, Washington, March 2020. MMWR Morb Mortal Wkly Rep 2020;69:377–381.  

  4. Baggett TP, Keyes H, Sporn N, Gaeta JM. COVID-19 outbreak at a large homeless shelter in Boston: Implications for universal testing. medRxiv [Preprint]. 2020 Jan 1;2020.04.12.20059618.  

  5. Day M. Covid-19: four fifths of cases are asymptomatic, China figures indicate. BMJ. 2020;369.  

  6. Rothe C, Schunk M, Sothmann P, Bretzel G, Froeschl G, Wallrauch C, et al. Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany. N Engl J Med. 2020 Jan 30;382(10):970–1.  

  7. Tong Z-D, Tang A, Li K-F, Li P, Wang H-L, Yi J-P, et al. Potential Presymptomatic Transmission of SARS-CoV-2, Zhejiang Province, China, 2020. Emerg Infect Dis J. 2020;26(5):1052.  

  8. Ye F, Xu S, Rong Z, Xu R, Liu X, Deng P, et al. Delivery of infection from asymptomatic carriers of COVID-19 in a familial cluster. Int J Infect Dis. 2020 May 1;94:133–8. 

  9. Bai Y, Yao L, Wei T, Tian F, Jin D-Y, Chen L, et al. Presumed Asymptomatic Carrier Transmission of COVID-19. JAMA. 2020 Feb 21. 

  10. He X, Lau EHY, Wu P, Deng X, Wang J, Hao X, et al. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat Med. 2020.

  11. Aguilar JB, Faust JS, Westafer LM, Gutierrez JB. Investigating the Impact of Asymptomatic Carriers on COVID-19 Transmission. medRxiv [Preprint]. 2020 Jan 1;2020.03.18.20037994.

Do the national testing numbers reflect community surveillance? 

Answered in May 10, 2020 Newsletter

  • Nationally, the Public Health Agency of Canada tracks the number of tests, cases (probable and confirmed), the percent positivity, and deaths across all provinces daily. As of May 9th, Ontario has the highest gross number of tests performed at currently 402,761 with a percent positivity (PP) ~5%. In contrast, Quebec has run 276,787 tests, but has a PP of ~11%.(1) However, if you look at it from number of tests performed per 1,000,000 population, for Ontario that would be 27,650 and for Quebec 32,621. The province or territory that currently has the highest number of tests performed per 1,000,000 is Northwest Territories with 39,932.

  • Across Canada, the testing criteria are focused on symptomatic patients. In order to predict community spread, asymptomatic testing is an important consideration given the evolving understanding of presymptomatic and asymptomatic transmission. However, the limitation of the RT-PCR test means that it is an imperfect candidate for a surveillance test in this population. Some provinces such as Alberta have started testing asymptomatic workers and residents at outbreak sites. As of May 9th, they have 166,327 total tests (including symptomatic and asymptomatic cases) performed to date with a PP ~3%.(1) They have completed 38,050 tests per 1,000,000.

  1. Public Health Agency of Canada. Epidemiological summary of COVID-19 cases in Canada. Last updated May 7, 2020.

When a patient’s chest CT has ground glass opacities, what should be on your differential diagnosis, besides COVID-19? 

Answered in May 10, 2020 Newsletter

  • Ground-glass opacity (GGO) refers to an area of “haziness” on CT imaging of the lung that does not obscure underlying bronchial structures or pulmonary vessels.(1)

  • Although GGO has been associated with COVID-19, it is not pathognomonic. Broadly, the differential for GGO includes infection (including other viral pneumonia, bacteria, and fungi), chronic interstitial diseases, and acute alveolar disease (including pulmonary edema).(1)

  • However, GGO with bilateral lung involvement, multi-lobar involvement, and peripheral distribution increases specificity for COVID-19 pneumonia.(2)    

  1. Assar M, Amini B, et al. Ground-glass opacification [Internet]. [Accessed May 6, 2020].  

  2. Salehi S, Abedi A, Balakrishnan S, Gholamrezanezhad A. Coronavirus Disease 2019 (COVID-19): A Systematic Review of Imaging Findings in 919 Patients. Am J Roentgenol [Internet]. 2020 Mar 14;1–7.

What is the current status of point of care (POC) RT-PCT testing in Canada? Are there any alternative testing strategies currently under development? 

Answered in May 10, 2020 Newsletter

  • In Canada, the Cepheid Xpert Xpress SARS-CoV-2 has become mainstream for POC testing. Although several platforms have been approved for use during this pandemic, the Xpert has shown to have the lowest limit of detection.(1,2) The Xpert has been mainly implemented into diagnostic hospitals rather than provincial public health labs, as it cannot perform the volume of tests necessary for centralized provincial laboratories.(2) 

  • The Spartan Cube from Spartan Biosciences Inc. has recently had its Health Canada licence modified to research only (from diagnostic) as a POC RT-PCR test. This is due primarily to suboptimal validation studies and issues with specimen collection, mainly inhibitory concerns when viral transport media is utilized.(3)

  • The most recent platform to be approved by Health Canada for potential use as a rapid test is the BioFire® Respiratory 2.1 (RP2.1) Panel with SARS-CoV-2.(4) This test is currently being validated in Canada laboratories, but has the potential to be as rapid as the Xpert.

  • A recent study also discussed the potential of using a LAMP-Seq, a barcoded reverse-transcription loop-mediated isothermal amplification (RT-LAMP) protocol for testing.(5) This testing algorithm would utilize barcoded amplicons that could be shipped to a testing center, pooled and analyzed in massive quantities, potentially millions of samples per day. Albeit promising, it must be noted that this study has not been validated with clinical specimens.

  1. Zhen W, Smith E, Manji R, Schron D, Berry GJ. Clinical Evaluation of Three Sample-To-Answer Platforms for the Detection of SARS-CoV-2. J Clin Microbiol. doi: 10.1128/JCM.00783-20. 

  2. Moran A, Beavis KG, Matushek SM, Ciaglia C, Francois N, Tesic V, Love N. The Detection of SARS-CoV-2 using the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 Assays. J Clin Microbiol. doi: 10.1128/JCM.00772-20.

  3. CBC-COVID-19. Health Canada pauses regulatory approval for COVID-19 rapid test. May 03 2020. 

  4. Health Canada - Medical Devices. Diagnostic devices for use against coronavirus (COVID-19): List of authorized devices. May 08 2020.

  5. Schmid-Burgk J L, Li D, Feldman D, Słabicki M, Borrajo J, Strecker J, Cleary B, Regev A, Zhang F. LAMP-Seq: Population-Scale COVID-19 Diagnostics Using a Compressed Barcode Space. Biorxiv [Preprint]. 2020 April 08.

What is the diagnostic use of serology for SARS-CoV-2? Can it be used to measure individual immunity? 

Answered in May 1, 2020 Newsletter

  • The use of serology to measure SARS-CoV-2 antibodies is debated among countries worldwide. At this time, Canada has decided to not utilize the presence of IgG or IgM as a diagnostic tool to rule out COVID-19.(1) This is primarily due to the delay between symptom onset and serological detection,(2,3,4) suggesting that testing would be less reliable in the first week after symptom onset. Also, cross-reactivity of IgG against other endemic coronaviruses does occur,(3) leading to false positivity.

  • The detection of IgG and/or IgM does not correlate with individual immunity. A plaque reduction assay is critical to determining the percentage of neutralizing antibodies in a specimen(4) (i.e. antibodies that can actually eliminate a viral pathogen). Canada’s National Microbiology Laboratory (NML) is currently in the process of validating such assays, but these assays require biosafety level 3 facilities and are highly laborious to perform. In time, ELISA’s that detect IgG and/or IgM may be used as a measure of seroprevalence and may act as an imperfect surrogate for immunity.

  • Notably, in a study of 175 patients with mild illness, 30% did not develop adequate quantities of neutralizing antibodies either during or after infection with SARS-CoV-2.(4) Furthermore, a preprint study showed that prior exposure to other human coronaviruses does not confer any discernible cross-reactivity to SARS-CoV-2.(5)

  1. Canadian Public Health Laboratory Network Best Practices for COVID-19 V1.0 APRIL 23, 2020 Respiratory Virus Infections Working Group.

  2. Government of Canada. Serology test for use against COVID-19. Date modified April 24, 2020. Accessed April 28, 2020.

  3. Wölfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Müller MA, et al. Virological assessment of hospitalized patients with COVID-2019. Nature. 2020;

  4. Wu F, Wang A, Liu M, Wang Q, Chen J, Xia S, et al. Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. medRxiv [preprint]. 2020 Jan 1;2020.03.30.20047365.

  5. Amanat F, Stadlbauer D, Strohmeier S, Nguyen T, Chromikova V, McMahon M, et al. A serological assay to detect SARS-CoV-2 seroconversion in humans. medRxiv [preprint]. 2020 Jan 1;2020.03.17.20037713.

What is the viral structure of SARS-CoV-2? How is the angiotensin-converting enzyme 2 (ACE2) involved in the pathophysiology of COVID-19 compared to SARS?

Answered in May 1, 2020 Newsletter

  • SARS-CoV-2 is an enveloped single-stranded RNA virus. Starting from the outside of the virion towards the center, the key proteins used in diagnostic testing include:(1

    • Spike (S) proteins, giving its classical “crown” appearance in images taken by electron microscopy

    • Envelope (E) proteins

    • Phosphorylated nucleocapsid (N) proteins that enclose the central RNA

  • SARS-CoV specifically targeted ACE2 found in the lower respiratory tract (LRT),(2) even though higher expression of ACE2 has been demonstrated in the nasal epithelial cells.(3) The virus uses ACE2 as a receptor for cell entry. ACE2 is also found throughout the body, with highest levels appearing in the small intestine, testis, kidneys, heart, thyroid, and adipose tissue.(4)  

  • SARS-CoV-2 has a broader clinical picture, affecting both the LRT and the upper respiratory tract (URT). One hypothesis suggests that SARS-CoV-2’s binding interface contains more Van der Waals forces and hydrogen bonds with ACE2, which increases its likelihood of binding to ACE2 and thereby allowing for cell entry.(5)

  • Another theory involves the presence of an unique polybasic cleavage site within SARS-CoV-2, which may improve pathogenicity by synthesizing added O-linked glycans.(6) These O-linked glycans may function to shield key residues on the S protein and allow for immunoevasion.

  1. Jin Y, Yang H, Ji W, Wu W, Chen S, Zhang W et al. Virology, Epidemiology, Pathogenesis, and Control of COVID-19. Viruses. 2020;12(4):372. 

  2. Shang J, Ye G, Shi K, Wan Y, Luo C, Aihara H et al. Structural basis of receptor recognition by SARS-CoV-2. Nature. 2020. 

  3. Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature Medicine. 2020. 

  4. Li M, Li L, Zhang Y, Wang X. Expression of the SARS-CoV-2 cell receptor gene ACE2 in a wide variety of human tissues. Infectious Diseases of Poverty. 2020;9(1). 

  5. Shang J, Ye G, Shi K, Wan Y, Luo C, Aihara H et al. Structural basis of receptor recognition by SARS-CoV-2. Nature. 2020.

  6. Andersen K, Rambaut A, Lipkin W, Holmes E, Garry R. The proximal origin of SARS-CoV-2. Nature Medicine. 2020;26(4):450-452.

During the national shortage of specimen collection supplies, what alternatives are available for diagnostic use? 

Answered in May 1, 2020 Newsletter

  • Nationally there has been an ongoing shortage of nasopharyngeal (NP) swabs for many weeks, as described in our March 21, 2020 newsletter. This is primarily due to limitations in production, supply-chain disruptions and swab contaminations. 

  • As a result, various countries have adopted strategies to overcome this concern. Recently, the provincial lab in Manitoba has utilized ethylene oxide to sterilize many of their contaminated NP swabs. Ethylene oxide has been previously shown to be effective in decontamination.(1) 

  • Canada, USA and other countries are also exploring 3D printed swabs as an alternative to the traditionally used flocked swab. These could be easily mass-produced,(2,3) but their diagnostic utility is still to be determined. 

  • Very recently, the Canada’s National Microbiology Laboratory (NML) has shown that non-standard swabs (wood, cotton and 3D-printed plastic), previously thought to be inhibitory to RT-PCR, had Ct values equitable to standard NP swabs (note: data being submitted for publication).

  1. Wilson-Wilde L, Yakovchyts D, Neville S, Maynard P, Gunn P. Investigation into ethylene oxide treatment and residuals on DNA and downstream DNA analysis. Science & Justice. 2017; 57(1): 13-20.  

  2. Callahan CJ, Lee R, Zulauf KE, Tamburello L, Smith KP, Previtera J, Cheng A, Green A, Azim AA, Yano A, Doraiswami N, Kirby JE, Arnaout R. Rapid Open Development and Clinical Validation of Multiple New 3D-Printed Nasopharyngeal Swabs in Response to the COVID-19 Pandemic. medRxiv [preprint]. April 17, 2020. 

  3. Allen K. Ontario received 100,000 contaminated, unusable swabs for COVID-19 tests. The Toronto Star. April 10, 2020.

What is the probability of false negative SARS-CoV-2 testing?

Answered in April 24, 2020 Newsletter

  • Accuracy of RT-PCR is influenced by a number of factors such as the platforms and protocols used,(1) disease severity,(2) specimen type,(3) and time of collection.(3,4,5) For further details on each of these factors, please see March 27,2020 newsletter.

  • Generally, the sensitivity of RT-PCR for SARS-CoV-2 is highest when performed as close as possible to time of symptom onset.(3,4) However, false negatives can still occur, particularly in the week immediately following symptom onset. False negatives also seem to be more common later in the disease course as symptoms begin to wane. This may impact the practice of serial monitoring for viral clearance and may account for the observed “recurrence” in those thought to have initially cleared the virus.(5,6)

  1. Pan Y, Long L, Zhang D, Yan T, Cui S, Yang P, et al. Potential false-negative nucleic acid testing results for Severe Acute Respiratory Syndrome Coronavirus 2 from thermal inactivation of samples with low viral loads. Clin Chem. 2020 Apr 4. 

  2. Tahamtan A, Ardebili A. Real-time RT-PCR in COVID-19 detection: issues affecting the results. Expert Rev Mol Diagn. 2020 Apr 16;p1–2. 

  3. Wikramaratna P, Paton RS, Ghafari M, Lourenco J. Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR. medRxiv [preprint]. 2020 Jan 1;2020.04.05.20053355. 

  4. Kucirka L, Lauer S, Laeyendecker O, Boon D, Lessler J. Variation in False Negative Rate of RT-PCR Based SARS-CoV-2 Tests by Time Since Exposure. medRxiv [preprint]. 2020 Jan 1;2020.04.07.20051474. 

  5. Li Y, Yao L, Li J, Chen L, Song Y, Cai Z, et al. Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19. J Med Virol. 2020 Mar 26. 

  6. Xiao AT, Tong YX, Zhang S. False-negative of RT-PCR and prolonged nucleic acid conversion in COVID-19: Rather than recurrence. J Med Virol. 2020 Apr.

Why is viral isolation in cell culture important? What information does it give us compared to RT-PCR?

Answered in April 24, 2020 Newsletter

  • SARS-CoV-2 is most commonly grown in the Vero-E6 cell line using minimum essential medium or Dulbecco's modified eagle medium and incubated at 37°C. Cytopathic effects have been observed 72 hours post infection of Vero-E6 cells.(1,2,3,4)

  • Isolation of the virus is critical for the development of new diagnostic tests and therapeutics including:

    • Drug susceptibility testing against SARS-CoV-2

    • Vaccine development for active immunization

    • Development of plaque reduction neutralization assays to determine long-term immunity

    • Validation of RT-PCR assays for SARS-CoV-2 detection

  1. Harcourt S, Tamin A, Lu X, Kamili S, Kumar S, et al. Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient. bioRxiv [preprint]. 2020 bioRxiv 2020.03.02.972935 [posted 2020 Mar 17]: [16p.]. 

  2. Kim JM, Chung YS, Jo HJ, Lee NJ, Kim MS, et al. Identification of coronavirus isolated from a patient in Korea with COVID-19. Osong Public Health Res Perspect. 2020; 11(1):3-7. 

  3. Banerjee A, Nasir JA, Budylowski P, Yip L, Aftanas P, et al. Isolation, sequence, infectivity and replication kinetics of SARS-CoV-2. bioRxiv [preprint]. 2020 bioRxiv 2020.04.11.037382 [posted 2020 Apr12]: [22p.]. 

  4. Haveri A, Smura T, Kuivanen S, Österlund P, Hepojoki J, et al. Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020. Euro Surveill. 2020; 25(11): 2000266.

What are the consequences on diagnostic laboratory testing when public resources are focused on SARS-CoV-2?

Answered in April 24, 2020 Newsletter

  • During viral pandemics, it is expected that diagnostic laboratories alter routine testing protocols and infrastructure in response to the atypical demands placed on them, irrespective of testing volume.(1,2)

  • For instance, across Canadian laboratories, many routine tests that are normally run once a week are now being run every two weeks to allow for more timely SARS-CoV-2 testing. In Manitoba, assays performed mostly for academic purposes have been suspended.

  • Besides the changes made by diagnostic laboratories, there has been a significant decrease in sample volumes for many standard tests at tertiary hospitals from January to March, a trend that is anticipated to continue in April.

  1. Crawford JM, Stallone R, Zhang F, Gerolimatos M, Korologos DD, Sweetapple C, de Geronimo M, Dlugacz Y, Ginocchio CC. Laboratory surge response to pandemic (H1N1) 2009 outbreak, New York City metropolitan area, USA. Emerg Infect Dis. 2010 Jan; 16(1): 8-13.  

  2. Isaac-Renton JL, Chang Y, Prystajecky N, Petric M, Mak A, Abbott B, Paris B, Decker KC, Pittenger L, Guercio S, Stott J, Miller JD. Use of Lean response to improve pandemic influenza surge in public health laboratories. Emerg Infect Dis. 2012 Jan; 18(1): 57-62.

How is SARS-CoV-2 detected by RT-PCR (reverse transcriptase - polymerase chain reaction)?

Answered in April 17, 2020 Newsletter

  • Shortly after sequencing of SARS-CoV-2 was completed in Wuhan, China(1) the WHO determined several core gene targets that are currently used in laboratory developed testing (LDTs): RNA-dependant RNA polymerase (RdRp), envelope (E), nucleocapsid (N), and open reading frame (ORF1) genes.(2) 

  • Detection of these genes constitutes a cycle threshold (Ct) that is used to quantitate each PCR assay. Studies from centers in Wuhan, China have reported Ct values in symptomatic patients ranging from 16-38,(3,4) with no significant differences between symptomatic and asymptomatic patients.(5) It is important to note that RT-PCR is a semi-quantitative test (a set Ct value determines whether a result is positive or negative), while the reported results is qualitative (positive, negative, inconclusive).

  • Initially, detection of 2-3 gene targets was required to confirm positivity, but with proper validation, most countries have adopted a single target approach thus simplifying the test and reducing the required reagents.(6) The use of sample pooling has also dramatically increased testing capacity in most centres, especially for community monitoring.(7) 

  • In recent months, many companies have developed platforms to automate LDTs and improve throughput. Canada has authorized 13 PCR-based detection systems to date.(8) The Spartan Cube was most recently approved by Health Canada and it may help provide rapid diagnostics that would be particularly helpful for remote locations.(9) Scientists at Canada’s National Microbiology Laboratory are currently validating its diagnostic use. 

  1. Sah R, Rodriquez-Morales AJ, Jha R, Chu DKW, Gu H, et al. Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal. 2020; 9(11);1-3.

  2. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance. 2020;25(3):1–8. 

  3. Zou L, Ruan F, Huang M, Liang L, Huang H, et al. SARS-CoV-2 viral load in upper respiratory specimens of infected patients. NEJM. 2020;382(12):1177-179. 

  4. Xu T, Chen C, Zhu Z, Cui M, Chen C, et al. Clinical features and dynamics of viral load in imported and non-imported patients with covid-19. Int J Infect Dis. 2020; Mar 12]: [21p.].

  5. Kimball A, Hatfield KM, Arons M, James A, Taylor J, et al. Asymptomatic and presymptomatic SARS-CoV-2 infection in residents of a long-term care skilled nursing facility- King County, Washington, March 2020. MMWR Morb Mortal Wkly Rep. 2020; 69(13):377-381. 

  6. World Health Organization. Laboratory testing for coronavirus disease 2019 (‎‎COVID-19)‎‎ in suspected human cases: interim guidance. WHO, 2020.

  7. Hogan CA, Sahoo MK, Pinsky BA. Sample Pooling as a Strategy to Detect Community Transmission of SARS-CoV-2 [published online ahead of print April 6, 2020]. JAMA. 

  8. Health Canada - Medical Devices. Diagnostic devices for use against coronavirus (COVID-19): List of authorized products. April 17, 2020.

  9. Spartan Bioscience Receives Health Canada Approval for Fast, Portable COVID-19 Test.

Are any inflammatory markers indicative of prognosis in COVID-19?​

Answered in April 17, 2020 Newsletter

  • Studies have shown the CRP, ESR, and ferritin are significantly higher in severe cases of COVID-19 than moderate cases.(1,2,5)

  • Elevated IL-6 predicts clinical deterioration and correlates with the development of “cytokine storm”.(3,4,5) This is why anti-IL-6 monoclonal antibodies are being considered in some clinical trials for treatment of COVID-19 (see March 27, 2020 newsletter).

  • It is also worth noting that increased procalcitonin values have been associated with severe cases. It is not yet clear whether this is reflective of a bacterial superinfection.(5,6)

  1. Lippi G, Plebani M. Laboratory abnormalities in patients with COVID-2019 infection. Clin Chem Lab Med. 2020;(0):20200198.

  2. Guan W, Ni Z, Hu Y, Liang W, Ou C, He J, et al. Clinical Characteristics of Coronavirus Disease 2019 in China. N Engl J Med. 2020 Feb 28. 

  3. Ulhaq ZS, Soraya GV. Interleukin-6 as a potential biomarker of COVID-19 progression. Med Mal Infect. 2020 Apr 4;S0399-077X(20)30088-3.  

  4. Wan S, Yi Q, Fan S, Lv J, Zhang X, Guo L, et al. Characteristics of lymphocyte subsets and cytokines in peripheral blood of 123 hospitalized patients with 2019 novel coronavirus pneumonia (NCP). medRxiv [preprint]. 2020 Jan 1;2020.02.10.20021832.  

  5. Chen G, et al. Clinical and immunological features of severe and moderate coronavirus disease 2019. J Clin Invest. 2020. 

  6. Lippi, G., & Plebani, M. (2020). Procalcitonin in patients with severe coronavirus disease 2019 (COVID-19): A meta-analysis. Clinica chimica acta; international journal of clinical chemistry, 505, 190-191.

Does viral load correlate with symptoms or infectivity?

Answered in April 10, 2020 Newsletter

  • Initial studies suggest that severe cases of COVID-19 are associated with higher viral loads(1) and longer lasting viral detection as compared to mild cases. 90% of mild cases are PCR-negative at 10 days post symptom onset.(2)

  • Contrary to this, recent work has suggested that in mild cases of COVID-19, viral RNA detection may peak 3-8 days post symptom onset.(3) As well, sputum samples remained positive longer than upper respiratory specimens.

  • Viral load detection in asymptomatic patients has not been thoroughly studied. Carriage and transmission of SARS-COV-2 have been described previously, but their contribution to population prevalence of SARS-CoV-2 is not clear.(4,5,6)

  1. Li R, Pei S, Chen B, Song Y, Zhang T, Yang W et al. Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2). Science. 2020.

  2. Liu Y, Yan L, Wan L, Xiang T, Le A, Liu J et al. Viral dynamics in mild and severe cases of COVID-19. The Lancet Infectious Diseases. 2020.

  3. Wölfel R, Corman V, Guggemos W, Seilmaier M, Zange S, Müller M et al. Virological assessment of hospitalized patients with COVID-2019. Nature. 2020.

  4. Hu Z, Song C, Xu C, Jin G, Chen Y, Xu X, et al. Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing, China. Sci China Life Sci. 2020.

  5. Bai Y, Yao L, Wei T, Tian F, Jin D-Y, Chen L, et al. Presumed Asymptomatic Carrier Transmission of COVID-19. JAMA. 2020 Feb 21.

  6. Dong X, Cao Y, Lu X, Zhang J, Du H, Yan Y, et al. Eleven faces of coronavirus disease 2019. Allergy. 2020 Mar 20;n/a(n/a).

Why are we not screening asymptomatic people? Can healthcare workers (HCW) become infected from asymptomatic patients? 

Answered in April 10, 2020 Newsletter

  • Truly asymptomatic patients (never develop symptoms) may be a cause of potential super-spreading since presymptomatic patients are likely to self-isolate once symptoms develop.(1,2,3)

  • Although less comparable to urban settings, mathematical modelling studies from the infamous Diamond Princess cruise-ship (Feb 2020) demonstrated that 51.7% of all cases were presymptomatic, and only 17.9% never developed symptoms.(4) 

  • Currently, there have been no documented cases of transmission to a HCW from a truly asymptomatic COVID-19 patient. Still, literature suggests that transmission can and does occur from both asymptomatic and presymptomatic patients, although this is likely the minority of cases.(5,6)

 

  1. Han Y, Yang H. The transmission and diagnosis of 2019 novel coronavirus infection disease (COVID-19): A Chinese perspective [published online ahead of print March 6, 2020]. J Med Virol.

  2. Nishiura H, Kobayashi T, Suzuki A, et al. Estimation of the asymptomatic ratio of novel coronavirus infections (COVID-19) [published online ahead of print March 13, 2020]. Int J Infect Dis.

  3. Li C, Ji F, Wang L, Wang L, Hao J, Dai M, Liu Y, Pan X, Fu J, Li L, Yang G, Yang J, Yan X, Gu B. Asymptomatic and Human-to-Human Transmission of SARS-CoV-2 in a 2-Family Cluster, Xuzhou, China [published online ahead of print March 31, 2020]. Emerg Infect Dis. 2020;26(7).

  4. Mizumoto K, Kagaya K, Zarebski A, Chowell G. Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020. Euro Surveill. 2020 Mar;25(10):2000180.

  5. Bai Y, Yao L, Wei T, Tian F, Jin DY, et al. Presumed asymptomatic carrier transmission of COVID-19. JAMA. 2020;jama.2020.2565.

  6. Hu Z, Song C, Xu C, Jin G, Chen Y, et al. Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing, China. Sci China Life sci. 2020;s11427-020-1661-4.

What role does serology play in monitoring COVID-19 disease progression and population surveillance? Has SARS-CoV-2 serology been applied to "return to work" policies?

Answered in April 3, 2020 Newsletter

  • IgM and IgG antibodies against SARS-CoV-2 may be detected as early as 2-4 days post symptom onset.1 However, seroconversion usually occurs after 10-13 days post symptom onset for IgM and 12-14 days for IgG.(1,2,3,4)

  • Severe COVID-19 has been associated with an early and strong IgM response.(5,6)

  • In one study, only 4.3% of close contacts of COVID-19 cases with negative nasopharyngeal RT-PCR were positive for IgG and/or IgM.(1)

  • Serology may play a role in population surveillance and “return to work” policies, but this has not yet been studied nor implemented.

  1. Long Q, Deng H, Chen J, Hu J, Liu B, et al. Antibody responses to SARS-CoV-2 in COVID-19 patients: the perspective application of serological tests in clinical practice. medRxiv [preprint]. 2020 medRxiv 2020.03.18.20038018 [posted 2020 Mar 20; cited 2020 April 1]: [20 p.].

  2. Guo L, Ren L, Yang S, Meng X, Chang D, et al. Profiling early humoral response to diagnose novel coronavirus disease (COVID-19). Clin Infect Dis. 2020; ciaa310.

  3. Lou B, Li T, Zhen S, Su Y, Li Z, et al. Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset. medRxiv [preprint]. 2020 medRxiv 2020.03.23.20041707 [posted 2020 Mar 27; cited 2020 April 1]: [26 p.].

  4. Zhao J, Yuan Q, Wang H, Liu W, Liao X, et al. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019. medRxiv [preprint]. 2020 medRxiv 2020.03.02.20030189 [posted 2020 Mar 3; cited 2020 April 1]: [28 p.].

  5. Tan W, Lu Y, Zhang J, Wang J, Dan Y, et al. Viral kinetics and antibody responses in patients with COVID-19. medRxiv [preprint]. 2020 medRxiv 2020.03.24.20042382 [posted 2020 Mar 26; cited 2020 April 1]: [29 p.].

  6. Wang Z, Li H, Li J, Yang C, Guo X, et al. Elevated serum IgM levels indicate poor outcome in patients with coronavirus disease 2019 pneumonia: a retrospective case-control study. medRxiv [preprint]. 2020 medRxiv 2020.03.22.20041285 [posted 2020 Mar 27; cited 2020 April 1]: [16 p.].

What Point of Care Testing (POCT) is currently available for SARS-CoV-2?

Answered in April 3, 2020 Newsletter

  • The use of POCT is ideal for emerging outbreaks due to decreased turn-around time (0.5-1 hours), technical simplicity, and portability which would be particularly beneficial for rural and remote settings.(1)

  • Currently, the only product approved for use in Canada is the Gene Xpert Xpress SARS-CoV-2, with six other systems pending approval.(2)

  • This test, among most others on the market, utilizes a nucleic acid amplification approach (e.g.: RT-PCR).(3)

  1. Kozel T R & Burnham-Marusich A R. Point-of-Care Testing for Infectious Diseases: Past, Present, and Future. Jour. Clin. Micro. 2017, 55(8).

  2. Health Canada - Medical Devices. Diagnostic devices for use against coronavirus (COVID-19): List of authorized products. April 1 2020.

  3. Cepheid, Gene Xpert. Xpert® Xpress SARS-CoV-2 - For Use Under an Emergency Use Authorization (EUA) Only. Product Insert. March 2020.

What laboratory findings are consistent with COVID-19?

Answered in April 3, 2020 Newsletter

  • The most frequent laboratory abnormalities include: lymphopenia, increased LDH, increased CRP and ESR, increased D-dimer, anemia, and decreased serum albumin.(1,2)

  • In addition to the derangements above, severe cases are marked by: thrombocytopenia, transaminase elevation, and increased procalcitonin. However, the latter likely indicates bacterial superinfection.(1,3)

  • A minority of COVID-19 cases are associated with myocarditis and increased troponin. 

  • In one study, 15 of 21 (71%) patients with fatal COVID-19 fulfilled the criteria for DIC with increased fibrinogen degradation products.(4)

  1. Lippi G, Plebani M. Laboratory abnormalities in patients with COVID-2019 infection. Clin Chem Lab Med. 2020;(0):20200198.

  2. Guan W, Ni Z, Hu Y, Liang W, Ou C, He J, et al. Clinical Characteristics of Coronavirus Disease 2019 in China. N Engl J Med. 2020 Feb 28.

  3. Han H, Yang L, Liu R, Liu F, Wu K, Li J, et al. Prominent changes in blood coagulation of patients with SARS-CoV-2 infection. Clin Chem Lab Med. 2020;(0):20200188.

  4. Tang N, Li D, Wang X, Sun Z. Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia. J Thromb Haemost. 2020 Apr 1;18(4):844–7.

Can saliva be used as a specimen to detect SARS-CoV-2?

Answered in March 27, 2020 Newsletter

  • Non-invasive and does not require healthcare worker to collect.(1)

  • So far the data available shows sensitivity may be as high as 91.7% to detect SARS-CoV-2 in saliva, but this was based on a series of only 12 patients.(1)

 

  • Throat wash and saliva specimens have previously been shown to outperform nasopharyngeal aspirate (NPA) in detection of respiratory viruses in general.(3)

 

  • Currently no widespread clinical use and requires further studies to determine suitability for SARS-CoV-2 detection compared to other methods.

  1. To KK-W, Tsang OT-Y, Yip CC-Y, Chan K-H, Wu T-C, Chan JM-C, et al. Consistent Detection of 2019 Novel Coronavirus in Saliva. Clin Infect Dis. 2020 Feb 12.

  2. Wang W-K, Chen S-Y, Liu I-J, Chen Y-C, Chen H-L, Yang C-F, et al. Detection of SARS-associated coronavirus in throat wash and saliva in early diagnosis. Emerg Infect Dis. 2004 Jul;10(7):1213–9. 

  3. To KK-W, Tsang OT-Y, Leung W-S, Tam AR, Wu T-C, Lung DC, 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 Mar 24.

What is the ideal sample type based on clinical syndrome?

Answered in March 27, 2020 Newsletter

  • Respiratory samples are the most sensitive for SARS-CoV-2 detection, with lower tract specimens BAL and sputum having highest positivity rates, 80-93% and 75-89%, respectively.(1,2,3)

  • For upper tract specimens, nasopharyngeal swabs showed higher positivity rates (63-73%) over oropharyngeal swabs (32-60%).(2,3)

  • Anal swabs (25-39% positivity) appear to remain PCR-positive ~2 days longer than oral swabs.(2,4) SARS-CoV-2 has also been detected (29-35% positivity)(2,3) in stool up to 3 weeks after the onset of symptoms(5), suggesting possibility of transmission by fecal-oral route. However, note virus did not grow in cell culture.(5)

  • Other specimens including blood, urine, amniotic fluid and breast milk have little to no detectable viral RNA.(1,2,6)

  1. Liu R, Han H, Liu F, Lv Z, Wu K, et al. Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in Wuhan, China, from Jan to Feb 2020. Clinica Chimica Acta. 2020 June, 505. 

  2. Wang W, Xu Y & Gao R. Detection of SARS-CoV-2 in Different Types of Clinical Specimens. JAMA. 2020 March.

  3. Yang Y, Yang M, Shen C, Wang F, Yuan J, Li J, Zhang M, et al. Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. MedRxiv (Pre-Print), 2020 February.

  4. Yun L, Shui-Bao X, Yi-Xiao L, Di T, Zhao-Qin Z, et al. Persistence and clearance of viral RNA in 2019 novel coronavirus disease rehabilitation patients. Chin. Med. Jour, 2020 February.

  5. Wölfel R, Corman V M, Guggemos W, Seilmaier M, Zange S, et al. Virological assessment of hospitalized cases of coronavirus disease 2019. MedRxiv (Pre-Print), 2020 March.

  6. Chen H, Huo J, Wang C, Luo F, et al. Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records. Lancet, 2020, 395.

How are specimens stored before testing?

Answered in March 27, 2020 Newsletter

  • With a national shortage of universal transport media (UTM), labs across the country have adopted to in-house made viral transport media (VTM).

  • Other suitable alternatives, including saline(1), alcohol(2,3) and even dry flocked swabs(1,2), have been used in the past for many respiratory viruses with similar viral RNA recovery rates to UTM.

  1. Druce J, Garcia K, Tran T, Papadakis G & Birch C. Evaluation of Swabs, Transport Media, and Specimen Transport Conditions for Optimal Detection of Viruses by PCR. Jour Clin Micro. 2012, 50(3).

  2. Luinstra K, Petrich A, Castriciano S, Ackerman M, et al. Evaluation and Clinical Validation of an Alcohol-Based Transport Medium for Preservation and Inactivation of Respiratory Viruses. Jour Clin Micro. 2011, 49(6).

  3. World Health Organization. Collecting, preserving and shipping specimens for the diagnosis of avian influenza A(H5N1) virus infection. Guide for field operations. WHO, 2006.

How useful is a chest CT scan in detecting COVID-19?

Answered in March 27, 2020 Newsletter

  • In a study of 1,014 COVID-19 cases from China, CT scans had a sensitivity of 97%, specificity of 25%, positive predictive value of 65%, and negative predictive value of 83%.(1)

  • When serial RT-PCRs were obtained, initial positive chest CTs were consistent with COVID-19 (60-93%) 6-8 days after symptom onset.(1)

  • CT scans from 0-2 days less sensitive (44%) than 3-12 days (91-96%) after symptom onset.(2)

  1. Ai T, Yang Z, Hou H, et al. Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases. Radiology. 2020 Feb 26;200642.

  2. Bernheim A, Mei X, Huang M, et al. Chest CT Findings in Coronavirus Disease-19 (COVID-19): Relationship  to Duration of Infection. Radiology. 2020 Feb 20;200463.

In the context of a growing national shortage of supplies for sample collection and testing reagents, what are the current guidelines for testing?

Answered in March 21, 2020 Newsletter

  • Most countries are screening symptomatic individuals (fever, cough, LRTI) with epidemiologic risk factors (<14 day international travel, including US)(1,2,3).

  • In Manitoba, priority testing is being given to ICUs, outbreaks, Northern RHA residents, and healthcare workers.

  • At the national level, investigations are ongoing for alternative testing strategies (specimen type, swab type, media, PCR protocols, etc.).

  1. Bajema K, Oster A, McGovern O, et al. Persons Evaluated for 2019 Novel Coronavirus - United States, January 2020. Morbidity and Mortality Weekly Report (CDC). 2020;69(6).

  2. Bordi L, Nicastri E, Scorzolini L, et al. Differential diagnosis of illness in patients under investigation for the novel coronavirus (SARS-CoV-2), Italy, February 2020. Euro Surveill. 2020;25(8).

  3. Chinese Centre for Disease Control and Prevention. Partie du diagnostic et traitement: COVID-19 prevention et le controle des. Chinese Centre for Disease Control and Prevention; 2020 p.1-3.

 

 

What is the effectiveness of screening?

Answered in March, 21, 2020 Newsletter

  • Screening ≠ Testing

  • Current data suggests that arrival and/or departure screening (mainly looking for fever) is likely to detect only 30-53% of true cases.(1,2)

  • Contact tracing is crucial to containment and may help identify asymptomatic patients. In a cohort of 24 asymptomatic COVID-19 positive individuals identified by contact tracing, 70.8% had abnormal chest CT findings and 16.7-33.4% had lymphopenia and/or leukopenia.(3)

  1. Gostic K, Gomez A, Mummah R, et al. Estimated effectiveness of symptom and risk screening to prevent the spread of COVID-19. eLife. 2020;9.  

  2. Quilty B, Clifford S, CMMID nCoV working group, Flasche S, Eggo R. Effectiveness of airport screening at detecting travellers infected with novel coronavirus (2019-nCoV). Euro Surveill. 2020;25(5). 

  3. Hu Z, Song C, Xu S, et al. Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing, China. Science China Life Sciences. 2020;63.