Autopsy case room for forensic and hospital autopsies


Guidelines updated October 9, 2020.

Modifications are highlighted

COVID-19 Testing Policy and Guidelines

This document is adopted from the Public Health Ontario guidelines and other Health Unit guideline resources to instruct COVID-19 testing process and practice for the Erie St. Clair and South West health region. The Testing Policy Advisory Council convenes regularly to review and update the content of these guidelines, as well as direct the testing priorities in situations of swab and other resource limitations.

All swabs for the Erie St. Clair and South West region are being allocated through the Ministry of Health to HMMS for local dissemination to health units and hospitals. Health units and hospitals can now use the online order form below to request a swab allocation. If you are in a community organization, please contact your local public health unit who is responsible for ordering and distributing swabs for your region. To all organizations, please monitor your inventory closely so that your request is placed prior to a depletion of stock. To access the online order form, please click on the link below:

Click here to order swabs.

Who to test:

Refer to the COVID-19 Provincial Testing Guidance Update on the Ministry of Health website for descriptions of individual categories and testing guidance. Click here for more information.

Effective September 24, 2020, the Ministry of Health recommends that low risk, asymptomatic individuals should not be considered for testing.


Testing Priorities

The following prioritization framework should be used by all regional stakeholder groups, based in hospital and community health, to inform operational decision making when faced with constrained resources.


Testing Priorities

Testing Guidance to Support Isolation and De-escalation Process for Persons Under Investigation

The recommendations outlined below are intended to guide COVID-19 testing requirements appropriate for isolation and de-escalation practices, including those for healthcare workers returning to work. For more detailed guidance on testing, quarantine, and self-isolation, refer to your local Health Unit and Institutional document. Isolation and de-escalation should always be conducted in consultation with local Medical Officers of Health, Infection Prevention and Control, or Occupational Health and Safety, as relevant.


Patients in Hospital and other Institutions

  1. Symptomatic with positive test for COVID-19
  • Isolation required until two negative tests are obtained 24 hours apart
  • Retesting is not required if patient discharged home and still within 14-day self-isolation period
  • Retesting criteria for patients discharged from hospital to long-term care facilities or other institutions should be directed by local guidelines
  1. Symptomatic with negative test for COVID-19
  • Retesting only required if symptoms change, persist, or worsen

Healthcare Workers and Return to Work

  1. Symptomatic with positive test for COVID-19
  • Self-isolation for a minimum of 14 days from symptom onset
  • For work-self-isolation, two negative tests obtained 24 hours apart are necessary if a clearance swab policy is locally endorsed. Continue to work-self-isolate until 14 days from symptom onset is reached
  1. Symptomatic with negative test for COVID-19
  • At minimum, self-isolation until 24 hours after symptoms are fully resolved
  • Retesting only required if symptoms change, persist, or worsen
  1. Symptomatic with negative test for COVID-19 following high-risk exposure to a positive case
  • Retesting is not indicated to support 14-day self-isolation criteria
  • Retesting for essential HCW is not routinely recommended.

Healthcare Centre Streams

Instructions in the sections below are specific to the healthcare centres within each stream.

  • Thames Valley Cerner Hospital Sites
  • London Assessment Centres
  • Hospital Sites Not on Thames Valley Cerner
  • Assessment Centres Outside of London
  • Community Care

What Samples to Collect

  • Collect one nasopharyngeal swab in viral transport medium
  • Nasopharyngeal specimens are the PREFERRED choice for swab-based SARS-CoV-2 testing
  • Collection of a nasopharyngeal swab should be guided by the experience and comfort of the healthcare professional. Swab types with a flexible shaft and a small tip are ideal but may not be available for use
  • Deep nasal specimen
  • Throat/oropharyngeal combined with anterior nares/nostril specimen
  • When a preferred specimen site cannot be collected, the following are ACCEPTABLE collection sites:
  • Throat/oropharyngeal specimen
  • Anterior nares/nasal/nostril (both sides)
  • For the PaLM COVID-19 Swab Specimen Collection Guide, Click Here
  • For inpatients, one additional lower respiratory sample can be collected, if clinically warranted
  • Expectorated sputum; do NOT induce sputum specimen
  • Tracheal aspirate
  • Bronchoalveolar lavage; do NOT perform bronchoscopy unless medically indicated
  • Ensure collection traps are replaced by a screw-cap lid on specimen containers

Test Order, Specimen Collection Requirements and Routing Requirements

PaLM Microbiology is currently following the Spring/Summer algorithm for influenza and other respiratory virus testing.

  • Testing will only be performed on patients in Critical Care Areas (as identified on the submitted requisition for non-Cerner sites)
  • Samples for testing will be processed on Monday, Wednesday and Friday only
  • Testing on any other patients will require consultation with the Microbiologist On-Call (Pager # 19000)

  1. Thames Valley Cerner Hospital Sites
  • In Cerner, click the COVID19 Screen button
  • Complete the COVID Screening PowerForm by populating the required fields, and click the SIGN button
  • From the orders workspace, proceed to order the appropriate COVID-19 order (diagnostic or screen), and RPCR as appropriate
  • A paper requisition does not need to be completed
  • Specimens to be routed to PaLM Microbiology for testing

  1. London Assessment Centres
  • In Cerner, click the COVID19 Screen button
  • Complete the COVID Screening PowerForm by populating the required fields, and click the SIGN button
  • From the orders workspace, proceed to order the appropriate COVID-19 order (diagnostic or screen)
  • Specimens to be routed to PaLM Microbiology for testing

  1. Hospital Sites Not on Thames Valley Cerner
  • Order COVID-19 testing, as per local LIS procedure
  • Complete the PaLM Microbiology COVID19 paper requisition for COVID-19, and Respiratory Virus Testing, as per local seasonal respiratory virus testing policy
  • LHSC COVID Requistion
  • Both COVID19 and Respiratory Virus orders can be applied to a single swab collection device, labeled accordingly
  • Specimens to be routed to PaLM Microbiology for testing

  1. Assessment Centres outside of London
  • Follow established local guidelines to facilitate specimen flow and testing at designated laboratory

  1. Community Care
  • Complete the PHO COVID-19 Virus Test paper requisition
  • Specimens to be routed to PHO London for testing or onwards routing

Be sure to screw cap on firmly to prevent leaking and test cancellation. Place specimen in biohazard bag and seal. Specimens should be stored at 2 to 8C following collection and transported either to the designated referral laboratory


Testing Algorithms and Specimen Pooling

Currently, PaLM Microbiology is supporting COVID-19 PCR testing primarily for hospital in-patients and assessment centre patient flows. Expansion of testing for influenza and other respiratory viruses for hospital in-patients and other targeted patient settings is being planned for the beginning of November.

On September 22nd, PaLM Microbiology will begin pooling community-collected specimens for COVID-19 detection. Specifically, swab specimens from multiple individuals will be combined, or pooled, into a single PCR test. The pooling strategy will be applied to:


  • All specimens received from Assessment Centres (symptomatic and asymptomatic individuals)

  • All specimens received from asymptomatic patients/staff in Long-Term Care facilities and surveillance screening for other congregate living settings

Specimen pooling is a quality assured approach that will allow PaLM Microbiology to increase testing capacity without compromising the diagnostic performance or turnaround time of the COVID-19 PCR test.

Our clinical validation demonstrated 100% diagnostic accuracy and, importantly, all true positive specimens were detected when pooled with known negative specimens. Specimens with a low viral load that would otherwise be interpreted as indeterminate in an unpooled setting may be interpreted as negative when pooled with other specimens.

The pooling algorithm will combine four specimens into a single reaction and results will be interpreted as follows:


  • All specimens from a negative pool will be reported as NEGATIVE with the comment, "This specimen was tested using a pooling algorithm. For more information consult LHSC COVID-19 Testing Policy Guidelines." Following the Ministry of Health guidelines, any patient with high index of suspicion of infection (symptoms/exposure) with a negative result should be reassessed and retested if clinically indicated.
  • All specimens from a POSITIVE, INDETERMINATE or INVALID pool will be reflexed to individual un-pooled testing from the original specimen and reported accordingly.

Our pooling algorithm will be re-evaluated as the pandemic evolves and is subject to change.

Test Frequency and Turnaround Time (TAT)

Specimens processed in PaLM Microbiology:

  • Testing will be performed up to four times daily, 7 days a week
  • The majority of reports will be issued within 24 hours of receiving the specimen in PaLM Microbiology
  • Those requiring additional testing will be completed within 48 hours of being received
  • All testing in this stream is CRITICAL by eligibility and treated as STAT on the next available run. There is no need to call to prioritize, as all needs are processed as STAT.

Specimens processed by the Public Health Laboratories: see details

Reporting

Do NOT call the PaLM Microbiology laboratory for results of CRITICAL investigations. Significant human resources are in place to manage reporting and verbal notification of these results within 24 hours of specimen receipt.


Thames Valley Cerner Hospital Sites

  • Reports will be available in Cerner
  • Positive COVID19 results for inpatients will be verbally communicated to the MRP/clinical unit by PaLM Microbiology
  • All COVID19 positive results will be reported to the appropriate Health Unit by PaLM Microbiology

London Assessment Centres

  • Hardcopy reports will be delivered by fax to the respective Health Unit by PaLM Microbiology

Hospital Sites Not on Thames Valley Cerner

  • Hardcopy Reports will be delivered by fax, or established printer connections, to the referring hospital laboratory indicated on the COVID-19 requisition
  • Positive COVID19 results will be verbally communicated to the referring hospital laboratory contact provided on the COVID-19 requisition by PaLM Microbiology
  • Positive and Indeterminate COVID19 final results will be reported to the appropriate Health Unit by PaLM Microbiology

Assessment Centres outside of London

    Those affiliated with a Hospital Referring Laboratory
  • Hardcopy Reports will be delivered by fax, or established printer connections, to the referring hospital laboratory indicated on the COVID-19 requisition
  • Positive and Indeterminate COVID19 final results will be reported to the appropriate Health Unit by PaLM Microbiology
    Those Not Affiliated with a Hospital Referring Laboratory
  • Hardcopy reports will be delivered by fax to the respective Health Unit by PaLM Microbiology

Community Care

  • Reports will be issued by one of many potential laboratories working in the provincial network

Test Method and Interpretation

Initially, WHO recommendations for COVID-19 testing in geographic areas with low virus circulation suggested the use of at least two genomic targets for COVID-19 confirmation. Aligning with these recommendations and the test methodology implemented at the Public Health Ontario Laboratory (PHOL), PaLM Microbiology implemented molecular screening for the E-gene target (highly sensitive) and confirmation of all E-gene positives with a second target, the RNA-dependent RNA polymerase, on March 18th.

Now that Ontario is experiencing a higher degree of COVID-19 transmission, PHOL has updated and streamlined its testing algorithm to screen for a single discriminatory target, effective, March 29th. As of April 2nd, 2020, PaLM Microbiology has also implemented a simplified test algorithm and no longer requires PHOL support for confirmation.


Specimens processed in PaLM Microbiology:

  • The assay used by PaLM Microbiology to detect SARS CoV-2 from nasopharyngeal swab specimens exhibits and overall agreement of 98.5% in comparison to parallel testing performed by the Public Health Laboratory of Ontario. Discordant results were limited to two specimens (of 136) that were interpreted as Indeterminate (weak signal) by PaLM Microbiology and negative by the Public Health Laboratory
  • The analytical sensitivity (limit of detection) of the assay was estimated to be 14.4 copies/reaction (216 copies/ml of specimen sample), which is in alignment with data reported in the literature
  • There was no cross-reactivity observed with the assay when tested against other respiratory pathogens, including Influenza, RSV, and seasonal Coronaviruses. In other words, other respiratory pathogens do not cause false positive COVID-19 PCR results
  • To date, the analytical performance of 12 swab collection devices and a mix of nasopharyngeal, nasal, and throat specimens has been validated with the molecular assay. The clinical performance of these various specimen collection devices is not known due to the absence of a gold standard to confirm a positive case
  • False negative samples are infrequent but do occur and would appear to result from insufficient sample collection. A negative result does not rule out the possibility of infection, particularly for cases with a high probability of COVID-19 disease
  • Clinical judgement and multiple lines of evidence, including symptoms, medical imaging results, and contact with confirmed cases should be considered when making decisions for patient care and staff protection
  • This is especially important for the interpretation of indeterminate results were a weak signal is observed

Interpretations include, NEGATIVE, POSITIVE, INDETERMINATE, INCOMPLETE, and UNDER INVESTIGATION.

Limitations of Interpretation:

  • UNDER INVESTIGATION: specimens that require additional testing following initial testing. These results can be expected within 48 hours of the specimen being received by PaLM Microbiology.
  • INDETERMINATE: In a minority of tests, specimens with a weak-positive signal for the E-gene cannot be confirmed as positive by a confirmatory target. For inconclusive reports on patients where there is a strong suspicion of infection, another specimen should be tested no sooner than 24 hours later. We are currently exploring testing alternatives to confirm those instances in-house.
  • NEGATIVE: For negative reports on a patient with high index of suspicion for COVID-19 infection, additional specimens, including those from the lower respiratory tract, should be collected and tested. Factors that can lead to a negative result in an infected individual include:
  • Poor quality of the specimen, containing little patient material
  • Specimen collected late or very early in the infection
  • Specimen not handled and shipped appropriately

Specimens processed by Public Health Laboratory: see details


Schulich School of Medicine and Dentistry London Health Sciences CentreSt. Joseph's Health Care LondonWestern University