COVID Testing and Clinical Diagnosis

Throughout the fall and winter of 2023, RAT kits will be available through select City of Hamilton locations. Beginning in September 2023, primary care providers have been able to order RAT kits for their patients free of charge. Pharmacies and participating grocery stores will continue to have kits available as long as their current supplies last. The goal of this distribution plan is to allow easy access to COVID-19 testing so that people can receive antiviral treatments sooner.

A list of participating City of Hamilton locations where RAT kits are available is presented on the city’s website.

Ministry of Health updated eligibility criteria for PCR testing for COVID-19.

Only a small group of patients and workers are eligible for PCR testing.

  • A positive RAT is now accepted as confirmation of COVID diagnosis and follow-up PCR testing is not required.
  • If two consecutive RATs, separated by 24-48 hours, are both negative, the symptomatic individual most likely does not have COVID-19 infection. PCR is not required. The individual is advised to self-isolate until symptoms are improving for at least 24 hours (or 48 hours if gastrointestinal symptoms). The household members of the symptomatic individual with two negative tests may also discontinue self-isolation.
  • If RAT or PCR testing is not available, diagnosis is made on the basis of the clinical symptom algorithm at the bottom of the page

Criteria for eligibility for PCR testing

Primary care patients

Patients must be symptomatic AND in one of the five groups below

  1. In the group for whom COVID-19 treatment is being considered
  • Individuals aged 18 and over who are immunocompromised (have an immune system that is weakened by a health condition or medications);
  • Individuals aged 70 and over;
  • Individuals aged 60 and over with fewer than three vaccine doses; and
  • Individuals aged 18 and over with fewer than three vaccine doses and at least one risk condition (e.g., a chronic medical condition)
  • Immunocompromised individuals not expected to mount an adequate response to vaccination regardless of age and vaccination status.

2. Underhoused or homeless

3. Pregnant

4. First responders (including fire, police, and paramedics)

Symptomatic OR Asymptomatic

  • Individuals who are from a First Nation, Inuit, Métis community, and/or who self-identify as First Nation, Inuit, and Métis and their household members.
  • Individuals travelling into First Nation, Inuit, Métis communities for work.
Healthcare and congregate settings:
  1. Symptomatic patients who are:
  • Hospitalized Patients
  • Patients seeking emergency care, at the discretion of the treating clinician
  • Patient-facing healthcare workers
  • Staff, volunteers, residents/inpatients, essential care providers, and visitors in highest risk settings (hospitals and congregate living settings, including Long-Term Care, retirement homes, First Nation elder care lodges, group homes, shelters, hospices, temporary foreign worker settings, and correctional institutions)

  • Household members of workers in highest risk settings above and patient-facing health care workers

2. Asymptomatic but require PCR testing for work self-isolation (see page 11 of guidance)

3. Symptomatic elementary and secondary students and education staff who have received a PCR self-collection kit through their school.

Other guidance for testing eligibility of contacts in outbreaks in high risk settings or other aspects of care related to hospital admission / treatments for particular conditions or related to congregate settings can be found in the full guidance.

If your patient is calling about COVID-19 symptoms and fits criteria, direct them to the City of Hamilton COVID-19 testing page for information on eligibility, how to book and how to access test results as well as other FAQs about testing and assessment centres.

Where to Access PCR Testing

People with COVID-19 symptoms may seek PCR tests if eligible. Publicly funded PCR tests are available to eligible people in Hamilton through participating pharmacies. To find the closest pharmacy to get a COVID-19 PCR test, please visit Ontario’s COVID-19 Testing Locations.

Please note that all pharmacies require a booked appointment to receive a test and that you are encouraged to follow public health measures when going for your appointment. This includes bringing a well-fitting mask (as masking may be required), and cleaning hands frequently.

Public Health Services (289-778-1465) will continue to connect vulnerable individuals in need of support with the City Emergency Operations Centre (EOC) to facilitate the following:

  • Emergency food delivery for those in self isolation or deemed medically vulnerable who have no other supports such as friends, family or neighbours to assist.
  • Delivery of masks and gloves to individuals identified by PH as COVID positive
  • Arranging transportation to the assessment centres via DARTS for individuals requiring testing for COVID-19

If a patient is homebound,  EMS can do the swab – call Public Health testing number, and it can be arranged.

Testing for suspected COVID should only be done with COVID nasopharyngeal PCR swabs. It can be done in clinics for those meeting new provincial guidelines for testing. It can be done in clinics for those meeting new provincial guidelines for testing.

A positive rapid antigen test is now considered diagnostic of COVID in the current high prevalence situation. A PCR is not needed to confirm.

Note that this accuracy will change as the community prevalence reduces. At low prevalence (low “pretest probability”) the proportion of positive RATs that are false positives increases, reducing the usefulness.

RATs are less sensitive for the Omicron variant compared to the Delta variant using nasal samples particularly in the first 2 days after infection. The ability to detect Omicron is improved by using a new oral-nasal sample collection technique (using the same swab). See instructions for collection below.

A single negative RAT does not reliably rule out infection.

Two negative RATs separated by a minimum of 24-48 hours are considered to rule out COVID diagnosis. This can be helpful in guiding management in patients who are higher risk and would need closer monitoring, to reduce the monitoring workload for this group. Symptomatic patients should still isolate until improving as per the current isolation recommendations. See Tab 8: Isolation Guidelines.

Ordering Supplies

RATs can be ordered through the same portal as COVID swabs (Ontario Health West) however note that there have been intermittent supply chain issues since mid-December (including local Hamilton suppliers).

Supplies of COVID-19 swabs for nasopharyngeal swabbing for PCR tests can be ordered through Ontario Health West.

Store between 2-25°  C

If you have no current supply of the provincial swab kits, Lifelabs will accept other swabs for PCR testing, in particular the UT COPAN swabs (used for chlamydia testing) as well as other sampling methods. See here for details.

Note: Use the same public health form – see below

Collection: RAT

Collection Techniques for adults and children

The most recommended swab technique for RATs for detecting the Omicron variant is an oral-nasal sample collected using the same swab. Individuals can collect these samples by initially swabbing the inside of both cheeks, followed by the back of the tongue or throat, and then both nostrils.

Video instructions for adults

Video instructions for children

Written instructions from Public Health Ontario: COVID-19 Rapid Antigen Tests: How to Collect a Sample

Collection: PCR

Use this requisition form

Swabs should be refrigerated (2-8°C) and can be stored overnight. They should be received by the lab within 24 hours.

Swab label should include:

  • Patient’s full name 
  • DOB or Health Card number 
  • Source of specimen 
  • Date and time of collection 

Specimen Collection Instructions:

  • Recommended full PPE (fit-tested N95 mask, eye protection and gown) should be worn.
  • Specimen Collection Instructions (Public Health Ontario):
  • Lifelabs and Dynacare will pick up swabs and forward to public health
  • Results generally take 2 days, longer in times of peak demand.

Other resources:

Recommendations and evidence about alternate sample collection methods can be found here: https://www.publichealthontario.ca/en/laboratory-services/test-information-index/covid-19

Video: How to Collect a Combined Throat and Nasal Specimen for COVID-19 Testing (Public Health Ontario)

RATs are being used in some settings (including primary care clinics) to reduce cases by regular screening of asymptomatic individuals. Because there is a delay between infection and development of a positive RAT (see the graph on the left), frequent screening is key to effective use.

Frequency

The graph on the right supports the current recommendation for testing between 3 and 5 times per week when using for screening.

Sensitivity of RAT in detecting COVID infection
(days since positive PCR)

Reduction in COVID cases with different frequencies of asymptomatic screening using RATs

Modified from Ontario Science Table: Use of Rapid Antigen Tests During the Omicron Wave

Interpretation

A positive rapid antigen test is now considered diagnostic of COVID in the current high prevalence situation. A PCR is not needed to confirm. Note that this accuracy will change as the community prevalence reduces. At low prevalence (low “pre test probability”) the proportion of positive RATs that are false positives increases, reducing the usefulness.

RATs are less sensitive for the Omicron variant compared to the Delta variant using nasal samples particularly in the first 2 days after infection. The ability to detect Omicron is improved by using a new oral-nasal sample collection technique (using the same swab). See instructions for collection below.

A single negative RAT does not reliably rule out infection

Two negative RATs separated by a minimum of 24-48 hours apart are considered to rule out COVID diagnosis. This can be helpful in guiding management in patients who are higher risk and would need closer monitoring, to reduce the monitoring workload for this group. Symptomatic patients should still isolate until improving as per the current isolation recommendations. (See #8 Isolation Guidelines)

Ordering Supplies

RATs can be ordered through the same portal as COVID swabs (Ontario Health West) however note that there have been intermittent supply chain issues since mid-December (including local Hamilton suppliers).

Video instructions from Ontario Science Table: Use of Rapid Antigen Tests During the Omicron Wave

Video instructions for adults

Video instructions for children

Written instructions from Public Health Ontario: COVID-19 Rapid Antigen Tests: How to Collect a Sample

Read more detail here: 

Ontario Science Table: Use of RATs During the Omicron Wave

An article from the BMJ provided useful “what you need to know” summary for interpreting test results in primary care:  

  • Interpreting the result of a test for covid-19 depends on two things: the accuracy of the test, and the pre-test probability or estimated risk of disease before testing  
  • A positive RT-PCR test for covid-19 test has more weight than a negative test because of the test’s high specificity but moderate sensitivity  
  • A single negative covid-19 test should not be used as a rule-out in patients with strongly suggestive symptoms  
  • Clinicians should share information with patients about the accuracy of covid-19 tests 
You can read the full paper here Download

Interpretation and management of previously cleared cases with new positive results can be found in the Ministry Guidance on Management of Cases and Contacts (Section 5.4)

1. From Lifelabs:

The following limitations of COVID-19 antibody testing should be considered:

  • Positive antibody (serology) test results do not infer immunity and protection from re-infection
  • Serology results should not be used to exclude active infection
  • Antibody testing performed < 3 weeks after onset of symptoms has reduced clinical sensitivity and may lead to false negative results
  • Rare false positive results may be due to cross-reactivity with other coronaviruses
  • Immunosuppressed individuals or those with mild disease may not produce measurable antibody levels
  • Some studies indicate that a small percentage of people infected with SARS-CoV-2 (<4%) do not have detectable antibodies.
  • The COVID-19 antibody test currently offered by LifeLabs cannot detect antibodies generated after vaccination.

2. From MOHLTC: COVID-19 Provincial Testing Guidance Update V. 14.0 November 10, 2021

Laboratory-based serology testing: detects antibodies to SARS-CoV-2

Purpose: Serology testing is available for clinical use under specific clinical indications:

  • Patients presenting with symptoms compatible with Multisystem Inflammatory Syndrome in Children (MIS-C) or Adults (MIS-A) who do not have laboratory confirmation of COVID-19 by molecular testing.
  • Testing may be considered for patients with severe illness who have tested negative for COVID-19 by molecular testing and where serology testing would help inform clinical management and/or public health action. Serology testing for these patients requires consultation and approval by the testing laboratory.

Serology should NOT be used for screening and diagnosis of acute COVID-19 infection, determining immune status, vaccination status.

3. From Public Health Ontario 

Coronavirus Disease 2019 (COVID-19) – Serology

COVID-19 serology should not be used as a diagnostic test, except in very rare circumstances, due to the potential for false negative and false positive results. SARS-CoV-2 antibodies do not correlate with recovery or infectivity. Serology also cannot be used to assess whether a person is immune to COVID-19 or to determine their COVID-19 vaccination status.

Testing Indications

This test is intended for use as an aid in determining if a patient with an adaptive immune response has been previously exposed to SARS-CoV-2. Currently, it is not known whether the presence of SARS-CoV-2 IgG antibodies correlates with immunity. It can take at least 7-14 days from symptom onset to develop a measurable SARS-CoV-2 IgG response with some individuals never seroconverting. In evaluations at PHO, the highest sensitivity of the assay was seen at >14-21 days from symptom onset. Further, the duration of the IgG response is variable, with a reduction in IgG levels and seronegativity in as little as 2-3 months in some patients.  Additional information about COVID-19 serology testing can be found here: What We Know So Far – COVID-19 and Serology Testing.  

In patients with a low pretest probability (e.g. no high-risk exposure or symptoms compatible with COVID-19), there is a risk that a positive COVID-19 serology result is a false positive, even with high test specificity. Conversely, there is an increased risk of a false negative result if serum is taken too early (i.e., <2-3 weeks after symptom onset) or too late (i.e. antibody waning), from a patient with a mild infection, or if the patient is immunocompromised. Given these caveats and significant gaps in our understanding of the immune response in COVID-19, serology testing has very limited clinical value for individual patients. Detection of viral RNA by molecular testing, such as PCR, is the gold standard for diagnosing COVID-19 in suspected patients. If the patient is symptomatic, a respiratory specimen should be tested by COVID-19 PCR Testing. 

Currently, the limited clinical value for individual patient testing precludes the widespread use of COVID-19 serology as a clinical diagnostic tool. It may be considered for clinical use as an adjunct to COVID-19 PCR testing in:

  • Patients suspected to have multisystem inflammatory syndrome in children (MIS-C) or adults (MIS-A) with a negative, indeterminate, or inconclusive PCR test result or who were not tested

Other clinical scenarios of severe illness with negative PCR tests, where serology results may be helpful for clinical management and/or public health action, will be considered following consultation and approval by a PHO Microbiologist before specimen collection. 

Specimens submitted for testing for indications other than MIS-C/MIS-A or without prior approval will be rejected.

Serology should NOT be used for:

  • The diagnosis of acute infection, reinfection, or determining the infectivity of the patient
  • Determining immune status of the patient (i.e. protection against future infection)
  • Determining COVID-19 vaccination status of the patient or serological response to vaccination

Interpretation

SARS-CoV-2 IgG testing should NOT be used to determine a patient’s immune status, vaccination status, or infectivity. Results should be interpreted in the context of clinical and exposure history.

A negative SARS-CoV-2 IgG test result:

  • Does not rule out current or previous SARS-CoV-2 infection
  • If clinical suspicion is high, consider retesting in 2-3 weeks
  • Negative results may occur if the specimen is collected too soon or too late following infection, if the patient is immunocompromised, or if the patient is too young to produce an effective adaptive immune response (eg. neonate)

A positive COVID-19 IgG test result:

  • Indicates recent or prior infection with SARS-CoV-2 virus
  • An individual with evidence of seroconversion over a 4-week interval, regardless of nucleic acid amplification testing (e.g. real-time PCR), is considered a “confirmed” case if the individual has not received a COVID-19 vaccination
  • An individual with antibody detected in a single serum specimen is considered a “probable” case if they have not yet received a COVID-19 vaccination AND had symptoms of COVID-19 AND had a high-risk exposure or epidemiological link AND antibody was detected within four weeks of symptom onset1
  • False-positive results may occur from cross-reaction due to prior infection with other human coronaviruses, including SARS-CoV-1 and certain seasonal coronaviruses (e.g. human coronavirus OC43) 

If the patient is symptomatic, a respiratory specimen should be collected and tested for SARS-CoV-2 using a molecular assay.

There is currently no data available to determine if these commercial assays can or cannot detect IgG antibodies produced in response to infection by SARS-CoV-2 variants of concern (VOCs).