Primary care assessment and testing for COVID-19
If a patient thinks they have symptoms, or is worried they have been exposed to COVID-19, they should complete the provincial COVID-19 Self-Assessment which gives guidance tailored to self-reported symptoms and exposure. If responses indicate possible COVID-19, patients will be directed to contact you as their family physician/primary care nurse practitioner, or Telehealth Ontario.
Putting it into practice
Patients with possible COVID-19 should be screened by video or phone, not in person. If an in-person visit is necessary and feasible, patients should be advised to wear their own mask (cloth or other) to the office/clinic, if available, and the primary care setting should undertake the following active and passive screening.
- Post information on clinic website or send an email to all patients on screening requirements and advise them to call prior to coming to the office/clinic. Consider mailing by post for those patients without email and/or internet.
- Where possible, post signage outside the office/clinic asking patients to call before entry for appropriate screening and direction.
- Post signage at the office/clinic entrance and at reception reminding patients that, regardless of symptoms, they are expected to wear a mask for the entirety of their visit and perform hand hygiene before reporting to reception. If office/clinic is in a shared building, post signage at building entrance.
- Before scheduling appointments, patients should be screened over the phone using the COVID-19 Patient Screening Guidance Document (MOH, June 11, 2020).
- If patients present in-person, patient and accompanying persons should be screened upon entry with the following precautions:
- To protect from contact/spread, staff conduction screening should be behind a plexiglass barrier, if available, or maintain a 2-metre distance from the patient.
- If a barrier or 2-metre distance is not possible, use contact/droplet precautions. This includes the following PPE: gloves, gown, a surgical/procedure mask, and eye protection (goggles, face shield). See Primary Care Operations in the COVID-19 Context > Personal protective equipment (PPE) for details.
Patients with severe symptoms should be directed to the emergency department. Otherwise, patients should be instructed to self-isolate until further discussion with their primary care provider.
Patients should be offered an assessment by video or phone, ideally on the same day. This discussion should include a thorough history-taking and assessment of symptoms and managing them, even if COVID-19 testing is being considered as part of the diagnostic plan.
Patients should be provided with a surgical/procedure mask and be advised to perform hand hygiene. Ensure patients do not leave their masks in waiting areas.
Patients should be immediately placed in an exam room alone with the door closed to avoid contact with other patients the office/clinic. If the is not possible, instruct patients to return outside (e.g. vehicle or parking lot, if available and appropriate) and inform them they will be texted or called when a room becomes available.
Patients should be provided with hand sanitizer (if available), access to tissue and a hands-free waste receptacle for their used tissues and used masks.
Instruct patients to cover their nose and mouth with a tissue when coughing and sneezing, dispose of the tissue in the receptacle and to use the hand sanitizer right afterwards. Patients may also be instructed to take their surgical/procedure mask home with them with instructions for doffing masks.
Patients with possible COVID-19 should be assessed by video or phone, not in person. If patients screen positive in-person, you may offer clinical assessment and examination only if you can follow Droplet and Contact precautions and know how to properly don and doff PPE, including gloves, gown, a surgical/procedure mask, and eye protection (goggles, face shield). See Primary Care Operations in the COVID-19 Context > Personal protective equipment (PPE) for details.
Any persons experiencing one of the following should be told to self-isolate and tested as soon as possible. When assessing for the symptoms below, focus on evaluating if they are new, worsening, or different from an individual’s baseline health status. Symptoms should not be chronic or related to other known causes or conditions:
- Fever (temperature of 37.8°C or greater)
- Cough, including croup (barking cough, making a whistling noise when breathing)
- Shortness of breath (dyspnea, out of breath, unable to breathe deeply, wheeze)
- Sore throat (painful or difficulty swallowing)
- Rhinorrhea (runny nose)
- Nasal congestion (stuffy nose)
- New olfactory or taste disorder (decrease or loss of smell or taste)
- Nausea and/or vomiting, diarrhea, persistent/ongoing abdominal pain
- Headaches (new and persistent, unusual, unexplained, or long-lasting)
- Conjunctivitis (pink eye)
- Fatigue, lethargy, or malaise (general feeling of being unwell, lack of energy, extreme tiredness)
- Myalgias (muscle aches and pain)
- Decreased or lack of appetite (for young children); difficulty feeding in infants
- New or unusual exacerbation of chronic conditions
- Tachycardia (fast heart rate; including age specific tachycardia for children)
- Low blood pressure for age
- Hypoxia (i.e. oxygen saturation less than 92%)
- Delirium (acutely altered mental status and inattention)
- Increased number of falls in older persons
- Acute functional decline
- Contact with a confirmed case in the last 14 days without proper PPE
See COVID-19 Reference Document for Symptoms (MOH, September 21, 2020) for a full list of signs and symptoms and examples of when symptoms may be related to other causes or conditions.
Keep in mind
A systematic review of 131 studies found that fever and cough were the most common symptoms, followed by nasal congestion, fatigue and sore throat, while approximately 19% of children were asymptomatic (EClinicalMedicine, June 26, 2020).
- Fatigue, lethargy or malaise
- Decreased or lack of appetite
- Age-specific tachycardia
- Difficulty feeding in infants
- Multisystem inflammatory vasculitis in children (for more information, see Emerging evidence: COVID-19 transmission, paediatric symptoms, and Rx research > Multisystem Inflammatory Syndrome in Children (MIS-C))
For suggested criteria for assessing the severity of COVID-19 disease in children, see The acute management of paediatric coronavirus disease 2019 (CPS, April 20, 2020).
It’s important to monitor atypical symptoms because COVID-19 presents itself differently among older adults. For example, an older patient may not experience a fever or may experience unexplained or an increased number of falls (RGP, April 2, 2020; MOH, September 21, 2020).
Refer to the Atypical COVID-19 Presentations in Frail Older Adults (RGP, April 2, 2020) for a summary of what to look for such as:
- Milder symptoms
- Delirium or acute functional decline
- Little or no temperature elevation
- Mild hypoxia (O2S <90%) without respiratory symptoms
- Unexplained or increased number of falls
When assessing patients by telephone or video, use the COVID-19 remote consultations infographic (BMJ, March 25, 2020) for guidance on setting up, connecting, taking a history and examination.
Although there are no evidence-based methods for assessing shortness of breath (dyspnea) by telephone or video, experts have recommended asking patients 7 key questions (Centre for Evidence-Based Medicine, March 23, 2020).
For information on differentiating between COVID-19 and heart failure exacerbation symptoms in patients with known heart failure, see Is it COVID-19 or Is It Heart Failure? (Canadian Cardiovascular Society, April 1, 2020).
- Send patient to emergency department. Phone ahead and arrange safe transfer of patient to minimize contact/spread.
- Tell patient to self-isolate immediately.
- Refer to COVID-19 assessment centre for testing or test in-office if you are safely able to do so. See Testing section below for additional guidance.
- Tell patient to self-isolate.
- See Managing COVID-19: Outpatient management and resolution for additional guidance.
If your practice does not have the capacity to perform tests on site, refer the patient to an assessment centre or emergency department for testing.
Frequently asked questions (FAQs)
Testing is available for the following populations:
- All people with at least one symptom of COVID-19.
- Asymptomatic people who have received a positive antigen point-of-care test result.
- Asymptomatic people who have been exposed to COVID-19, including people who are contacts of or may have been exposed to a confirmed case.
- Asymptomatic people who are at risk of exposure to COVID-19, including workers, residents and visitors of high-risk settings (e.g., long-term care homes, homeless shelters and other congregate settings). This includes residents and workers at specific outbreak sites.
- Asymptomatic people from certain populations but without known high-risk exposure may be considered for testing. This includes any individual identifies as part of a targeted testing campaign. For a list of groups, see COVID-19 Provincial Testing Guidance Update (May 26, 2021).
Testing in the primary care office/clinic can only be performed if the primary care provider is able to:
- follow Droplet and Contact precautions outlined by the Ministry of Health (November 9, 2020);
- has the appropriate tools and knowledge of how to test; and
- can ensure coordination of sample delivery to the Public Health Ontario Laboratory or an alternative laboratory providing COVID-19 testing.
A single upper respiratory tract specimen will be accepted for COVID-19 testing, including nasopharyngeal swab (NPS), deep nasal swab, anterior nasal swab or viral throat swab. NPS is the preferred specimen when swabs are available, followed by deep nasal swab. Due to global shortages, Public Health Ontario (April 30, 2021) has provided information on alternative collection kits that are acceptable for COVID-19 testing (see Specimen Collection and Handling).
Nasopharyngeal swab collection is not considered an aerosol generating procedure and can be performed in the office/clinic with appropriate contact/droplet precautions of gloves, gown, surgical/procedure mask, and eye protection (e.g., goggles, face shield). This is important as many people will cough or sneeze when the nasal swab is done. Links to resources on properly conducting NP swabs are available under ‘COVID-19 Care’ on OCFP’s Clinical Care- Office Readiness page.
If testing is conducted in the office/clinic, it is important to conduct the nasopharyngeal swab properly to minimize the risk of a false negative sample:
- Pre-label the swab so, once obtained, it can be placed in the bag without further handling.
- Place the specimen in the bag, and place the completed requisition in the attached pouch.
Diagnosing COVID-19 is done by laboratory testing (NAAT result by PCR or nucleic acid sequencing) on at least one specific genome target.
- A single positive result is sufficient to confirm COVID-19.
- A single negative result is sufficient to exclude COVID-19.
- A positive result might represent one of the following scenarios:
- current COVID-19 infection that is asymptomatic or pre-symptomatic, OR
- prior COVID-19 infection (+/- symptoms) as testing can remain positive for several weeks after infection, OR
- false positive result.
- If a patient has a medium/high pre-test probability of infection, a single positive result is sufficient to confirm current or prior infection.
- If a patient has a low pre-test probability of infection, a positive result should be immediately retested and may be cleared with a single negative retest (MOH, May 6, 2021). The patient must be managed as if they have current COVID-19 infection (i.e., immediate self-isolation) until cleared.
- A single negative result is sufficient to exclude COVID-19.
In a patient who tested positive for COVID-19 AND was cleared, retesting should generally not be done due to persistent shedding (viral detection has been identified in some cases well beyond 4 weeks (>70 days) in some cases).
If the patient is within their 14-day self-isolation due to known exposure, the patient should remain in self-isolation for the rest of the 14-day period, regardless of the negative result.
See COVID-19 Quick Reference Public Health Guidance on Testing and Clearance (MOH, May 21, 2021) for more detailed information.
A recent study retroactively compared the results from 353 patients who received both OP and NP simultaneously, and found that 73.1% of NP-positive cases were negative in OP swab. The authors concluded that while use of both swabs slightly increased the positive rate over using NP swab only, NP swabs “may be more suitable” than oropharyngeal swab (Int. J. Infect. Dis., April 22, 2020).
Testing for COVID-19 involves sending a respiratory tract specimen – nasopharyngeal swab (NPS) or viral throat swab; NPS is preferred– to a PHO laboratory or other suitable laboratory with capacity for RT-PCR testing. RT-PCR is a type of nucleic acid amplification testing (NAAT), the gold standard used in Canada and abroad for the diagnosis of active COVID-19 infection, that tests for the presence of viral RNA during active infection (Health Canada, May 26, 2021). At this time, serology testing and antigen testing should not be used for diagnosis of acute COVID-19 infection (MOH, May 26, 2021).
The turnaround time for COVID-19 testing at a PHO Laboratory is for 60% of results to be completed within 24 hours and 80% to be completed within 48, but will vary depending on what laboratory performs the testing (PHO, April 30, 2021).
As of September 10, 2020, PHO Laboratory implemented a validated pooling approach to testing, which will allow an increase in testing throughput without greatly compromising sensitivity (PHO, March 30, 2021) . For pooled testing, a portion of three individual specimens are combined into a single pool and run on the SARS-CoV-2 PCR assay as a single test.
- If the pool result is NOT DETECTED, all three specimens are individually reported as NOT DETECTED.
- If the pool result is DETECTED, INDETERMINATE or INVALD, each individual specimen is tested individually and reported based on individual result obtained.
Health Canada is prioritizing the review of point-of-care tests intended to diagnose COVID-19, including both nucleic acid-based tests and antigen-based tests, and have authorized several tests (Health Canada, May 26, 2021).
At this time, a positive result on a rapid test is considered a preliminary positive and should have a parallel sample taken for a confirmatory laboratory-PCR test (MOH, May 26, 2021).
Serology testing is only available for clinical use under specific clinical indications listed below. Serology testing should not be used for screening and diagnosis of acute COVID-19 infection, and a positive serology test does not mean a patient is immune to COVID-19 (MOH, May 26, 2021).
- Patients presenting with symptoms compatible with Multisystem Inflammatory Syndrome in Children (MIS-C) who do not have laboratory confirmation of COVID-19 by PCR.
- Patients with severe illness who have tested negative for COVID-19 by PCR 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.
- A study retrospectively analyzed the results of tests administered to more than 15,000 individuals in order to identify the prevalence of false negative results. Of those results studied, 2,699 individuals who tested negative initially were subsequently tested again, and 60 (2.2%) of these individuals were determined to have false negative results in their initial test. The study led the researchers to recommend repeat testing for suspected COVID-19 patients, particularly those with symptoms and other clinical factors consistent with COVID-19 and during periods of high COVID-19 incidence (Open Forum Infect Dis, Nov 24, 2020; Johns Hopkins Center for Health Security, December 4, 2020).
- The findings in a recently published systematic review (PLoS One, December 10, 2020) further reinforces the need for repeated testing in patients with suspicion of COVID-19 infection given that up to 54% of COVID-19 patients may have an initial false-negative RT-PCR. This is based on very low certainty of evidence.
- A cohort study has found that even rigorous RT-PCR testing protocols might miss a substantial proportion of SARS-CoV-2 infections, perhaps in part due to difficulties in determining the timing of testing in asymptomatic individuals for optimal sensitivity (Lancet, January 19, 2021).
- A recent study has determined that most false negative results were found to be due to low amounts of SARS-CoV-2 virus concentrations in patients with multiple specimens collected during different stages of infection. Post-test clinical evaluation of each patient is advised to ensure that rtRT-PCR results are not the only factor in excluding COVID-19 (Virol J, January 9, 2021).
- A recent retrospective observational cohort study identified clinical characteristics associated with false negative SARS-CoV-2 testing. The study found that negative test results were associated with anosmia/ageusia, having a COVID-19 positive contact, and having an elevated lactate dehydrogenase level. Demographics, symptom duration, other laboratory values, and abnormal chest imaging were not significantly associated with false negative test results in multivariable analysis (Infect Control Hosp Epidemiol, April 19, 2021).
For patients experiencing respiratory tract infection (RTI) symptoms who have tested negative for COVID-19, a viral RTI is the most likely diagnosis. These patients can usually be treated virtually with supportive management. For information on when an in-person visit might be indicated, see The Cold Standard 2nd Edition (Choosing Wisely Canada, October 15, 2020).
The following are being implemented as part on Ontario’s six-point variant action plan (Government of Ontario, January 29, 2021):
- Mandatory testing of travelers: On-arrival testing for international travellers at Toronto Pearson International Airport will be mandated starting February 1. Additional testing measures at Pearson International Airport and land border crossings will be explored in the coming weeks.
- Enhanced screening and sequencing: Led by Public Health Ontario (PHO), the provincial diagnostic lab network will screen all positive COVID-19 tests in Ontario for known variants within 2 to 3 days of initial processing starting February 3. By February 17, PHO will be sequencing up to 10% of all positive tests in an effort to identify new and emerging variants.
For more information on the COVID-19 variants, see COVID-19 Variants and vaccines
Screening / Assessment resources
- COVID-19 Screening Tools for Electronic Medical Records (EMRs) (eHealth Centre of Excellence, 2020).
- COVID-19 Patient Screening Guidance Document (MOH, June 11, 2020).
- COVID-19 Reference Document for Symptoms (MOH, September 21, 2020).