Guidance for repeated PCR testing in individuals previously positive for COVID-19

On this page

• Purpose
• Context
• Recommendations
• References

Purpose

To provide guidance on when to perform and how to interpret repeat polymerase chain reaction (PCR) testing for SARS-CoV-2 in individuals who have previously tested positive.

Context

A key question from the start of the COVID-19 pandemic has been whether individuals can become reinfected with SARS-CoV-2, and if so, the frequency of occurrence and timing relative to prior infection.

There are numerous studies that demonstrate prolonged detection of SARS-CoV-2 RNA that extends beyond the resolution of COVID-19 symptoms and can persist for several weeks or months.^{Footnote 1Footnote 2Footnote 3Footnote 4Footnote 5Footnote 6Footnote 7Footnote 8Footnote 9Footnote 10Footnote 11} In addition, it has been shown that detection of genetic material can be intermittent during the recovery phase, such that a person with a previously negative test can be positive again is re-tested a few days later. This was observed early in the pandemic where “tests of cure” were being used. In most individuals with competent immune systems and those recovered from mild or moderate illness, prolonged or renewed RNA detection is not believed to reflect infectious virus, but rather non-infectious viral fragments, as viable virus has rarely been reported to persist for longer than 10 days in these populations.^{Footnote 12Footnote 13Footnote 14Footnote 15Footnote 16} Shedding of infectious virus may persist longer in those with immune compromise or severe or persistent illness, but data are lacking.

Reinfection with common coronaviruses that cause seasonal respiratory infections can occur within months of previous infection with the same virus.^{Footnote 17Footnote 18Footnote 19Footnote 20} Neutralizing antibodies to SARS-CoV-2 develop in the majority of individuals within 1-2 weeks of infection, and start to decline within 1-2 months; exact correlates and the durability of protection from reinfection with SARS-CoV-2 is unknown.120^{Footnote 1Footnote 20Footnote 21Footnote 22Footnote 23Footnote 24}

There have been multiple reports of possible reinfection with SARS-CoV-2; however, supporting evidence is often insufficient to allow confirmation.^{Footnote 25Footnote 26Footnote 27Footnote 28Footnote 29Footnote 30} Recent publications and preprint articles present more convincing evidence for reinfection, including resolution of symptoms and PCR negativity followed by epidemiological support for reinfection (e.g., travel to an area with increasing transmission or cohabitation with someone with active COVID-19 infection), evidence of a high viral load with gradual decline and seroconversion, and performance of whole genome sequencing showing discordance of virus detected across episodes of infection.^{Footnote 31Footnote 32Footnote 33Footnote 34Footnote 35Footnote 36Footnote 37} Reported time intervals between episodes range from less than 2 to 4.5 months.^{Footnote 31Footnote 32Footnote 33Footnote 34Footnote 35Footnote 36Footnote 37Footnote 38Footnote 39} The risk of further transmission from an individual(s) who have been reinfected onto others is currently unknown. As of writing, transmission from an individual(s) who have been reinfected to another has not been demonstrated, but the data is very limited and may change.

Based on current evidence, individuals can become reinfected with SARS-CoV-2. After approximately six months of significant global transmission, reinfection appears to be uncommon, but the frequency of occurrence remains uncertain. Ongoing investigation and reporting will help to improve our understanding.

The following recommendations are based on what is currently known. As scientific knowledge evolves, these recommendations are expected to change. It is recognized that there may be variation in the extent to which provinces and territories will use these recommendations to inform their own operational decisions; local context should be considered, and judgment by clinicians, microbiologists, infection prevention and control, and regional public health authorities should be exercised.

Recommendations

1. A prior infection does not guarantee immunity and so individuals who have been infected with SARS-CoV-2 should be counseled about the possibility of reinfection and the importance of continued adherence to public health (e.g. physical distancing and masking) and infection prevention and control measures (e.g. use of recommended personal protective equipment by healthcare workers).
2. When individual(s) who were previously infected present to care or have already undergone re-testing for SARS-CoV-2, the decision to test and test interpretation should take into consideration the clinical and epidemiological context, and results of laboratory investigations where indicated (see proposed algorithm and table).
   • PCR positivity may persist or fluctuate for weeks or in some cases months, and positive results particularly within 3 months of a previous infection may not represent a true reinfection. However, it is not clear how soon after a COVID-19 diagnosis reinfection may occur and it has been reported within less than 2 months. Differential diagnoses along with relevant clinically appropriate investigations should be considered in the evaluation of any patient recovered from COVID-19 presenting with new onset of symptoms consistent with possible COVID-19 reinfection. When re-testing for SARS-CoV-2, consultation with local public health, institutional infection prevention and control, and/or infectious diseases specialists should be considered dependent on the context and the rationale for testing.
3. Individuals who have recovered from COVID-19 generally should not undergo testing for screening/surveillance purposes, if they are asymptomatic. If a test is done in a recovered individual with no symptoms and no known exposure and the result is positive, it should generally not be considered a new infection and should not trigger public health actions unless additional factors, such as a new exposure or renewed symptom becomes a factor. This may not be applicable to very high-risk situations such as outbreaks in long term care homes.
   • Local public health and/or facility infection prevention and control should be consulted with respect to recovered individual(s) who are asymptomatic with new exposure who have a high degree of interaction with populations who are at high risk of more severe disease or outbreaks. As evidence builds regarding reinfection and how it affects subpopulations (e.g., sex, gender, and other groups of diverse peoples), guidance may be updated to reflect differences, as needed.
4. If there is suspicion of reinfection, strong consideration should be given to genetic sequencing of the current and previous virus if samples are available and sufficient genetic material can be recovered to enable sequencing. Whole genome sequencing of SARS-CoV-2 samples enables differentiation between persistent viral shedding from a single episode of infection and reinfection with a new virus by comparing the genetic sequences of more than one sample from the same patient.

Figure 1: Proposed algorithm for PCR re-testing for SARS-CoV-2 in previously positive individuals

Figure 1 - Long description

Clinical support for re-testing?

• If yes, epidemiological support for re-testing?
• If no, re-testing generally not indicated

Epidemiological support for re-testing?

• If yes, recommend or strongly consider re-testing
• (see table)
• If no, consider re-testing if immunocompromised or hospitalized, persistently or severe ill

Figure depicts proposed steps or points of consideration for re-testing for SARS-CoV2 in previously positive individuals. First step to consider is whether there is clinical support for re-testing, if no, re-testing is generally not indicated. If there is clinical evidence to support testing then consider whether there is epidemiological support for testing. Generally when there is epidemiological support then re-testing is strongly considered. However, even when epidemiological support is lacking, retesting can be considered under special circumstances including in people who are immunocompromised or hospitalised or in those who are persistently or seriously ill.

Clinical support for re-testing:

• New symptoms of COVID-19 in a recovered case (a recovered case refers to an individual with complete resolution of symptoms associated with COVID-19, if present, or passage of sufficient time since first positive SARS-CoV-2 test in an individual(s) who are asymptomatic such that new symptoms are unlikely to be associated with a previous positive test);
• Immunocompromised or hospitalized, persistently and/or severely ill patients.

Epidemiological support for re-testing:

• New unprotected exposure to an unrelated (i.e. not epidemiologically linked to the individual’s past episode of infection) case or outbreak of COVID-19, or travel to or residence in an area with high community prevalence;
• High degree of interaction with populations who are at high risk of more severe disease or outbreaks (e.g., HCWs, staff and residents in LTCHs, prisons, shelters, single room occupancy residences, work camps).

Re-testing generally not indicated:

Asymptomatic testing and/or isolation regardless of testing may be recommended in some circumstances, for instance in recovered cases who have a new exposure to an unrelated (i.e. not epidemiologically linked to the individual’s past episode of infection) case or outbreak, and a high degree of interaction with populations who are at high risk of more severe disease or outbreaks [e.g., healthcare workers (HCWs), staff and residents in long term care homes, prisons, shelters, single room occupancy residences, work camps]. Please refer to local public health and/or facility infection prevention and control guidance for details.

Table 1: Example scenarios and guidance on indications to perform and how to interpret PCR re-testing for SARS-CoV-2 in previously positive individuals

Clinical support for re-testing	Epidemiological support for re-testing	Rationale for PCR testing	Interpretation of positive PCR result
New symptoms of COVID-19 in a recovered caseFootnote 1	New unprotected or high risk exposure to an unrelatedFootnote 2 case or outbreak	Testing recommended to inform public health and infection prevention and control measures to prevent transmission	May represent prior infection or reinfection. Laboratory consultation and additional testing may be considered.
New symptoms of COVID-19 in a recovered caseFootnote 1	Travel to or residence in an area with high community prevalence	Testing should be strongly considered to inform public health and infection prevention and control measures to prevent transmission	May represent prior infection or reinfection. Laboratory consultation and additional testing may be considered.
New symptoms of COVID-19 in a recovered caseFootnote 1	No known exposure to a new unrelated case or outbreakFootnote 2 case or outbreak or travel to or residence in an area with high community prevalence, but high degree of interaction with populations who are at high risk of more severe disease or outbreaks (e.g., HCWs, staff and residents in LTCHs, prisons, shelters, single room occupancy residences, work camps)	Testing should be strongly considered to inform public health and infection prevention and control measures to prevent transmission	May represent prior infection or reinfection. Laboratory consultation and additional testing may be considered.
New symptoms of COVID-19 in a recovered caseFootnote 1	No known exposure to a new unrelated case or outbreakFootnote 2 or travel to or residence in an area with high community prevalence, but high degree of interaction with populations who are at high risk of more severe disease or outbreaks (e.g., HCWs, staff and residents in LTCHs, prisons, shelters, single room occupancy residences, work camps)	Testing should be strongly considered to inform public health and infection prevention and control measures to prevent transmission	May represent prior infection or reinfection. Laboratory consultation and additional testing may be considered.
Immuno-compromised or hospitalized, persistently and/or severely ill patients	Re-testing could be considered under the above scenarios. Additionally, retesting in this population may be driven by the need to determine ongoing positivity in the context of potential for prolonged period of infectiousness	Testing may be considered to inform public health and infection prevention and control measures to prevent transmission, and to guide decision making with regard to clinical management.	May represent prior/persistent infection or reinfection. Laboratory consultation and additional testing may be considered. Consultation with local public health and/or institutional infection prevention and control authorities should be considered.
Footnotes Footnote 1 A recovered case refers to an individual with complete resolution of symptoms associated with COVID-19, if present, or passage of sufficient time since first positive SARS-CoV-2 test in an individual(s) who are asymptomatic such that new symptoms are unlikely to be associated with a previous positive test. Return to footnote 1 referrer Footnote 2 Refers to a case or outbreak that was not epidemiologically linked to the individual’s past episode of infection. Return to footnote 2 referrer

Laboratory consultation and additional testing:

PCR positivity is a necessary but not a sufficient condition for the diagnosis of reinfection due to evidence of prolonged detection that can last weeks or in some cases months after symptom resolution. Reinfection has been reported <2 months after a first episode of infection.

Additional testing beyond PCR:

• PCR cycle threshold (Ct) values: the higher the Ct value required to detect a gene target, the lower the number of viral copies present in a sample. Higher Ct values in the setting of new acute symptom onset may be more suggestive of old/persistent viral shedding. However, Ct values may also be higher with early case detection, and re-testing 48 hours later may be considered to assist with interpretation. If the Ct value on a subsequent sample is lower, this would add support for a diagnosis of a new infection. Ct values and cut-offs vary dependent upon the assay used and should be reviewed with the laboratory that performed the testing.
• Serology: serology is generally not helpful in the diagnosis of acute infection, but new seroconversion may assist with confirming reinfection.
• Genomic analysis: whole genome sequencing of virus from suspected separate episodes of infection can be used for comparative phylogenetic analysis to determine whether viruses are genetically distinct enough to support a diagnosis of reinfection. This is unlikely to be widely available with a turn-around-time that supports clinical and public health decision-making, but results may also inform studies that evaluate reinfection.

References