St. Louis Encephalitis Virus - Serology and PCR
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Background
This page provides serology and molecular testing information for the St. Louis Encephalitis virus (SLEV).
- The SLEV is a mosquito-borne RNA virus that is a member of the Flaviviridae family1.
- The primary route of SLEV transmission is through the bite of an infected mosquito in an endemic area, including the Central, Eastern and Southwest United States2.
Note: Requests for SLEV testing received at PHO will be considered on a case-by-case basis. Testing is available only upon special request via the US Centers for Disease Control and Prevention (CDC).
Updates
Effective July 2, 2025, submission of the new Vector-borne and Zoonotic Virus Testing Intake Form is mandatory, along with the General Test Requisition when requesting specific vector-borne or zoonotic virus tests. The new intake form replaces both the Arbovirus (Non-Zika) Testing Intake Form and the Mandatory Intake Form for Zika Virus Testing.
Testing Indications
Note: A clinical and epidemiological risk assessment for SLEV infection is recommended prior to submitting a test request. Due to the limited availability of SLEV testing, sufficient justification for these requests is necessary. Requests require approval by a PHO Microbiologist and may be cancelled if the above information and specimen requirements, are not received by PHO.
Testing for SLEV is available upon special request via the US CDC. A review of the individual’s clinical status, exposure, and travel history (including relevant dates) and consideration of alternative diagnoses should be completed prior to submitting a SLEV test request to PHO. This information will be required for the approval processes.
The following are considerations for SLEV testing eligibility:
- Infection with SLEV in Canada is rare3. The majority of human SLEV cases occur in the US2,4.
- Individuals with clinical signs/symptoms of infection with relevant travel to SLEV endemic areas (e.g. travel to the US and particularly to Southern states), mosquito bites and/or outdoor recreational activities in endemic areas up to 21 days prior to symptom onset.
- Infection with West Nile Virus (WNV) or other relevant arboviruses should be considered due to overlap in the geographic distribution of the mosquito vectors.
Most SLEV infections are asymptomatic, however, some individuals may become symptomatic with a mild, febrile illness which can progress to neuroinvasive disease.
Serology is the preferred testing method for individuals suspected of SLEV infection. Testing by PCR is not routinely recommended and may be best suited for individuals that are immune compromised4. Testing of asymptomatic individuals is not recommended.
Acceptance/Rejection Criteria
Specimens received without the appropriate forms, relevant clinical information, or approvals (See: Submission and Collection Notes) are subject to cancellation.
CSF specimens submitted without a paired serum will not be accepted.
Specimen Requirements
| Test Requested | Required Requisition(s) | Specimen Type | Minimum Volume | Collection Kit |
St. Louis Encephalitis (SLE) Virus serology |
Serum |
5.0 ml blood or 1.0 ml serum |
Red top or Serum Separator tubes (SST) |
|
St. Louis Encephalitis (SLE) Virus serology |
CSF |
1.0 ml |
Sterile container |
|
St. Louis Encephalitis (SLE) Virus PCR |
Serum |
5.0 ml blood or 1.0 ml serum |
Red top or Serum Separator tubes (SST) |
|
St. Louis Encephalitis (SLE) PCR serology |
CSF |
1.0 ml |
Sterile container |
Submission and Collection Notes
Label the specimen container(s) with the patient’s first and last name, date of collection, and one other unique identifier such as the patient’s date of birth or Health Card Number. For additional information see: Criteria for Acceptance of Patient Specimens. Failure to provide this information may result in rejection or testing delay.
Each specimen submitted for testing must be accompanied by a separate PHO General Test Requisition, with all fields completed.
It is MANDATORY to provide the clinical information, relevant travel(s), and relevant exposures for Vector-borne viruses requested on the Vector-borne and Zoonotic Virus Testing Intake Form. Test requests that are submitted without the appropriate mandatory information are subject to cancellation.
If submitting serum, acute and convalescent serum specimens must be sent together. If there is a suspicion of neuroinvasive disease, CSF must be paired with an acute serum for SLEV testing to be completed. CSF should only be collected if neurological symptoms are present and there is suspicion of neuroinvasive disease. Note: Submission of a CSF specimen alone will not be accepted.
Testing for WNV serology (IgM/IgG) is required by the CDC for any SLEV requests.
Testing for SLEV serology and PCR is not routinely performed and must be approved by a PHO Microbiologist. Submission of the mandatory Vector-borne and Zoonotic Virus Testing Intake Form will initiate the review process at PHO provided the form contains all necessary information. Requests received without the form, forms submitted with insufficient information or insufficient justification for testing are subject to cancellation.
Timing of Specimen Collection
Serology:
- Acute and convalescent sera must be submitted together for SLEV testing.
- The acute specimen should be collected within 10 days of the onset of symptoms.
- The convalescent serum specimen should be collected at least 2 to 3 weeks after the acute specimen.
Molecular (real-time RT-PCR) testing:
Collect specimens for molecular testing ASAP after symptom onset.
Limitations
Haemolysed, icteric, lipemic or microbial contaminated sera or plasma are not recommended for testing.
Storage and Transport
All clinical specimens must be shipped in accordance with the Transportation of Dangerous Goods Act/Regulations.
- For serum separator tubes: centrifuge sample prior to placing in biohazard bag.
- Place each specimen type in an individual biohazard bag and seal. Insert the corresponding requisition in the pocket on the outside of each sealed biohazard bag.
- Clotted blood/serum specimens should be stored at 2-8°C following collection and shipped to PHO on ice packs.
All specimens submitted for molecular testing should be stored at 2-8°C following collection and shipped to PHO on ice packs. If a delay in transport to PHO is anticipated (more than 72 hours), specimens should be frozen (at -80°C if possible) and shipped on dry ice.
Test Frequency and Turnaround Time (TAT)
Due to the limited access to SLEV testing, the TAT for SLEV serology and/or molecular testing will be determined at the time of specimen receipt in consultation with the National Microbiology Laboratory (NML) and CDC. TAT can be affected by shipping times, testing schedules and the need for confirmatory testing.
All SLEV requests, if approved by a PHO Microbiologist, are referred to the CDC in Fort Collins by the NML if all requirements and testing criteria are met.
Serology:
SLEV antibody screens are performed using an IgM capture enzyme-linked immunosorbent assay (ELISA) or indirect immunofluorescence assay (IFA), as appropriate4. Confirmatory testing is performed by plaque reduction neutralization tests (PRNT)4.
Molecular (real-time RT-PCR)
Tests to detect SLEV RNA are performed by reverse-transcription polymerase chain reaction (RT-PCR).
Algorithm
SLEV antibody screening is performed to detect the presence of IgM/IgG antibodies. Specimens that are antibody screen reactive will be tested for neutralizing antibodies by PRNT to determine whether the reactive screen is SLEV specific or due to cross-reactivity with another flavivirus infection (e.g., West Nile virus, Powassan virus) or non-specific reactivity.
Molecular testing by RT-PCR can be performed on specimens collected early in the disease course or from individuals that are immune compromised. A negative result does not rule out SLEV infection.
Reporting
The CDC laboratory will send all reports to the NML. The NML will then forward these reports to PHO for reporting.
Results are reported to the physician, authorized health care provider (General O. Reg 45/22, s.18) or submitter as indicated on the requisition.
Positive specimens are reported to the Medical Officer of Health as per the Ontario Health Protection and Promotion Act.
References
- International Committee on the Taxonomy of Viruses (ICTV). 2025. Flaviviridae. Available from: https://ictv.global/report/chapter/flaviviridae/flaviviridae/orthoflavivirus
- Centers for Disease Control and Prevention (CDC). 2024. St. Louis Encephalitis Virus – Historic Data (2003-2023). Available from: https://www.cdc.gov/sle/data-maps/historic-data.html
- Artsob H. 2000. Arthropod-borne disease in Canada: A clinician's perspective from the ‘Cold Zone’. Paediatrics and Child Health. 5(4): 206-212.
- Centers for Disease Control and Prevention (CDC). 2024. Clinical Testing and Diagnosis for St. Louis encephalitis. Available from: https://www.cdc.gov/sle/about/index.html
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