Sign in →

Test ID SCOFR Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA, Influenza Virus Type A and Type B RNA, and Respiratory Syncytial Virus (RSV) RNA Detection by PCR, Varies

Ordering Guidance

Due to the non-specific clinical presentation of COVID-19, influenza and respiratory syncytial virus during the early stages of flu-like illness, concurrent testing for these 4 respiratory tract viral pathogens may be warranted.


For the most up-to-date information and testing recommendations, visit:

Shipping Instructions

Ship specimens refrigerated (if less than 72 hours from collection to arrive at MCL) or frozen (if greater or equal to 72 hours from collection to arrive at MCL).

Specimen Required

Specimen Type: Nasopharyngeal (NP), oropharyngeal (OP ie, throat), nasal mid-turbinate, or nares/nasal swab


-Swab, Sterile Polyester, 10 per package (T507)

-Dacron-tipped swab with plastic shaft is acceptable

Container/Tube: Universal transport media, viral transport media, or equivalent (eg, Copan UTM-RT, BD VTM, MicroTest M4, M4-RT, M5)

Media should not contain guanidine thiocyanate (GTC).

For more information on acceptable transport media, see

Specimen Volume: Entire specimen with a minimum of 1.5 mL (maximum 3 mL) of transport media.

Collection Instructions:

1. Collect specimen by swabbing back and forth over nasal or pharyngeal mucosa surface to maximize recovery of cells. For more information on OP swab specimen collection, see COVID-19 Oropharyngeal Collection Instructions

2. NP and OP swab specimens may be combined at collection into a single vial of transport media but only one swab is required for analysis.

3. Swab must be placed into transport medium. Swab shaft should be broken or cut so that there is no obstruction to the sample or pressure on the media container cap.

4. Do not send in glass tubes, vacutainer tubes, or tubes with push caps.

5. Do not overfill with more than 3 mL total volume of media.


Specimen Type: Nasopharyngeal aspirate or nasal washings

Container/Tube: Sterile container

Specimen Volume: Minimum of 1.5 mL

Additional Information: Do not aliquot into viral transport media, glass tubes, vacutainer tubes, or tubes with push caps.

Useful For

Simultaneous detection and differentiation of COVID-19 (due to SARS-CoV-2), influenza A, influenza B, and respiratory syncytial viral infection in a single upper respiratory tract specimen from an individual with flu-like illness


See following websites on indications and recommendations for testing:

Profile Information

Test ID Reporting Name Available Separately Always Performed
COFLU SARS-CoV-2 and Influenza A+B PCR, V Yes Yes

Additional Tests

Test ID Reporting Name Available Separately Always Performed

Method Name

Real-Time Reverse Transcription Polymerase Chain Reaction (RT-PCR)

Reporting Name

SARS-CoV-2, Flu A+B, and RSV PCR, V

Specimen Type


Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Frozen (preferred) 14 days
  Refrigerated  72 hours

Clinical Information

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA virus that causes COVID-19. Like other coronaviruses that infect humans, SARS-CoV-2 can cause both upper and lower respiratory tract infection. Symptoms can range from mild (ie, the common cold) to severe (ie, pneumonia) in both healthy and immunocompromised patients. SARS-CoV-2 transmission occurs primarily via respiratory droplets. During the early stages of COVID-19, symptoms maybe nonspecific and resemble other common respiratory tract infections, such as influenza. If testing for other respiratory tract pathogens is negative, specific testing for SARS-CoV-2 may be warranted.


SARS-CoV-2 is likely to be at the highest concentrations in the nasopharynx during the first 3 to 5 days of symptomatic illness. As the disease progresses, the viral load tends to decrease in the upper respiratory tract, at which point lower respiratory tract specimens (eg, sputum, tracheal aspirate, bronchoalveolar fluid) would be more likely to have detectable SARS-CoV-2.


Influenza, also known as the "flu," is an acute, contagious respiratory illness caused by influenza A, B, and C viruses. Of these, only influenza A and B are thought to cause significant disease, with infections due to influenza B usually being milder than infections with influenza A. Influenza A viruses are further categorized into subtypes based on the 2 major surface protein antigens: hemagglutinin (H) and neuraminidase (N).


Common symptoms of influenza infection include fever, chills, sore throat, muscle pains, severe headache, weakness, fatigue, and a nonproductive cough. Certain patients, including infants, the elderly, the immunocompromised, and those with impaired lung function, are at risk for serious complications. In the northern hemisphere, annual epidemics of influenza typically occur during the fall or winter months. However, the peak of influenza activity can occur as late as April or May, and the timing and duration of flu seasons vary.


Influenza infection may be treated with supportive therapy, as well as antiviral drugs such as the neuraminidase inhibitors: oseltamivir (Tamiflu) and zanamivir (Relenza). These drugs are most effective when given within the first 48 hours of infection, so prompt diagnosis and treatment are essential for proper management.


Respiratory syncytial virus (RSV) is an infectious pathogen that infects the human respiratory tract causing an influenza-like illness. Most healthy people spontaneously recover from RSV infection in 1 to 2 weeks, but infection can be severe in infants, young children, and older adults. The virus is the most common cause of bronchiolitis (inflammation of the small airways in the lung) and pneumonia in children under 1 year of age in the United States, and it is recognized increasingly as a frequent cause of respiratory illnesses in older adults.


RSV can be detected by polymerase chain reaction in the human upper and lower respiratory tract specimens. Nasopharyngeal swabs or aspirates are the preferred specimen types for detection of RSV RNA. Nasal swabs may not yield as high detection rate as those of nasopharyngeal specimens for molecular detection of RSV RNA.

Reference Values



A "Detected" result indicates that the specific virus is present and suggests infection with the virus. Test results should always be considered in the context of patient's clinical history, physical examination, and epidemiologic exposures when making the final diagnosis.


An "Undetected" result indicates that the specific virus is not present in the patient's specimen. However, this result may be influenced by the stage of the infection, quality, and type of the specimen collected for testing. Result should be correlated with patient's history and clinical presentation.


An "Indeterminate" result of SARS CoV-2 RNA polymerase chain reaction (PCR) suggests that the patient may be infected with a variant SARS-CoV-2 or SARS-related coronavirus. Additional testing with an alternative molecular method is recommended on a newly collection specimen may be considered if the patient does not have signs and/or symptoms of COVID-19.


An "Inconclusive" result indicates that the presence or absence of the specific virus in the specimen could not be determined with certainty after repeat testing in the laboratory, possibly due to reverse transcription-polymerase chain reaction inhibition. Submission of a new specimen for testing is recommended.

Clinical Reference

1. Centers for Disease Control and Prevention (CDC). Overview of testing for SARS-CoV-2. CDC; Updated August 25, 2022. Accessed September 8, 2022. Available at

2. Centers for Disease Control and Prevention (CDC), National Center for Immunization and Respiratory Diseases (NCIRD). Information for clinicians on influenza virus testing. Updated August 29, 2022. Accessed September 8, 2022. Available at

3. US Food and Drug Administration. FAQs on testing for SARS-CoV-2. Updated January 22, 2022. Accessed September 8, 2022. Available at

4. National Center for Immunization and Respiratory Diseases (NCIRD), Division of Viral Diseases, Centers for Disease Control and Prevention (CDC). Respiratory syncytial virus infection (RSV). Updated December 18, 2020. Accessed September 8, 2022. Available at

Day(s) Performed

Monday through Sunday

Report Available

2 to 3 days

Test Classification

See Individual Test IDs

CPT Code Information



LOINC Code Information

Test ID Test Order Name Order LOINC Value
SCOFR SARS-CoV-2, Flu A+B, and RSV PCR, V 95941-1


Result ID Test Result Name Result LOINC Value
610295 Influenza A RNA PCR 92142-9
610296 Influenza B RNA PCR 92141-1
610294 SARS CoV-2 RNA PCR 94500-6
CFLUS SARS-CoV-2 & Flu A/B Specimen Source 31208-2
CFRAC Patient Race 72826-1
CFETH Patient Ethnicity 69490-1