H1N1 (Swine Flu) RNA Detection by Real Time PCR - Swab

Bacterial/ Viral

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No Fasting Required

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RT-PCR is the gold standard for diagnosing active H1N1 infection

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H1N1 (Swine Flu) RNA Detection by Real Time PCR - Swab

Why is it done?
- Detects the presence of H1N1 influenza A virus RNA in respiratory specimens using highly sensitive and specific real-time polymerase chain reaction (PCR) technology
- Confirms suspected H1N1 infection in patients presenting with acute respiratory illness symptoms including fever, cough, sore throat, and body aches
- Performed during acute phase of illness, ideally within 3-4 days of symptom onset for optimal sensitivity, though can be conducted up to 7-10 days after symptom initiation
- Used for epidemiological surveillance, outbreak investigation, and clinical decision-making regarding antiviral therapy and infection control measures
- Guides appropriate patient isolation and treatment initiation, particularly in hospitalized patients and high-risk populations
Normal Range
- Negative Result: No H1N1 RNA detected in specimen. Indicates absence of acute H1N1 infection or specimen collected after viral shedding has ceased.
- Positive Result: H1N1 RNA detected in specimen (expressed as detected/positive). Confirms active H1N1 influenza A virus infection.
- Cycle Threshold (Ct) Value: Some laboratories provide Ct values (typically <30 indicates higher viral load, >30 may indicate lower viral load or borderline positivity)
- Indeterminate/Inconclusive: Rare result indicating suboptimal specimen quality or borderline detection requiring repeat testing
Interpretation
- Positive H1N1 RNA Detection: Confirms active H1N1 infection with high specificity (typically >98%). Indicates patient is infectious and requires antiviral therapy (neuraminidase inhibitors such as oseltamivir/Tamiflu or zanamivir) if clinically indicated. Warrants respiratory isolation precautions.
- Negative H1N1 RNA Detection: Indicates absence of H1N1 infection. However, negative results do not exclude influenza if clinical suspicion is high (consider repeat testing within 24 hours, test for other respiratory viruses, or perform rapid antigen testing if available). Sensitivity ranges from 75-95% depending on specimen type and timing.
- Timing Impact on Interpretation: Testing within first 3-4 days provides optimal sensitivity. Testing after 7-10 days may yield false negatives due to decreased viral shedding. Specimens collected from lower respiratory tract (nasopharyngeal or bronchoalveolar lavage) are more sensitive than oropharyngeal swabs.
- Factors Affecting Results: Improper specimen collection, transport delay, storage temperature variations, immunocompromised status (may have prolonged shedding), and prior antiviral administration can influence test accuracy and viral load quantification.
- Cross-reactivity and Specificity: Real-time PCR is highly specific for H1N1 and does not cross-react with seasonal influenza A (H3N2), influenza B, or other respiratory viruses when properly designed assays are used.
Associated Organs
- Primary Organ System: Respiratory system, including upper respiratory tract (nose, pharynx, throat) and lower respiratory tract (trachea, bronchi, lungs)
- Direct Complications: Acute viral pneumonia, bronchitis, sinusitis, otitis media. Severe disease can progress to acute respiratory distress syndrome (ARDS) requiring mechanical ventilation.
- Secondary Bacterial Infections: Secondary bacterial pneumonia caused by Streptococcus pneumoniae, Staphylococcus aureus (including MRSA), or Haemophilus influenzae can occur following H1N1 infection
- Extrapulmonary Manifestations: Myocarditis (heart muscle inflammation), encephalitis (brain inflammation), myositis, rhabdomyolysis, and exacerbation of underlying chronic diseases
- High-Risk Populations: Pregnant women, immunocompromised patients, elderly individuals, persons with chronic lung disease (asthma, COPD), cardiac disease, diabetes, obesity, and neurological disorders face increased risk of severe complications
- Associated Conditions: Influenza-like illness (ILI), pandemic influenza, nosocomial (hospital-acquired) infection, severe acute respiratory infection (SARI)
Follow-up Tests
- If Positive H1N1 Result: Chest X-ray to assess for pneumonia or pulmonary involvement; complete blood count (CBC) to evaluate for lymphopenia or thrombocytopenia; comprehensive metabolic panel and liver function tests to assess organ involvement
- Secondary Infection Screening: Blood cultures if secondary bacterial infection is suspected; sputum culture and gram stain for hospitalized patients with pneumonic presentation
- If Negative Result with High Clinical Suspicion: Repeat H1N1 PCR within 24 hours from fresh specimen; test for other influenza types (seasonal influenza A H3N2, influenza B); multiplex respiratory panel to detect other viral pathogens (rhinovirus, coronavirus, RSV, parainfluenza, adenovirus, enterovirus)
- Complications Monitoring: Troponin and BNP if myocarditis is suspected; electrocardiography and echocardiography for cardiac evaluation; brain imaging (CT/MRI) if neurological symptoms develop
- Coinfection Assessment: COVID-19 PCR (SARS-CoV-2) if concurrent pandemic or seasonal concerns; testing for other respiratory pathogens in immunocompromised hosts or unusual presentations
- Monitoring Frequency: Hospitalized patients may require serial chest imaging and laboratory monitoring every 24-48 hours; intensive care unit patients require continuous hemodynamic and respiratory monitoring; repeat testing generally not recommended to document cure
- Public Health Follow-up: Reporting to local health departments; contact tracing and monitoring; antiviral susceptibility testing if resistance is suspected
Fasting Required?
- Fasting Required: No
- Patient Preparation: No special preparation required. Patient can eat and drink normally before the test. Test can be performed at any time of day.
- Specimen Collection: Nasopharyngeal or oropharyngeal swab specimens are obtained using sterile plastic-shafted swabs with synthetic fiber tips (avoid calcium alginate or wooden shaft swabs). Specimen should be placed in appropriate transport medium (viral transport medium or saline) immediately after collection.
- Timing Considerations: Ideally collect specimen during acute phase within 3-4 days of symptom onset. Avoid specimen collection immediately after eating, drinking, or smoking in oropharyngeal swab procedures to prevent dilution of secretions.
- Specimen Transport: Transport specimen to laboratory within 2 hours if refrigerated (2-8°C); if longer transport time expected, use viral transport medium designed to preserve virus integrity. Store at 2-8°C, do not freeze unless using specific preservative media.
- Medications: No medications need to be avoided or withheld before testing. Continue all regular medications as prescribed. However, if antiviral medications (oseltamivir) have already been initiated, inform the laboratory as this may affect viral detection timing.
- Special Instructions: Wear standard precautions including gloves and mask during specimen collection; use appropriate respiratory hygiene protocols; label specimen correctly with patient identifiers and collection time; maintain chain of custody documentation throughout transport and handling.

How our test process works!