Friday, August 22, 2025

by Adam Irvine, Staff Writer, Physicians Office Resource

Point-of-care (POC) testing has transformed clinical decision-making by enabling rapid diagnostic results in outpatient clinics, urgent care centers, emergency departments, and even at the bedside. Two of the most widely utilized POC diagnostic modalities for infectious diseases are antigen testing and molecular testing (including nucleic acid amplification tests, or NAATs).

While both aim to identify the presence of a pathogen, their methodologies, performance characteristics, and practical implications differ significantly. Understanding these differences is essential for physicians to select the most appropriate test for a given patient, clinical setting, and operational workflow.

Overview of Antigen and Molecular Testing

Antigen Testing
Antigen tests detect specific proteins on the surface of a pathogen, often using lateral flow immunoassay technology. These tests are generally designed for rapid detection, with turnaround times as short as 10–30 minutes. Common POC antigen tests include those for influenza, respiratory syncytial virus (RSV), group A streptococcus, and SARS-CoV-2.

Molecular Testing
Molecular tests detect the genetic material (DNA or RNA) of a pathogen, usually via polymerase chain reaction (PCR) or other nucleic acid amplification techniques such as isothermal amplification (e.g., LAMP, TMA). Historically, these were laboratory-based due to the complexity of equipment and processes. However, recent advances in microfluidics, cartridge-based platforms, and portable analyzers have brought molecular testing into the POC environment, with turnaround times as short as 15–45 minutes.

Benefits of Antigen Testing at the POC

1. Speed and Simplicity

Antigen tests typically provide results in less than 30 minutes without requiring specialized laboratory equipment or personnel. This is particularly beneficial in acute care settings where immediate treatment or isolation decisions are needed.

2. Cost-Effectiveness

Antigen tests are generally less expensive than molecular tests, both in terms of equipment and per-test cost. For high-volume outpatient clinics or resource-limited settings, this can be a significant advantage.

3. Ease of Use

Most antigen tests are CLIA-waived, enabling use in a wide range of clinical settings without the need for high-complexity laboratory certification. Minimal training is required for staff, and sample preparation is often straightforward.

4. Suitability for High Prevalence Scenarios

When disease prevalence is high, the positive predictive value (PPV) of antigen testing increases, making rapid antigen results particularly useful during peak seasonal outbreaks.

Drawbacks of Antigen Testing at the POC

1. Lower Sensitivity

Antigen tests generally have lower sensitivity than molecular tests, especially in cases with low viral or bacterial load. This increases the risk of false-negative results, particularly early or late in the infection course.

2. Variable Performance by Pathogen

While some antigen tests (e.g., group A strep) have relatively strong performance, others (e.g., influenza and SARS-CoV-2) may vary considerably in sensitivity depending on the manufacturer, specimen quality, and timing of testing.

3. Need for Confirmatory Testing

Because of their reduced sensitivity, antigen test negatives may require follow-up molecular testing when clinical suspicion remains high. This can delay final diagnosis and treatment in some cases.

Benefits of Molecular Testing at the POC

1. High Sensitivity and Specificity

Molecular assays are generally considered the gold standard for infectious disease detection due to their ability to amplify and detect minute amounts of pathogen genetic material. Sensitivity often exceeds 95%, even in early infection.

2. Broad Pathogen Detection

Many modern molecular POC platforms are multiplex-capable, enabling detection of multiple pathogens from a single sample (e.g., SARS-CoV-2, influenza A/B, and RSV in one assay). This is especially valuable in patients with overlapping clinical presentations.

3. Improved Diagnostic Confidence

The high accuracy of molecular testing reduces the need for confirmatory testing and minimizes false negatives, enabling more confident clinical decision-making.

4. Utility in Low Prevalence Settings

Because of their high specificity, molecular tests maintain strong positive predictive value even when disease prevalence is low—something antigen tests struggle with due to higher false-positive rates under these conditions.

Drawbacks of Molecular Testing at the POC

1. Higher Cost

Molecular POC instruments and consumables are significantly more expensive than antigen tests. This includes the upfront investment in analyzers and the per-cartridge cost for each test.

2. Longer Turnaround Time

Although much faster than traditional lab-based PCR, molecular POC tests typically require 15–45 minutes to produce results—longer than most rapid antigen assays. In high-volume settings, this can create workflow bottlenecks.

3. More Complex Operation

While simplified compared to central lab PCR, many molecular systems still require more operator training and careful handling to prevent contamination. Some platforms are CLIA moderate complexity, restricting use in certain settings.

4. Maintenance and Supply Chain Considerations

POC molecular instruments require calibration, periodic maintenance, and reliable access to proprietary test cartridges—factors that may complicate deployment in smaller or resource-limited facilities.

Comparative Performance in Clinical Practice

To illustrate the differences, consider SARS-CoV-2 testing:

• Antigen POC Tests: Sensitivity around 80–85% in symptomatic patients within the first five days of symptom onset; specificity typically >97%.
• Molecular POC Tests: Sensitivity >95% and specificity >99% across a wider time frame, including pre-symptomatic and later stages of illness.

In influenza, antigen tests have sensitivities ranging from 50–80% depending on the patient population and test brand, while molecular influenza assays typically exceed 95% sensitivity.

Clinical Decision-Making at the Point of Care

Choosing between antigen and molecular testing at the POC involves balancing diagnostic accuracy, turnaround time, cost, and clinical urgency.

• When speed outweighs sensitivity: In scenarios such as school or workplace clearance, rapid antigen testing offers a practical solution, particularly when positive results will be acted upon immediately and negative results are unlikely to alter management.
• When accuracy is paramount: In high-risk patient populations (immunocompromised, elderly, comorbidities) or when the consequences of a missed diagnosis are significant, molecular testing is the preferred choice.
• Hybrid approaches: Some facilities deploy antigen testing for initial screening with reflex molecular testing for negatives in high-suspicion cases. This strategy can balance speed, cost, and accuracy.

Operational Considerations for Physicians

When implementing POC testing protocols, physicians should consider:

1. Regulatory Requirements – Determine whether the test is CLIA-waived or moderate complexity.
2. Staff Training – Even simple tests require competency training and ongoing quality control.
3. Workflow Integration – Consider how testing fits into patient flow and result documentation in the EHR.
4. Cost-Benefit Analysis – Factor in not only per-test cost but also the potential cost savings from reduced follow-up visits, hospitalizations, or unnecessary treatments.
5. Supply Chain Reliability – Ensure consistent access to test kits, reagents, and maintenance services.

Future Directions in POC Infectious Disease Testing

The gap between antigen and molecular testing is narrowing. Emerging technologies such as ultrasensitive digital immunoassays are boosting antigen sensitivity to near-PCR levels, while molecular test manufacturers continue to reduce turnaround times and device costs. Additionally, the expansion of multiplex respiratory panels in POC formats will allow physicians to rapidly differentiate between pathogens that present with similar symptoms, streamlining both diagnosis and treatment.

Key Takeaways

• Antigen tests offer speed, simplicity, and affordability, making them valuable in high-prevalence or resource-limited settings, but their lower sensitivity requires careful interpretation.
• Molecular tests deliver superior accuracy and diagnostic confidence, especially in low-prevalence settings or high-risk patients, but come with higher costs and slightly longer turnaround times.
• A strategic, patient-centered approach—possibly combining both modalities—can optimize care while balancing cost and efficiency in point-of-care settings.