Influenza “PCR vs. Rapid Antigen Test”: Which Should You Choose? A Complete Guide to Accuracy, Cost, and Discomfort

When you develop a fever and visit a hospital, the influenza testing performed will primarily involve two types: the “Rapid Antigen Test” and the “PCR Test (Genetic Test).”

The Rapid Antigen Test is appealing for its convenience, offering results in 15 minutes, but it carries the risk of false negatives. This accuracy can plummet to below 50% after 48 hours post-onset. In contrast, the PCR test boasts nearly perfect accuracy, ranging from 99.5% to 100%, but it comes with the drawbacks of time and cost.

Influenza “PCR vs. Rapid Antigen Test” Thorough Comparison (2025 Japan)

ItemRapid Antigen Test (15-Minute Nasal Swab)PCR Test (Genetic Test)
Time to Result5–15 minutes (On the spot)40 minutes – Next day (Varies by hospital)
Accuracy (Sensitivity)Type A: 88–95%Type B: 70–85%
False Negative Rate (12–36 hours)Type A: 5–10%Type B: 15–25%
False Negative Rate (48+ hours)50–90%Nearly 0% (Still detectable even after 72 hours)
Cost (30% Co-pay)¥600–¥1,500¥1,800–¥3,500
Insurance Coverage HurdleAlmost 100% applicable to anyoneOnly when a doctor deems it “necessary”
Discomfort of Sample CollectionNose 2cm: ★★★★☆Throat: ★★★☆☆
Simultaneous TestingFlu + COVID + RSV is standardAlso possible (Nearly all kits are multi-target)
Actual Frequency of Use99% of people receive this firstOnly 1–3% of people receive this
Doctor’s Trust LevelType A positive → 100% trustNegative → 50–80% trust
Medication Dispensation on Negative ResultCommonly prescribed if symptoms are strongRarely prescribed if negative

Current Usage Scenarios in 2025

SituationTest Actually Used
Common cold symptoms + fever→ 100% Antigen Test
Antigen test negative but symptoms strongly suggest flu→ Another Antigen test the next day, or medication without a test if symptoms are severe
Elderly, underlying conditions, or difficulty breathing→ PCR from the start
Fourth day of high fever despite two negative antigen tests→ Switch to PCR
Need to know the exact strain type for school/facility→ PCR
Went to the emergency room with a fever at 9 PM→ Antigen Test (PCR results available the next morning)

Summary (The Reality in 2025)

What You Want to KnowThe Correct Answer
“I want results fast, cheap, and reasonably accurate.”→ Antigen Test is sufficient.
“I absolutely cannot afford a mistake (hospitalization, high risk).”→ PCR is the only choice.
Those who think “Antigen Negative = Not the flu”→ This is completely wrong! (Doctors only half-trust the negative result.)

Most people will finish with the Antigen Test. PCR is reserved for “those who absolutely must know 100%” and “high-risk individuals.”

At-Home Testing Kit Ranking (Combined COVID-19 and Influenza)

Here is the English translation of the ranking table for at-home diagnostic kits that test for both COVID-19 and Influenza A/B:

RankProduct Name (Manufacturer)Targets DetectedSensitivity (Detection Rate) (Estimate: 12-48h Post-Onset)Result TimeApproximate Price (Per Test)Suitability for Pregnant Women / ChildrenKey Features & Availability
1Panbio COVID-19/Flu A&B COVID + Flu A/BCOVID: Approx. 90%Flu: Approx. 85%15 mins¥1,980 – ¥2,480◎ (Shallow Nasal Swab)
2クイックナビ-Flu+COVIDSame (COVID + Flu A/B)COVID: 88%Flu: 80–85%15–20 mins¥1,780 – ¥2,200◎ (Designed for children’s use)
3KBMラインチェック nCoV/Flu Same (COVID + Flu A/B)COVID: 85%Flu: Approx. 80%15 mins¥1,480 – ¥1,980
4イージードック Flu&COVID-19 Same (COVID + Flu A/B)COVID: 87%Flu: 82%15 mins¥2,200 – ¥2,600◎ (Many cases of use by pregnant women)