# PCR

> Polymerase chain reaction. Molecular method for detecting viral DNA or RNA. For hantaviruses: sensitivity ~92%, specificity 100%, result in a few hours.

Canonical source: https://hantatracker.fr/en/glossary/pcr/

**Aliases**: RT-PCR, RT-qPCR, PCR test, polymerase chain reaction

**PCR** (polymerase chain reaction) is a molecular biology technique that amplifies a target DNA or RNA fragment millions of times. For RNA viruses like hantavirus, **RT-PCR** (reverse-transcription PCR) is used, which first transcribes viral RNA into DNA. PCR is the tool of choice for early diagnosis of hantavirus diseases: it was by PCR that Andes virus was identified in MV Hondius patients on 3 May 2026.

## Technical principle

### Exponential amplification

PCR relies on thermal cycles that denature DNA, attach oligonucleotide primers specific to the target sequence, then polymerise a new strand. With each cycle the number of copies doubles. In 30 to 40 cycles, a single original copy can produce up to a billion copies, making the target detectable.

### RT-PCR for RNA viruses

Hantaviruses have an RNA genome. RT-PCR adds a preliminary step of **reverse transcription**: viral RNA is transcribed into complementary DNA (cDNA) by a reverse transcriptase enzyme, then amplified like a standard PCR. RT-qPCR ("quantitative") measures in real time the amount of amplified DNA at each cycle, allowing both detection and viral load estimation in the sample.

## Performance for hantavirus diagnosis

### Sensitivity and specificity

A reference study published in *PLOS Neglected Tropical Diseases* evaluated the performance of an RT-qPCR developed for the diagnosis of hantavirus pulmonary syndrome in South America:

- **Clinical sensitivity**: 92.5%
- **Clinical specificity**: 100%
- **Overall accuracy**: 97.6%
- **Analytical detection limit**: 0.9 viral RNA copy per microlitre

These performances make RT-qPCR the reference test for early diagnostic confirmation, especially in outbreak settings.

### Detection window

Viral load in blood peaks within the **first 5 days of symptoms**, with detection possible up to **about day 11**. Beyond that, PCR sensitivity declines rapidly and serology (searching for IgM then IgG) takes over for diagnosis and epidemiological follow-up.

## Application to MV Hondius

### Identification of the pathogen

For the MV Hondius event, it was PCR that on **3 May 2026** enabled the identification of Andes virus in patients on board. Samples collected during medical evacuations (Saint Helena, South Africa) were sent to European reference virology laboratories for confirmation. Rapid identification triggered international surveillance measures and WHO outbreak notification.

### Contact surveillance

Identified passengers and contacts can benefit from RT-PCR upon onset of any suggestive symptom during the 42-day surveillance period. An early negative test does not exempt from surveillance until the end of the period, since incubation can extend up to 6 weeks.

## Limits and precautions

### False positives and false negatives

No test is perfect. An RT-qPCR may be negative very early (before the viraemic phase), during the recovery phase, or in case of a poor-quality sample. Conversely, laboratory contamination can generate rare false positives. Medical decisions always rely on combining the PCR result with the clinical and epidemiological context.

### Transport logistics

Potentially infectious samples are transported in triple packaging **UN3373** ("biological substance, category B") to reference laboratories. This logistics introduces delays that must be anticipated in clinical management — the result is typically available in 24 to 48 hours rather than a few hours.