The Omicron variant of COVID-19 has raised questions about the accuracy of PCR testing. PCR tests are considered the gold standard for detecting SARS-CoV-2, the virus that causes COVID-19. However, some mutations in Omicron may affect the ability of PCR tests to accurately detect infection. Here we review the evidence on PCR test accuracy for Omicron and discuss the implications.
How PCR tests work
PCR (polymerase chain reaction) tests detect the genetic material of SARS-CoV-2 in respiratory samples such as nasal swabs. The test uses primers – short nucleic acid sequences – that bind to specific target regions of the SARS-CoV-2 genome. Using repeated cycles of heating and cooling, the viral RNA is amplified to detectable levels.
Most PCR tests target multiple genes including the N, S, and Orf1ab genes. The S gene encodes the spike protein that the virus uses to infect cells. Mutations in the S gene could potentially interfere with primer binding resulting in false negatives.
Omicron mutations and PCR test targets
Omicron contains over 30 mutations in the spike protein gene. Of particular concern is a mutation called H69/V70 deletion which is located in the S gene target of many PCR tests including the Thermo Fisher TaqPath assay.
Some but not all PCR tests also target the N and Orf1ab genes which are less prone to mutations. PCR tests targeting multiple genes are expected to be more resilient to variants with S gene mutations.
Examples of PCR assays and their targets
- Thermo Fisher TaqPath – S, N, and Orf1ab genes
- Roche cobas – Orf1ab and E genes
- Cepheid Xpert Xpress – E and N2 genes
Evidence on PCR accuracy for Omicron
Studies evaluating PCR tests with the Omicron variant have found:
- S gene target failure (SGTF) occurs with Omicron due to the H69/V70 deletion. This results in an altered PCR profile compared to other variants.
- Despite SGTF, most PCR tests accurately detect Omicron infection when multiple gene targets are used.
- In one UK study, the Roche cobas test (no S target) detected Omicron with equal sensitivity as Delta.
- PCR tests performed better compared to rapid antigen tests in detecting Omicron.
Based on these results, the CDC notes that SGTF PCR results indicate probable Omicron infection that should be confirmed with genomic sequencing when possible.
Implications and limitations
The evidence so far indicates that PCR maintains high accuracy for Omicron detection provided multiple gene targets are used. However, there are some caveats:
- Not all PCR protocols have been directly evaluated for Omicron. More studies are needed.
- SGTF does not rule out Delta or other variants. Only genomic sequencing can definitively identify variants.
- Factors like sample collection and handling can affect PCR sensitivity regardless of mutations.
While PCR remains the most reliable COVID-19 testing method, limitations include:
- Turnaround times of 1-3 days on average, allowing time for spread.
- Many tests still rely on timely reagents and supplies.
- Does not indicate infectiousness.
Interpreting positive and negative PCR results
When interpreting PCR results, cycle threshold (Ct) values provide a semiquantitative measure of viral load. Lower Ct values indicate higher viral load. Studies suggest:
- Omicron infections tend to have lower Ct values compared to Delta early in illness.
- Ct values 30 are less likely to be infectious.
- However, there is no clear Ct cutoff that guarantees infectivity or non-infectivity.
Factors like specimen type and collection technique also affect Ct values. As with previous variants, negative PCR tests cannot completely rule out SARS-CoV-2 infection.
Rapid antigen tests vs PCR
Rapid antigen tests detect SARS-CoV-2 proteins directly unlike PCR tests. Compared to PCR, advantages of antigen tests include:
- Quick results within 15-30 minutes.
- Lower cost and can be performed anywhere.
- Potential to detect infectious virus.
However, antigen tests have lower sensitivity than PCR tests, especially early in infection. Their accuracy depends on:
- Proper sample collection technique.
- Timing during the course of infection.
- Test brand and quality.
Studies show rapid tests detect Omicron but may have reduced sensitivity compared to Delta. Despite limitations, regular rapid testing remains a useful public health strategy.
Conclusions
In summary:
- Most PCR tests accurately detect Omicron infections with minimal impacts from S gene mutations.
- SGTF PCR results can indicate likely Omicron infection.
- PCR maintains higher sensitivity for Omicron than rapid antigen tests.
- Ct values provide an indication of viral load but definitive cutoffs are lacking.
- Negative PCR results cannot rule out infection, especially early on.
- Rapid antigen testing is useful for frequent screening despite slightly lower accuracy.
While promising, data on PCR accuracy for Omicron remains limited. More studies on clinical specimens with genomic confirmation are needed. PCR testing capacity, speed, and access remains a challenge. Testing strategies should utilize both PCR and rapid antigen tests in a tailored and systematic approach based on indication, resources, and community prevalence.