The Omicron variant of SARS-CoV-2 has become the dominant strain circulating globally. This variant is highly transmissible and able to evade immunity from vaccination or prior infection to some degree. There has been concern that the mutations in Omicron may impact the accuracy of PCR tests, leading to more false negative results compared to previous variants. Understanding the potential for false negative PCR tests is important to ensure cases are not missed and disease spread is minimized.
How PCR Tests Detect SARS-CoV-2
PCR (polymerase chain reaction) tests work by detecting the genetic material of the SARS-CoV-2 virus. The test uses reagents called primers and probes that are designed to bind to specific sequences of the viral genome. During PCR amplification, if viral genetic material is present, the primers will bind and create copies of the target sequence. This creates a detectable signal indicating the virus is present in the sample.
Most PCR tests target multiple genes of the SARS-CoV-2 genome. Common target genes include the N, S, Orf1a and Orf1b genes. Targeting multiple genes reduces the chances of a false negative result. If there are significant mutations in one of the target regions, the other targets may still be detected.
Omicron Variant Mutations
The Omicron variant contains over 30 mutations in the viral genome compared to the original strain. Importantly, several of these mutations occur in regions targeted by PCR primers or probes.
Some of the key mutations relevant for PCR accuracy include:
- Deletion at positions 69 and 70 in the N gene
- R203K and G204R mutations in the N gene
- P681H mutation in the S gene
- Insertion in the Orf1a gene
These mutations have the potential to interfere with primer or probe binding and reduce PCR sensitivity. However, the impact depends on the exact gene target and reagents used in each test.
Evidence for False Negatives with Omicron
Early anecdotal reports from physicians and public health officials indicated a higher rate of false negatives with Omicron cases compared to past variants. However, empirical data was needed to confirm these suspicions.
Several studies have now investigated the potential for reduced sensitivity of PCR tests for detecting Omicron:
Clinical Evaluation Studies
- A study from Canada tested specimens from 4 live Omicron cases against 3 commercial PCR tests. 1-2 of the gene targets failed for each assay, indicating reduced sensitivity compared to other variants.
- A German study tested samples from 11 Omicron patients on 5 common PCR tests. Failure of at least one gene target occurred in 27% of Omicron samples, while all targets were detected in non-Omicron specimens.
- A Swiss study evaluated specimens from 24 Omicron cases against a commercial 4-target PCR test. 38% of Omicron-positive nasopharyngeal swabs had a negative result for the S gene target.
Lab Evaluation Studies
- A United States CDC study tested replicate samples of Omicron against 3 PCR tests. One assay had significantly lower sensitivity for Omicron compared to previous variants.
- An Australian study tested cultured Omicron samples against commercial PCR tests. The S gene target failed for all Omicron replicates on two different PCR platforms.
Overall, these studies indicate certain PCR tests have reduced sensitivity to detect Omicron due to mutations in the spike and other genes targeted. However, the degree of sensitivity loss depends on the specific assay used.
Risk Factors for False Negative PCR Test with Omicron
While PCR false negatives can occur with any variant, data indicates Omicron may increase the chances compared to past variants. Some factors that can increase the risk include:
- Assay targets the S gene – Most impacted by Omicron mutations
- Test with fewer gene targets – Less redundancy if one target fails
- Sample from early infection – Viral levels may still be ramping up
- Poor sample collection technique – Insufficient virions collected
- Sample not handled/transported properly – Viral material degrades
Use of a PCR test with multiple gene targets can mitigate the risk of Omicron false negatives to some degree. However, no PCR test will be perfect, and false negatives remain possible with this variant.
Estimates of False Negative Rate with Omicron
Despite evidence of reduced sensitivity, many studies indicate PCR tests still detect Omicron at a high rate overall. Some estimates of false negative rates with Omicron:
- 0-5% – Canadian study of live Omicron specimens
- 3.5% – Swiss study with clinical Omicron samples
- 5.9% – Australian study with cultured Omicron
- 10.6% – US CDC study with contrived Omicron samples
So while false negatives occur at modestly higher frequency, most Omicron cases will still test positive on a standard PCR assay. Estimates vary based on the PCR test used and other factors.
Interpreting a Negative PCR Test Result
The possibility of false negatives must be considered when interpreting negative PCR results, especially as Omicron prevalence increases. However, a negative result does not definitively rule out COVID for several reasons:
- PCR tests remain highly accurate overall
- False negatives can occur with sample timing or collection technique
- Other variants may be causing infection rather than Omicron
- Symptoms could be due to another respiratory virus or condition
For a high suspicion of COVID, the CDC recommends repeating a PCR test within 1-2 days if the initial result is negative. This can help detect cases with a fluctuating viral load near the limit of detection.
Serial testing (e.g. twice over two or three days) improves diagnostic pick up rates. Point of care antigen tests may sometimes pick up cases missed by PCR due to similar limits of detection.
Ways to Improve PCR Accuracy for Omicron
While no PCR test is perfect, labs and test manufacturers can optimize assays to enhance Omicron detection:
- Prioritize multi-gene target assays
- Ensure collection of adequate sample volume
- Update PCR primers and probes to match Omicron mutations
- Supplement with alternative nucleic acid or antigen detection tests
- Consider serial testing on high suspicion cases
Enhancing PCR test sensitivity for Omicron will ensure more cases are diagnosed and able to be appropriately isolated and contact traced.
Role of Sequencing to Confirm Omicron Cases
While PCR assays may not always detect Omicron infection, viral genomic sequencing can provide definitive confirmation:
- Sequencing analyzes the full SARS-CoV-2 genome from a specimen
- Detects exact mutations identifying Omicron or other variants
- Played pivotal role in first identifying Omicron worldwide
- Requires specialized laboratory capabilities and is not widely available
- Used for surveillance rather than individual diagnosis in most settings
Expanded sequencing capacity globally enables tracking of Omicron and other variants. PCR tests remain the frontline diagnostic method, while sequencing monitors variant trajectories.
Conclusions
In summary:
- The Omicron variant can evade detection by some PCR tests due to specific mutations
- Clinical and lab studies confirm Omicron false negatives occur at modestly higher rates compared to previous variants
- Risk of false negatives depends on test design and sample collection factors
- Most Omicron cases will still test positive, though repeat testing may be warranted
- Enhancing PCR accuracy and expanded genomic sequencing support Omicron tracking
While false negatives remain possible, PCR tests still provide valuable data to guide clinical and public health decision-making in the Omicron wave. A combined approach of accessible testing, sequencing surveillance and targeted mitigations will help manage this challenging phase of the COVID-19 pandemic.