The story so far: The Omicron variant of the SARS-CoV-2 virus has been confirmed in India and in at least 30 other countries by the World Health Organization (WHO). While the variant can only be reliably confirmed with genome sequencing, the WHO has also recommended that certain commonly used COVID-19 detection tests, with ‘S-gene dropout’ capabilities, can be used to quickly screen for an Omicron infection.
What is the S-gene drop out?
Tests usually look for three target genes related to parts of the virus: S (spike), N2 (nucleocapsid or inner area) and E (envelope or outer shell). The S-gene refers to the gene that codes for the spike protein, or the most distinctive part of the coronavirus. The SARS-CoV-2, like many other coronaviruses, has key protein-regions that define its structure: The envelope protein (E), thenucleocapsid protein(N), the membrane protein (M) and the spike protein (S). To accurately identify the virus, diagnostic tests are made that can identify characteristic genes that make these proteins. To maintain the balance between cost, turn-around time and efficiency, makers of diagnostic kits usually target 1-3 genes on these regions. The SARS-CoV-2 virus incidentally has one of the largest genomes in the coronavirus family. One popular kit, called the TaqPath COVID-19 assays, identifies three gene targets from three regions one of which is the S region to confirm or rule out the presence of the coronavirus. Some versions of the coronavirus, notably B.1.1.7, known as the Alpha variant, and the Omicron variant (B.1.1.529), have characteristic amino acids missing on the S protein. Amino acids are the building blocks of protein.
When tests designed to look for the ‘S’ gene encounter these coronaviruses with the missing amino acids, they show up as negative for the S gene and this is called the S Gene Targeted Failure or popularly S-gene drop out. Despite the negative ‘S’, the test will return positive in case of the presence of the SARS-CoV-2 virus because the genes on the ‘E’ and ‘N’ will likely signal a match. Some parts of the coronavirus are more conserved, or don’t change too much, and make for more reliable test targets. The spike protein can change a lot—the coronavirus is continually evolving, trying to adapt to antibodies created from vaccines or prior infections—and tests too must keep changing to find appropriate targets.
How is this useful in the case of Omicron?
On November 26, the WHO declared Omicron as a variant of concern, practically the highest level of risk that it attributes to specific variants. It noted that several labs from around the world indicated that for “one widely used PCR test”, one of the three target genes is not detected and this therefore could be used as a marker for this variant, pending sequencing confirmation. Using this approach, this variant had been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.
The WHO appeared to be referencing the TaqPath test but this by no means is the most widely used test in India. A challenge with RT-PCR tests is that companies often don’t reveal what primers, or chemical tools, they employ to look for specific viral genes. Therefore, it is hard to determine which test is best for certain variants and which can fail. “The TaqPath is one of the few that looks for three genes whereas India’s official rules are that they must only be equipped to detect at least two,” said a genome scientist, who declined to be identified. “Their test is a useful surrogate and a quick fix. Other variants and mutations can also cause a dropout and it is possible that the TaqPath doesn’t pick it up.” If a person manifests symptoms and is returning positive on a RT-PCR test, that also returns negative on the S gene, then it’s a sign that the sample ought to be sent for a genome scan.
India only scans a small percentage of positive samples to ascertain genomes and so a test that throws up intriguing results such as an S-gene dropout, may be prioritised for a more thorough genome scan.
What is the most reliable way to check for the new variant?
The Union Health Ministry has stated that all of the standardised RT-PCR tests coupled with genome sequencing are effective at detecting Omicron. While factors such as clinical symptoms and viral loads help in determining the virus, a variant can only be confirmed by genome sequencing which means waiting for a day or even weeks depending on available facilities.
