S-gene Drop Out

S-gene Drop Out

Subject – Science and Tech

Context – 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.

Concept –

• 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), the nucleocapsid 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.