Variants, Sublineages, and Recombinants: The Constantly Changing Genome of SARS-CoV-2

Subject: Science and technology

Section: Biotechnology

Mutation

When a virus replicates, it makes copies of all of its genes. In the process, it makes mistakes, like typos in the string of 30,000 letters that make up the SARS-CoV-2 genome. Those mistakes may result in changes in the amino acids that make up a protein, altering its structure. Usually, those mistakes are called mutation

Variants

When a population of viruses with the same set of mutations is found in enough hosts, that group is labeled a variant

Variants of Cocern

Variants that have the potential or demonstrated ability to be much more transmissible, immune evasive, or virulent are closely monitored and may be designated as variants of interest (VOIs), or variants of concern (VOCs)
The World Health Organization has designated five variants as VOCs and given them the Greek letter names Alpha, Beta, Gamma, Delta, and Omicron

Classification of SARS-CoV-2 viruses

A clade or lineage is a group of genetically similar viruses with a common ancestor.
A sublineage is a group of similar viruses within a lineage.
A subvariant is a sublineage of a variant, usually referring to a variant of concern.
The WHO includes all of the sublineages of a lineage within its labels for variants of concern.

What is the cause of recent increase in Covid cases

Every time SARS-CoV-2 infects a person and replicates, mutations will occur.As long as SARS-CoV-2 continues to spread, it will evolve and new variants will emerge
In the summer of 2021, a Delta subvariant, now called AY.1, was detected with an additional mutation that was associated with the ability to evade the immune system
More recently, another sublineage of Delta, called AY.4.2, was detected in at least 42 countries. It had three potentially worrisome mutations and began to increase in prevalence in some areas, although it did not reach very high levels worldwide.
Many of the monoclonal antibody treatments that are effective against the Delta variant, for example, are ineffective against the BA.1 sublineage of Omicron
Natural infection too has been found to be less protective against re-infection by the Omicron sub-lineages
Hybrid immunity caused by vaccination and infection was generally seen to offer slightly better protection against infection. But with the Omicron sub-lineages, even hybrid immunity offers no advantage in terms of protecting against re-infections

What is S-Gene Dropout or S-Gene Target Failure (SGTF) test

SGTF was a quick, inexpensive way to track the Omicron variant as it spread throughout the world. Unlike sequencing, which requires more specialized equipment and trained personnel, the SGTF feature allows diagnostic laboratories to detect possible Omicron cases.