In the little under two months since the variant that came to be named as Omicron was detected in southern Africa, fresh surges have been reported in multiple countries the world over. India, too, has seen its share of positive tests shoot up. While Omicron (Pango lineage B.1.1.529) sparked worries over the number of mutations it had gathered, the latest WHO-designated variant of concern (VoC) has since been found to have spawned three subtypes — BA.1, BA.2, BA.3 — the first of which is now reported to be swiftly moving to replace the thus far dominant Delta variant in Maharashtra. Here’s what you need to know.
What Is A Sub-lineage?
Mutations are certainly peculiar. In the normal course, most viruses would prefer to avoid them since they may introduce errors into its genetic code and hamper replication and, hence, the way they spread. Humans, on the other hand, are wary about them since they may end up conferring an evolutionary advantage on the virus, making it tougher to deal with.
The Omicron variant was found to have gathered an unprecedented number of mutations, with more than 30 in its spike protein itself, which the novel coronavirus uses to attack and enter human cells. That despite this virus having a proof-reading mechanism to prevent errors in its genetic code while making copies of itself inside the human body.
Now, a new variant is said to arise when it displays mutations that are unique enough to substantially set it apart from other variants. Typically, these are changes that make the virus able to spread more easily, evade antibodies from infection and vaccines, etc. Lineage connotes “a genetically closely related group of virus variants derived from a common ancestor".
Coming to sub-lineage, the US FDA says that “a new variant or sub-lineage of Sars-CoV-2 may have one or more mutations that differentiate it from the reference sequences or predominant virus variants already circulating in the population", that is other existing variants or the parent lineage.
What Is The BA.1 Sub-lineage?
The WHO says that the “Omicron variant includes Pango lineages B.1.1.529, BA.1, BA.2 and BA.3". It adds that BA.1 accounts for more than 99 per cent of sequences submitted to GISAID as of December 23.
According to a report in The Times Of India, scientists at the Indian Sars-CoV-2 Genomics Consortium, or INSACOG, which is tasked with tracking the mutations of the novel coronavirus through genome sequencing, have found that BA.1 subtype is spreading in tandem with the original Omicron variant “and rapidly replacing the Delta variant in Maharashtra and some other states".
The report quotes a senior scientist as saying that INSACOG is seeing the presence of “more BA.1 sub-lineage now than the original Omicron strain". However, cases linked to BA.1 are classified under the Omicron designation since it is a sub-lineage of the B.1.1.529 variant.
The report said that the BA.2 subtype, too, has shown up in genomic tests, “but this presence is comparatively far too low". They added that no instances of the BA.3 sub-lineage has so far been identified in India.
According to online resource outbreak.info, which sources its data from GISAID, BA.1 is so far the most well-travelled of the members of the B.1.1.529 family, showing up in more than 200,000 sequences since the lineage was identified with its presence now detected in at least 98 countries as of January 10, 2022. Compare that with B.1.1.529, which has been detected in 1,212 sequences and reported in 36 countries.
The BA.2 lineage was detected in 1,617 sequences from a total of 21 countries while only 32 sequences of BA.3 had been detected from seven countries.
What Are The Challenges The Sub-lineages Present?
While WHO has noted that there is “consistent evidence that Omicron has a substantial growth advantage over Delta" and that it is “spreading significantly faster than the Delta variant in countries with documented community transmission, with a doubling time of 2-3 days", data on clinical severity while growing “is still limited". However, it has found that “early data… suggest a reduced risk of hospitalisation for Omicron compared to Delta".
In determining the need for classifying sub-lineages of Omicron, experts had noted that genomes uploaded from multiple countries “whilst having many of the defining mutations of B.1.1.529 do not have the full set and also have a number of their own unique mutations". While the impact of these unique mutations is under investigation as to whether they behave differently from the parent Omicron variant, BA.2 demonstrates a change that has led to it being termed the “stealth" variant.
The reason for BA.2 picking up the moniker is that it does not have the 69-70 deletion in the spike protein that has enabled the presence of Omicron to be picked up by a simple RT-PCR test. RT-PCR tests look for certain markers in the novel coronavirus to return a positive result, but the absence of the 69-70 deletion in a positive sample gives Omicron away. However, the BA.2 subtype does not display the 69-70 deletion and hence cannot be captured in RT-PCR tests.
While the scope for Omicron’s confirmation through an RT-PCR test is seen as a simple expedient to determine the presence of the new VoC, WHO has pointed out that samples need to be certified via genomic sequencing since the deletion in question is also found in other VoCs like Alpha and “subsets of Gamma and Delta, which are circulating at low levels worldwide".