The Omicron storm seems to be on. The lineage has been throwing out a series of sub-lineages within a short span of around 4-month. After the XE variant, two more new variants within the Omicron lineage have recently been identified via genome sequencing in the United Kingdom.
The two newly designated variants are BA.4 and BA.5. The Variant Technical Group (VTG) of the UK has identified these two variants as a part of horizontal scanning On April 4, 2022. These two have been categorised as Variant of Interest (VOI). As data on transmissibility and immunity is not available, therefore, they are yet to get entry into the VOC (a variant of concern) club.
As per the UK Health Security Agency (UHSA), the new variant BA.4 shares all the mutations or deletions with the most dominant BA.2 lineage of the Omicron variant. Except for the spike 69/70 deletion that will result in an undetectable S-gene target (S-gene target failure) in the Taqpath assay (test). In the BA.4, the L438F reverted to WT (wild type). Many more mutations in spike and nucleotides are different from BA.2.
Does BA.4 Have New Origin?
The UKHSA report reveals that the earliest BA.4 sample was from South Africa that was collected on January 10, 2022. However, the study by the top UK agency shows the accumulation of genomes and geographic spread as more recent. Countries reporting BA.4 genomes via GISAID now include South Africa (41 genomes), Denmark (3), Botswana (2) and England and Scotland reporting one each.
This has been put under watch as a Variant of Interest (VOI), despite the number of total genomes being small. The big reason behind this is the variant's apparent geographic spread, which suggests that it is transmitting successfully, the report added.
As per the technical data shared by the UKHSA, BA.5 shares the same mutations/deletions as BA.4 except for the following: M: D3N; ORF 7b: L11 (WT); N: P151 (WT); synonymous SNPs: A27038G, and C27889T.
Currently, there are 27 sequences reported with this lineage, all from South Africa. This lineage shows samples collected between February 25 and March 25, 2022.
XE - Picking Up Pace?
The data released by UKHSA on April 7, 2022 hints at gaining pace in the country. When there were 736 XE genomes sequenced as of March 22, 2022, the genomes of the variant were found in 1179 samples as of April 5, 2022.
A look at the numbers tells the tale. For a period of Jan 19 - March 22, the UK had reported only 736 cases. But between March 23 and Apr 5, the XE cases detected in the UK touched 443. This shows the number is picking up pace.
For this, the UKHSA model has pegged XE's growth rate now at 12.6 percent from the earlier rate of 9.8 percent. This growth rate is calculated vis-a-vis the growth rate of other variants like BA.2.
However, the big revelation by the top UK Health agency is in the last 3 weeks, the growth rate had been over 20.9 percent. Cases of XE are being reported mostly from London, Yorkshire and Humber.
The news of respite so far has been that the epi-curve of XE doesn't show consistency. As a consequence, the virologists and molecular scientists are keeping their fingers crossed.
XE In India
After a denial over the detection of the first XE case in Mumbai, it becomes official today that the XE variant has made its debut in the country. The recombinant variant XE variant was detected in a 67-year-old Gujarat man, who had tested positive on March 12. The significant indicator here is the Gujarat resident had travelled from Mumbai to Vadodara and had tested positive for the virus upon arrival.
Only yesterday, BMC had announced the detection of the first XE case in Mumbai, which was later denied by the INSACOG - the country's apex genome sequencing body.
The sequences to date hint that more cases will surface in the coming days. and Mumbai seems to be playing the hub of XE variant in the country.
As of now, there are no significant clues of severity. The XE positive man had returned to Mumbai after giving his sample for sequencing, reports suggest.
XE Age-Group Wise Infection
A study of the limited data provided by UKHSA reveals that maximum XE infections in the UK have been detected in the age group of 20-49 years followed by 50-69 years and 0-9 years.
The gender data shows the female proportion in infections was higher than males in the UK - the only country that has detected the Omicron recombinant.
NHS New Symptom List
After the emergence of a large number of variants, the National Health Service, a publicly funded healthcare system in England, has published a total of new nine symptoms recently. Take a look.
• Loss of appetite
• Feeling very sick
• Blocked or running nose
• Sore throat
• Aching body
• Feeling tired or exhausted
• Shortness of breath
• Continuous cough - means coughing a lot in an hour or 3 or more cough episodes in 24 hr
• Fever with chills