In the last two weeks, virologists and genomic experts from all over the world have discovered a slew of new Omicron variants, BA.2 subvariants and third-generation subvariants, as well as BA.2 recombinant variants, all of which are circulating and spreading in different parts of the world.
Since December 2021, experts around the world have been warning about such a scenario, and the advent of many new variants, subvariants, and recombinant variants will completely alter the kinetics of the COVID-19 pandemic, as we will see more reinfections and coinfections in non-stop cycles, as well as more new variants produced in these cycles, as well as sub-lineages that can evade vaccine induced immunity, natural immunity, antivirals, and existing
In most cases, the majority of people may experience mild or asymptomatic infections with these new mutations of virus, but they can also cause serious health and medical conditions and we can expect an exponential rise in excess deaths from heart failures, strokes, kidney and liver failures, CVSTs, etc., as these new strains can literally switch off the human host’s initial immune responses.
However, among these many new sub-lineages, at least one potentially fatal mutation has been discovered.
BA.4 and BA.5 mutations
Dr. Cornelius Roemer, a Swiss biophysicist, discovered the BA.4 and BA.5 mutations.
Both the BA.4 and BA.5 lineages have been found in South Africa, where they are now predominating, as well as Germany, Denmark, the United Kingdom, and other European and African countries.
The BA.4/5 have certain common mutations, such as nuc: G12160A, S:L452R, and S:F486V, but not the S:Q493R. (in contrast to all other Omicrons).
The BA.4 variant also known as BA.1.1.529.4 variant having following unique mutations: nuc:27788T, nuc:27259C Key mutations: Spike L452R, F486V, 493Q-reversion; N:P151S
In comparison to BA, COV-spectrum forecasts a large growth advantage over 1/2.
While the BA.5 variant also known as BA.1.1.529.5 variant carries following unique mutations: nuc:27889T, nuc:283 30G Key mutations: Spike L452R, F486V, 493Q-reversion; M:D3N.
COV-spectrum forecasts a significant growth advantage over BA.1/2.
The number of sequences revealing these two variants in various online sequencing databases, such as GISAID, is increasing as of the time of publishing of this article.
New XE Variant of Omicron
The XE variant is one of several recently reported recombinant variants and is essentially a unique fusion of the BA.1 and BA.2 variants. It is the sixth known recombinant variant involving the Omicron variant. (There are other such recombinant BA.1 and BA.2 variants, but the XE has the specific mutations observed exclusively in this lineage.)
A total of 637 cases of XE were confirmed by the British Health Security Agency, with the first reported on January 19.
XD and XF are combinations of delta and omicron BA.1, according to the British Health Security Agency.
There have been 38 cases of XF in the United Kingdom, all of which occurred before mid-February, and there is no evidence that this strain of the virus is spreading within the country.
In global databases, 49 cases of XD have been reported, with the majority occurring in France.
XE has infected roughly 600 persons in the United Kingdom since January. It’s unclear whether XE is more contagious than BA.2, and there’s no evidence that it causes more serious illness.
XE, on the other hand, has demonstrated a fluctuating growth rate and is now being identified in countries like as India, the United States, Canada, Germany, Thailand, and Singapore.
There is insufficient information to draw any judgments concerning transmissibility, severity, vaccination effectiveness, or actual growth benefit at this time.
Other recombinant BA.1/BA.2 variants that are currently in play include:
XP – BA.1.1/BA.2 Recombinant (UK, Scotland)
XQ- BA.1.1/BA.2 Recombinant (UK, Wales)
XR- BA.1.1/BA.2 Recombinant (Wales)
BA.2 subvariants lineage
Early reports link the emergence of BA.2.2 subvariants, such as BA.2.2, which caused a massive outbreak in Hong Kong, to the BA.2.7 subvariant identified in the US.
BA.2.8 (B.1.1.529.2.8) is a Scottish variant with the following mutations: Orf3a:A31T + Nuc:T21048C (2400+ sequences) followed by Orf3a:T9K (2000+ sequences).
According to COV-spectrum, it has a global growth advantage of 34% over BA.2 and >100% over BA.1.1
BA.2.9 also known as B.1.1.529.2.9 prevalent in Denmark and Poland carried key mutations: ORF3a: H78Y, having a global growth advantage of -15% over BA.2 and 15% over BA.1.1, according to the COV-spectrum.
BA.2.10 also known as BA.1.1.529.1.10) identified in India, Singapore and Australia carried key mutation: ORF1b:S959P and has a global growth advantage of -15% over BA.2 and 15% over BA.1.1
BA.2.11 also known as BA.1.1.529.2.11 variant was identified in France as having key mutations: ORF1a:S2519P+S:L452R and has a global growth advantage of 55% over BA.2 and 149% over BA.1.1 (sample size is low – these numbers are not reliable yet).
BA.2.12 variant also known as BA.1.1.529.2.12 was first identified in Canada with key mutations: Spike S704L having a 3% global growth advantage over BA.2 and 47% over BA.1.1.
BA.2.3 Sub-variants also known as third-generation mutations
BA.2.3.1 strain having key mutation Spike: Q677E also known as B.1.1.529.2.3.1 was identified in Japan having a 15% advantage over BA.2 and 59% over BA.1.1 in Japan.
BA.2.3.2 strain also called B.1.1.529.2.3.2 was detected in Vietnam and Japan. Unique Key Mutation found: (Envelope Protein : S55F) and has a 12% advantage over BA.2 and 64% over BA.1.1.
BA.2.10.1 also known as B.1.1.529.2.10.1 was detected in Singapore and some other countries. Unique key mutations: Spike: G798D and it has an 11% growth advantage over BA.2 and 43% over BA.1.1 in Singapore.
BA.2.12.1, also known as BA.1.1.529.12.1, was discovered in the United States and parts of Europe and was found to carry the crucial mutation Spike: L452Q, 47 of the 213 BA. This Spike L452Q mutation has been found in two New York sequences in the last 15 days. This mutation was discovered for the first time in the Lambda variant! and surprisingly it has a 32% growth advantage over BA.2 and 105% over BA.1.1.
Other emerging Variants of Interest under the same linage
South Africa: BA.2 variant found with S:L452R and S:F486V (79 sequences as of 2022-04-05)
UK: BA.2 was found with N:Q39L & ORF1a:S2535LD
Denmark: BA.2 said to have Spike P681R mutation (9 sequences)
Norway and UK: BA.2 found with S:K356R and also has orf1a: s2193f mutations in Norway and UK
With the ORF1ab:E973K mutation, a possible Omicron BA.6 Variant was discovered in Peru and Chile.
Variants of Concern
The BA.2.12.1 variant, also known as BA.1.1.529.12.1, which has been found in New York and other parts of the United States, may turn out to be the most fatal BA.2 sub-variant yet, as it carries the Spike mutation L452Q, which was last seen in the Lambda version.
The L452Q mutation has been associated with enhanced cell fusogenicity, which contributes to disease severity.
To date, all patients who have tested positive for this novel strain are either in intensive care units or have died!
L452R – another deadly variant
Another worrying mutation that boosts fusogenicity and infectivity is the L452R mutation, which is beginning to emerge on many BA.2 subvariants and third-generation types, as well as in the new BA.4 and BA.5 variants. It can be found in many new forms in the UK, South Africa, Denmark, and the rest of Europe, as well.
Increased fusogenicity has been linked to an increase in disease severity and mortality. Long COVID conditions are often severe, with considerable weariness and crippling effects for those who survive.
Future variants
Due to the current dynamics of the COVID-19 outbreak and the lifting of measures and travel restrictions, as well as less testing and sequencing, more Delta subvariants and third and fourth generation variants are also emerging, along with many potential new clades appearing soon.
More worrying strains are expected to surface in the U.K., the U.S., Germany, Denmark, Thailand, and the African continent in the coming weeks, according to specialists.
Image Credit: Getty
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