variants of concern of SARS-CoV-2 depicted in a tree scaled radially by genetic distance, derived from Nextstrain on 1 December 2021 Nomenclature On 26 November, the WHO's Technical Advisory Group on SARS-CoV-2 Virus Evolution declared PANGO lineage B.1.1.529 a variant of concern and designated it with the Greek letter<unk> . Greek letters are used to identify variants of SARS-CoV-2. The WHO skipped the preceding letters nu and xi in the Greek alphabet to avoid confusion with the similarities of the English word "new" and the Chinese surname Xi. The previous designation was for the "variant of interest" Mu. Possibly due to a lack of familiarity with the Greek alphabet among some English speakers and the relative frequency of the Latin prefix "omni" in other common speech, the name of the variant has also occasionally been mispronounced and misspelled as "Omnicron". The GISAID project has assigned it the clade identifier GR/484A, and the Nextstrain project has assigned it the clade identifiers 21K and 21L, both belonging to a larger<unk>  group 21M. Mutations File:SARS-CoV-2<unk>  (BA.1) variant.The genomic sequence of the<unk>  variant is pictured above. + Gene Amino acid ORF1ab nsp3: K38R nsp3: V1069I nsp3: Δ1265 nsp3: L1266I nsp3: A1892T nsp4: T492I nsp5: P132H nsp6: Δ105-107 nsp6: A189V nsp12: P323L nsp14: I42V Spike A67V Δ69-70 T95I G142D, Δ143-145 Δ211 L212I ins214EPE G339D S371L S373P S375F K417N N440K G446S S477N T478K E484A Q493R G496S Q498R N501Y Y505H T547K D614G H655Y N679K P681H N764K D796Y N856K Q954H N969K L981F E T9I M D3G Q19E A63T N P13L Δ31-33 R203K G204R Sources: UK Health Security Agency CoVariants The variant has many mutations, some of which have concerned scientists. The<unk>  variant has a total of 60 mutations compared to the reference / ancestral variant: 50 nonsynonymous mutations, 8 synonymous mutations, and 2 non-coding mutations. Thirty-two mutations affect the spike protein, the main antigenic target of antibodies generated by infections and of many vaccines widely administered. Many of those mutations had not been observed in other strains. The variant is characterised by 30 amino acid changes, three small deletions, and one small insertion in the spike protein compared with the original virus, of which 15 are located in the receptor-binding domain (residues 319–541). It also carries a number of changes and deletions in other genomic regions. Additionally, the variant has three mutations at the furin cleavage site. The furin cleavage site increases SARS-CoV-2 infectivity. The mutations by genomic region are the following: * Spike protein: A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F * Half (15) of these 30 changes are located in the receptor binding domain-RBD (residues 319–541) * ORF1ab * nsp3: K38R, V1069I, Δ1265, L1266I, A1892T * nsp4: T492I * nsp5: P132H * nsp6: Δ105-107, A189V * nsp12: P323L * nsp14: I42V * Envelope protein: T9I * Membrane protein: D3G, Q19E, A63T * Nucleocapsid protein: P13L, Δ31-33, R203K, G204R A link with HIV infection may explain a large number of mutations in the sequence of the<unk>  variant. Indeed, in order to be affected by such a high number of mutations, the virus must have been able to evolve a long time without killing its host, nor being eliminated. One such situation occurs in people with a weakened immune system but receiving enough medical care to survive. This is the case in HIV patients in South Africa, who represent more than 20% of the population. Due to lack of access to clinics, fear of stigmatisation and disrupted healthcare, millions living with HIV in the region are not on effective HIV therapy. HIV prevention could be key to reducing the risk of uncontrolled HIV driving the emergence of Covid variants. In addition, it is believed that one of these many mutations, comprising a 9-nucleotide sequence, may have been acquired from another coronavirus (known as HCoV-229E), responsible for the common cold. This is not entirely at times, viruses within the body acquire and swap segments of genetic material from each other, and this is one common means of mutation. One hypothesis to explain the novel mutations is that SARS-CoV-2 was transmitted from humans to mice and mutated in a population of mice sometime between mid-2020 and late 2021 before reinfecting humans. Sublineages and BA.2 subvariant Researchers have established the existence of three sublineages of<unk> . The 'standard' sublineage is now referred to as BA.1 (or B.1.1.529.1), and the two other sublineages are known as BA.2 (or B.1.1.529.2) and BA.3 (or B.1.1.529.3). They share many mutations, but also significantly differ. In general, BA.1 and BA.2 share 32 mutations, but differ by 28. This makes them as different as some other major variants, and it has been suggested that BA.2 should receive its own Greek-letter name. BA.1 has itself been divided in two, the original BA.1 and BA.1.1, where the main difference is that the latter has a R346K mutation. A laboratory study on hamsters and mice in Japan published as a non-peer-reviewed preprint in mid-February 2022 suggested that BA.2, is not only more transmissible than BA.1, but may cause more severe disease. Therapeutic monoclonal antibodies used to treat people infected with COVID did not have much effect on BA.2, which was "almost completely resistant" to casirivimab and imdevimab, and 35 times more resistant to sotrovimab than the original B.1.1 virus. The researchers proposed that BA.2 should be recognised as a unique variant of concern, which would be given its own Greek letter. Detection Ordinary COVID-19 tests, both PCR and rapid, can detect all<unk>  subvariants as COVID-19, but further tests are necessary to distinguish the subvariants from each other and from other COVID-19 variants. A notable difference between the 'standard'<unk>  subvariant and BA.2 is that the latter lacks the characteristic S-gene target failure (SGTF)-causing deletion (Δ69-70) by which many qPCR tests are able to rapidly detect a case as an<unk>  (or Alpha) variant, from the previously dominant Delta variant. Thus, countries that primarily rely on SGTF for detection may overlook BA.2, and British authorities consider SGTF alone as insufficient for monitoring the spread of<unk> . This has resulted in it having been nicknamed 'Stealth<unk> '. Because BA.2 still can be separated from other variants through normal full sequencing, or checks of certain other mutations, the nickname is however inaccurate. Some countries, such as Denmark and Japan, use a variant qPCR that tests for several mutations, including L452R. It can also distinguish Delta, which has L452R, and all<unk>  sublineages, which do not have L452R. As<unk>  became dominant and the Delta variant became rare, the SGTF mutation that had made Delta and BA.2 similar in qPCR tests could now be used for easily separating BA.1 and BA.2 from each other. As a consequence, BA.2 could now be regarded as decidedly un-stealthy. The third<unk>  sublineage, BA.3, is very rare. It has the same SGTF deletion (Δ69-70) as BA.1. In April 2022 the WHO announced it was tracking BA.4 and BA.5 subvariants with BA.4 having been detected in South Africa, Botswana, Denmark, Scotland and England.Early indications from data collected in South Africa suggested BA.4 and BA.5 have a significant growth advantage over BA.2. In addition, there were two new subvariants detected in New York State, USA, which are BA.2.12 and BA.2.12.1, both of which have a significant growth advantage of 23-27% over BA.2 and contributing to a rise in infections in central New York State, centred on Syracruse and Lake Ontario. Affected countries and transmissibility According to early research, BA.2 is roughly 30% to 60% more transmissible than BA.1. As a consequence, it may prolong a COVID-19 wave when it overtakes BA.1, although it is difficult to assess what part is caused by the higher transmissibility of BA.2 in countries that simultaneously reduce restrictions (allowing easier transmission than in earlier periods with more restrictions). A new BA.1–BA.2 recombinant isolated from the UK in January 2022, dubbed the "XE" recombinant, was found by the WHO to be potentially 10% more transmissible than BA.2, making it about 43% to 76% to more transmissible than BA.1, and making the XE recombinant the most contagious variant identified. On 7 April 2022 Brazilian authorities announced the first detected case of a person infected with<unk>  XE. The first known sequence of BA.2 was in a sample from 15 November 2021. In mid-December 2021, BA.2 still appeared to be rare with relatively few sequences from half a dozen countries having been uploaded to GISAID, but subsequently numbers rapidly increased. As of 17 January 2022, BA.2 had been detected in at least 40 countries and in all continents except Antarctica. By 31 January, it had been detected in at least 57 countries. In global samples collected from 4 February to 5 March and uploaded to GISAID, BA.2 accounted for c. 34%, compared to 41% for BA.1.1, 25% for BA.1 and less than 1% for BA.3. In a review two weeks later, covering 16 February to
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