SARS-CoV-2 Omicron variant

The Omicron variant is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first reported to the World
Health Organization (WHO) from South Africa on 24 November 2021.[1] On 26 November 2021, the WHO designated it
as a variant of concern and named it "Omicron", the fifteenth letter in the Greek alphabet.[2][3]

The variant has an unusually large number of mutations, several of which are novel[4][5] (see § Mutations) and a significant
number of which affect the spike protein targeted by most COVID-19 vaccines at the time of discovering the Omicron
variant. This level of variation has led to concerns regarding its transmissibility, immune system evasion, and vaccine
resistance, despite initial reports indicating that the variant causes less serious disease than previous strains. The variant was
quickly designated as being "of concern", and travel restrictions were introduced by several countries in an attempt to slow
its international spread. As of 15 December 2021, the variant has spread to over 80 countries.

The new variant was detected on 22 November 2021 in laboratories in Botswana[6] and South Africa.[7] The global
Omicron variant and other major or
patient zero was a man arriving in Hong Kong from South Africa via Qatar on 11 November.[8] Another early case on 19
previous variants of concern of
November was later identified in the Netherlands.[9]
SARS-CoV-2 depicted in a tree
scaled radially by genetic distance,
derived from Nextstrain on 1
Contents December 2021

Classification
Nomenclature
Mutations
Stealth variant
Possible consequences
Signs and symptoms
Characteristics
Contagiousness
Virulence
Diagnosis
Prevention
Treatment
Epidemiology
Statistics
History
Reported cases
Market reactions
International response
See also
Notes
References
Further reading
External links

Classification

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 omicron.[1][2][3] 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.[2][3][10][11] The previous designation was
for the "variant of interest" mu. [12][13][3]

Possibly due to a lack of familiarity with the Greek alphabet among some English speakers, the name of the variant has also occasionally been mispronounced as
"Omnicron".[14][15][16][17]

The GISAID project has assigned it the clade identifier GR/484A,[18] and the Nextstrain project has assigned it the clade identifier 21K.[19]

Mutations
 Genomic sequence

The variant has many mutations, some of which have concerned scientists.[21] The Omicron variant has a total of 60 mutations compared to the original Wuhan
variant: 50 nonsynonymous mutations, 8 synonymous mutations, and 2 non-coding mutations.[5] 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.[22][23] 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.[24] The furin cleavage site increases SARS-CoV-2 infectivity.[25] The mutations by genomic region are the
following:[26][27]

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 Omicron variant.[29] 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.[30] This is the case in HIV patients in South Africa, who represent more than 20% of the
population.[31] 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 that uncontrolled HIV is driving the emergence of Covid variants.[32]

Stealth variant

Researchers have established the existence of two variants of Omicron. The 'standard' one is now referred to as BA.1/B.1.1.529.1, and a second variant of
Omicron is known as BA.2/B.1.1.529.2. BA.2 has been nicknamed 'Stealth Omicron' because it differs from the 'standard' variety by not having the characteristic
SGTF-causing deletion (Δ69-70) by which many PCR tests were able to detect it as an Omicron, or Alpha, variant.[33] Some countries, including Denmark, use a
variant qPCR that tests for several mutations, including Δ69-70, E484K, L452R and N501Y.[34] It can also distinguish Delta (the heavily dominant variant
worldwide, prior to the spread of Omicron), which has L452R but not N501Y,[35] and both Omicron sublineages, which have N501Y but not L452R.[36][37]

Possible consequences

The WHO is concerned that a large number of mutations may reduce immunity in people who were previously infected and in vaccinated people. It is also
possible the omicron variant might be more infective in this regard than prior variants. The effects of the mutations, if any, are unknown as of late November 2021.
The WHO warns that health services could be overwhelmed especially in nations with low vaccination rates where mortality and morbidity rates are likely to be
much higher, and urges all nations to increase COVID-19 vaccinations.[38]

Professor Paul Morgan, immunologist at Cardiff University, also recommends vaccination. Morgan said, "I think a blunting rather than a complete loss [of
immunity] is the most likely outcome. The virus can't possibly lose every single epitope on its surface, because if it did that spike protein couldn't work any more.
So, while some of the antibodies and T cell clones made against earlier versions of the virus, or against the vaccines may not be effective, there will be others,
which will remain effective. (...) If half, or two-thirds, or whatever it is, of the immune response is not going to be effective, and you're left with the residual half,
then the more boosted that is the better."[39]
Professor Francois Balloux of the Genetics Institute at University College London said, "From what we have
learned so far, we can be fairly confident that – compared with other variants – Omicron tends to be better Defining mutations in the
SARS-CoV-2 Omicron variant
able to reinfect people who have been previously infected and received some protection against COVID-19.
That is pretty clear and was anticipated from the mutational changes we have pinpointed in its protein Gene Amino acid
structure. These make it more difficult for antibodies to neutralise the virus."[40] nsp3: K38R

On 15 December, the European Centre for Disease Prevention and Control assessed that, even if the variant nsp3: V1069I
turns out to be milder than Delta, its spread will very likely increase hospitalizations and fatalities due the nsp3: Δ1265
exponential growth in cases caused by increased transmissibility.[41]
nsp3: L1266I
nsp3: A1892T
Signs and symptoms
ORF1ab nsp4: T492I

No unusual symptoms had been associated with the variant as of 26 November 2021, and, as with other nsp5: P132H
variants, some individuals are asymptomatic.[42] Angelique Coetzee, chair of the South African Medical nsp6: Δ105-107
Association, said she had first encountered the variant in patients who had fatigue, aches and pains, but no
nsp6: A189V
cough or change in sense of smell or taste.[43]
nsp12: P323L
British epidemiologist Tim Spector said in mid-December 2021 that the majority of symptoms of the Omicron nsp14: I42V
variant were the same as a common cold, including headaches, sore throat, runny nose, fatigue and sneezing,
so that people with cold symptoms should take a test. "Things like fever, cough and loss of smell are now in A67V
the minority of symptoms we are seeing. Most people don’t have classic symptoms." People with cold Δ69-70
symptoms in London (where Covid was spreading rapidly) are "far more likely" to have Covid than a
T95I
cold.[44]
G142D,

Characteristics Δ143-145
Δ211
Many of the mutations to the spike protein are present in other variants of concern and are related to increased L212I
infectivity and antibody evasion. Computational modeling suggests that the variant may also escape cell-
ins214EPE
mediated immunity.[23] On 26 November, the ECDC wrote that an evaluation of the neutralizing capacity of
convalescent sera and of vaccines is urgently needed to assess possible immune escape, saying these data are G339D
expected within two to three weeks.[27] S371L
S373P
Contagiousness S375F
K417N
It was not known in November 2021 how the variant would spread in populations with high levels of
immunity. It was also not known if the omicron variant causes a milder or more severe COVID-19 infection. N440K
According to pharmaceutical companies, vaccines could be updated to combat the variant "in around 100 G446S
days" if necessary.[45]
S477N
Relating to naturally acquired immunity, Anne von Gottberg, an expert at the National Institute for T478K
Communicable Diseases, believed at the beginning of December 2021 that immunity granted by previous Spike
E484A
variants would not protect against Omicron.[46]
Q493R
On 15 December 2021 Jenny Harries, head of the UK Health Security Agency, told a parliamentary G496S
committee that the doubling time of COVID-19 in most regions of the UK was now less than two days,
despite the majority of the population being vaccinated. She said that the Omicron variant of COVID-19 is Q498R
"probably the most significant threat since the start of the pandemic", and that the number of cases in the next N501Y
few days would be "quite staggering compared to the rate of growth that we've seen in cases for previous
Y505H
variants".[47]
T547K
Work made available online by researchers at the University of Hong Kong on 15 December 2021 before D614G
peer review reports that Omicron grew seventy times faster than Delta in bronchial tissue, which could help
explain the variant's rapid transmission. Omicron also grew ten times slower in lung tissue, which the authors H655Y
suggest could indicate lower disease severity. The researchers said that the result needed to be interpreted N679K
with caution; in particular, even a less virulent variant could cause more cases of severe disease and death by P681H
infecting more people, concluding that "the overall threat from the Omicron variant is likely to be very
significant".[48][49] N764K
D796Y

Virulence N856K
Q954H
Fergus Walsh wrote in November 2021 "South Africa has a young population and it is encouraging that N969K
doctors there are reporting that Omicron is causing mild symptoms with no increase in hospital admissions.
But we need to see what happens when the variant moves into older age groups who are the most vulnerable L981F
to Covid."[50] However, in an update on the variant, the World Health Organization stated "Preliminary data E T9I
suggests that there are increasing rates of hospitalization in South Africa",[51] even if it has not been
D3G
determined that this is attributed to this specific variant.
M Q19E
On 4 December 2021, the South African Medical Research Council reported that from 14 to 29 November A63T
2021 at a hospital complex in Tshwane, inpatients were younger than in previous waves and the ICU and
oxygen therapy rates were lower than in earlier waves. These observations are not definitive and the clinical P13L
profile could change over the following two weeks, allowing for more accurate conclusions about disease Δ31-33
severity.[52] Excess deaths nearly doubled in the week of 28 November, suggesting under-reporting, but the N
R203K
level was still much lower than that seen in the second wave in mid-January.[53] On 12 December, director-
general of the World Health Organization Tedros Adhanom asserted that it was "wrong for people to G204R
consider Omicron as mild". This is because high exposure to previous infections in South Africa likely Sources: UK Health Security Agency[20] CoVariants[19]
 Illustration of the locations of the Omicron mutations in the spike protein, top view (left) and side view (right), showing amino acid substitutions (yellow), deletions (red),
and insertions (green). In this trimeric structure, two monomers (gray and light blue) have their receptor-binding domains in the "down" conformation while one (dark blue) is
in the "up" or "open" conformation. Mutation data from WHO,[1] structure from PDB: 6VYB (https://www.rcsb.org/structure/6VYB).[28]

affects the clinical course of the new infections.[54] As of 15 December 2021, 20 days after the first significant uptick in South Africa cases, there was still no
significant uptick in COVID deaths. This contrasted with the previous two waves, in both of which a substantial increase in deaths occurred starting 12 days after
the first uptick in cases.[55]

A preliminary study by Neil Ferguson and others at Imperial College London reported on 18 December 2021 found that vaccines were substantially less effective
against Omicron than Delta, and found no evidence that Omicron was milder than Delta. Vaccine protection against symptomatic infection was 4.5% less potent
than against other variants, although much better after a third "booster" dose. However, the early data suggest that protection against infection severe enough to
require hospitalisation remained at 80–86% sixty days after a booster, compared to over 95% for Delta. While 80% is good protection individually, at population
level it would lead to many cases requring treatment.[56]

Diagnosis
The FDA has published guidelines on how PCR tests will be affected by Omicron."SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests" (https://www.fd
a.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests). FDA. 16 December 2021. Retrieved
16 December 2021. Tests that detect multiple gene targets will continue to identify the testee as positive for COVID-19. S-gene dropout or target failure has been
proposed as a shorthand way of differentiating Omicron from Delta.

The variant may be identified by sequencing and genotyping.[57] The BA.1 lineage, but not the BA.2 lineage, can be identified by S gene target failure (SGTF) of
the TaqPath assay, a trait shared with subsets of SARS-CoV-2 Alpha variant.[33] Several other commercial assays can also be used, though they test for different
amino acid substitutions.[a]

Prevention
As with other variants, the WHO recommended that people continue to keep enclosed spaces well ventilated, avoid crowding and close contact, wear well-fitting
masks, clean hands frequently, and get vaccinated.[1][58]

On 26 November 2021, BioNTech said it would know in two weeks whether the current vaccine is effective against the variant and that an updated vaccine could
be shipped in 100 days if necessary. AstraZeneca, Moderna and Johnson & Johnson were also studying the variant's impact on the effectiveness of their
vaccines.[59] On the same day, Novavax stated that it was developing an updated vaccine requiring two doses for the Omicron variant, which the company
expected to be ready for testing and manufacturing within a few weeks.[60][61] On 29 November 2021, The Gamaleya Institute said that Sputnik Light should be
effective against the variant, that it would begin adapting Sputnik V, and that a modified version could be ready for mass production in 45 days.[62] Sinovac said it
could quickly mass-produce an inactivated vaccine against the variant and that it was monitoring studies and collecting samples of the variant to determine if a new
vaccine is needed.[63] On 7 December 2021, at a symposium in Brazil with its partner Instituto Butantan, Sinovac said it would update its vaccine to the new
variant and make it available in three months.[64]

On 29 November 2021, the WHO said cases and infections are expected among those vaccinated, albeit in a small and predictable proportion.[65]

On 7 December 2021, preliminary results from a laboratory test conducted at the Africa Health Research Institute in Durban with 12 people who received the
Pfizer-BioNTech vaccine found a 41-fold reduction in neutralizing antibody activity against the variant in some of the samples. This is a big reduction, but it does
not mean that the variant can escape vaccines completely, so vaccination with current vaccines is still recommended. Neutralizing antibody activity against the
variant was greater in those fully vaccinated after being infected about a year earlier. Effectiveness estimates will likely change as more data is collected, as
antibodies generated by vaccination vary widely between individuals and the sample was small.[66][67][68] On 8 December 2021, Pfizer and BioNTech reported
that preliminary data indicated that a third dose of the vaccine would provide a similar level of neutralizing antibodies against the variant as seen against other
variants after two doses.[69] A preprint from Germany also suggests that many of the people who receive three doses of an mRNA vaccine can form antibodies to
omicron.[70]

On 10 December 2021, the UK Health Security Agency reported that early data indicated a 20- to 40-fold reduction in neutralizing activity for Omicron by sera
from Pfizer 2-dose vaccinees relative to earlier strains and a 20-fold reduction relative to Delta. The reduction was greater in sera from AstraZeneca 2-dose
vaccinees, falling below the detectable threshold. An mRNA booster dose produced a similar increase in neutralising activity regardless of the vaccine used for
primary vaccination. After a booster dose (usually with an mRNA vaccine),[71] vaccine effectiveness against symptomatic disease was at 70%–75%, and the
effectiveness against severe disease was expected to be higher.[72]

On 26 November 2021 the WHO asked nations to do the following:

Enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
Submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
Report initial cases/clusters associated with virus-of-concern infection to WHO through the IHR mechanism.
Where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to
improve understanding of the potential impacts of the virus of concern on COVID-19 epidemiology, severity, and the effectiveness of public
health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.[73]

On December 14, Davide Corti et al. released a preprint suggesting that previous infection with COVID-19 with no vaccine or two doses of the Johnson &
Johnson, Sinopharm or Sputnik vaccines were not generating significant antibodies to a virus with an Omicron spike, but many of the health care workers who
had had two doses of the Pfizer or Moderna vaccines and had also previously recovered from COVID-19 did generate antibodies.[74]
Treatment
Corticosteroids such as dexamethasone and IL6 receptor blockers such as tocilizumab(Actemra) are known to be effective for managing patients with the earlier
strains of severe COVID-19. The impact on the effectiveness of other treatments was being assessed in 2021.[75][76]

On 29 November 2021, Pfizer CEO Albert Bourla said that Pfizer had submitted an Emergency Use Authorization application to the FDA for development of the
RNA virus antiviral drug Paxlovid, and the company was confident that it could treat the Omicron variant.[77] Merck and Ridgeback were evaluating the anti–
RNA virus drug molnupiravir for omicron treatment at the time.[78]

Relating to monoclonal antibodies (moAb) treatments, similar testing and research is undergoing. Preclinical data on in vitro pseudotyped virus data demonstrate
that some moAbs designed to use highly conserved epitopes retain neutralizing activity against key mutations of Omicron substitutions.[79]

A preprint of early December 2021 suggests that casirivimab/imdevimab may no longer be effective at inhibiting Omicron.[70] According to another preprint, the
monoclonal antibody sotrovimab may be effective against viruses similar to Omicron.[80] A third preprint suggests that sotrovimab and DXP-604 may function at
reduced efficacy against Omicron, and that the variant may escape tixagevimab/cilgavimab, casirivimab/imdevimab, bamlanivimab/etesevimab and
amubarvimab.[81] Davide Corti et al. released a preprint suggesting that casirivimab/imdevimab and bamlanivimab/etesevimab were generating fewer neutralizing
antibodies, but sotrovimab and Vir-7832 seem to be holding up.[82]

Epidemiology
On 26 November 2021, the South African National Institute for Communicable Diseases announced that 30,904 COVID-tests (in one day) detected 2,828 new
COVID infections (a 9.2% positivity rate).[83] One week later, on 3 December 2021, the NICD announced that 65,990 COVID tests had found 16,055 new
infections (5.7 times as many as seven days before; positive rate 24.3%) and that 72 percent of them were found in Gauteng.[84][85] This province of South Africa
is densely populated at about 850 inhabitants per km2 . Gauteng's capital Johannesburg is a megacity (about 5.5 million inhabitants in the city itself plus 9.5 million
in the urban region).

In November 2021 the transmissibility of the Omicron variant, as compared to the Delta variant or other variants of the COVID-19 virus, was still uncertain.[86]
Omicron is frequently able to infect previously Covid-positive people.[87][88]

It has been estimated the Omicron variant diverged in late September or early October 2021, based on Omicron genome comparisons.[89] Sequencing data
suggests that Omicron had become the dominant variant in South Africa by November 2021, the same month where it had been first identified in the
country.[90][91] "Phylogeny suggests a recent emergence. Data from South Africa suggests that Omicron has a pronounced growth advantage there. However, this
may be due to transmissibility or immune escape related, or both."[92]

Detectable changes in levels of COVID-19 in wastewater samples from South Africa's Gauteng province were seen as early as 17–23 October (week 42).[93] The
National Institute for Communicable Diseases reports that children under the age of 2 make up 10% of total hospital admissions in the Omicron epicentre Tshwane
in South Africa.[94]

A study suggests that Omicron has picked up one of its mutations, ins214EPE, from HCoV-229E, a common cold coronavirus strain, a genetic sequence also
present in the human genome. This appears to aid the virus in circumventing the human immune system.[95][96][97]

In the UK, the logarithmic growth rate of Omicron-associated S gene target failure (SGTF) cases over S gene target positive (SGTP) cases was estimated at 0.41
per day,[b] which is exceptionally high.[98] Furthermore, by 13 December it appears to have become the most dominant strain.[c][99] Without presuming behavior
change in response to the variant, a million infections per day by December 24 are projected for a 2.5 days doubling time.[d][57] In Denmark, the growth rate has
been roughly similar with a doubling time of about 2–3 days (with some geographical differences), it having reached about one-third of all COVID-19 cases on 14
December.[100][101] Switzerland is not far behind and neither is Germany.[102][103] In Scotland, Omicron apparently became the most prevalent variant around 11
December,[104] or otherwise may occur early in the week afterwards. In Ontario it appears to have become the most prevalent strain around 13 December.[105]
Other countries may not have enough timely information, as they may not use Thermo Fisher TaqPath Assay or equivalent for their PCR tests to indicate Omicron.

Data on the SGTF status of sampled cases in South Africa indicates a similar growth of 21% per day relative to Delta, generating an increased reproduction
number by a factor of 2.4[e]. Omicron became the majority strain in South Africa around 10 November.[106][107] Another analysis showed 32% growth per day in
Gauteng, South Africa, having become dominant there around 6 November.[108]

Statistics
The chance of detecting a case particularly depends on a country's sequencing rate. For example, South Africa
sequences far more samples than any other country in Africa, but at a considerably lower rate than most
Western nations.[109][110] Furthermore it can take up to two weeks to return a viral sequence in places with
the technical capability, hence solid statistics on confirmed cases lag the actual situation.[111] Denmark and
Norway regard cases found by their variant qPCR test, which is relatively fast and checks several genes,[34]
as sufficient for counting it as an Omicron, also before full sequencing.[112][113]

Cumulative confirmed Omicron variant cases by

country and territory
10,000–99,999 10–99
1,000–9,999 1–9
100–999 0
 Confirmed and suspected cases by country and territory

Country/Territory Confirmed cases (GISAID)[114] Confirmed cases (other sources)

Suspected cases
as of 19 December as of 19 December

South Africa 1,247 872[115] 19,070[116]

United Kingdom 6,713 24,968[117] 200,000[111][118], 76,705[119]

Denmark 273 15,452[120] -

Canada 71 799[121] 2,674[122]

Norway 179 2,060[112] -

United States 836 321[123] –

Australia 344 406[124] -

Germany 249 77[125] -

Belgium 164 17[126] –

Netherlands 151 105[127] –

France 71 133[128] –

Switzerland 142 13[126] –

Argentina 2 119[129][130] 80[131]

South Korea 9 114[132] -

Israel 90 67[133] -

Botswana 84 23[134] –

Japan 8 65[135] –

Spain 69 14[125] –

India 40 50[136] –

Zimbabwe – 50[137] –

Ghana 40 33[134] –

Ireland 32 39[138] –

Portugal 23 37[139] 6[140][126]

Sweden 52 28[141] –

Estonia – 26[142]

Namibia 17 18[143] –

Hong Kong 18 8[144] –

Austria 69 17[126] –

Russia 3 16[145] –

Italy 48 13[146] –

Brazil 23 11[147] –

Iceland – 12[148] 4[149]

Thailand 12 11[150] 5

Zambia – 11[151] –

Finland 3 34[152][153]
Romania 2 13[154][155] –

Singapore 28 24[156] -

Nigeria 11 6[157] –

Uganda 1 7[158] –

Rwanda 1 6[145] –

Turkey 3 6[159] –

Montenegro 1 5[160] –

Slovenia 2 4[161] –

Greece 2 3[126] –

Croatia 2 3[126] –

Cyprus – 3[162] –

Kenya – 3[163] –

Senegal 7 3[164] –

Egypt – 3[145] –

Malawi 3 3[165] –
 Palestinian Territory – 3[145] –

Taiwan – 3[166] –

Slovakia 3 3[167] –

Fiji – 2[168] –

Jordan 4 2[169] –

Latvia – 2[170] –

Lebanon 4 2 [171] –

Nepal 2 2[172] –

Philippines 2 2[173] –

Reunion 7 2[174] –

Bangladesh 2 2[175] –

Czech Republic 8 2[126] –

Chile 2 2[176] –

Hungary – 2[177] –

Lithuania 3 2[178] –

Mauritius – 2[179] –

Mozambique 17 2[180] –

Oman – 2[181] –

Algeria - 1[145] -

Bahrain - 1[182] -

Cambodia 1 1[183] -

China 1 4[184][185][186] -

Cuba - 1[187] -

Ecuador 1 1[188] -

Indonesia 3 3[189] -

Kuwait - 1[190] -

Liechtenstein 2 1[191] –

Luxembourg 1 1[126] –

Malaysia 2 13[192] –

Maldives 1 1[193] –

Mexico 7 1[194] –

Morocco – 1[195] –

New Zealand 1 1[196] –

Pakistan 1 1[197] -

Poland 2 1[145] -

Puerto Rico 3 1[198] -

Sierra Leone 1 1[199] –

Saudi Arabia – 1[200] –

Sri Lanka 2 1[201] –

Trinidad and Tobago 1 1[202] –

Tunisia – 1[203] –

United Arab Emirates – 1[204] –

World total (92 countries and territories) 11,206 46,211 >200,000

History

Reported cases

On 24 November 2021, the variant was first reported to the WHO from South Africa,[1] based on samples that had been collected from 14 to 16 November.[205]
South African scientists were first alerted by samples from the very beginning of November where the PCR tests had S gene target failure (occurs in a few
variants, but not in Delta which dominated in the country in October) and by a sudden increase of COVID-19 cases in Gauteng; sequencing revealed that more
than 70 percent of samples collected in the province between 14 and 23 November were a new variant.[206][207] The first confirmed specimens of Omicron were
collected on 8 November 2021 in South Africa,[91][208] and on 9 November in Botswana.[23] Likely Omicron (SGTF) samples had occurred on 4 November
2021 in Pretoria, South Africa.[209]

When WHO was alerted on 24 November, Hong Kong was the only place outside Africa that had confirmed a case of Omicron; one person who traveled from
South Africa on 11 November, and another traveler who was cross-infected by this case while staying in the same quarantine hotel.[207][210][211]

On 25 November, one confirmed case was identified in Israel from a traveler returning from Malawi,[212] along with two who returned from South Africa and one
from Madagascar.[213] All four initial cases reported from Botswana occurred among fully vaccinated individuals.[214]

On 26 November, Belgium confirmed its first case; an unvaccinated person who had travelled from Egypt via Turkey on 11 November.[215][216][217] All three
initial confirmed and suspected cases reported from Israel occurred among fully vaccinated individuals,[212] as did a single suspected case in Germany.[218]

On 27 November, two cases were detected in the United Kingdom, another two in Munich, Germany and one in Milan, Italy.[219]

On 28 November, 13 cases were confirmed in the Netherlands among the 624 airline passengers who arrived from South Africa on 26 November.[220]
Confirmation of a further 5 cases among these passengers followed later.[221] Entry into the Netherlands generally required having been vaccinated or PCR-tested,
or having recovered. The passengers of these two flights had been tested upon arrival because of the newly imposed restrictions (which were set in place during
their flight), after which 61 tested positive for SARS-CoV-2.[222] A further two cases were detected in Australia. Both people landed in Sydney the previous day,
and travelled from southern Africa to Sydney Airport via Doha Airport. The two people, who were fully vaccinated, entered isolation; 12 other travellers from
southern Africa also entered quarantine for fourteen days, while about 260 other passengers and crew on the flight have been directed to isolate.[223] Two
travellers from South Africa who landed in Denmark tested positive for COVID-19; it was confirmed on 28 November that both carried the Omicron
variant.[224][225] On the same day, Austria also confirmed its first Omicron case.[226] A detected Omicron case was reported in the Czech Republic, from a
traveler who spent time in Namibia.[227] Canada also reported its first Omicron cases, with two from travelers from Nigeria, therefore becoming the first North
American country to report an Omicron case.[228]

On 29 November, a positive case was recorded in Darwin, Australia. The person arrived in Darwin on a repatriation flight from Johannesburg, South Africa on 25
November, and was taken to a quarantine facility, where the positive test was recorded.[229] Two more people who travelled to Sydney from southern Africa via
Singapore tested positive.[230] Portugal reported 13 Omicron cases, all of them members of a soccer club.[231] Sweden also confirmed their first case on 29
November,[232] as did Spain, when a traveler came from South Africa.[233]

On 30 November, the Netherlands reported that Omicron cases had been detected in two samples dating back as early as 19 November.[234] A positive case was
recorded in Sydney from a traveller who had visited southern Africa before travel restrictions were imposed, and was subsequently active in the community.[235]
Japan also confirmed its first case.[236] Two Israeli doctors have tested positive and have entered isolation. Both of them had received three shots of the Pfizer
vaccine prior to testing positive.[237] In Brazil, three cases of the Omicron variant were confirmed in São Paulo.[238] Another five are under suspicion.[239][240] A
person in Leipzig, Germany with no travel history nor contact with travellers tested positive for Omicron.[241]

On 1 December, the Omicron variant was detected in three samples in Nigeria that had been collected from travelers from South Africa within the last
week.[242][243] On the same day, public health authorities in the United States announced the country's first confirmed Omicron case. A resident of San Francisco
who had been vaccinated returned from South Africa on 22 November, began showing mild symptoms on 25 November[244] and was confirmed to have a mild
case of COVID-19 on 29 November.[245] Ireland and South Korea also reported their first cases.[246] South Korea reported its cases from five travelers arriving in
South Korea from Nigeria.[247]

On 2 December, Dutch health authorities confirmed that all 14 passengers with confirmed Omicron infection on 26 November had been previously
vaccinated.[248] The same day, the Norwegian Institute of Public Health confirmed that 50 attendees of a company Christmas party held at a restaurant in
Norway's capital, Oslo, were infected with the Omicron variant.[249] France has confirmed only 25 cases of the new Omicron variant but officials say the number
could jump significantly in the coming weeks.[250]

By 6 December, Malaysia confirmed its first case of the variant. The case was a South African student entering to study at a private university.[251] Namibia
detected 18 cases of the variant out of 19 positive COVID-19 cases.[252] Fiji also confirmed two positive cases of the variant. They travelled from Nigeria arriving
in Fiji on November 25.[253]

On 8 December, WHO announced the variant had been detected in 57 countries.[254]

On 9 December, Richard Mihigo, coordinator of the World Health Organisation's Immunisation and Vaccine Development Programme for Africa, announced that
Africa accounted for 46% of reported cases of the Omicron variant globally.[255]

On 13 December, the first death of a person with Omicron was reported in the UK.[256]

On 16 December, New Zealand confirmed its first case of the Omicron variant, an individual who had traveled from Germany via Dubai.[257]

Market reactions

Worry about the potential economic impact of the Omicron variant led to a drop in global markets on 26 November, including the worst drop of the Dow Jones
Industrial Average in 2021, led by travel-related stocks. The price of Brent Crude and West Texas Intermediate oil fell 10% and 11.7%, respectively.[258]
Cryptocurrency markets were also routed.[259][260][261] The South African rand has also hit an all-time low for 2021, trading at over 16 rand to the dollar, losing
6% of its value in November.[262][263][264]

In early December 2021, the chairman of the Federal Reserve, Jerome Powell, testified before the U.S. Senate Committee on Banking that "The recent rise in
Covid-19 cases and the emergence of the Omicron variant pose downside risks to employment and economic activity and increased uncertainty for inflation."[265]

International response

On 26 November, WHO advised countries not to impose new restrictions on travel, instead recommending a "risk-based and scientific" approach to travel
measures.[266] On the same day, the European Centre for Disease Prevention and Control (ECDC) reported modeling indicating that strict travel restrictions would
delay the variant's impact on European countries by two weeks, possibly allowing countries to prepare for it.[27]
After the WHO announcement, on the same day, several countries announced travel bans from southern Africa in response to the identification of the variant,
including the United States, which banned travel from eight African countries,[267] although it notably did not ban travel from any European countries, Israel,
Canada, or Australia where cases were also detected at the time the bans were announced. Other countries that also implemented travel bans include Japan,
Canada, the European Union, Israel, Australia, the United Kingdom, Singapore, Malaysia, Indonesia, Morocco, and New Zealand.[268][269]

The Brazilian Health Regulatory Agency recommended flight restrictions regarding the new variant.[270] The state of New York declared a state of emergency
ahead of a potential Omicron spike, although no cases had yet been detected in the state or the rest of the United States.[271] On 27 November, Switzerland
introduced obligatory tests and quarantine for all visitors arriving from countries where the variant was detected, which originally included Belgium and Israel.[272]

In response to the various travel bans, South African Minister of Health Joe Phaahla defended his country's handling of the pandemic and said that travel bans
went against the "norms and standards" of the World Health Organization.[273]

Some speculate that travel bans could have a significant impact on South Africa's economy by limiting tourism and could lead to other countries with economies
that are reliant on tourism to hide the discovery of new variants of concern. Low vaccine coverage in less-developed nations could create opportunities for the
emergence of new variants, and these nations also struggle to gain intellectual property to develop and produce vaccines locally.[274] At the same time, inoculation
has slowed in South Africa due to vaccine hesitancy and apathy, with only 35% of the population being fully vaccinated as of November 2021.[275]

On 29 November 2021, the WHO warned countries that the variant poses a very high global risk with severe consequences and that they should prepare by
accelerating vaccination of high-priority groups and strengthening health systems. WHO director-general Tedros Adhanom described the global situation as
dangerous and precarious and called for a new agreement on the handling of pandemics, as the "current system disincentivizes countries from alerting others to
threats that will inevitably land on their shores." CEPI CEO Richard Hatchett said that the variant fulfilled predictions that transmission of the virus in low-
vaccination areas would accelerate its evolution.[65]

In preparation for the Omicron variant arriving in the United States, president Joe Biden has stated that the variant is "cause for concern, not panic" and reiterated
that the government is prepared for the variant and will have it under control. He also stated that large-scale lockdowns, similar to the ones in 2020 near the
beginning of the pandemic, are "off the table for now."[276]

On 13 December it was reported that cases in Denmark, due to the Omicron variant were doubling every two days, furthermore it would overtake Delta variant as
the dominant variant in a matter of days.[277]

See also
Timeline of the SARS-CoV-2 Omicron variant
COVID-19 pandemic in Africa
COVID-19 vaccination in Africa
COVID-19 vaccination in Botswana
COVID-19 vaccination in South Africa
Variants of SARS-CoV-2
Other variants of either interest or concern: Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Theta, Iota, Kappa, Lambda, Mu

Notes
a. ECDC rapid risk assessment of Omicron,[41] annex 1.
b. Logarithmic growth rate of 0.41/day means that the log odds loge(SGTF/SGTP) is increasing by 0.41 in a day. So SGTF/SGTP was increasing
by a multiplicative factor of exp(0.41) ~ 1.51. This is substantially higher than a naive increase to 100%+41%. The difference is mathematically
due to compound growth within the day, which does not imply that epidemically people are already infectious within a day. Rather, simplified
(non-delay) differential equations are used for convenience for the modeling. This also indicates a doubling time of log_e(2)/(0.41/day) ~ 1.69
days for the Omicron to Delta prevalence ratio.
c. Referring to ref 6 in the reference, where the x-axis is crossed at 13 December
d. A doubling time of 2.5 days corresponds to an exponential growth rate of ln(2)/(2.5 days) ~ 28%/day. Direct comparison to the logistic growth
rate needs to take the growth/decline of Delta into account
e. With a presumed an identical person-to-person serial interval of log_e(2.4)/0.21 ~ 4.2 days, or a distribution thereof to the same effect.

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Further reading
WHO: Update on Omicron (https://www.who.int/news/item/28-11-2021-update-on-omicron)
Live Omicron Variant Location Map (https://omicronvariant.com)
Omicron variant: What have COVID vaccine makers said and are they working on new doses? (https://www.euronews.com/next/2021/12/02/o
micron-variant-what-have-covid-vaccine-makers-said-and-are-they-working-on-new-doses)
Callaway, Ewen; Ledford, Heidi (2 December 2021). "How bad is Omicron? What scientists know so far" (https://www.nature.com/articles/d41
586-021-03614-z). Nature. 600 (7888): 197–199. doi:10.1038/d41586-021-03614-z (https://doi.org/10.1038%2Fd41586-021-03614-z).
PMID 34857948 (https://pubmed.ncbi.nlm.nih.gov/34857948). S2CID 244840636 (https://api.semanticscholar.org/CorpusID:244840636).
Retrieved 3 December 2021.

External links
Corum, Jonathan; Zimmer, Carl (9 February 2021). "Coronavirus Variant Tracker" (https://www.nytimes.com/interactive/2021/health/coronaviru
s-variant-tracker.html). The New York Times. Archived (https://web.archive.org/web/20211130040553/https://www.nytimes.com/interactive/202
1/health/coronavirus-variant-tracker.html) from the original on 30 November 2021. Retrieved 1 December 2021. "Constantly Updated"
Archived video:
Mohale F, Phaahla J, Oliveira T, Lessels R, Gottberg A, Moore P, Crisp N (25 November 2021). Health Department briefs media about a
new so-called super-variant (https://www.youtube.com/watch?v=b4aTIoZDQk4) (Internet video live stream). South Africa: eNCA.
 Retrieved 27 November 2021. Archived at the Wayback Machine (https://web.archive.org/web/20211125215908/https://www.youtube.com/
watch?v=b4aTIoZDQk4) and Ghostarchive (http://ghostarchive.org/varchive/b4aTIoZDQk4).
Oliveira T, Kamwendo S (26 November 2021). Professor Tulio de Oliviera on the new COVID-19 variant (https://www.youtube.com/watch?
v=dMlqRsJ8vuU) (Internet video live stream). South Africa: SABC News. Archived (https://ghostarchive.org/varchive/dMlqRsJ8vuU) from
the original on 29 November 2021. Retrieved 27 November 2021. Archived at the Wayback Machine (https://web.archive.org/web/202111
26125647/https://www.youtube.com/watch?v=dMlqRsJ8vuU) and Ghostarchive (https://ghostarchive.org/varchive/dMlqRsJ8vuU)

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