SARS-CoV-2 Omicron variant

Omicron (BA.1) has many mutations, some of which have concerned scientists.[28][29]

The genomic sequence of the Omicron variant is pictured above

Omicron (BA.1) has more mutations than any previous SARS-CoV-2 variant with 50 mutations and approximately 32 of these pertain to the spike protein which most vaccines target to neutralise the virus.[30] Many of the mutations are novel and are not found in previous variants of the virus.[31] 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).[32] It also carries a number of changes and deletions in other genomic regions. Additionally, the variant has three mutations at the furin cleavage site which facilitate transmission of the virus.[33][34]

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,[35] structure from PDB: 6VYB​.[36]

Omicron did not evolve from any other variant, but instead diverged on a distinct track, perhaps in mid-2020.[41][42] Competing hypotheses are being examined.

One origin hypothesis is that various mutations in the Omicron variant, comprising a 9-nucleotide sequence, may have been acquired from another coronavirus (known as HCoV-229E), responsible for the common cold.[43] This is not entirely unexpected — at times, viruses within the body acquire and swap segments of genetic material from each other, and this is one common means of mutation.[43]

A link with HIV infection may explain a large number of mutations in the sequence of the Omicron variant.[44] 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, which can occur in people with a weakened immune system who receive enough medical care to survive.[44][45] This is the case in HIV patients in South Africa, who represent about 14% of the population (as of 2017).[46] HIV prevention could be key to reducing the risk of uncontrolled HIV driving the emergence of SARS-CoV-2 variants.[44]

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.[42]

On 24 November 2021, the variant was first reported to the WHO from South Africa based on samples that had been collected from 14 to 16 November.[37] 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.[47]

The first confirmed specimens of Omicron were collected on 8 November 2021 in South Africa and on 9 November in Botswana.[31] Likely Omicron (SGTF) samples had occurred on 4 November 2021 in Pretoria, South Africa.

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.[39]

On 25 November, one confirmed case was identified in Israel from a traveler returning from Malawi,[48] along with two who returned from South Africa and one from Madagascar.[49] All four initial cases reported from Botswana occurred among fully vaccinated individuals.[50]

On 26 November, Belgium confirmed its first case; an unvaccinated person who had travelled from Egypt via Turkey on 11 November.[40] All three initial confirmed and suspected cases reported from Israel occurred among fully vaccinated individuals,[48] as did a single suspected case in Germany.[51]

On 27 November, two cases were detected in the United Kingdom, another two in Munich, Germany and one in Milan, Italy.[52]

On 28 November, 13 cases were confirmed in the Netherlands among the 624 airline passengers who arrived from South Africa on 26 November.[53] Confirmation of a further 5 cases among these passengers followed later.[54] 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.[55] 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 were directed to isolate.[56] 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.[57][58] On the same day, Austria also confirmed its first Omicron case.[59] A detected Omicron case was reported in the Czech Republic, from a traveler who spent time in Namibia.[60] 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.[61]

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.[62] Two more people who travelled to Sydney from southern Africa via Singapore tested positive.[63] Portugal reported 13 Omicron cases, all of them members of a soccer club.[64] Sweden also confirmed their first case on 29 November,[65] as did Spain, when a traveler came from South Africa.[66]

On 30 November, the Netherlands reported that Omicron cases had been detected in two samples dating back as early as 19 November.[67] 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.[68] Japan also confirmed its first case.[69] Two Israeli doctors tested positive and entered isolation. Both of them had received three shots of the Pfizer vaccine prior to testing positive.[70] In Brazil, three cases of the Omicron variant were confirmed in São Paulo.[71] Another five are under suspicion.[72][73] A person in Leipzig, Germany with no travel history nor contact with travellers tested positive for Omicron.[74]

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.[75][76] 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[77] and was confirmed to have a mild case of COVID-19 on 29 November.[78] Ireland and South Korea also reported their first cases.[79] South Korea reported its cases from five travelers arriving in South Korea from Nigeria.[80]

On 2 December, Dutch health authorities confirmed that all 14 passengers with confirmed Omicron infection on 26 November had been previously vaccinated.[81] 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.[82] France has confirmed only 25 cases of the new Omicron variant but officials say the number could jump significantly in the coming weeks.[83]

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.[84] In Namibia, 18 cases out of 19 positive COVID-19 samples that had been collected between 11 and 26 November were found to be Omicron, indicating a high level of prevalence in the country.[85] Fiji also confirmed two positive cases of the variant. They travelled from Nigeria arriving in Fiji on November 25.[86]

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.[87]

On 13 December, the first death of a person with Omicron was reported in the UK.[88]

On 16 December, New Zealand confirmed its first case of the Omicron variant, an individual who had traveled from Germany via Dubai.[89]

The first death of a person with Omicron was reported in Germany on 23 December[90] and in Australia on 27 December.[91]

By Christmas 2021, the Omicron Strain became dominant in the US.[92]

On 3 January 2022, South Korea reported the first two deaths of people who tested positive post mortem for Omicron.[93]

On 29 March 2022, Omicron subvariant BA.2 became the dominant strain in the U.S.[94][95][96]

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.[97] 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.[98][99] 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.[100] 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.[101]

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.[102] On 2 December, the Finlay Institute was already developing a version of Soberana Plus against the variant.[103] Pfizer hoped to have a vaccine targeted to immunize against Omicron ready by March 2022.[104]

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.[35][105] On 29 November 2021, the WHO said cases and infections were expected among those vaccinated, albeit in a small and predictable proportion.[106] 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.[107]

On 26 November 2021, WHO advised countries not to impose new restrictions on travel, instead recommending a "risk-based and scientific" approach to travel measures.[108] 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.[109]

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,[110] 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.[111][112]

The Brazilian Health Regulatory Agency recommended flight restrictions regarding the new variant.[113] 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.[114] 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.[115]

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.[116]

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.[117] At the same time, inoculation has slowed in South Africa due to vaccine hesitancy and apathy, with a nationwide vaccination rate of only 35% as of November 2021.[118]

On 29 November, 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.[106]

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."[119]

In mid-December, multiple Canadian provinces reinstated restrictions on gatherings and events such as sports tournaments, and tightened enforcement of proof of vaccination orders. British Columbia expressly prohibited any non-seated "organized New Year's Eve event",[120][121][122] while Quebec announced a partial lockdown on 20 December, ordering the closure of all bars, casinos, gyms, schools, and theatres, as well as imposing restrictions on the capacity and operating hours of restaurants, and the prohibition of spectators at professional sporting events.[123]

On 18 December, the Netherlands government announced a lockdown intended to prevent spread of the variant during the holiday period.[124]

In late December, some countries shortened the typical six-month interval for a booster dose of the vaccine to prepare for a wave of Omicron, as two doses are not enough to stop the infection. UK, South Korea and Thailand reduced to three months; Belgium, four months; France, Singapore, Taiwan, Italy and Australia, five months. Finland reduced it to three months for risk groups. Other countries continued with a six-month booster schedule. While antibody levels begin to drop at four months, a longer interval usually allows time for the immune system's response to mature.[125]

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.[126] Cryptocurrency markets were also routed.[127][128] 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.[129][130][131]

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."[132]

BA.1 is the original strain of the Omicron variant.

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.[140] Therapeutic monoclonal antibodies used to treat people infected with COVID-19 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 BA.1 subvariant.

According to early research, BA.2 is roughly 30% to 60% more transmissible than BA.1.[141][142]

The first known sequence of BA.2 was in a sample from 15 November 2021.[143] As of 17 January 2022, BA.2 had been detected in at least 40 countries and in all continents except Antarctica.[144] By 31 January, it had been detected in at least 57 countries.[145] 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.[146] In a review two weeks later, covering 16 February to 17 March, BA.2 had become the most frequent.[147] However, the data is geographically skewed due to sequencing rate and speed; for example, among the c. 205,000 COVID-19 sequences from March that had been uploaded to GISAID as of 22 March, United Kingdom and Denmark accounted for more than 3⁄4, and most of the remaining were from other European countries, Australia, Canada and the United States (altogether, c. 6,000 were from Africa, Asia and Latin America).[148] Based on GISAID uploads, BA.1 peaked in early January 2022, after which it was overtaken by both BA.1.1 and BA.2.[149] In North America, parts of Europe and parts of Asia, BA.1 was first outcompeted by BA.1.1. For example, in the United States, France and Japan, BA.1.1 became the dominant subvariant in January 2022.[150][151][152]

By late December 2021/early January 2022, BA.2 appeared to have become dominant in at least parts of India (already making up almost 80 percent in Kolkata in late December 2021[153]) and the Philippines, had become frequent in Scandinavia, South Africa and Singapore, and was showing signs of growth in Germany and the United Kingdom.[154][155][156][157] In Japan, which has quarantine and detailed screening of all international travellers, as of 24 January, the vast majority of BA.2 had been detected in people that had arrived from India or the Philippines with cases going back at least to 1 December 2021 (far fewer BA.1 or other variants were detected among arrivals from the two countries in that period), but small numbers had also been detected in people arriving from other countries.[158][159][160]

In Denmark, the first BA.2 was in a sample collected on 5 December 2021 and extremely few were found in the directly following period.[161] By week fifty (13–19 December) it had started to increase, with BA.2 being at around 2 percent of sequenced cases compared to 46 percent BA.1 (remaining Delta). The frequency of both Omicron subvariants continued to increase throughout the last half of December; in week fifty-two (27 December–2 January), BA.2 had reached 20 percent and BA.1 peaked at 72 percent. In January 2022, BA.1 began decreasing, whereas BA.2 continued its increase. By the second week (10–16 January) of 2022, the frequency of the two was almost equal, both being near 50 percent (around one percent was the rapidly disappearing Delta).[161] In the following week, BA.2 became clearly dominant in Denmark with 65 percent of new cases being the BA.2 subvariant.[162] Trends from the other Scandinavian countries, India, South Africa and the United Kingdom also showed that BA.2 was increasing in proportion to the original BA.1.[163][164] In early February 2022, it had become the dominant subvariant in South Africa, in late February it had become dominant in Germany and in early March it had become dominant in the United Kingdom.[165][166][167] In early March, BA.1.1 was still heavily dominant in the United States (having overtaken BA.1 in January), but BA.2 was increasing in frequency, later becoming dominant in the US by 29 March.[150][168]

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.[169]

There were two new BA.2 subvariants detected in the US state of New York, which are BA.2.12 (or B.1.1.529.2.12) and BA.2.12.1 (or B.1.1.529.2.12.1), 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, centred on Syracuse and Lake Ontario, which later became dominant by May 24 in the US.[170]

The subvariant BA.2.75 (or B.1.1.529.2.75, nicknamed Centaurus by the media[171]), first detected in India in May 2022, has been classified as variant under monitoring by the WHO.[172] Additional newer mutations in this line (like BA.2.75.2 aka B.1.1.529.2.75.2 or Chiron) may be capable of escape neutralizing antibodies.[173]

XBB, a recombinant of the BA.2.10.1 and BA.2.75 sublineages,[174] is an Omicron subvariant first detected in August 2022.[175] Described as "immune-evasive", it has caused a small surge of cases in countries including Singapore and Bangladesh.[176]

On 20 October 2022, the chief scientist of the World Health Organization (WHO), Soumya Swaminathan, warned that the XBB subvariant of Omicron may cause infections in some countries while the severity of the new variants is not yet known.[177]

The third Omicron sublineage, BA.3, is very rare. It has the same S-gene target failure (SGTF) deletion (Δ69-70) as BA.1.

In April 2022, the WHO announced it was tracking the BA.4 and BA.5 subvariants with BA.4 having been detected in South Africa, Botswana, Denmark, Scotland and England.[178] Early indications from data collected in South Africa suggested BA.4 and BA.5 have a significant growth advantage over BA.2, which by 12 May earned the status Variant of Concern by the European Centre for Disease Prevention and Control, and, by 20 May, by the UK Health Security Agency.[179][180][181][182] BA.5 was dominant in Portugal by 25 May, accounting for two-thirds of all new cases there.[183] By 24 June, BA.4 and BA.5 together had become dominant variants in the UK and Germany.[184][185][186][187] These two subvariants became dominant in the United States by 28 June.[188][189] By late June, BA.5 became the dominant subvariant in France, with 59% of new cases linked to it.[190][191]

On 10 May 2022, a case of a new subvariant BA.5.2.1 was reported in California.[192] On 10 July, the city of Shanghai reported its first case of BA.5.2.1, in a man who had flown in from Uganda, sparking a new wave of testing.[193] On 22 July, the province of Ontario, Canada announced that subvariant BA.5.2.1 overtook BA.2.12.1 as the main variant in circulation in Ontario around 2 July.[194] Regeneron is reporting that BA.5.2.1 is the main variant in Australia, Belgium, Brunei, Greece and Iceland.[195] The government of Canada is also reporting that in late June and July, of the travelers arriving by air who test positive for COVID-19, a substantial proportion are BA.5.2.1.[196]

BQ.1 (or B.1.1.529.5.3.1.1.1.1.1, nicknamed Typhon by the media) and BQ.1.1 (or B.1.1.529.5.3.1.1.1.1.1.1, nicknamed Cerberus) are new subvariants of BA.5.[197][198][199]

In January 2022, William Schaffner, professor of infectious diseases at Vanderbilt University Medical Center, compared the contagiousness of the Omicron variant to that of the measles.[200]

It was not known in November 2021 how Omicron would spread in populations with high levels of immunity or if it causes a milder or more severe disease. On 15 December 2021, Jenny Harries, head of the UK Health Security Agency, told a parliamentary committee that the doubling time of COVID-19 in most regions of the UK was now less than two days despite the country's high vaccination rate. She said that the Omicron variant of COVID-19 is "probably the most significant threat since the start of the pandemic", and that the number of cases in the next few days would be "quite staggering compared to the rate of growth that we've seen in cases for previous variants".[201]

Relating to naturally acquired immunity, Anne von Gottberg, an expert at the South African National Institute for Communicable Diseases, believed at the beginning of December 2021 that immunity granted by previous variants would not protect against Omicron.[202]

A study suggests that mutations that promote breakthrough infections or antibody-resistance "like those in Omicron" could be a new mechanism for viral evolution success of SARS-CoV-2 and that such may become a dominating mechanism of its evolution.[203] A preprint supports such an explanation of Omicron's spread, suggesting that it "primarily can be ascribed to the immune evasiveness rather than an inherent increase in the basic transmissibility".[204][205] Studies showed the variant to escape the majority of existing SARS-CoV-2 neutralizing antibodies, including those in sera from vaccinated and convalescent individuals.[206][207][208][209] Nevertheless, current vaccines are expected to protect against severe illness, hospitalizations, and deaths due to Omicron[210] and, on an individual level, the Omicron variant is milder than earlier variants that evolved when the antibody/vaccination share was lower than it was when Omicron emerged.[211]

In contrast to other investigated variants, Omicron showed substantial, population-level, evasion of immunity from prior infection as well as a higher ability to evade immunity induced by vaccines.[212]

In February 2022, the first confirmed case infecting a wild animal was confirmed by researchers at Pennsylvania State University in white-tailed deer in Staten Island, N.Y.[213]

Although transmission via fomites is rare, preliminary data indicate that the variant lasts for 194 hours on plastic surfaces and 21 hours on skin, compared with just 56 and 7 hours, respectively, for the original strain.[214][215]

In December, studies, some of which using large nationwide datasets from either Israel and Denmark, found that vaccine effectiveness of multiple common two-dosed COVID-19 vaccines is substantially lower against the Omicron variant than for other common variants including the Delta variant, and that a new (often a third) dose – a booster dose – is needed and effective, as it substantially reduces deaths from the disease compared to cohorts who received no booster but two doses.[217][218][219][220][221][222] 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 significant 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.[223][224][225] 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.[226]

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),[227] vaccine effectiveness against symptomatic disease was at 70%–75%, and the effectiveness against severe disease was expected to be higher.[228]

Many of the mutations to the spike protein are present in other variants of concern and are related to increased infectivity and antibody evasion. Computational modeling suggests that the variant may also escape cell-mediated immunity.[31]

Vaccines continue to be recommended for BA.1. Professor Paul Morgan, immunologist at Cardiff University 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."[229]

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 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 structure. These make it more difficult for antibodies to neutralise the virus."[230]

On 23 December 2021, Nature indicates that, though Omicron likely weakens vaccine protection, reasonable effectiveness against Omicron (BA.1) may be maintained with currently available vaccination and boosting approaches.[231][232]

In May 2022, a preprint indicated Omicron subvariants BA.4 and BA.5 could cause a large share of COVID-19-reinfections, beyond the increase of reinfections caused by the Omicron lineage, even for people who were infected by Omicron BA.1 due to increases in immune evasion, especially for the unvaccinated. However, the observed escape of BA.4 and BA.5 from immunity by a BA.1 infection is more moderate than of BA.1 against studied prior cases of immunity (such as immunity from specific vaccines).[233][234]

Immunity from an Omicron infection for unvaccinated and previously uninfected was found to be weak "against non-Omicron variants",[235] albeit at the time Omicron is, by a large margin, the dominant variant in sequenced human cases.[236]

As of June 2022, researchers, health organizations and regulators are discussing, investigating (including with preliminary laboratory studies and trials) and partly recommending COVID-19 vaccine boosters that mix the original vaccine formulation with Omicron-adjusted parts – such as spike proteins of a specific Omicron subvariant – to better prepare the immune system to recognize a wide variety of variants amid substantial and ongoing immune evasion by Omicron.[237]

Omicron BA.1 multiplies around 70 times faster than the Delta variant in the bronchi (lung airways) but evidence suggests it is less severe than previous variants, especially compared to Delta.[246][211] BA.1 might be less able to penetrate deep lung tissue.[247] Omicron infections are 91 percent less fatal than the delta variant, with 51 percent less risk of hospitalization.[248] However, the estimated difference in the intrinsic risk of hospitalization largely decreases to 0–30 percent when reinfections are excluded.[249]

The risk of hospitalisation is the same in BA.1 and BA.2 based on reviews from Denmark, India, South Africa and the United Kingdom.[250][146][162][251] Norwegian studies show that the amount of virus in the upper airways is similar in those infected with BA.1 and BA.2.[164]

Studies from Denmark and Qatar found that after an infection with BA.1, the vast majority of people were well-protected against a BA.2 infection, although it is unknown how long this protection lasts.[146][252][253] Laboratory studies also show that antibodies for BA.1 generally protect against BA.2.[253] In Denmark, preliminary data found breakthrough rates in people that had been vaccinated that were similar to the breakthrough rates seen for BA.1.[162] An initial study by the UK Health Security Agency found that vaccines afford similar levels of protection against symptomatic disease by BA.1 and BA.2, and in both it is considerably higher after two doses and a booster than two doses without booster.[254][255] Because of the gradually waning effect of vaccines, further booster vaccination may later be necessary.[167]

The FDA has published guidelines on how PCR tests will be affected by Omicron.[262] 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 can also be identified by sequencing and genotyping.[263]

A notable difference between the BA.1 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 Omicron (or Alpha) variant, from the previously dominant Delta variant.[264][265] Thus, countries that primarily rely on SGTF for detection may overlook BA.2,[264] and British authorities consider SGTF alone as insufficient for monitoring the spread of Omicron.[250] This has resulted in it having been nicknamed 'Stealth Omicron'.[250] 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.[137][266] Some countries, such as Denmark and Japan, use a variant qPCR that tests for several mutations, including L452R.[259][158] It can also distinguish Delta, which has L452R,[267] and all Omicron subvariants, which do not have L452R.[268][144] As Omicron became dominant and the Delta variant became rare in early 2022, the SGTF mutation that had made Delta and BA.2 similar in qPCR tests was found to be useful for separating BA.1 and BA.2 from each other.[269]

In January 2022 the medicine and therapeutic regulatory agency Therapeutic Goods Administration (TGA) of the Australian Government found that only one of their 23 approved COVID-19 rapid antigen tests (RAT) stated that it detected Omicron.[270] In June 2022 the German federal Paul-Ehrlich-Institute published their findings, that most RATs detect the Omicron Variant. [271]