the variant. the case was a south african student entering to study at a private university. 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. fiji also confirmed two positive cases of the variant. they travelled from nigeria arriving in fiji on november 25. 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. on 13 december, the first death of a person with omicron was reported in the uk. on 16 december, new zealand confirmed its first case of the omicron variant, an individual who had traveled from germany via dubai. the first death of a person with omicron was reported in germany on 23 december and in australia on 27 december. by christmas 2021, the omicron strain became dominant in the us. on 3 january 2022, south korea reported the first two deaths of people who tested positive post mortem for omicron. on 29 march 2022, omicron subvariant ba.2 overtook ba.1 and became the dominant strain in the u.s. as of may 2022, ba.2.12.1 was spreading in the us and two new subvariants of omicron named ba.4 and ba.5, first detected in january 2022, spread in south africa. all 3 subvariants have spike protein mutations of l452 and elude immunity from prior ba1 infection. reactions vaccine producers 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. 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. 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. 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. 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. on 2 december, the finlay institute was already developing a version of soberana plus against the variant. pfizer hoped to have a vaccine targeted to immunize against omicron ready by march 2022. world health organization on 26 november 2021, the who asked nations to enhance surveillance and sequencing efforts, 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. 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. 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. 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. on 29 november 2021, the who said cases and infections were expected among those vaccinated, albeit in a small and predictable proportion. international response 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, although as of 30 november 2021 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. on 26 november 2021 the brazilian health regulatory agency recommended flight restrictions regarding the new variant. 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. on 27 november 2021, switzerland introduced obligatory tests and quarantine for all visitors arriving from countries where the variant was detected, which originally included belgium and israel. on 26 november 2021 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. some speculated 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 were struggling to gain intellectual property to develop and produce vaccines locally. at the same time, inoculation had slowed in south africa due to vaccine hesitancy and apathy, with a nationwide vaccination rate of only 35% as of november 24, 2021. 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. in preparation for the omicron variant arriving in the united states, president joe biden stated that the variant is "cause for concern, not panic", reiterated that the government was prepared for the variant and would have it under control and that large-scale lockdowns, similar to the ones in 2020 near the beginning of the pandemic, were "off the table for now." in mid-december 2021, 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", while quebec announced a partial lockdown on 20 december 2021, 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. on 18 december 2021, the netherlands government announced a lockdown intended to prevent spread of the variant during the holiday period. in late december 2021, 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. market reactions on 26 november 2021, worry about the potential economic impact of the omicron variant led to a drop in global markets, 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 cryptocurrency markets were also routed. and the south african rand also hit an all-time low for 2021, trading at over 16 rand to the dollar, losing 6% of its value in november. in early december 2021, jerome powell, the chairman of the federal reserve, 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." biology the genomic sequence of the omicron variant is pictured above mutations as of june 2022, omicron had about 50 mutations, which is more than any previous sars-cov-2 variant, 32 of which pertained to the spike protein, which most vaccines target to neutralise the virus. as of december 2021, many mutations were novel and not found in previous variants. as of april 2022 the variant was 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). as of december 2022 the virus carried a number of changes and deletions in other genomic regions. for example three mutations at the furin cleavage site, which facilitates its transmission. 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, structure from pdb: 6vyb​. comparison of mutation prevalence for orf1a, orf1b, and s genes of omicron lineages that are designated variants of concern. characteristic mutations for a lineage are defined as nonsynonymous substitutions or deletions that occur in > 75% of sequences within that lineage. subvariants several subvariants of omicron have been discovered and new ones continue to emerge. there are 310 pango lineages currently associated with the omicron variant. 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). in mid-2022, ba.4 (or b.1.1.529.4) and ba.5 (or b.1.1.529.5) were detected in several countries. they share many mutations, but also significantly differ. in general, ba.1 and ba.2 share 32 mutations, but differ by 28. ba.1 has itself been divided in two, the original ba.1 and ba.1.1 (or b.1.1.529.1.1) where the main difference is that the latter has a r346k mutation. standard pcr and rapid tests continue to detect all omicron subvariants as covid-19, but further tests are necessary to distinguish the subvariants from each other and from other covid-19 variants. defining mutations in thesars-cov-2 omicron variant 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 ba.2 a preprint released in february 2022 (published in may) suggested that ba.2 is more transmissible than ba.1 and may cause more severe disease. this was later disproven by a study in late-october 2022, that found ba.2 actually caused less severe disease relative to ba.1 (which in turn, caused less severe disease compared to the delta variant). 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 ba.1 subvariant. affected countries and transmissibility according to early research, ba.2 is roughly 30% to 60% more transmissible than ba.1. the