sars-cov-2 omicron variant sars-cov-2 omicron variant omicron (b.1.1.529) is a variant of sars-cov-2 first reported to the world health organization (who) by the network for genomics surveillance in south africa on 24 november 2021. it was first detected in botswana and has spread to become the predominant variant in circulation around the world. following the original b.1.1.529 variant, several subvariants of omicron have emerged including: ba.1, ba.2, ba.3, ba.4, and ba.5. since october 2022, two subvariants of ba.5 called bq.1 and bq.1.1 have emerged. sars-cov-2 variantomicronscientifically accurate atomic model of the external structure of sars-cov-2. each "ball" is an atom.general detailswho designationomicronlineageb.1.1.529first detectedsouth africadate reported24 november 2021 (2021-11-24)statusvariant of concernsymptomsasymptomatic infection, body ache, cough, fainting, fatigue, fever, headache, loss of smell or taste, — less common nasal congestion or running nose night sweats, — unique omicron symptom, upper respiratory tract infection skin rash, sneezing, sore throatcases mapcumulative confirmed omicron variant cases by country and territory 100,000–999,999 10,000–99,999 1,000–9,999 100–999 10–99 1–9 0major variants alpha (b.1.1.7) beta (b.1.351) gamma (p.1) delta (b.1.617.2) omicron (b.1.1.529) ba.1 (b.1.1.529.1)ba.2 (b.1.1.529.2)ba.3 (b.1.1.529.3)ba.4 (b.1.1.529.4)ba.5 (b.1.1.529.5) three doses of a covid-19 vaccine provide protection against severe disease and hospitalisation caused by omicron and its subvariants. for three-dose vaccinated individuals, the ba.4 and ba.5 variants are more infectious than previous subvariants but there is no evidence of greater sickness or severity. classification part of a series on thecovid-19 pandemicscientifically accurate atomic model of the external structure of sars-cov-2. each "ball" is an atom. covid-19 (disease) sars-cov-2 (virus) cases deaths timeline 2019 2020 january responses february responses march 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sars-cov-2 virus evolution declared pango lineage b.1.1.529 a variant of concern and designated it with the greek letter omicron. the who skipped the preceding letters nu and xi in the greek alphabet to avoid confusion with the similarities of the english word "new" and the chinese surname xi. the name of the variant has occasionally been mistaken as "omnicron" among some english speakers, due to a lack of familiarity with the greek alphabet, and the relative frequency of the latin prefix "omni" in other common speech. the gisaid project has assigned it the clade identifier gr/484a, and the nextstrain project has assigned it the clade identifiers 21k and 21l, both belonging to a larger omicron group 21m. history omicron was first detected on 22 november 2021 in laboratories in botswana and south africa based on samples collected on 11–16 november, with the first known samples collected in johannesburg, south africa on 8 november 2021. the first known cases outside of south africa were two people who travelled on 11 november: one who flew from south africa to hong kong via qatar, and another who travelled from egypt to belgium via turkey. on 26 november 2021, who designated b.1.1.529 as a variant of concern and named it "omicron", after the fifteenth letter in the greek alphabet. as of 6 january 2022, the variant had been confirmed in 149 countries. origin hypotheses omicron did not evolve from any other variant, but instead diverged on a distinct track, perhaps in mid-2020. 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. 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. a link with hiv infection may explain a large number of mutations in the sequence of the omicron variant. indeed, in order to be affected by such a high number of mutations, the virus must have been able to evolve a long time without killing its host, which can occur in people with a weakened immune system who receive enough medical care to survive. this is the case in hiv patients in south africa, who represent about 14% of the population (as of 2017). hiv prevention could be key to reducing the risk of uncontrolled hiv driving the emergence of sars-cov-2 variants. 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. on 1 december 2022, a team of researchers from the charité (berlin) published a study in science (journal) that claimed that "data revealed genetically diverse omicron ancestors already existed across africa by august 2021". after a re-analysis because of doubts, the team has retracted the article on 20 december 2022 due to contamination of the samples. spread 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. 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. the first confirmed specimens of omicron were collected on 8 november 2021 in south africa and on 9 november in botswana. 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. on 25 november, one confirmed case was identified in israel from a traveler returning from malawi, along with two who returned from south africa and one from madagascar. all four initial cases reported from botswana occurred among fully vaccinated individuals. on 26 november, belgium confirmed its first case; an unvaccinated person who had travelled from egypt via turkey on 11 november. all three initial confirmed and suspected cases reported from israel occurred among fully vaccinated individuals, as did a single suspected case in germany. on 27 november, two cases were detected in the united kingdom, another two in munich, germany and one in milan, italy. on 28 november, 13 cases were confirmed in the netherlands among the 624 airline passengers who arrived from south africa on 26 november. confirmation of a further 5 cases among these passengers followed later. 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. 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. 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. on the same day, austria also confirmed its first omicron case. a detected omicron case was reported in the czech republic, from a traveler who spent time in namibia. 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. 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. two more people who travelled to sydney from southern africa via singapore tested positive. portugal reported 13 omicron cases, all of them members of a soccer club. sweden also confirmed their first case on 29 november, as did spain, when a traveler came from south africa. on 30 november, the netherlands reported that omicron cases had been detected in two samples dating back as early as 19 november. 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. japan also confirmed its first case. two israeli doctors tested positive and entered isolation. both of them had received three shots of the pfizer vaccine prior to testing positive. in brazil, three cases of the omicron variant were confirmed in são paulo. another five are under suspicion. a person in leipzig, germany with no travel history nor contact with travellers tested positive for omicron. 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. 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 and was confirmed to have a mild case of covid-19 on 29 november. ireland and south korea also reported their first cases. south korea reported its cases from five travelers arriving in south korea from nigeria. on 2 december, dutch health authorities confirmed that all 14 passengers with confirmed omicron infection on 26 november had been previously vaccinated. 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. france has confirmed only 25 cases of the new omicron variant but officials say the number could jump significantly in the coming weeks. by 6 december, malaysia confirmed its first case of