Timeline of the SARS-CoV-2 Omicron variant

South African scientists begin seeing samples where PCR tests have S-gene target failure (which occurs in a few variants, but not in Delta which by far dominated in the country in October), alerting them to a change in epidemiology.[3]

The first confirmed sample of what would eventually be named the Omicron variant by the World Health Organization (WHO) is collected in South Africa.[4][5][6]

Other samples of the Omicron variant are collected in Botswana by South African scientists[7][8] under the aegis of Network for Genomic Surveillance South Africa (NGS-SA).

More than 70 percent of sequenced samples from Gauteng province in South Africa are Omicron, indicating that it already has become the dominant variant in the province.[9]

South Africa makes its first report of B.1.1.529 (as it is scientifically known) to WHO,[1] based on samples that had been collected from 14 to 16 November.[10]

The variation first comes to public notice[11] at a virtual press conference called by the Health Department of South Africa, Richard Lessells, an infectious-diseases physician at the University of KwaZulu-Natal,[12] remarked that “There’s a lot we don’t understand about this variant... The mutation profile gives us concern, but now we need to do the work to understand the significance of this variant and what it means for the response to the pandemic.” Professor Penny Moore, a virologist at the University of the Witwatersrand[13] said of the pace of this research that “We’re flying at warp speed[,]”[7] At this point there are 87 cases in five countries and an estimated 990 probable cases, with the most confirmed cases in South Africa at 77.[14]

On 26 November at an emergency meeting in Geneva, Switzerland WHO's Technical Advisory Group on SARS-CoV-2 Virus Evolution designated PANGO lineage B.1.1.529 a variant of concern (VOC) and gave it the designation Omicron (skipping Nu and Xi, the next letters in the Greek alphabet in keeping with its nomenclature protocol introduced for the Delta variant).[15][16][17] At this point there are 96 confirmed cases worldwide in South Africa, Botswana,[18] England,[19] Hong Kong,[20] Italy,[21] Israel,[22] and Belgium,[23] and 2 probable cases in Germany[24] and 1 in Czech Republic.[25][26]

The first two cases in the United Kingdom are announced. Additionally it was announced via Twitter that Malawi, Mozambique, Zambia and Angola were to be added to the UK's Red List as of Sunday at 4:00 a.m. GMT [27] genomic sequencing having been performed overnight, thus joining South Africa, Botswana, Lesotho, Eswatini, Zimbabwe, and Namibia.[28] Furthermore Switzerland adds the UK to its "at risk" list along with other countries with cases.[29]

Two Danish returnees from South Africa test positive,[30] and another two people with recent travel in Nigeria test positive in Ottawa, Canada. A third case is detected in the UK, but the individual concerned, who had traveled from southern Africa, is no longer in the country, instigating high-level contact tracing.[31] Israel bans entry to all foreign nationals and puts travel to fifty African countries on its red list. Morocco closes its borders for two weeks.[32] [33]

The first 13 cases are identified among 61 SARS-CoV-2 cases from two flights[34] from South Africa to The Netherlands on November 26; the passengers involved, numbering approximately 624, were in mid-flight when EU restrictions were imposed.[35][36] Five additional cases among these passengers were confirmed a week later.[37]

Two cases were detected in Sydney, Australia. Both people had landed in Sydney the previous day, and had traveled from southern Africa to Sydney via Doha, Qatar. The two people, who were fully vaccinated, entered isolation; 12 other travelers from southern Africa also entered quarantine for fourteen days, while about 260 other passengers and crew on the flight have been directed to isolate.[38]

South African President Cyril Ramaphosa addressed the Nation at 20:00 SAST.[39][40] Ramaphosa highlighted a few key points in his address.[41] Firstly he explained the arrival of the new Omicron Variant and stated that over the next 2 weeks, South African scientists will be working on understand and testing the effectiveness of vaccines against this new Variant.[42] He called for nations who closed borders to reopen then cited that the closure “is not informed by science, nor will it be effective in preventing the spread of the Omicron coronavirus variant”.[43][44] Secondly, he called for the country to vaccinate.[45] Finally he announced the country would not go into lockdown, but introduced a minor curfew and a limit on gathering.[46] A further address is set to take place next week on 5 December 2021 to evaluate whether a lockdown is needed.[47][48]

The affairs ministry of South Africa said that it was dismayed by its 'punishment' for discovering the variant and that 'excellent science should be applauded and not punished'.[49]

Australia records its third case of the variant in a national repatriated from Johannesburg. He was undertaking mandatory isolation in the Howard Springs quarantine facility in the Northern Territory.[50] The first six cases are identified in Scotland (bringing the total in the UK to nine): four in the Lanarkshire area and two in Greater Glasgow and Clyde area.[51] Spain and Sweden report their first cases, the latter from a sample taken less than a week prior from a traveler from South Africa.[52] India announces that a portion of the stock of its own vaccines (under the aegis of COVAX) shall be shipped to afflicted African nations.[53] At a special session of the World Health Assembly WHO presents the variant as having a very high global risk.[54]

Ecuador and Japan impose international travel restrictions. The U.S. also tightens its restrictions. Japan reports its first case as does France (on the Indian Ocean island of Réunion). China's leader Xi Jinping pledges 30m doses of its own vaccine to Africa by way of addressing global vaccine inequity, with 400m to follow (produced by Chinese-owned companies in Africa).[55] In The Netherlands, two additional cases are identified in older samples that were retroactively checked for the new variant, dating back to 19 and 23 November.

United States,[56] Saudi Arabia,[57] Ghana, South Korea, Norway and Nigeria announce their first cases. The Dutch health ministry announces that its first cases date back to November 19 and 23. WHO advises the COVID-vulnerable, including those over 60, not to travel,[58][59] and more than fifty countries have implemented new travel restrictions.[60] Ireland announces its first case, apparently from community transmission.[61]

United Arab Emirates announces its first cases. The number of cases in South Africa has increased exponentially in the prior two weeks, with Omicron rapidly becoming the dominant strain.[62]

A case is found in the greater Paris, France region, reports BFM TV; the infected person had recently returned from Nigeria.[63] This is the first case in mainland France.[64] Iceland also reports its first case, a triply-vaccinated individual who had not traveled abroad;[65] Greece announces its first case (in Crete), an individual who had traveled to South Africa.[66] Finland reports its first case, an individual who had traveled from Sweden with a group.[67]

Singapore preliminarily reports its first two cases.[68] The U.S. reports its second case (and its first case of community transmission) in a Minnesota resident who in late November had attended an anime convention in New York City, Anime NYC 2021; vaccination had been required for attendance.[69] The event had 53,000 attendees, all of whom were urged to get tested (along with staff and exhibitors) inasmuch as authorities feared it as having been a superspreader event.[70][71][72]

Malaysia announced its first case of the variant. The case was detected on 26 November, a South African student entering the country to study at a private university.[73] There are now ten cases in the U.S., in California, Colorado, Minnesota, and New York, and in Hawaii, where the person had no recent travel history.[74] Réunion reported its second confirmed case. Both cases were linked to travel from mainland Africa.[75] More than a dozen cases have been found in the U.S. spread over at least ten states.[76]

The official number of cases in South Korea is now nine (after the initial first three). Officials fear that a church gathering of hundreds on 28 November may have been a superspreader event. Concurrently the country is undergoing a record Delta surge. The Cook Islands reports its first case, a young vaccinated boy repatriated from New Zealand. 97% of the eligible population is double-dosed.[77] Officials in Norway officially regard a corporate Christmas party held on 26 November as a superspreader event, being the single largest outbreak outside of South Africa. At least 14 people of the 120 participants were infected.[78]

Eight cases of community transmission, unrelated to each other, are reported in New York. A woman who recently traveled from South Africa became both New Jersey and Georgia’s first confirmed case. Maryland has its first three cases, and Pennsylvania and Missouri one each. Nebraska's number of cases increases to six, all in its southeast.[79]

Fiji confirmed its first two cases of the variant. The two cases traveled from Nigeria arriving in the country from Hong Kong on 25 November.[80]

The Omicron variant features as such for the first time in the overview of WHO's weekly operational update, namely "Supporting Omicron variant detection and COVID-19 response in southern Africa." As of December 2, Botswana and South Africa have reported 19 and 172 Omicron variant cases, respectively, accounting for 62% of global cases. A surge team is being deployed. Globally, more than twenty countries have reported cases to date.[81]

Queensland, Australia health authorities detect the first case of the variant in the state, alongside the first identification ever of a genetically distinct 'Omicron-like' variant.[82]

WHO announces that the variant had been detected in 57 countries.[83]

WHO announces that "Of 899,935 Covid-19 test samples sequenced and uploaded to the global Covid database in the last 60 days, 897,886 (99.8%) were confirmed to be Delta, while 713 (0.1%) were Omicron." Cases in South Africa rise by 110% in one week. [84] Cuba reports its first case, in a person who had traveled from Mozambique. [85]

Singapore detects its first case of community transmission, an airport frontline worker. In the U.S, more than 40 people have been found to be infected, more than 75% of whom had been vaccinated. [86]

Bangladesh reports its first two cases, female cricketers who had recently returned from Zimbabwe. [87]

64 new cases are reported in New South Wales, Australia. [88]

The first Briton infected with the Omicron variant dies;[89] the variant now accounts for 20% of the cases in the UK.[90] China reports its first case (a returnee from overseas),[91] in Tianjin.[92] Puerto Rico confirms its first case. [93]

France reports 130 cases.[94] In England 20 cases are in hospital.[94] Studies continue to show that while current vaccines are not as effective against Omicron that boosters are beneficial nevertheless.[95]

Algeria reports its first case, A foreign national who entered Algeria on December 10, 2021 tested positive on his arrival in the International Airport of Algiers.[96]