Type of the virus first detected in November 2021
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.
As of September 28, 2024, a new subvariant of Omicron labeled XEC has emerged. The new variant is found in Europe, and in 25 states in the United States of America, including three cases in California.
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.
On 26 November 2021, 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. 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, the WHO designated B.1.1.529 as a variant of concern and named it "Omicron", after the fifteenth letter in the Greek alphabet. By 6 January 2022, the variant had been confirmed in 149 countries.
Retrospectively, Omicron cases have been detected as occurring earlier, in October 2021.
Origin hypotheses.
Omicron did not evolve from any other variant, but instead diverged on a distinct track, perhaps in 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 2020 and 2021 before reinfecting humans.
On 1 December 2022, a team of researchers from the Charité (Berlin) published a now-retracted study in Science 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 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 the 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 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 25 November.
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.
In February 2022, Omicron accounted for 98% of publicly available genetic sequences worldwide.
On 29 March 2022, Omicron subvariant BA.2 overtook BA.1 and became the dominant strain in the US.
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.
On 16 March 2023, without seeing a reduction in the threat to public health, the WHO stopped classifying Omicron as a variant of concern in order to maintain this classification only for new threats. Instead, the WHO classified its subvariants as variants of interest and under monitoring.
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 &amp; 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