WHO’s unusual speed

In recent days, a new novel Coronavirus variant b.1.1.529 has been detected in South Africa, Botswana and other African countries. Experts say the mutant strain has a large number of mutations and could be more contagious. The World Health Organization (WHO) called an emergency meeting on November 26 local time to discuss the new strain.

On 26 November 2021, the mutant B.1.1.529 was officially named Omicron by WHO and designated as a worrying variant (VOC), the same grade as the Delta mutant that has taken the world by surprise.

This was also the most rapid response by WHO of all the mutants: only two days passed between the first report on B.1.1.529 and Omicron’s inclusion in the VOC.

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5 mutant strains of VOC listed by WHO at present: screenshots from WHO official website

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People get vaccinated against COVID-19 on the “vaccine train” at East London Railway Station in South Africa, Oct. 8, 2019. The South African government has launched the “Vaccine Train” to make it easier for people living along the railway, especially in remote areas, to be vaccinated at railway stations along the railway.

The loci of variation for B.1.1.529 were very different

Variants of VOC and VOI, which are named after the Greek alphabet, will be among the Variants that the World Health Organization (WHO) has listed as noteworthy. Such as the Delta (Delta) strain, which has been the main strain circulating globally in recent times.

TULIO DE Oliveira, director of the South African Centre for Epidemic Response and Innovation, said at a press conference held by the South African Department of Health on 25 November that the variation of the B.1.1.529 strain was very different from other VOCs and VOI strains. There are more than 30 mutation points in the spike protein (S protein) part of the novel Coronavirus, and about 50 in the whole genome.

Spike proteins are responsible for recognizing and binding receptors on the surface of host cells and play an important role in the first step of viral infection. In addition to inactivated vaccines, S protein is the main target of all vaccine candidates for other technical routes.

Moreover, there is a key part of S protein named RBM, which is the receptor binding motif of spike protein. RBM directly contacts ACE2 receptor on the surface of human cells, and then infects human cells. TULIO DE OLIVEIRA, director of the South African Centre for Epidemic Response and Innovation, said there were 10 mutated loci in the B.1.1.529 strain in the RBM portion, compared with two in the circulating Delta strain and three in the Beta strain.

“Some of these loci are familiar to us, but there are a lot of loci that are unfamiliar to us.” Richard Lessells, an infectious disease expert at the University of KwaZulu-Natal in Durban, South Africa, said the B.1.1.529 strain may not only be more transmissible, but also more likely to breach the body’s immune system, given the known mutation sites.

TULIO DE OLIVEIRA said some of the mutants had been linked to higher infectivity in previous studies, but the effect of others on infectivity and pathogenicity was unknown.

Omicron has numerous mutations, with more than 30 mutations in the spike protein alone, including 10 mutations in the key ACE2 receptor RBD region. In contrast, the Beta mutant had 3 mutations (K417N, E484K, N501Y) in the RBD region, while the Delta mutant had only 2 mutations (L452R, T478K) in the same region.

Dr Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation in South Africa, commented: “This mutant really surprised us, it was a big step forward in evolution and there were many more mutations than we expected.”

More studies are needed to find out the specific characteristics of the B.1.1.529 strain.

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From left to right, comparison of mutations of alpha, Beta, Gamma, Dental and Omicron, and omicron with the most mutations on the right (source: GISAID)

The speed of transmission is amazing

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Waves of outbreaks and corresponding strains in South Africa. According to a press release from the South African Department of Health.

The new mutant strain Omicron is spreading rapidly in South Africa. As of 23:47 PM Beijing time on November 26, the number of new cases in South Africa continued to rise by more than 1,000 a day.

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Omicron (B.1.1.529) is far more virulent than the Beta and Delta variants, and it does not have the buffer phase of the initial outbreak of the Beta and Delta variants.

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It can be seen from the above table that it took 100 days for Beta strain to reach about 50% and 100 days for Delta strain to reach 90%, but it only took 10 days for B.1.1.529 to reach 90%.

But there are some conflicting claims about the speed of transmission, the WHO said in a statement, noting that previous laboratory tests have found that for the widely used PCR test, loss of the S gene (one of the three target genes is not detected) is a high suspicion of Omicron, pending confirmation by further sequencing. At present, South Africa has detected a faster growth rate in Omicron in this way than before, suggesting that Omicron may have a spreading advantage.

But some scientists think otherwise. William Hanage, an epidemiologist at Harvard, for example, says that the absolute number of new daily infections in South Africa remains low, making it hard to tell if the mutant strain has swept the country quickly. “It’s too early to tell.”

The b.1.1.529 strain may cause a new wave of outbreaks

In November 2020, says Richard Lessells, the Beta strain became the dominant epidemic strain detected in South Africa, causing the second wave of the Novel Coronavirus pandemic; Earlier this year, the Delta strain began to emerge as the dominant strain circulating in South Africa, causing the third wave of COVID-19. A variant called C.1.2 was also detected in South Africa a few months ago, but it remained low in all the sequenced strains and did not become a major circulating strain in subsequent months of surveillance.

But quite unlike the C.1.2 variant, the proportion of reports of THE B.1.1.529 strain in the South African Novel Coronavirus sequencing surveillance system has risen sharply in the past few weeks alone, and is now close to 75%.

Currently, reports of the outbreak in South Africa are mainly concentrated in Gauteng, South Africa, where the B.1.1.529 strain identified by genetic sequencing is also concentrated. But Richard Lessells says preliminary results from nucleic acid tests in other provinces suggest the new strain may already be circulating in other provinces in South Africa.

“Because the strain has a specific mutation site in the S protein, it allowed us to initially label the strain using an existing PCR assay, which allowed us to get a basic understanding of the transmission of the strain before doing the full genome sequencing.” Lessells says PCR tests from several other provinces in South Africa have also seen a rapid increase in the proportion of new markers. Although these provinces have not reported as many new cases as Gauteng, it gives us concern that the B.1.1.529 strain may already be widespread in South Africa.

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B.1.1.529 strain mutation loci. According to a press release from the South African Department of Health.

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Who called in experts to study the new strain

Maria Van Kerkhove, director of the WHO’s COVID-19 Technical Department, said at a press conference on Monday, “There are fewer than 100 cases of b.1.1.529 that have been sequenced, and our understanding of it is very limited. What we do know is that this strain does have a large number of mutation loci, and the concern is that if you have a large number of mutation loci, you can change the behavior of the virus.”

“It is good to see that the new mutation is being detected and that our system is working well.” Dr. Van Kerkhoff said scientists were discussing together what the b.1.1.529 mutation might mean and what it might mean for existing vaccines, diagnostics and treatments in humans. It could take several weeks for experts to determine the strain’s impact on the pandemic, decide whether to add it to the WHO’s list of mutant strains to watch (VOI) and give the strain a name with a Greek letter.

“Everyone needs to understand that the more widespread the virus is in the world, the more likely it is that it will mutate.” Van Kerkhov called for vaccination and other prevention and control measures to reduce the spread of the virus. She particularly thanked scientists in South Africa and Botswana for their surveillance and called on everyone not to stigmatize specific countries or regions because of the discovery of new virus variants.

The world’s reaction

Governments around the world reacted swiftly to the threat of Omicron. Dozens of countries have imposed restrictions on travel to and from South Africa and neighboring countries, media said on Friday. The United States will impose travel restrictions on non-U.S. citizens from eight African countries — South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi — starting Monday, following who’s announcement that the newly mutated virus has been classified as VOC.

China Central Television news reported that the UK was the first to suspend flights from South Africa, Namibia, Lesotho, Botswana, Zimbabwe and Eswatini on The 25th, and British passengers returning from these regions must be quarantined. Britain has put South Africa on a “blacklist” for tourism.

Subsequently, Germany, Spain, France, Canada, Switzerland, Turkey, Singapore, the Philippines and so on have followed suit.

In addition, a number of countries have not adopted a flight ban against southern Africa, but have issued a warning. Japan has tightened border controls; India imposes stringent screening tests on travellers from these “high-risk” areas; Australia says it will tighten border controls if the situation worsens. Jordan imposed entry restrictions on people with travel history to seven African countries; Russia will restrict the entry of people from some countries and regions; Denmark, Israel and Malaysia have also tightened border controls.

Cases of infection with the new variant of the virus have been reported outside Africa. Hong Kong, China, said Thursday it had detected the first new strain of the virus in South Africa, with two cases at the Regal Airport hotel carrying the B.1.1.529 strain. The Centre for Health Protection (CHP) of the Hong Kong Department of Health has arranged quarantine for hotel staff, and there are no confirmed cases at present. Belgium also reported a case of B.1.1.529 on Friday, becoming the first country in Europe to find a variant of the coronavirus strain. Israel reported its first case of B.1.1.529 in an incoming passenger on Friday, and Prime Minister Bennett quickly sounded a warning that the country was on the brink of crisis. Also on Friday, Israel issued a travel ban on most southern African countries and announced the purchase of 10 million PCR tests specifically for the virus.

BioNTech: Assess impact of new virus in two weeks, worst-case 100 shelves of new vaccine

In its first response to the Omicron virus that has rattled global capital markets, vaccine developer BioNTech said on Friday it had started a laboratory trial of the effectiveness of its vaccine against the virus and expected to have more laboratory data within two weeks.

In a response on Friday, BioNTech also said b. 1.1.529 was “significantly different” from the previously observed variant, but emphasized the company’s ability to develop its technology quickly and iteratively.

BioNTech stressed that it and its partner Pfizer took action months ago to ensure that, in the event that the current vaccine became ineffective against the virus, the mRNA vaccine could be adjusted within six weeks, allowing the first batches of the new vaccine to be shipped within 100 days.

In addition to BioNTech/ Pfizer, Johnson & Johnson and Astrazeneca said on Friday they were studying the impact of the new strain on their vaccines.

Medical wounds xiaobian press:

To sum up, the new variant is thought to be structurally unrecognisable, and with some known structures that enhance transmission and reduce vaccine effectiveness, and many more unknown, the South African epidemic seems to be growing at an extraordinary rate, scientists are getting nervous.

It will take two weeks of laboratory time to confirm the effectiveness of the current vaccine. If it is confirmed to be ineffective, it will take six weeks to design the new mrna vaccine and 100 days to ship the first vaccine after design. It looks fast, but if the virus is spreading as fast as those slides in South Africa, I think the speed of vaccine production seems to be lagging behind.

If this virus is really so strong, but it can buy some time for the scientific community to study the virus, and this is true, so how strong the virus is, how fierce it can be, then we still wait for the scientists’ conclusions.

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