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What would making a new vaccine for the Omicron South African variant look like? How long will it take and how does it happen? Adam Whipple, Science Editor of The Times, looks at the process in the 100 days it would take Pfizer to do this in this excellent article that anticipates and answers readers questions. New mutations are shown to be taking place in the virus, it is shown here that UK and world capabilities have also increased to tackle the problem in the last 18 months.

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The danger of new variants emerging with increased mutations is greater with a failure to tackle HIV in African countries says the Science editor of The Guardian. Omicron variant mutations in South Africa shows how this is already happening.

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Protection from hospitalization for Omicron variants can drop to 57% from 81% after 6 months from second dose, and can be pushed back up to 90% using booster shots for Pfizer and Moderna vaccines, according to a large CDC study in the US. For Delta variant period last year the vaccine effectiveness against hospitalization was 90% from about two weeks after dose two till 6 months, dropping to 81% after 6 months, and up to 94% after a booster shot. For Omicron variant the currently vaccine effectiveness for same periods is 81%, 57%, and 90%.

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The third or booster dose of vaccine is needed to take out the Omicron variant. The UK Health Security Agency analyzed data from 581 Omicron cases and thousands of Delta cases to calculate how effective vaccines such as Pfizer and Astra Zeneca were against the Omicron variant. This early analysis shows a third booster dose prevents around 75% of people from getting any coronavirus symptoms. The double dose of the vaccine however provides good protection against severe coronavirus that needed hospital treatment says the UK Health Security Agency. Of equal concern is the rate of spread of the Omicron variant. Here this BBC report shows graphs of UK National Health Security Agency which show the rate of spread is rapid with cases doubling every 2-3 days. For the UK which on December 10 had about 1265 cases this means says this BBC report that the number of Omicron cases could be well above 100,000 in the UK by the end of December. The BBC graph shows the curve for Omicron cases moving in a close to vertical direction upwards. Reports say the experience in South Africa where the Omicron variant was first detected is similar in pattern causing rapid spread. ...

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Manon Ragonnet-Cronin, MRC Fellow at Imperial College, London, looks at how scientists today have tackled the challenge from coronavirus and its many variants, using scientific tools in real time.

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Pfizer says a third dose of Pfizer vaccine neutralized the Omicron variant in lab tests. The two dose was much less effective at blocking the virus. A third dose increased antibodies 25 fold compared two doses for the omicron variant. Pfizer CEO Albert Bourla says- "Although two doses of the vaccine may still offer protection against severe disease caused by Omicron strain, it's clear from these preliminary data that protection is improved with a third dose of our vaccine."

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German Heath Minister Karl Lauterbach says vaccine mandates are the only way out of this pandemic. Speaking to German daily Welt he said, gaining immunity through infection was a "dirty vaccination" that made little sense as it would not protect one against a more harmful variant. He saiid that it "would be naive to think that omicron is the end of the pandemic." Omicron would not make one immune to the next viral variant. "No one can guarantee that a variant will not develop soon that is much more dangerous."

Lauterbach says 25 million doses of the Moderna vaccine have been procured that would be enough for 50 million booster shots to be done in the first quarter of 2022.

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Omicron cases are up in an almost vertical line on a graph with cases doubling every 2-3 days in the UK, similar to the pattern in South Africa during the beginning of the spread in South Africa. Since then early data in South Africa show the trend in the province of Gauteng, center of the omicron outbreak in South Africa in the Johannesburg area, has reached its peak. On Dec. 16 it recorded 27% of national infections compared to 70% the week before. Head of the National Institute of Communicable Diseases in South Africa, Michael Groome, says "we had areally dramatic increase in Gauteng, which has now leveled off."  Hospital admissions in South Africa show a different pattern than earlier hospital admission rates in previous waves, with only 1.7% of cases being hospitalized in this Omicron wave compared to 19% for the Delta variant wave at a similar point in the wave, says Health Minister Joe Phaahla. In UK as of Dec. 14, this WSJ report cites health authorites saying 73% of cases in London are omicron variant, doubling every 1-2 days, with omicron making up 41% of all cases in England. In the US the Centers for Disease Control show Omicron variant making up 2.9% of all cases in US as of Dec. 11, with highest concentration in New York, New Jersey of 13.1%. Proportion of positive tests went up from 3.3% to 5% in New York City. A convention in New York City, Anime convention at Javits Center, November 23, 2021, shown in a recent NYT report, could potentially have acted as a super spreader event in New York according to NYT though not confirmed, similar to football stadiums events in Italy in March 2020. Dense atmosphere and large crowds increase the risk of a super spreader event happening, say experts. ...

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In the manner it has handled Omicron variant South Africa is a beacon of transparency and hope, and of scientific advancement, says this report in the WSJ. Stephanie Nolan in her reports in NYT which Lyrarc commended as exemplary, shows how South African frontline workers were fighting the pandemic, and other reports showed how the scientific community in South Africa was using its advanced labs working with the US and Europe to tackle the variant. This is the opposite of what happened with China, says Marc Siegel, clinical professor of medicine at NYU Langone Health.

 

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JN.1 is the latest mutation of the Omicron virus. it is spreading in France and other countries. The NYT looks at this new variant and the threat it poses in November 2023.

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This analysis in The Times looks at the latest information on the omicron variant gathered in the UK and what it means for the capital London and the UK. It looks at the hospital admissions in January 2021 that could be expected in the UK compared to  January 2020. A big spike infections with a sharp fall is the scenario seen as expected based on experience in South Africa, with 2% of cases as hospital admissions as in the prior January, or in a "milder" scenario somewhat smaller percentage.

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The US booster vaccine drive is lagging behind as only 30% of Americans fully vaccinated have taken the booster vaccine, according to CDC. Only half of Americans over ager 65 have taken the booster shot. In New York City only 1.5 million Americans out of 8 million have taken the booster vaccine. This report in NYT shows Dr. Oshita's 3 urgent care clinics in Sacramento, California, and no rush of people to get the booster vaccine. It is scary, he says, of the lack of a rush of people into the vaccine centers. This is happening as the new omicron variant is spreading.

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France is tightening up on vaccine passes making them mandatory and imposing bigger penalties for fake passes. Fine of 5 years in jail or 75,000 euros for use of fake vaccine passes and stricter penalties for stores not checking the pass. Vaccine passes are mandatory in stores, public transport and venues in France. The goal is to get the remaining unvaccinated to get vaccines as omicron variant of the virus reaches 200,000 new cases a day in France. 

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The key role played by National Institutes of Health scientists in the development of the Moderna covid vaccine was not accepted in the application for patents by Moderna, leading to a dispute with the NIH. Moderna has now dropped the patent application saying it is a distraction on work for tackling the Omicron variant. That patent application had not listed scientists of NIH who worked on the invention.

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South Africa feels a sense of relief as omicron cases follow a pattern of very steep upward increase, followed by a short period of a month, and then a very steep decrease. Cases in South Africa with a population of 60 million, about the size of Britain, dropped from 27,000 at the peak to about 15,000 on December 21, 2021. The area around Johannesburg was hardest hit. The median age is 27 years in South Africa, 40 in UK and 43 in Italy. With younger populations in India and parts of Asia South African population demographic is closer to India than it is to Europe where populations are much older. Scientists do not want to extrapolate from the South African experience with Omicron for this reason. Immunity from vaccination and prior infection could be contributory causes to the less severity of omicron say NCID scientists. "In South Africa this is the epidemiology. Omicron is behaving in a way that is less severe," says Dr. Cheryl Cohen, of the National Institute for Communicable Diseases (NCID). "Compellingly together our data really suggest a positive story of a reduced severity of omicron compared to other variants," he said at a conference with other scientists on Wednesday, Dec. 22.  ...

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In 2020 soccer at filled football stadiums in northern Italy acted as superspreader events. Here the NYT looks at conventions as superspreader events and one recent convention in New York City, Anime (Japanese animation) convention at Javits Center, in late November 2021, that potentially could have acted as a spreader event though not confirmed according to NYT. Dense atmosphere and large crowds increase the risk of a super spreader event happening say experts.This happens as the new omicron variant in South Africa is seen in several countries. 

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New York Governor Kathy Hochul said Friday that the state recorded 21,027 new covid cases surpassing the previous record of 19,942 set in January. Of 263,000 tested about 8% were positive- health officials say positivity rate doubled over 3 day period through Sunday.

William Lee, vp science at Helix, population-genomics company that does surveillance and testing, says Omicron will likely be the dominant strain in the US within a week. He says it is growing so much faster as a proportion of cases, than any previous variants.

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The first spread event for Omicron outside of South Africa is now known to be in Norwegian capital of Oslo. Some workers of renewable energy company Scatec SA returning from South Africa where the company has a solar panel project attended an annual holiday party. The party was at Louise an upscale Oslo restaurant, with 120 people all vaccinated, and tested the day before. More than half have tested positive for covid 19, with at least 13 having the new variant Omicron. Oslo municipal health department says it expects more Omicron cases among the 64 coronavirus cases as remaining workers get tested. The results so far are anecdotal and thin to be sure, yet they show none of the infected employees were seriously ill, says this report in WSJ, citing a company spokesman. The spokesman says people had different sysmptoms but none were severe. Tine Ravlo, assistant superintendent of the Oslo municipal government says- all of them are under isolation at home. And  for now they have what they describe as mild symptoms such as headache, cough, sore throat, and flulike symptoms.  Norway has 80% of population of 5.4 million people fully vaccinated. Mask mandates are in place again in Norway, private indoor gatherings limited to fewer than 100 people. ...

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With staff shortages and the spread of omicron variant some German states are no longer doing contact tracing. Contact tracing is not happening in Berlin or Hamburg says this report in DW.com. The chair of the Federal Association of Doctors, Dr. Teichert, in an interview with RND says "comprehensive followup is almost no longer taking place at the moment." He also said there is a "massive fluctuation" in staffing levels for nearly two years. Experts even say that because of staff leaves and office closures infection rates will not be really known till later, a "sink into ignorance" says a medical statistician.

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In tackling the new Omicron variant president Biden is choosing to avoid the toughest restrictions and broad mandates that American would find it tough to accept and which affect upward mobility and the economy, and widen gaps between red and blue states. The fatigue is high as well as mental health impact says one of Biden's advisors. Biden announced stricter travel restrictions and a mandate for masks for public transit but avoided mention of lockdowns and shutdowns.

New York Governor Kathy Hochul says the situation is different now that 70% of the population is fully vaccinated and children over 5 are being vaccinated. She said "its a different situation right now and we don't need to have a knee-jerk reaction."

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The market for oil field equipment is tight with 90% utilization, making it harder for larger oil producers to drill more oil wells for shale oil in the US. Large US shale oil producers reduced production when oil prices plunged and did not come back leaving smaller oil producers to increase production as prices went back up in 2021. Oil prices are now expected to reach $100 per barrel for the first time since 2014.  Saudis and Russia are not expected to increase production say experts. The possible Russian invasion of Ukraine and shortage of energy supplies is also a factor. Oil demand in the US and Europe has rebounded with milder covid-19 from Omicron variant and fewer lockdowns. Automobile use is also up in the US with November showing 12% increase in miles driven over the prior year, according to the Federal Highway Administration. Low inventories and resilient demand, and low spare capacity will keep prices surging to $100 from today's price of Brent crude oil at $89 in January 2022.   ...