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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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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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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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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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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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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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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 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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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 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.   ...

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In a factory the size of 5 football fields located in Gurnee, Illinois, Abbott Labs makes its BinaxNow Covid-19 home tests. Abbott turned out 1 billion tests in 2021 and at one point had 80% of the market. Along with Pfizer vaccine, BinaxNow Home covid-19 tests are a dominant product during the pandemic. Abbott generated a fifth of its $43 billion in revenue from these home tests. Abbott faced several hurdles along the way. It gained when the US government authorized it to make the test. Yet after vaccination took off by mid 2021 the demand for tests declined and Abbott nearly idled its giant factory in Gurnee. Delta and Omicron variants led to a sudden reversal and surge in demand. Abbott developed its test based on an existing design it used in the US for flu tests, by a company it inherited by acquisition called Binax. To do that test one sends a swab up the nose, add that sample and a liquid mixture to a rectangular paper card, and close the card shut. The liquid then travels up the paper strip, revealing one or two pink lines, one for negative, two for positive. This is done in 15 minutes and the simple design described as a lollipop shape, put Abbott far ahead of competitors. The US FDA authorized Becton Dickinson and Quidel to make the tests before it authorized Abbott, but these rival companies had a poor and complex design. The Trump administration gave Abbott a $760 million contract to buy 150 million tests for distribution to health departments, long termcare facilities, nursing homes, and schools. And by October 2020 Abbott was already making 50 million tests a month. When it comes to distribution Abbott tapped into its pharmacy connections for baby products such as Similac baby formula. This gave it an advantage over Quidel and others who also lacked the manufacturing knowhow for large scale ramp up. The BinaxNow in pharmacies was sold at $24 for a box of two tests, while government paid $5 for one test. Abbott says it makes $ 7 per single consumer test. Yet there was one problem waiting to hit Abbott in 2021- demand dried up as the vaccination campaign took off. In fact the plant manager, Mr. Rodriguez, planned to move to another job inside Abbott as production declined. Then came the Delta variant and he was asked to ramp up production again. With Omicron demand soared. The Biden administration committed $3 billion to help boost test production and asked Kroger and Walmart to sell over the counter tests at cost for 3 months. Abbott had to lure workers from Amazon at $25 an hour for the Gurnee plant expansion. What was learned by the government and Abbott from this experience? The US government now looks for ideas in meeting demand volatility, supply challenges and production needs,. Sustaining production capacity is important for future virus flareups- a new government-industry partnership is required for maintaining test making infrastructure. With government help Abbott plans now to keep the facility at Gurnee operating indefinitely. ...

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Dr. Ezekiel Emmanuel of the University of Pennsylvania gives this early warning on the risks of the sudden U turn in China's zero covid policy to complete reopening. He says the switch from zero covid to population wide immunity via viral spread is coming on too suddenly without preparation. He says China made three mistakes. First, the economic cost of zero covid that dropped growth and created high youth unemployment of over 20%. Second, not procuring Pfizer and Moderna mRNA vaccines with newer technologies. Third, moving to abruptly end the zero covid policy 180 degrees in a sudden move that lacks preparation. Precipitiously ending the zero covid policy for 800 million people means rapid spread says Dr. Emmanuel. He says the key variable the R statistic that measures how many people get infected from one covid patient on average, has moved from 2 to 3 during the early stages of the pandemic to 10 with the omicron variant. Chinese officials report the R to be at 16 in China today, says Dr. Emmanuel. ...

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Latin America has made a huge turnaround through successful vaccination drives. Today more people are vaccinated as a percentage of the population in Latin America at 62% than in the US at 56% or Europe at 60%, according to Our World in Data project at Oxford University. There is little resistance to vaccines in Latin America after successful vaccine campaigns against yellow fever and other diseases. During the first year of the pandemic Latin America had one third of the deaths in the world with 8% of the population. Deaths after vaccination drives have dropped to 8%.  Brazil with 617,000 deaths from coronavirus was second only to the US with 800,000 deaths. Brazil is now back to normal after a successful vaccination drive that has 66% of the population fully vaccinated, and 80% with one dose, some of the highest rates in the world, according to Our World in Data at Oxford University. In Colombia with 50 million population about 50% of people are fully vaccinated. Cases have dropped from 30,000 in June to 2000 a day and deaths from 700 daily that month to 50 a day in December 2021. In Buenos Aires, Argentina's capital, 83% of three million population are fully vaccinated, 14% have received a booster. Buenos Aires city health minister says Argentine society has an affinity for vaccination campaigns. "They rapidly accepted receiving them," he says. Yet from the point of view of new variants emerging there is a different situation in rural areas. In industrial states such as Sao Paulo 78% are fully vaccinated, yet less than 40% are fully vaccinated in poor Amazon state of Roraima.   We make it a point to honor the brave reporters in these countries who provide the reports in the WSJ, as we did earlier for NYT Stephanie Nolan's reports from South Africa and Zambia about frontline workers against Omicron in Africa.  Luciana Magalhaes in Sao Paulo, Jenny Carolina Gonzalez in Bogota, and Sylvina Frydlewsky in Buenos Aires and Kejal Vyas writing this report from San Salvador. ...

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Nationally the new Omicron offshoot variant, the XBB.1.5 represents 40.5% of the cases in the US by Dec. 31, according to the Centers for Disease Prevention and Control or CDC. In New England and New York it is about 75% of cases and is a rapidly rising variant in Europe also. Only 38% of persons over 65 years in the US have got the updated covid booster bivalent vaccine shot.