Charts: Omicron Variants Spread Rapidly in South Africa

COVID cases exploded last week

No Omicron Variant in the last 2 weeks on Nov 1, 2021

25% Cases are caused by Omicron Variant in the last 2 weeks of Nov 15, 2021

88% Omicron cases on Nov 29, 2021

Source : Our World in Data

WHO Names New COVID Variant of Concern Omicron, Cautions Against Travel Measures

Stephanie Nebehay and Alexander Winning wrote . . . . . . . . .

The World Health Organisation (WHO) on Friday classified the B.1.1.529 variant detected in South Africa as a SARS-CoV-2 “variant of concern,” saying it may spread more quickly than other forms.

Preliminary evidence suggested there is an increased risk of reinfection and there had been a “detrimental change in COVID-19 epidemiology,” it said in a statement after a closed meeting of independent experts who reviewed the data.

Infections in South Africa had risen steeply in recent weeks, coinciding with detection of the variant now designated as omicron, WHO said.

“This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other (variants of concern), it said.

“This variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage,” the WHO said.

Current PCR tests continue to successfully detect the variant, it said.

Global authorities reacted with alarm to the new variant detected in South Africa, with the EU and Britain among those tightening border controls as scientists sought to find out if the mutation was vaccine-resistant.

“At this point, implementing travel measures is being cautioned against,” WHO spokesman Christian Lindmeier told a U.N. briefing in Geneva. “The WHO recommends that countries continue to apply a risk-based and scientific approach when implementing travel measures.”

It would take several weeks to determine the variant’s transmissibility and the effectiveness of vaccines and therapeutics against it, he said, noting that 100 sequences of the variant have been reported so far.

People should continue to wear masks whenever possible, avoid large gatherings, ventilate rooms and maintain hand hygiene, Lindmeier added.

Mike Ryan, WHO’s emergency director, praised South African public health institutions for picking up the signal of the new variant.

But he warned that while some countries had systems in place to do this, the situation elsewhere was often unclear.

“So it’s really important that there are no knee-jerk responses here. Especially with relation to South Africa,” he said. “Because we’ve seen in the past, the minute that there is any mention of any kind of variation, then everyone is closing borders and restricting travel.”

Source : Reuters

Read also at CTV

Doug Ford calls new COVID-19 variant concerning as Canada implements travel ban . . . . .

A New COVID Delta Descendant Is Rising in the UK

Tara John wrote . . . . . . . . .

British and international authorities are closely monitoring a subtype of the Delta variant that is causing a growing number of infections in the United Kingdom.

This descendant of the Delta variant, known as AY.4.2, accounted for an estimated 6% of cases in the week of September 27 — the last week with complete sequencing data — and is “on an increasing trajectory,” a report by the UK Health Security Agency said.

Little is known about AY.4.2. Some experts have suggested it could be slightly more transmissible than the original Delta variant, though that has not yet been confirmed. While it accounts for a growing number of infections, it is not yet classified in the UK as a “variant of concern.” It currently remains rare beyond Britain, with a small number of cases being recorded in Denmark and the US, expert Francois Balloux told the Science Media Center (SMC) on Tuesday.

“As AY.4.2 is still at fairly low frequency, a 10% increase its transmissibility could have caused only a small number of additional cases. As such it hasn’t been driving the recent increase in case numbers in the UK,” Balloux, Professor of Computational Systems Biology and Director at the UCL Genetics Institute, told the SMC.

While new variants have repeatedly overtaken one another to become the dominant strain globally in the past year, experts say it is too soon to know whether AY.4.2 will become significant. In the UK, “Delta very rapidly in a matter of weeks” outpaced the Alpha variant by the summer, Deepti Gurdasani, a senior epidemiology lecturer at Queen Mary University of London, told CNN. “That’s not what we’re seeing here, we’re seeing sort of a slow increase in proportion that suggests that it’s not hugely more transmissible, it might be slightly more transmissible.

Balloux agreed, telling SMC that “this [is] not a situation comparable to the emergence of Alpha and Delta that were far more transmissible (50% or more) than any strain in circulation at the time. Here we are dealing with a potential small increase in transmissibility that would not have a comparable impact on the pandemic.”

Source: CNN

Antibodies to Early Strains of COVID May Not Fight New Variants: Study

Antibodies from current COVID-19 vaccines don’t bind well to the new variants of the virus, a study finds.

Researchers collected data from previously published papers about the sequence of antibodies produced by the vaccines. They focused on antibodies against the spike protein, a part of the virus that binds to receptors on human cells to infect them. It’s the target of most vaccines.

“Antibody response is quite relevant to everything from understanding natural infection and how we recover from infection to vaccine design,” lead researcher Nicholas Wu said in a news release from University of Illinois Urbana-Champaign. He is a professor of biochemistry.

The body can make an estimated 1 trillion different antibodies, so when people are making similar antibodies to a particular virus, it means vaccines can be designed to elicit it. It also means it is likely going to improve responsiveness to it, Wu explained.

This study found that many antibodies converged into two groups, indicating an immune response to the virus.

“We really focused on characterizing the antibodies created in those infected with the original strain of the virus,” said first author Timothy Tan, a graduate student.

He noted that variants hadn’t been much of a problem before the study began. But, Tan added, once they emerged, researchers wanted to see whether common antibodies were able to bind to newer variants.

“Even though this antibody response is very common with the original strain, it doesn’t really interact with variants,” Wu said. “That, of course, raises the concern of the virus evolving to escape the body’s main antibody response. Some antibodies should still be effective — the body makes antibodies to many parts of the virus, not only the spike protein — but the particular groups of antibodies that we saw in this study will not be as effective.”

Researchers said they would like to do similar studies of antibody responses to Delta and other variants, to see if they also produce a response and how it differs from the original strain.

The findings were published recently in the journal Nature Communications.

Source: HealthDay

COVID-19 Booster Shots Alone Might Not Stop Delta and Other Variants

Frank Diamond wrote . . . . . . . . .

Recently booster shots were approved—and are now available—to people with compromised immune systems, thanks to action taken by the Food and Drug Administration and the Centers for Disease Control and Prevention as evidence mounts that the efficacy of COVID-19 vaccines wane over time.

This week, plans are in the works to offer booster shots come October to other higher-risk populations in the United States, including infection preventionists and other health care professionals, residents in nursing homes, and Americans aged 60 or older. In other words, the booster shots will be offered in more or less the same order in which the original vaccines were distributed.

But as Sakia V Popescu, PhD, MPH, MA, CIC, a member of Infection Control Today®’s (ICT®’s) Editorial Advisory Board (EAB) wrote in the December 2020 issue of ICT®, effective infection prevention and control should follow the Swiss cheese model championed by virologist Ian Mackay, PhD. Popescu wrote: “In one succinct image, this captures what we do in infection prevention—stress the additive layers that are needed to reduce the spread of infection. From masking to government messaging and vaccines, these layers all work cohesively to reduce the risk of not only COVID-19 infection, but also transmission. Really, this is a concept we have been reinforcing and growing in the field of infection prevention—a wholistic approach to disease prevention.”

Talk about booster shots over the weekend grabbed headlines. Francis Collins, MD, PhD, the director of the National Institutes of Health, said of the delta virus that “this is going very steeply upward with no signs of having peaked out,” according to the Associated Press (AP). The US saw an average of 129,000 new infections a day over the last seven days, according to the Johns Hopkins Coronavirus Resource Center. That’s a 700% increase from the beginning of July and the number could rise to 200,000, which has not been seen since the January/February surge.

Thanks to the vaccines, we will not see the horrendous death rates of those surges. But as ICT® EAB member Kevin Kavanagh, MD, has argued for over year, mortality isn’t the only metric that needs to be taken into account. For instance, medical experts still don’t know exactly what the long-term effects of COVID-19 are. In a recent interview with ICT®, Kavanagh pointed out that “COVID-19 is not just respiratory, it affects every organ of the body. This is a serious type of infection. And we need to be focusing on trying to keep this virus from spreading, plus protecting our young.”

Anthony Fauci, MD, the director of the National Institute of Allergy and Infectious Diseases and President Biden’s chief medical advisor, said that “if it turns out as the data come in, we see we do need to give an additional dose to people in nursing homes, actually, or people who are elderly, we will be absolutely prepared to do that very quickly.

But that won’t be enough, Kavanagh argues in an article scheduled to be printed in an upcoming issue of ICT®.

“SARS-CoV-2 has continued to evolve,” Kavanagh writes. “It has now become evident that with each emerging variant, the virus has appeared to progressively become more infective. Variants which increase viral load may also increase transmissibility and the opportunity to mutate, along with overwhelming a host’s immune system and becoming more virulent.” And there seems to be wave after wave of variants.

Kavanagh adds that “to make matters worse, SARS-CoV-2 is infecting a number of animals, including cats, large cats, dogs and gorillas. Most recently, concern has been raised that it may have found an animal host in white tail deer, with SARS-CoV-2 antibodies identified in 40% of surveyed animals.”

Peter Hotez, MD, PhD, professor of the departments of pediatrics, molecular virology & microbiology and health policy scholar at Baylor College of Medicine, tells ICT®’s sister publication Contagion that recent data has indeed suggested that COVID-19 vaccine-induced immunity from infection is “not as high as it was.” It remains unclear whether that is due to waning immunity or decreased vaccine effectiveness versus the delta variant—a matter which is difficult to discern because the delta outbreak is occurring well into the post-vaccination phase for most adults in the US.

“Right now, the data are showing that the protective efficacy against hospitalization and deaths are holding, but the question is will that start to slip over time as well, and at what point do we pull the trigger?” Hotez said. “And how generalizable do we make it—do we keep it restricted over a certain age, are there other criteria, or do we just open it up the whole population?”

Kavanagh has always said that COVID-19 vaccines alone are not a panacea in stopping the pandemic. And although booster shots are crucially important, one should also not rely on booster shots alone, either.

There must be a multi-pronged approach to COVID-19 if we have any hope of returning to our pre-COVID normal lives, Kavanagh writes in his article. That includes:

  • Upgrade recommendations for mask usage and to use N95 or KN95 masks whenever possible.
  • Everyone who can needs to become vaccinated. Similar to Israel, we should fast track approval for mRNA boosters to those who are at higher risk, including those who are immunosuppressed and over the age of 60 and 5 months out from vaccination.
  • Upgrade building ventilation systems to increase air exchanges and air sanitization.
  • Expand testing capabilities to be able to test frontline workers and school children at least twice a week, and other workers at least once a week.
  • Limiting sizes of gatherings, including podding in schools and plans for permanent hybrid instruction to limit class sizes.
  • Businesses, including restaurants, need to offer online ordering along with curbside pickup and when possible, home delivery.
  • Everyone needs to be vaccinated. Mandatory vaccines should be required in many settings, including health care. Vaccine passports or green cards are being implemented in Israel and France and need to be implemented in the United States.

    Source : Infection Control Today