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Study of coronavirus variants predicts virus evolving to escape current vaccines

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Study of coronavirus variants predicts virus evolving to escape current vaccines

A new study of the U.K. and South Africa variants of SARS-CoV-2 predicts that current vaccines and certain monoclonal antibodies may be less effective at neutralizing these variants and that the new variants raise the specter that reinfections could be more likely.

The study was published in Nature on March 8, 2021. A preprint of the study was first posted to BioRxiv on January 26, 2021.The study’s predictions are now being borne out with the first reported results of the Novavax vaccine, says the study’s lead author David Ho, MD. The company reported on Jan. 28 that the vaccine was nearly 90% effective in the company’s U.K. trial, but only 49.4% effective in its South Africa trial, where most cases of COVID-19 are caused by the B.1.351 variant.”Our study and the new clinical trial data show that the virus is traveling in a direction that is causing it to escape from our current vaccines and therapies that are directed against the viral spike,” says Ho, the director of the Aaron Diamond AIDS Research Center and the Clyde’56 and Helen Wu Professor of Medicine at Columbia University Vagelos College of Physicians and Surgeons.””If the rampant spread of the virus continues and more critical mutations accumulate, then we may be condemned to chasing after the evolving SARS-CoV-2 continually, as we have long done for influenza virus,” Ho says. “Such considerations require that we stop virus transmission as quickly as is feasible, by redoubling our mitigation measures and by expediting vaccine rollout.”

After vaccination, the immune system responds and makes antibodies that can neutralize the virus.Ho and his team found that antibodies in blood samples taken from people inoculated with the Moderna or Pfizer vaccine were less effective at neutralizing the two variants, B.1.1.7, which emerged last September in England, and B.1.351, which emerged from South Africa in late 2020. Against the U.K. variant, neutralization dropped by roughly 2-fold, but against the South Africa variant, neutralization dropped by 6.5- to 8.5-fold.

“The approximately 2-fold loss of neutralizing activity against the U.K. variant is unlikely to have an adverse impact due to the large ‘cushion’ of residual neutralizing antibody activity,” Ho says, “and we see that reflected in the Novavax results where the vaccine was 85.6% effective against the U.K. variant.”

Data from Ho’s study about the loss in neutralizing activity against the South Africa variant are more worrisome.

“”The drop in neutralizing activity against the South Africa variant is appreciable, and we’re now seeing, based on the Novavax results, that this is causing a reduction in protective efficacy,” Ho says.

The new study did not examine the more recent variant found in Brazil (B.1.1.28) but given the similar spike mutations between the Brazil and South Africa variants, Ho says the Brazil variant should behave similarly to the South Africa variant.


“We have to stop the virus from replicating and that means rolling out vaccine faster and sticking to our mitigation measures like masking and physical distancing. Stopping the spread of the virus will stop the development of further mutations,” Ho says.

The study also found that certain monoclonal antibodies used now to treat COVID patients may not work against the South Africa variant. And based on results with plasma from COVID patients who were infected earlier in the pandemic, the B.1.351 variant from South Africa has the potential to cause reinfection.

New study contains comprehensive analysis of variants

The new study conducted an extensive analysis of mutations in the two SARS-CoV-2 variants compared to other recent studies, which have reported similar findings.

The new study examined all mutations in the spike protein of the two variants. (Vaccines and monoclonal antibody treatments work by recognizing the SARS-CoV-2 spike protein.)

The researchers created SARS-CoV-2 pseudoviruses (viruses that produce the coronavirus spike protein but cannot cause infection) with the eight mutations found in the U.K. variant and the nine mutations found in the South African variant.

They then measured the sensitivity of these pseudoviruses to monoclonal antibodies developed to treat COVID patients, convalescent serum from patients who were infected earlier in the pandemic, and serum from patients who have been vaccinated with the Moderna or Pfizer vaccine.

Implications for monoclonal antibody treatments

The study measured the neutralizing activity of 18 different monoclonal antibodies — including the antibodies in two products authorized for use in the United States.

Against the U.K. variant, most antibodies were still potent, although the neutralizing activity of two antibodies in development was modestly impaired.

Against the South Africa variant, however, the neutralizing activity of four antibodies was completely or markedly abolished. Those antibodies include bamlanivimab (LY-CoV555, approved for use in the United States) that was completely inactive against the South Africa variant, and casirivimab, one of the two antibodies in an approved antibody cocktail (REGN-COV) that was 58-fold less effective at neutralizing the South Africa variant compared to the original virus. The second antibody in the cocktail, imdevimab, retained its neutralizing ability, as did the complete cocktail.

“Decisions of the use of these treatments will depend heavily on the local prevalence of the South Africa and Brazil variants,” Ho says, “highlighting the importance of viral genomic surveillance and proactive development of next-generation antibody therapeutics.”

Reinfection implications

Serum from most patients who had recovered from COVID earlier in the pandemic had 11-fold less neutralizing activity against the South Africa variant and 4-fold less neutralizing activity against the U.K. variant.

“The concern here is that reinfection might be more likely if one is confronted with these variants, particularly the South Africa one,” Ho says.

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Warming of Antarctic deep-sea waters contribute to sea level rise in North Atlantic, study finds

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Analysis of mooring observations and hydrographic data suggest the Atlantic Meridional Overturning Circulation deep water limb in the North Atlantic has weakened. Two decades of continual observations provide a greater understanding of the Earth’s climate regulating system.

A new study published in the journal Nature Geoscience led by scientists at University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, and the National Oceanic and Atmospheric Administration’s Atlantic Oceanographic and Meteorological Laboratory, found that human-induced environmental changes around Antarctica are contributing to sea level rise in the North Atlantic.

The research team analyzed two decades of deep sea oceanographic data collected by observational mooring programs to show that a critical piece of Earth’s global system of ocean currents in the North Atlantic has weakened by about 12 percent over the past two decades.

“Although these regions are tens of thousands of miles away from each other and abyssal areas are a few miles below the ocean surface, our results reinforce the notion that even the most remote areas of the world’s oceans are not untouched by human activity,” said the study’s lead author Tiago Biló, an assistant scientist at the Rosenstiel School’s NOAA Cooperative Institute for Marine and Atmospheric Studies.

As part of the NOAA-funded project DeepT (Innovative analysis of deep and abyssal temperatures from bottom-moored instrument), the scientists analyzed data from several observational programs to study changes over time in a cold, dense, and deep water mass located at depths greater than 4,000 meters (2.5 miles) below the ocean surface that flow from the Southern Ocean northward and eventually upwells to shallower depths in other parts of the global ocean such as the North Atlantic.

This shrinking deep-ocean branch — that scientists call the abyssal limb — is part of the Atlantic Meridional Overturning Circulation (AMOC), a three-dimensional system of ocean currents that act as a “conveyer belt” to distribute heat, nutrients, and carbon dioxide across the world’s oceans.

This near-bottom branch is comprised of Antarctic bottom water, which forms from the cooling of seawater in the Southern Ocean around Antarctica during winter months. Among the different formation mechanisms of this bottom water, perhaps the most important is the so-called brine rejection, a process that occurs when salty water freezes. As sea ice forms, it releases salt into the surrounding water, increasing its density. This dense water sinks to the ocean floor, creating a cold, dense water layer that spreads northward to fill all three ocean basins — the Indian, Pacific, and Atlantic oceans. During the 21st century, the researchers observed that the flow of this Antarctic layer across 16°N latitude in the Atlantic had slowed down, reducing the inflow of cold waters to higher latitudes, and leading to warming of waters in the deep ocean.

“The areas affected by this warming spans thousands of miles in the north-south and east-west directions between 4,000- and 6,000-meters of depth,” said William Johns, a co-author and professor of ocean sciences at the Rosenstiel School. “As a result, there is a significant increase in the abyssal ocean heat content, contributing to local sea level rise due to the thermal expansion of the water.”

“Our observational analysis matches what the numerical models have predicted — human activity could potentially impose circulation changes on the entire ocean,” said Biló. “This analysis was only possible because of the decades of collective planning and efforts by multiple oceanographic institutions worldwide.”



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Octopus inspires new suction mechanism for robots

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A new robotic suction cup which can grasp rough, curved and heavy stone, has been developed by scientists at the University of Bristol.

The team, based at Bristol Robotics Laboratory, studied the structures of octopus biological suckers, which have superb adaptive suction abilities enabling them to anchor to rock.

In their findings, published in the journal PNAS today, the researchers show how they were able create a multi-layer soft structure and an artificial fluidic system to mimic the musculature and mucus structures of biological suckers.

Suction is a highly evolved biological adhesion strategy for soft-body organisms to achieve strong grasping on various objects. Biological suckers can adaptively attach to dry complex surfaces such as rocks and shells, which are extremely challenging for current artificial suction cups. Although the adaptive suction of biological suckers is believed to be the result of their soft body’s mechanical deformation, some studies imply that in-sucker mucus secretion may be another critical factor in helping attach to complex surfaces, thanks to its high viscosity.

Lead author Tianqi Yue explained: “The most important development is that we successfully demonstrated the effectiveness of the combination of mechanical conformation — the use of soft materials to conform to surface shape, and liquid seal — the spread of water onto the contacting surface for improving the suction adaptability on complex surfaces. This may also be the secret behind biological organisms ability to achieve adaptive suction.”

Their multi-scale suction mechanism is an organic combination of mechanical conformation and regulated water seal. Multi-layer soft materials first generate a rough mechanical conformation to the substrate, reducing leaking apertures to just micrometres. The remaining micron-sized apertures are then sealed by regulated water secretion from an artificial fluidic system based on the physical model, thereby the suction cup achieves long suction longevity on diverse surfaces but with minimal overflow.

Tianqi added: “We believe the presented multi-scale adaptive suction mechanism is a powerful new adaptive suction strategy which may be instrumental in the development of versatile soft adhesion.

“Current industrial solutions use always-on air pumps to actively generate the suction however, these are noisy and waste energy.

“With no need for a pump, it is well known that many natural organisms with suckers, including octopuses, some fishes such as suckerfish and remoras, leeches, gastropods and echinoderms, can maintain their superb adaptive suction on complex surfaces by exploiting their soft body structures.”

The findings have great potential for industrial applications, such as providing a next-generation robotic gripper for grasping a variety of irregular objects.

The team now plan to build a more intelligent suction cup, by embedding sensors into the suction cup to regulate suction cup’s behaviour.



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One third of China’s urban population at risk of city sinking, new satellite data shows

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Land subsidence is overlooked as a hazard in cities, according to scientists from the University of East Anglia (UEA) and Virginia Tech.

Writing in the journal Science, Prof Robert Nicholls of the Tyndall Centre for Climate Change Research at UEA and Prof Manoochehr Shirzaei of Virginia Tech and United Nations University for Water, Environment and Health, Ontario, highlight the importance of a new research paper analysing satellite data that accurately and consistently maps land movement across China.

While they say in their comment article that consistently measuring subsidence is a great achievement, they argue it is only the start of finding solutions. Predicting future subsidence requires models that consider all drivers, including human activities and climate change, and how they might change with time.

The research paper, published in the same issue, considers 82 cities with a collective population of nearly 700 million people. The results show that 45% of the urban areas that were analysed are sinking, with 16% falling at a rate of 10mm a year or more.

Nationally, roughly 270 million urban residents are estimated to be affected, with nearly 70 million experiencing rapid subsidence of 10mm a year or more. Hotspots include Beijing and Tianjin.

Coastal cities such as Tianjin are especially affected as sinking land reinforces climate change and sea-level rise. The sinking of sea defences is one reason why Hurricane Katrina’s flooding brought such devastation and death-toll to New Orleans in 2005.

Shanghai — China’s biggest city — has subsided up to 3m over the past century and continues to subside today. When subsidence is combined with sea-level rise, the urban area in China below sea level could triple in size by 2120, affecting 55 to 128 million residents. This could be catastrophic without a strong societal response.

“Subsidence jeopardises the structural integrity of buildings and critical infrastructure and exacerbates the impacts of climate change in terms of flooding, particularly in coastal cities where it reinforces sea-level rise,” said Prof Nicholls, who was not involved in the study, but whose research focusses on sea-level rise, coastal erosion and flooding, and how communities can adapt to these changes.

The subsidence is mainly caused by human action in the cities. Groundwater withdrawal, that lowers the water table is considered the most important driver of subsidence, combined with geology and weight of buildings.

In Osaka and Tokyo, groundwater withdrawal was stopped in the 1970s and city subsidence has ceased or greatly reduced showing this is an effective mitigation strategy. Traffic vibration and tunnelling is potentially also a local contributing factor — Beijing has sinking of 45mm a year near subways and highways. Natural upward or downward land movement also occurs but is generally much smaller than human induced changes.

While human-induced subsidence was known in China before this study, Profs Nicholls and Shirzaei say these new results reinforce the need for a national response. This problem happens in susceptible cities outside China and is a widespread problem across the world.

They call for the research community to move from measurement to understanding implications and supporting responses. The new satellite measurements are delivering new detailed subsidence data but the methods to use this information to work with city planners to address these problems needs much more development. Affected coastal cities in China and more widely need particular attention.

“Many cities and areas worldwide are developing strategies for managing the risks of climate change and sea-level rise,” said Prof Nicholls. “We need to learn from this experience to also address the threat of subsidence which is more common than currently recognised.”



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