Tag: coronavirus

Immunity to Other Coronaviruses Confers COVID Protection

Transmission electron micrograph of SARS-CoV-2 virus particles (gold) within endosomes of a heavily infected nasal Olfactory Epithelial Cell. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID

Researchers have discovered another component beside previous infection or vaccination that contributes to SARS-CoV-2 immunity – previous antibody responses to other, harmless coronaviruses. “People who have had strong immune responses to other human coronaviruses also have some protection against SARS-CoV-2 infection,” said Alexandra Trkola, head of the Institute of Medical Virology at University of Zurich.

The study, published in Nature Communication, used a specially developed assay to analyse antibody levels against four other human coronaviruses in 825 serum samples taken before  the emergence of SARS-CoV-2, as well as 389 samples from donors infected with the virus. Combining these analyses with computer-based models enabled the team to precisely predict how well the antibodies would bind to and neutralise invading viruses.

The researchers were able to demonstrate that people who caught SARS-CoV-2 had lower levels of antibodies against coronaviruses that cause common colds compared to uninfected people. In addition, people with high levels of antibodies against harmless coronaviruses were less likely to have been hospitalized after catching SARS-CoV-2. “Our study shows that a strong antibody response to human coronaviruses increases the level of antibodies against SARS-CoV-2. So someone who has gained immunity to harmless coronaviruses is therefore also better protected against severe SARS-CoV-2 infections,” says Trkola. This type of immune response is referred to as cross-reactivity, and it also occurs with T cell responses,  the additional line of the immune system in the defense against infections.

People are only fully protected against SARS-CoV-2 shortly after they have recovered from an infection or have received an effective vaccination. This is when antibody levels against the virus are still very high. As these levels drop over time, infection is no longer prevented, but the immunological memory quickly reactivates the body’s defenses, the production of antibodies as well as the T cell defense. “Of course, immune responses targeting SARS-CoV-2 that are mounted by the memory cells are far more effective than cross-reactive responses. But even though the protection isn’t absolute, cross-reactive immune responses shorten the infection and reduce its severity. And this is exactly what is also achieved through vaccination, just much, much more efficiently,” said Trkola.

Whether cross-reactivity also works in the opposite direction is not yet known. “If SARS-CoV-2 immunity also offers some degree of protection from infection with other coronaviruses, we would be a significant step closer to achieving comprehensive protection against other coronaviruses, including any new variants,” the virologist explains. This idea is also supported by the fact that cross-reactive protection is not only based on antibodies, but very likely also on T cells.

Source: University of Zurich

Bat Coronavirus 94.5% Similar to SARS-CoV-2 Found

Researchers in China and Australia have reported the discovery of novel bat coronaviruses with a similarity of up to 94.5% to SARS-CoV-2. 

This finding further illuminates the diversity and complex evolutionary history of these viruses. A pre-print version of the research paper is available on the bioRxiv server.

Now, Weifeng Shi from Shandong First Medical University & Shandong Academy of Medical Sciences in Taian, China and colleagues have conducted a meta-transcriptomic analysis of samples collected from 23 bat species in Yunnan province in China during 2019 and 2020.  

Using a combination of genome sequencing and sampling studies, researchers identified a number of SARS-CoV-2-related coronaviruses in wildlife species that together pointed to underestimation of the phylogenetic and genomic diversity of coronaviruses.

“Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China,” said the team.

Bats are hosts to a broad range of viruses that can infect humans, and four of the seven known human coronaviruses have zoonotic origins.  They are also host to many coronaviruses, but sometimes “intermediate” hosts such as dromedary camels (MERS-CoV) are involved in the jump to humans.

Retrospective genome sequencing and sampling studies identified a number of SARS-CoV-2-related coronaviruses in wildlife species. These included the RaTG13 virus, which is the closest known relative of SARS-CoV-2,  found in the Rhinolophus affinis bat. SARS-CoV-2-related viruses have also been identified in various other Rhinolophid bats across Asia.

“Collectively, these studies indicate that bats across a broad swathe of Asia harbour coronaviruses that are closely related to SARS-CoV-2 and that the phylogenetic and genomic diversity of these viruses has likely been underestimated,” said Shi and colleagues.

Notably, one of these novel bat coronaviruses – RpYN06 – exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome, with key similarities in certain genes. Low genopmic sequence identity in the spike gene made RpYN06 the second closest relative of SARS-CoV-2, next to RaTG13. This is far more similar than seen in other SARS-CoV-2-like viruses identified in wildlife species.

Indeed, while the other three SARS-CoV-2-related viruses identified here were almost identical in sequence, the spike protein sequences formed an independent lineage that was separated from known sarbecoviruses (a  viral subgenus or the coronaviruses that  includesSARS-CoV-2)   by a relatively long branch.

“Collectively, these results highlight the extremely high, and likely underestimated, genetic diversity of the sarbecovirus spike proteins, which likely reflects their adaptive flexibility,” wrote Shi and colleagues.

The researchers say studies have previously shown that host switching of coronaviruses among bats is a frequent occurrence.

Source: News-Medical.Net

Journal information: Shi W, et al. Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. bioRxiv. 2021. doi: https://doi.org/10.1101/2021.03.08.434390

Improved Treatment Results in 18% Fall in COVID Death Rates

In a piece for The Conversation, Professor Monica Gandhi at the University of California, writes how, thanks to improved treatment as a results of experience gained, survival rates for COVID patients have dramatically risen.

In three New York hospitals, out of 1724 patients hospitalised for COVID in March, 430 died. In August, 134 hospitalised and five died. However, this may have been due to more vulnerable patients being infected. Therefore, to avoid bias, the researchers accounted for age of patients at hospitalisation, race, amount of oxygen support individuals needed on arrival and such risk factors as being overweight, smoking, high blood pressure, diabetes, lung disease. Even so, they found that patients were three times as likely to survive when admitted in August as compared to March, which indicates that this is due to improved treatment resulting from research into and experience with the disease.

A similar study in the UK looked at COVID patient survival rates in high-dependency units (HDU) and ICU, and found a continuous improvement in survival rates of 12.7% per week in the HDU and 8.9% per week in ICU.

Prof Gandhi attributes this to a better understanding of the disease, and the regular use of remdesivir and dexamethasone as treatments.

Source: The Conversation

Extreme “Super-spreader” Events Boost COVID Spread

The SARS-CoV-2 virus has a reproduction number of three, indicating that on average it will infect three other individuals over the course of the infection. However, a study at the Massachusetts Institute of Technology (MIT) found that extreme “super-spreader” events, such as the one that happened at a White House event in September, seem to generate more infections than would otherwise be expected due to random distributions.

“Super-spreading events are likely more important than most of us had initially realized. Even though they are extreme events, they are probable and thus are likely occurring at a higher frequency than we thought. If we can control the super-spreading events, we have a much greater chance of getting this pandemic under control,” said James Collins, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering, and the senior author of this study. 

The researchers analysed a number of documented “super-spreader events” that have taken place over the COVID pandemic. When they ran statistical analyses on super-spreader events, they found that instead of the expected “bell curve” of normal distribution, they found a “fat tail” of extreme events.

Lead author, MIT postdoc Felix Wong said, “This means that the probability of extreme events decays more slowly than one would have expected. These really large super-spreading events, with between 10 and 100 people infected, are much more common than we had anticipated.”

Source: Medical Xpress

Speech Recognition AI Detects COVID in Coughs

An AI system originally developed at the Massachusetts Institute of Technology (MIT) to research speech patterns in people with Alzheimer’s was repurposed when the COVID pandemic hit to become an indicator for COVID in asymptomatic patients. 

“The sounds of talking and coughing are both influenced by the vocal cords and surrounding organs,” says research scientist Brian Subirana of MIT.
“This means that when you talk, part of your talking is like coughing, and vice versa. It also means that things we easily derive from fluent speech, AI can pick up simply from coughs, including things like the person’s gender, mother tongue, or even emotional state. There’s in fact sentiment embedded in how you cough.”

The system was based on a neural network that was trained on a thousand hours of human speech, then on a database on words spoken in different emotional states and finally a database of coughs. The result was a system that could detect a cough in an asymptomatic person with COVID with 97.1% accuracy. However, this is not a true test of COVID but an enhanced early indicator. The advantage of this technology is that it can be developed as an early warning system that can be incorporated into something as ubiquitous as a smartphone.

Source: Science Alert

COVID DNA of White House “Superspreader Event” Analysed

On September 26, numerous high-profile individuals, contracted COVID at a large official White House gathering. This White House “superspreader event” as it was known became something of a case study in how COVID can spread in large groups of people.

Although President Trump contracted the virus, it is not known if this was a result of attending that event. The event, which had over a dozen guests, resulted in 34 individuals including White House staff testing positive for COVID by October 7.

Whilst contact tracing is difficult with COVID, genome sequencing offers a chance for insights into its development and spread. The researchers analysed SARS-CoV-2 genomes from nasal swabs taken from the patients at the White House superspreader event, and analysed it, looking for mutations. They found two variants, WH-2 and WH-2. They determined that these viruses descended from those widely in circulation in Florida, New York, Texas, Connecticut, and Washington – as well as certain countries such as  New Zealand.

Source: News-Medical.Net

Rights Group Supports No Patents for COVID Vaccines

Business Live reports on the recent call by South Africa and India for COVID vaccines not to be patented. Human Rights Watch added its support by stating that vaccines obtained by public funding should be shared as widely as possible, and their intellectual property status waived.

Some 44 vaccine candidates are being trialled around the world. Wealthy countries have placed orders in order to secure stockpiles of the vaccines. South Africa has no vaccine scheme of its own and is instead has expressed interest in (without signing up to) the global Covax scheme, which involves the World Health Organization and which aims to have two billion doses to be shipped out by the end of 2021.

HRW researcher Margaret Wurth said, “You can’t fight a global pandemic by allowing publicly funded vaccines to go to the highest bidder, at whatever price pharmaceutical companies set. When a safe and effective vaccine is found, it should be available and affordable for everyone, everywhere.”

COVID Cough Droplets Can Travel up to 6.6m

Researchers in Singapore have employed fluid physics to add to the growing body of research surrounding the airborne transmission of the SARS-CoV-2 virus. 

“In addition to wearing a mask, we found social distancing to be generally effective, as droplet deposition is shown to be reduced on a person who is at least one metre from the cough,” said study author Fong Yew Leong.

The researchers found that the results were highly dependent on ambient air characteristics, such as temperature and humidity, as well as assumptions about the viability of the virus

“An evaporating droplet retains the non-volatile viral content, so the viral loading is effectively increased,” said author Hongying Li.

Source: IOL

Air Pollution May Increase COVID Mortality Risk by 11%

Air pollution, a persistent problem around the world, is known to cause lung diseases, and existing lung diseases are known to exacerbate COVID. According to new research reported on by The Guardian, air pollution has been shown to be a significant factor for dying from COVID – increasing the risk of death by 11%.

The gold standard for assessing an association between COVID and air pollution would be getting a large enough sample of participants and acquiring personal details so that their age, smoking history and other details can be taken into account. However, such levels of individual details are not yet available, so researchers are looking to group studies to provide the data, albeit at reduced quality. Hundreds of group studies are awaiting review, but the evidence so far appears compelling.

Prof Francesca Dominici at Harvard University, the research leader says that there is definitely enough evidence to act on already. “We already have an overwhelming amount of evidence of the adverse health effects of fine particle pollution, so even without Covid, we should implement more stringent regulation. But the amount of [Covid-related] evidence is also big enough now that there is absolutely nothing to lose, and only benefits, to prioritise some of the more vulnerable areas.”

Efforts to help mitigate the effect of air pollution on potential COVID patients could include air pollution reduction measures and distributing PPE in priority areas.