Category: COVID

Cheaper Way of Monitoring Coronavirus Variants

Researchers at Karolinska Institutet in Sweden have developed a technology for cost-effective surveillance of the global spread of new SARS-CoV-2 variants.  This could help low- and middle-income countries monitor variants in their own borders.

From the beginning of the pandemic, thousands of viral genomes have been sequenced in order to reconstruct the evolution and global spread of the coronavirus. Dependent on these is the identification of particularly concerning variants.

To achieve global surveillance of the SARS-CoV-2 genome, the sequencing and analysis of numerous samples cost-effectively is key. Therefore, researchers in the Bienko-Crosetto laboratory at Karolinska Institutet and Science for Life Laboratory (SciLifeLab) in Sweden have developed a new method, COVseq, that can be used for surveillance of the viral genome on a massive scale at a low cost.

Multiplex PCR (polymerase chain reaction) is used to make more copies of the virus. The samples are then labeled and pooled together in the same sequencing library, using a previous method developed in their laboratory and now adapted for SARS-CoV-2 analysis.

“By performing reactions in very small volumes and pooling together hundreds of samples into the same sequencing library, we can sequence potentially thousands of viral genomes per week at a cost of less than 15 dollars per sample,” said co-first author Ning Zhang, postdoctoral researcher at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet.

Comparative analyses of 29 SARS-CoV-2 positive samples revealed that COVseq could detect small changes in the genome as well as standard methods. Analysing 245 additional samples, they showed that COVseq could also detect emerging variants of concern well. COVseq’s key advantage over existing methods is cost-effectiveness.

“Our inexpensive method could immediately be used for SARS-CoV-2 genomic surveillance by public health agencies and could also be easily adapted to other RNA viruses, such as influenza and dengue viruses,” said last author Nicola Crosetto, senior researcher at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet.

Source: Karolinska Institutet

Journal information: COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance. Nature Communications, 23 June 2021, DOI: 10.1038/s41467-021-24078-9

Tech Transfer for Local mRNA Vaccine Production

South Africa is planning to make vaccines locally using messenger RNA, the breakthrough technology of the global COVID vaccination effort – and once nearly consigned to the dustbin of medical research history.

The World Health Organization (WHO) and its COVAX partners are working with a South African consortium comprising Biovac, Afrigen Biologics and Vaccines, a network of universities and the Africa Centres for Disease Control and Prevention (CDC) to establish its first COVID mRNA vaccine technology transfer hub.

This follows WHO’s global call for Expression of Interest to establish COVID mRNA vaccine technology transfer hubs to scale up production and access to COVID vaccines. The partners will negotiate details with the South African government and public and private partners both local and international.

South African President Cyril Ramaphosa said: “The COVID pandemic has revealed the full extent of the vaccine gap between developed and developing economies, and how that gap can severely undermine global health security. This landmark initiative is a major advance in the international effort to build vaccine development and manufacturing capacity that will put Africa on a path to self determination. South Africa welcomes the opportunity to host a vaccine technology transfer hub and to build on the capacity and expertise that already exists on the continent to contribute to this effort.”

“This is great news, particularly for Africa, which has the least access to vaccines,” said Dr Tedros Adhanom Ghebreyesus, WHO Director-General. “COVID has highlighted the importance of local production to address health emergencies, strengthen regional health security and expand sustainable access to health products.”

The announcement follows the recent visit to South Africa by French President Emmanuel Macron, who gave his country’s commitment to aiding local vaccine production.

“Today is a great day for Africa. It is also a great day for all those who work towards a more equitable access to health products. I am proud for Biovac and our South African partners to have been selected by WHO, as France has been supporting them for years,” said President Macron. “This initiative is the first of a long list to come, that we will keep supporting, with our partners, united in the belief that acting for global public goods is the fight of the century and that it cannot wait.”

Technology transfer hubs are training facilities where the technology is established at industrial scale and clinical development performed. Interested manufacturers from low- and middle-income countries can receive training and any necessary licences to the technology, assisted by the WHO and partners.

Biovac is a bio-pharmaceutical company resulting from a partnership formed with the South African government in 2003 to establish local vaccine manufacturing capability for the provision of vaccines for national health management and security.

Afrigen Biologics and Vaccines is a biotechnology company focuses on product development, bulk adjuvant manufacturing and supply and distribution of key biologicals to address unmet healthcare needs.

The organisations complement one another, and can each take on different roles within the proposed collaboration: Biovac will be the developer while Afrigen is the manufacturer, with a consortium of universities as academic supporters providing mRNA know-how. Africa CDC will provide technical and regional support.

The South African consortium has existing operating facilities with available capacity and experience in technology transfers. It is also a global hub that can start training technology recipients immediately.

The WHO is speaking to a number of pharmaceutical manufacturers about establishing the hub, though the talks are so far mainly with “smaller companies,” said Soumya Swaminathan, WHO’s chief scientist. “We are having discussions with the larger companies with proven mRNA technology,” she added.

The mRNA vaccines may be produced in South Africa within 9 to 12 months, she said. WHO’s call for expressions of interest has so far generated 28 offers to either provide technology for mRNA vaccines or to host a technology hub or both. 

It is the first time that messenger RNA technology has been used to make vaccines, which has been used by Moderna and Pfizer/BioNTech. They have proven very effective against the original SARS-CoV-2 strains and even against its more recent variants.

Source: World Health Organization

Common Gut Bacteria Could Inhibit SARS-CoV-2

Bifidobacterium eriksonii, stained with fluorescent antibodies. Source: Public Health Image Library

South Korean researchers have found that certain common gut bacteria produce compounds that inhibit SARS-CoV-2. 

The research was presented on June 20 at World Microbe Forum, an online meeting of the American Society for Microbiology (ASM), the Federation of European Microbiological Societies (FEMS), and several other societies that taking place online June 20-24.

Previous clinical findings had shown that some patients with moderate to severe COVID experience gastrointestinal symptoms, while others show signs of infection in the lungs only.

“We wondered whether gut resident bacteria could protect the intestine from invasion of the virus,” said Mohammed Ali, a PhD student in Medicine at Yonsei University in South Korea.

To investigate this hypothesis, the researchers screened dominant bacteria inhabiting the gut for activity against SARS-CoV-2. Their efforts revealed that Bifidobacteria, already shown to suppress other bacteria such as H. pylori and have proven active against irritable bowel syndrome, had such activity, said Ali. Bifidobacteria are common in the guts of breast fed infants, which is partly driven by the bifidogenic activities of specific mother milk-derived oligosaccharides

The researchers also searched for potential illness-fighting compounds in databases containing microbially produced molecules, and discovered some that might also be useful against SARS-CoV-2. “To train our model we leveraged previous coronavirus datasets in which several compounds were tested against targets from coronaviruses,” explained Ali. “This approach seems to be significant as those targets share features in common with SARS-CoV-2.”

Ali emphasised the ecological nature of his approach to this work, pointing out that numerous existing antibiotics and cancer therapies are themselves compounds that bacteria use to compete with each other within the gastrointestinal tract, and that these were initially purified from microbial secretions.

“Finding microbes that secrete anti-coronavirus molecules will be a promising method to develop natural or engineered probiotics to expand our therapeutics prevention techniques, to provide a more sustainable way to combat the viral infection,” said Ali.

Source: American Society for Microbiology

Brazil COVID Deaths Pass Half a Million

Brazil’s COVID deaths passed 500 000 in Brazil, days after the US reported passing 600 000 deaths. Experts warn of a worsening outbreak amid slow vaccination and the onset of winter.

President Jair Bolsonaro refuses to back measures like social distancing even as the virus continues to take its toll. With only 11% of adults vaccinated, Brazil’s health institute Fiocruz says the situation is “critical”.

Heavy criticism has been directed at President Bolsonaro for not implementing a co-ordinated national response and for his vaccine scepticism, lockdowns and mask-wearing requirements, which he has sought to loosen.

The country has reported, on average, 70 000 cases and 2 000 deaths daily in the past week. Most new cases were among those aged 20-59, Fiocruz said, warning that the start of winter in the southern hemisphere this week could result in more infections.

Yet governors and mayors have already relaxed nonpharmaceutical interventions. Restaurants, bars and shops have reopened in many cities, while many people in the streets are not wearing face masks or following social distancing.

“People in Brazil are tired and they normalise death now,” Dr Natalia Pasternak Taschner, a microbiologist at the Question of Science Institute, told the BBC, adding that they have a long way to go.

“If we’re not successful in changing the behaviour of people and if we don’t have campaigns for mask wearing, social distancing and vaccinations coming directly from the central government we’re not going to be able to control it.”

On Saturday, protests against President Bolsonaro were held in cities across the country, with demonstrators accusing him of delaying the purchase of vaccines yet prioritising unproven treatments, such as hydroxychloroquine.

More transmissible variants of the virus have driven Brazil’s outbreak, including the one first identified in the Amazon region which is now known as Gamma. Occupancy rate for intensive care unit beds remains at or above 80% in most states, while cities struggle with vaccine supplies.

Faced with a crumbling healthcare system without the relief of lockdowns, a ‘Covid Kit‘ of ivermectin and azithromycin has been touted by the government, and which is widely prescribed. Ironically, its creator, a doctor in Mato Grosso state, died of COVID last September. In a country notorious for its excessive pill-taking, doctors are finding it difficult to recruit people into trials who have not taken ivermectin.

The Brazilian Senate is looking into President Bolsonaro’s handling of the pandemic. The opposition is accusing him of delaying vaccine orders for political reasons, as he has consistently downplayed the pandemic’s severity.

But President Bolsonaro maintains he has done all he can to buy vaccines from several countries, and insists the impacts of a lockdown would be worse than the pandemic.

The president has not commented on the 500 000 deaths although on Twitter, Health Minister Marcelo Queiroga expressed solidarity with relatives of those who had died.

Source: BBC News

COVID Shown to Damage The Testes

Photo by Fusion Medical Animation on Unsplash

Researchers at the University of Texas Medical Branch have discovered SARS-CoV-2 in the testes of infected hamsters, findings which may explain certain COVID symptoms reported in men.

Clinicians are finding that COVID affects more than just the lungs; some patients have reported testicular pain and some reports have shown decreases in testosterone. Autopsies have also shown evidence of significant disruption of the testes at the cellular level, severe in some cases, and presence of immune cells. Since SARS-CoV-2 has an affinity for ACE-2 receptors, and ACE-2 receptor expression is high in the testes, this could explain why this tissue becomes an infection target for COVID.

“Given the magnitude of the COVID pandemic, it is critical to investigate how this disease can impact the testes, and the potential consequences for disease severity, reproductive health and sexual transmission,” said Dr Rafael Kroon Campos, the study’s lead author and postdoctoral fellow in the laboratory of Dr Shannan Rossi at UTMB.

For a number of years, the Rossi lab had been studying Zika virus infection in the testes and wondered if SARS-CoV-2 could cause a similar disease. Hamsters are common models for COVID since they develop similar signs of disease to humans. Virus was detected in the testes of all infected hamsters during the first week but tapered off. The authors think this may represent what could occur in men with mild to moderate COVID disease.

“These findings are the first step in understanding how COVID impacts the male genital tract and potentially men’s reproductive health,” said Rossi, an associate professor in the Departments of Pathology and Microbiology & Immunology. “We have much more to do before we have the full picture. Moving forward, we will investigate ways to blunt this impact, including using antivirals, antibody therapies and vaccines.”

Future research could also include conditions associated with severe COVID, such as pre-existing conditions like obesity and diabetes and SARS-CoV-2 variants of concern, the study authors said.

Source: University of Texas Medical Branch at Galveston

SAMA Head Urges Stronger Lockdown; Two-thirds of Cases in Gauteng

Photo by Maxim Zhgulev on Unsplash

The South African Medical Association (SAMA) had said that early indications showed that the third wave of South Africa’s COVID pandemic would be worse than the previous two.

As infections surge around the country, particularly in Gauteng Province, the government  moved to Level 3, strengthening some curbs, including liquor sale restrictions, an extended curfew and a cap on the number of people allowed at gatherings. However, there has been no outright ban on alcohol.

As of Thursday, 11767 new COVID infections have been confirmed, with nearly two-thirds (7502) being recorded in Gauteng. The overall case positivity rate is 22.6%

SAMA chairperson Dr Angelique Coetzee said that the government’s measures were implemented far too late.

“People carry on as if everything is right. Everything is not right. We are in a pandemic, we are in a third wave and a third wave that’s going to be worse. At this stage, all the indications are that it is going to be worse than the second wave.”

Speaking to the SABC, she said Gauteng was running out of beds and oxygen. “If you want a bed in Gauteng you are going to struggle so this is what we’re seeing and if we want to get out of this we need to make tough decisions. But it seems like it’s not going to happen so for now it is what it is and no one should be astonished if the numbers go up,” says Coetzee.

Dr Coetzee also warned that allowing schools to remain open was a bad decision.

“Without proper, effective and decisive measures to curb the spread of COVID, our infection and fatality numbers are going to climb even further. In addition, schools are still open, travel is still allowed and public transport can still operate as they currently are. This should not have been allowed.”

The Basic Education Department had already dismissed suggestions that schools should be closed as well as part of the COVID containment efforts. She also argued against a  simple tightening of curfews and alcohol sales.

“Nothing significant has changed. The stricter curfew measures and limitations on alcohol sales will simply mean people change their behaviour to accommodate for these restrictions and will have little impact on people’s daily routines. This is actually where restrictions should have been targeted.”

Speaking to Jacaranda, she said, “For us, it doesn’t make sense, we need people at home. We don’t want people in a shopping centre or anywhere else, if we can manage to do that for three to four weeks we can get the numbers down but for now, I don’t see that happening.”

Source: EWN

Inhaled Corticosteroid Could Shorten Moderate COVID

Source: Pixabay

Early treatment with inhaled budesonide shortens recovery time by a median of three days in community-treated patients with COVID who are at higher risk of more severe illness, according to preliminary results from an Oxford University trial.

Inhaled budesonide is a safe, fairly cheap and readily available corticosteroid commonly used in inhalers for the treatment of asthma and chronic obstructive pulmonary disease

Based on an interim analysis using the latest data from 25th March 2021, the results showed the estimated median time to self-reported recovery for inhaled budesonide was three days shorter compared to usual care, with a high probability of being superior to the usual standard of care. Of those taking inhaled budesonide, 32% recovered within the first 14 days and stayed well until the 28 day endpoint, compared to 22% receiving usual care. Budesonide group participants also reported greater wellbeing after two weeks. 

Among patients who had completed the study, 8.5% (59/692) in the budesonide group were hospitalised with COVID compared with 10.3% (100/968) in the usual care group, with an estimated percentage benefit of 2.1%. However as fewer than expected people were admitted to hospital in the trial, and with COVID cases falling in the UK, it is not clear from this interim analysis whether budesonide reduces hospitalisations.

Patients with COVID symptoms that started within 14 days and who are at higher risk of a poor outcome from the illness were eligible to join the trial and those who tested positive for SARS-CoV-2 were included in the main analysis. Patients receiving inhaled budesonide were asked to inhale 800 micrograms twice a day for 14 days, with a 28 day follow-up.

Joint Chief Investigator, Professor Chris Butler, a South Wales GP and Professor of Primary Care from the University of Oxford’s Nuffield Department of Primary Care Health Sciences, said, “PRINCIPLE, the world’s largest platform trial of community-based treatments for COVID-19, has found evidence that a relatively cheap, widely available drug with very few side effects helps people at higher risk of worse outcomes from COVID recover quicker, stay better once they feel recovered, and improves their wellbeing. We therefore anticipate that medical practitioners around the world caring for people with COVID in the community may wish to consider this evidence when making treatment decisions, as it should help people with COVID recover quicker.”

When the data has been obtained and analysed, detailed results on time to recovery and hospitalisations will be published. The full pre-print is available on the MedRxiv server.

Source: University of Oxford

A Common Cold Virus Could Stifle COVID

Photo by Kelly Sikkema on Unsplash

There might be an unexpected benefit to the rhinovirus, or the most frequent cause of the common cold — protection against COVID, according to a study at Yale University.

Around 200 viruses cause the common cold, of which rhinovirus is the most common. Researchers found that the rhinovirus kick-starts interferon-stimulated gene activity. Within airway tissues infected with the rhinovirus, this also can halt replication of the SARS-CoV-2 virus.

Setting off these defences early in the course of COVID infection might prevent or treat the infection, said Ellen Foxman, assistant professor of laboratory medicine and immunobiology at the Yale School of Medicine and senior author of the study. One method is treating patients with interferons, an immune system protein which is also available as a drug.

“But it all depends upon the timing,” Prof Foxman clarified.

In later stages of COVID, high interferon levels correlate with worse disease and may fuel overactive immune responses, according to previous research. But recent genetic studies show that interferon-stimulated genes may actually also be protective in cases of COVID infection.

Prof Foxman’s lab wanted to study this defence system early in the course of COVID infection.

Earlier studies by the lab had shown that common cold viruses may protect against influenza, so they decided to find out whether rhinoviruses would have the same beneficial impact against the COVID virus. The researchers infected lab-grown human airway tissue with SARS-CoV-2 and found that for the first three days, viral load in the tissue doubled about every six hours. However, replication of the coronavirus was completely halted in tissue which had been exposed to rhinovirus. When antiviral defences were blocked, the SARS-CoV-2 could replicate in airway tissue previously exposed to rhinovirus.

The same defences slowed down SARS-CoV-2 infection even without rhinovirus, but only with a low infectious dose, suggesting that the viral load at the time of exposure affects whether the body can effectively fight the infection.

The researchers also studied nasal swab samples from patients diagnosed close to the start of infection. They found evidence of rapid growth of SARS-CoV-2 in the first few days of infection, followed by activation of the body’s defenses. According to their findings, the virus typically increased rapidly for the first few days of infection, before host defenses kicked in, doubling about every six hours; in some patients the virus grew even faster.

“There appears to be a viral sweet spot at the beginning of COVID, during which the virus replicates exponentially before it triggers a strong defence response,” Foxman said.

Interferon treatment is promising but could be tricky, she said, because it would be mostly effective in the days immediately after infection, when many people are asymptomatic. In theory, interferon treatment could be used prophylactically in people at high risk who have been in close contact with others diagnosed with COVID. Interferon is being trialled in COVID, and there appears to be a benefit when given early, but not late.

The study helps explain why influenza infections are lowered at times of the year when the common cold is prevalent, Prof Foxman said. The easing of social distancing measures could cause the common cold and flu viruses, which have been suppressed, to spring back with greater force. Respiratory viruses interference with each other could be a mitigating factor, creating an ‘upper limit’ on the degree to which respiratory viruses circulate together, she said.

“There are hidden interactions between viruses that we don’t quite understand, and these findings are a piece of the puzzle we are just now looking at,” Prof Foxman said.

Source: Yale University

Journal information: Cheemarla, N.R., et al. (2021) Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics. Journal of Experimental

Tougher Restrictions for Gauteng Being Debated

Image by Quicknews

As COVID cases continue to rise virtually unabated by the move to Level 2 lockdown, there are reportedly discussions at the National Coronavirus Command Council to tighten the lockdown restrictions.

The Gauteng government wants the province to have tighter lockdown restrictions, as it is host to about half of daily new infections of COVID in the country. Despite the high infection rate in the province, many in Gauteng are against tougher restrictions, such as the Gauteng Education Department and South African Council of Churches. Acting Health Minister Mmamoloko Kubayi-Ngubane says that she will speak to the National Coronavirus Command Council about the issue.

The province’s premier David Makhura said the province is asking for increased measures. “Level 2 as we know it currently is not having a sufficient impact,” he said. “People are going on as if we are really not in the middle of a raging pandemic.”

With Charlotte Maxeke Academic Hospital being indefinitely closed, the pressure is mounting on both public and private facilities which running out of ICU beds.

“So, we talk to the private hospitals almost on a daily basis, and they do indicate to us that they are running almost at about 80% of their capacity for ICU. In the public hospitals, we are also running at about 70%,” said Thabo Masebe, communications head of the Gauteng government.

He confirmed that the province was looking for tougher restrictions to curb new infections.

“That’s what the premier had said. He will be raising that with national government to see what added restrictions could be made to help slow down the rate of infections in the province,” Masebe said.

Source: ENCA

Drop in Heart Attacks Linked to COVID Pandemic

Photo by camilo jimenez on Unsplash

A sharp drop in heart attacks in Finland last year seems to be a result of the COVID pandemic, doctors believe.

Cardiologist Mika Laine noticed a roughly 30 per cent reduction in the number of patients suffering myocardial infarction at Helsinki University Central Hospital in April and May 2020. But what was even more surprising was that this was not an isolated occurrence.

“When we started to study this further, we noticed that exactly the same phenomenon happened everywhere else in Finland and also in other countries in Europe and in the United States. So it was a kind of global phenomenon that happened during the COVID pandemic,” he told Euronews.

What was behind the drop?

Dr Laine is of the opinion that the fall in heart attack patient numbers results from changes made in response to the COVID outbreak.

“We have the exact same genes that we had a year ago, two years ago. So it has to be something in the environment that has changed,” he said. One major factor could be the massive global shift to remote working for many people, as a result of the lockdowns.

“People are at home, they are less stressed because they don’t need to go through morning traffic, hurry to work and so forth,” Dr Laine added.

EU Science Hub data shows that even before the pandemic, Finns worked remotely more than almost any other EU country. Last May, EU labour research body Eurofound revealed that Finnish workers made the fastest switch to teleworking in the EU, with nearly 60 per cent switching over.

“We also see this decrease in those people who are retired, who don’t go to work, so it cannot be just because you’re commuting,” said Dr Laine.
He however cautioned that there could be other factors behind the fall in heart attack patients.

Was there a real fall in heart attacks in 2020?

“We know that many people stopped smoking because smoking was associated with severe COVID mortality,” he said.

Better air quality in urban areas as a result of the lockdown could be another cause, Laine said, since airborne particles are known to be a risk factor for heart disease.

However not all are convinced that the pandemic had a positive impact on patients with all types of heart conditions.

Research published in the Journal of the American College of Cardiology in January found that, during the early phase of the pandemic, deaths due to ischaemic heart disease and hypertensive diseases increased in some parts of the US. Some patients may have died as a result of avoiding hospital visits due to infection fears, the researchers noted. 

A temporary or permanent effect?

With Finland, however,Dr Laine believes that was not the case.

“We haven’t seen any increase in mortality in cardiac diseases and so currently we think that it’s a true decrease in the number of cases and not because patients are not seeking help,” he said. “People were not dying at home to myocardial infarction”.

According to Dr Laine, the number of heart attack patients in Finland remains about 5 per cent lower than average, despite the easing of COVID restrictions.

“I think this is a typical example that environmental factors can have profound effects on myocardial infarction. And I think it’s motivating us to change our lifestyle healthier,” Dr Laine said.

Source: EuroNews