Tag Archives: RNA

The E484K mutation is potentially linked to SARS-CoV-2 adaptive fitness | Instant News


A team of Brazilian scientists recently conducted a genomic and phylogenetic analysis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome to better understand the process of viral evolution. Their analysis revealed that the E484K mutation variant of SARS-CoV-2 was present in three different lineages in four regions of Brazil and that the mutation could serve as a general solution for viral evolution. Studies are currently available at bioRxiv* preprint server.

Background

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes Coronavirus disease 2019 (COVID-19), is a member of the Coronaviridae family, which is enveloped in positive sense single-strand RNA viruses with a larger genome size of about 30 kb. Since its appearance in December 2019 in China, researchers around the world have sequenced nearly 4.10,000 SARS-CoV-2 genomes and have shared information in the Global Initiative on Sharing All Influenza Data (GISAID) database.

Several epidemiological studies of the SARS-CoV-2 genomics have been conducted, with the majority focusing on viral mutations. spike protein, surface glycoproteins SARS-CoV-2 is responsible for binding to the host angiotensin-converting enzyme 2 (ACE2) and initiating viral entry. Current research mainly focuses on three viral lineages, B.1.1.7, B.1.351, and P.1. because of its significant impact on viral transmission and pathogenicity. From this lineage, the P.1 lineage is prevalent in Brazil with three mutations (K417T, E484K, and N501Y) in the spike receptor binding (RBD) domain. In Brazil, many viral genomes harbor the E484K mutation, which is associated with increased viral transmission and immune evasion.

In the current study, scientists evaluated mutation characteristics and phylogenetic relationships in currently known lineages in Brazil to understand the adaptive evolutionary process of SARS-CoV-2.

A mutation histogram frequently observed in the Brazilian SARS-CoV-2 genome which stores the E484K mutation.  The red label above the bar indicates the absolute nucleotide position and the blue label indicates the effect of this mutation on the corresponding protein.  Since P.1 has only 19 represented genomes and a handful of mutations, only the major mutations of concern were highlighted.  UTR: Areas that have not been translated;  Syn: Synonym substitution;  del: deletion;  ORF: Open Reading Frame;  Nsp: Non-structural protein;  S: Surge;  E: Envelope;  M: Membrane;  N: Nucleocapsid.

A mutation histogram frequently observed in the Brazilian SARS-CoV-2 genome that stores the E484K mutation. The red label above the bar indicates the absolute nucleotide position and the blue label indicates the effect of this mutation on the corresponding protein. Since P.1 has only 19 represented genomes and a handful of mutations, only the major mutations of concern were highlighted. UTR: Areas that haven’t been translated; Syn: Synonym substitution; del: deletion; ORF: Open Reading Frame; Nsp: Non-structural protein; S: Surge; E: Envelope; M: Membrane; N: Nucleocapsid.

An important observation

The results revealed that the SARS-CoV-2 variant with the E484K mutation was widespread in many regions in Brazil. This mutation was introduced in Brazil in October 2020. Because the E484K mutation was found in different viral lineages at the same time as other mutations, scientists suggest that this particular amino acid substitution could act as a general driver for viral evolution in different genetic variants of SARS. -CoV-2. In the E484K mutation, a negatively charged amino acid (glutamic acid) is replaced by a positively charged amino acid (lysine). Thus, it is hoped that mutations will have a significant impact on viral survival and adaptive evolution.

Structural analysis revealed that a new site for ACE2 (75 amino acid) binding was generated due to the E484K mutation. This appears to create a significantly stronger interaction between ACE2 and the native binding site located at the RBD and ACE2 interface (amino acid 501).

A very diverse range of genetic mutations was observed in all Brazilian lineages with the E484K mutation. On average, about 19 and 30 mutations were observed in lineages B.1.1.33 and P.1, respectively. Further genomic analysis of the most recently emerging P.2 lineage showed that the P.1 and P.2 lineages were rapidly developing and had been circulating in Brazil for a longer period.

A new specific single substitution analysis was also carried out in this study. One such mutation, A27V, is present in the N-terminal domain (NTD) of the spike protein. Research has suggested that mutations in the NTD spike can allosterically change the dynamics of the spike RBD-ACE2 interaction and facilitate immune evasion. In addition, evidence suggests that viral lineages carrying the E484K mutation are associated with increased escape from antibody-mediated neutralization. Although the true impact of E484K and other substitutes on immune avoidance remains unclear, scientists argue that the E484K mutation is associated with improved viral fitness under pressure of natural selection.

Learn significance

Overall, the study suggests that the E484K mutation acts as an important evolutionary event for different viral lineages in terms of increased viral fitness. The E484K mutation has the potential to increase the infectivity and immune-avoidance potential of SARS-CoV-2. According to scientists, further research investigating the effectiveness of human serum anti-SARS-CoV-2 against the E484K mutation variant of SARS-CoV-2 is urgently needed.

* Important Notice

bioRxiv publishes a preliminary scientific report that is not peer reviewed and, therefore, should not be construed as a conclusion, a guide to health-related clinical / behavioral practice, or be treated as prescribed information

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The study exposed human olfactory and brain cells as targets of the original SARS-CoV-2 virus | Instant News


In a study published in iScience Jurnal, a research group from Switzerland showed that the receptor and entry gene for coronavirus 2 (SARS-CoV-2) severe acute respiratory syndrome is expressed in human olfactory nerve cells and the brain by observing key molecular players involved in the infection process.

The entry of SARS-CoV-2 which is the causative agent for the coronavirus disease pandemic (COVID-19) requires the use of a spike. glycoproteins to interact with the angiotensin-converting enzyme-2 (ACE2) receptor. Attached to the cell membrane are serine proteases TMPRSS2, which prioritizes glycoprotein spikes and facilitates viral entry.

As a result, the main target of the virus – namely the respiratory cells lining the respiratory tract – together express ACE2 and TMPRSS2. The nasal cavity also houses respiratory cells, but there is an area of ​​smell which is responsible for regulating the sense of smell.

And indeed, loss of smell is one of the causes symptoms of COVID-19; However, the notion that viruses can directly or indirectly affect the integrity and functioning of the sensory parts of the olfactory system is not new. Some viruses actually interfere with the neuroepithelium in various ways and often modify certain types of cells, including neurons.

But whether the olfactory dysfunction shown to be associated with SARS-CoV-2 infection originates from a generalized inflammatory process in the nasal cavity or from a targeted disorder of the olfactory neuroepithelium or olfactory bulb is unclear.

In this new paper, researchers from Switzerland (led by Dr. Leon Fodoulian of the University of Geneva) aim to investigate the distribution of the SARS-CoV-2 ACE2 receptor in human olfactory neuroepithelial cells, as well as in the brain.

Multidisciplinary methodological approach

This research effort was carried out using a multidisciplinary approach, based on its data and publicly available RNA-seq datasets, as well as immunohistochemical staining of mice and human tissue.

More specifically, the investigators have collected biopsies using endoscopic nasal surgery from four adult patients and then explored the potential for expression of ACE2 and TMPRSS2. Immunohistochemistry was then used to evaluate ACE2 expression in the human nasal cavity.

In their study, transcriptomic analysis of entire tissues and single cells of the human olfactory epithelium was pursued, and they have also explored two single-core RNA-seq data sets to assess ACE2 expression in the human brain precisely.

Sustentacular cells loaded with receptors

The results have revealed that a subset of olfactory support cells in the olfactory neuroepithelium (also known as support cells involved in odor transformation and xenobiotic metabolism) express ACE2, but not olfactory sensory neurons.

“In mice, where the olfactory mucosa is well structured both in terms of the pseudo layer and in terms of its very tight separation from the respiratory epithelium, we observed (similar to humans) clear ACE2 expression at the apical boundaries of the support cells”, explain the study authors.

However, this distribution is not homogeneous because ACE2 is observed in cells that are located very dorsally but completely absent in the more ventral zone of the olfactory neuroepithelium.

However, these cells were also found to express TMPRSS2, and the researchers also revealed ACE2 expression in a subset of brain cell types – including nerve cells and non-neurons.

Credible link with anosmia

In short, this study has shown that respiratory cells are not the only players in contact with the outside world which stores the molecular keys involved in the entry of SARS-CoV-2 in the nose. Sustentacular cells, located at the interface between the central nervous system and the olfactory cavity, have the same properties.

But what is the likelihood that the co-expression of ACE2 in olfactory-supporting cells and its direct connection to the brain is the underlying cause of SARS-CoV-2-induced anosmia?

“Taken together, and despite the fact that one cannot exclude inflammation and infection of other types of non-neuronal cells in the olfactory neuroepithelium as the origin of SARS-CoV-2- induced anosmia, the relationship between the means of entry of viral molecules is revealed by the olfactory support and SARS-CoV-2-induced chemosensory changes appear to be quite credible “, the study authors concluded.

However, the existence of a wide variety of neuronal and non-neuronal cell populations that express ACE2 in the human brain is a research interest that needs to be pursued, with possible practical applications in the future.

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Mobile phone contamination can be part of the SARS-CoV-2 chain of transmission in hospitals, the Brazilian case study suggests | Instant News


Researchers conducting the study at the 2019 coronavirus disease (COVID-19) intensive care unit (ICU) in São Paulo, Brazil, have warned that infection control guidelines need to include a universal policy regarding the disinfection of cell phones in hospitals.

A team from the University of São Paulo, Brazil, conducted a cross-sectional study in the ICU to investigate health workers’ knowledge of cross-contamination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – the agent responsible for COVID-19.

Although most workers understand the importance of cross-transmission and the importance of adhering to hand hygiene and mobile phone disinfection practices, SARS-CoV-2 ribonucleic acid (RNA) – the genetic material for the virus – is still being detected in some devices, said Evelyn Patricia Sanchez Espinoza and colleagues.

The researchers said the finding that healthcare workers’ cell phones could be contaminated with SARS-CoV-2 suggests these devices could be part of a chain of transmission in health care settings.

“Implementation of official hospital policies to guide health workers [healthcare workers] regarding disinfection and personal MP care [mobile phones] is needed, ”the team warned.

A preprinted version of the paper is available at medRxiv* server when articles undergo peer review.

Worries about cell phone in hospital

Espinoza and colleagues say that cell phones are now generally considered a working tool in hospitals.

However, although SARS-CoV-2 has been detected on the cell phones belonging to patients with COVID-19, the devices have not been identified as a potential source of transmission in a hospital setting.

At the same time, concerns are growing about cross-transmission of SARS-CoV-2, following recent descriptions of how the virus can survive on surfaces in hospitals, the team said.

“However, there is no official policy from the Centers for Disease Control and Prevention (CDC) about it [mobile phone] disinfection in health facilities, ”write the investigators. “Little is known about [the] viruses in MPs or their potential for cross-contamination. “

Investigate healthcare workers’ knowledge of the risks of cell phones

Espinoza and colleagues set out to investigate health workers’ knowledge of SARS-CoV-2 cross-transmission and whether they understand its potential to survive on their own cell phones and be part of the transmission chain.

They conducted a cross-sectional study involving staff members working in the adult ICU at a teaching hospital in São Paulo.

The ICU has 11 separate rooms for each patient. Health care staff use scrubs, N95 respirators and surgical caps as standard when working within the unit, and they also wear surgical gowns, face shields and gloves when entering patient rooms.

An educational campaign on cross-transmission of SARS-CoV-2 and mobile disinfection was launched at the start of the pandemic.

“Informative posters were left on units that had QR codes with access to campaign videos,” said Espinoza and the team.

In the video, health workers are advised to use 70% alcohol swabs to clean phones and screen protectors to keep the oleophobic coating. They are also advised to avoid using the device when providing patient care and while in the restroom.

Ten days after the campaign was held, researchers took participants’ cell phones and sent them for SARS-CoV-2 testing by reverse transcriptase-polymerase chain reaction (RT-PCR).

Electronic questionnaires on hand hygiene and mobile phone use and disinfection were also administered.

What did the research find?

Although most health care workers understood the importance of cross-transmission and increased their adherence to hand hygiene and mobile disinfection during the pandemic, SARS-CoV-2 RNA was still detected in two devices.

Fifty-one out of fifty-three staff members working in the unit participated in the survey and answered the questionnaire. Nine (18%) had covered their cell phones with kitchen plastic film in an effort to facilitate disinfection. Eleven (16%) said they did not remember the campaign and three (6%) said they had not changed their behavior.

Only four (8%) healthcare workers do not believe that the virus can survive on mobile phones and only one (4%) do not believe that the virus can survive on hand.

Ninety-eight percent of participants said they had washed their hands more since the start of the pandemic.

Of the fifty-one swabs collected from the cell phone, SARS-CoV-2 RNA was detected by RT-PCR on two devices.

There is a need for a universal policy regarding the care of electronic devices in hospitals

Espinoza and colleagues said the findings suggest that healthcare workers’ phones could be contaminated with SARS-CoV-2.

“So, maybe members of parliament [medical professionals] may be part of the chain of transmission of the virus in health care settings, ”they wrote.

“Our findings suggest the need for universal policies in infection control guidelines on how to care for electronic devices in hospitals,” the team concluded.

* Important Notice

medRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be construed as conclusions, guidelines for health-related clinical / behavioral practice, or are treated as defined information.

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Tiny balls of minerals better means for prospective mRNA therapy | Instant News


University of Wisconsin-Madison researchers have developed safer and more effective way to deliver promising new treatment for cancer and liver diseases and for vaccination, including COVID-19 vaccine from modern therapy, which was published in clinical trials with people.

The technology is based on the introduction in cells pieces of carefully designed RNA (mRNA), a strip of genetic material of human cells usually decode human DNA, to make beneficial proteins and to go about their business. Problems delivering RNAi safely and undamaged without breaking the immune system inhibit mRNA therapy, but UW-Madison researchers make little balls of minerals that seems to do the trick on mice.

These microparticles have pores on their surface, which are in the nanometer scale that will allow them to lift and carry molecules, such as proteins or RNA. They mimic something seen often in archaeology, when we find intact protein or DNA in the sample is bone or eggshell from thousands of years ago. The mineral components help to stabilize these molecules for all this time.”

William Murphy, Professor of biomedical engineering and Orthopaedics, UW-Madison

Murphy and UW-Madison collaborators used mineral-coated microparticles (ILMC), which in the diameter from 5 to 10 µm, the size of a man … in a series of experiments to deliver RNA into cells around the wound in diabetic mice. Wounds healed faster in MCM-treated mice, and cells in adjacent experiments have shown a much more efficient pickup of mRNA molecules are compared with other delivery methods.

The researchers described their findings today in the journal Science Progress.

In a healthy cell, DNA is transcribed into mRNA and the mRNA serves as the instructions the cell uses to produce proteins. Strip mRNA created in the laboratory can be replaced in the process to tell the cell to do something new. If something is of a certain type of antigen molecule that alerts the immune system to the presence potentially dangerous virus mRNA did the work of the vaccine.

At UW-Madison researchers encoded an mRNA with instructions directing the cells ribosomes to pump out the growth factor, a protein that encourages the healing process, which otherwise is slow to unfold or absent in diabetic mice (and many serious patients with diabetes).

mRNA short-lived, although in the body, so to deliver enough cells usually means of the introduction of large and frequent doses, in which mRNA strands is carried out containers made of molecules called cationic polymers.

“Often the cationic component is non-toxic. The more mRNA you put, the more therapeutic benefit you will receive, but the greater the likelihood that you’re going to see a toxic effect. So, it is a compromise,” says Murphy. What we found when we ship out of the ILMC, we do not see toxicity. And because the supply mkm protects mRNA from degradation, you can get more mRNA where you want it, to reduce toxic effects.”

The new study also paired mRNA with the immune system inhibiting protein, to make sure that the target cell did not take mRNA as foreign bodies and destroy or remove it.

Successful delivery of mRNA, as a rule, keeps the cells working on new instructions for about 24 hours, and molecules that they produce to disperse throughout the body. This is sufficient for vaccines and antigens they produce. To maintain the long processes of growing replacement tissue to repair the skin or organs, proteins and growth factors produced by cells want to hang around here much longer.

“What we saw with mcms is once the cells absorb the mRNA and start to take protein is that the protein will bind right back to MICRON particles,” says Murphy. “Then he was released within weeks. We basically take something that would normally last maybe hours or even a day, and we do it in the past for a long time.”

Because MCMS are large enough that they do not get into the bloodstream and disappear, they stay where they need to keep releasing useful therapy. In mice that therapeutic activity to continue for more than 20 days.

“They are made of minerals similar to tooth enamel and bone, but designed to be absorbed into the body when they are not useful anymore,” says Murphy, whose work is supported by the Agency for environmental protection, the National institutes of health and the national science Foundation, and donations from University of Wisconsin-Madison alum Michael and Mary sue Shannon.

“We can control their lives, adjusting as they are made so they dissolve harmlessly, when we want.”

The technology underlying the microparticles were patented by research Fund of the graduates of the University of Wisconsin and is licensed to Dianomi therapy in the company Murphy co-founder.

The researchers are now working on growing bone and cartilage tissue and restore injury to the spinal cord with the mRNA made by the ILMC.

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How COVID-19 affects the nervous system | Instant News


A new paper published in the journal JAMA Neurology in May 2020 discussed the presentation and complications of COVID-19 with respect to the nervous system.

The COVID-19 pandemic has caused hundreds of thousands of cases of severe pneumonia and respiratory disorders, in 188 countries and regions in the world. The causative agent, SARS-CoV-2, is a new coronavirus, with well-recognized lung complications. However, evidence is increasing that the virus also affects other organs, such as the nervous system and heart.

The Coronaviruses: A Glimpse

That corona virus is a group of large spread RNA viruses that infect animals and humans. Human infections are known to be caused by 7 coronaviruses, namely human coronavirus (HCoV) –229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, MERS-CoV, SARS-CoV-1, and SARS-CoV-2.

Among these, the last three are known to cause severe human disease. While HCoV is more associated with respiratory manifestations, three of them are known to infect neurons: HCoV-229E, HCoV-OC43, and SARS-CoV-1.

Current research aims to contribute to the knowledge of the SARS-CoV-2 neurotropism, as well as post-infectious neurological complications. This virus infects humans through ACE2 receptors in various tissues, including airway epithelium, kidney cells, small intestine, proper lung tissue, and endothelial cells.

Because endothelium is found in blood vessels throughout the body, this offers a potential route for CoV to be localized in the brain. In addition, a recent report shows that ACE2 is also found in brain neurons, astrocytes, and oligodendrocytes, especially in areas such as substantia nigra, ventricles, middle temporal gyrus, and olfactory bulb.

Interestingly, ACE2 in neuron tissue is expressed not only on the surface but also in the cytoplasm. This finding could imply that SARS-CoV-2 can infect neuronal and glial cells in all parts of the central nervous system.

How does neuroinvasion occur with SARS-CoV-2?

Current knowledge indicates the possibility of nerve cell virus invasion by several mechanisms. These include the transfer of viruses across synapses of infected cells, entering the brain through the olfactory nerve, infection of endothelial blood vessels, and migration of infected white blood cells across the blood-brain barrier (BBB).

The corona virus has been shown to spread back along the nerves from the edge of the peripheral nerves, across synapses, and thus into the brain, in several small animal studies. This is facilitated by a pathway for endocytosis or exocytosis between motor cortex neurons, and other secretory vesicular pathways between neurons and satellite cells.

Axonal transport occurs rapidly using axonal microtubules, which allow the virus to reach the body of neuron cells with a retrograde version of this mechanism.

The possibility of spreading the olfactory route is marked by the occurrence of isolated anosmia and age. In such cases, the virus can pass through the latticed plate to enter the central nervous system (CNS) of the nose. However, more recent unpublished research shows that olfactory neurons lack ACE2, whereas cells in the olfactory epithelium do so. This could mean that a viral injury to the olfactory epithelium, and not the olfactory neuron, is responsible for anosmia, but further studies will be needed to confirm this.

Cross the BBB

This virus can also pass through the BBB through two separate mechanisms. In the first case, infected vascular endothelial cells can move the virus across blood vessels to neurons. Once there, the virus can start to bud and infect more cells.

The second mechanism is through infected white blood cells that pass through the BBB – a mechanism called Trojan horse, which is famous for its role in HIV. Inflamed BBB allows the entry of immune cells and cytokines, and even, possibly, viral particles into the brain. T-lymphocytes, however, do not allow viruses to replicate even though they can be infected.

Neurological features of COVID-19

From limited data on neurological manifestations related to COVID-19, it is clear that headaches, anosmia, and age are among the most common symptoms. However, other findings include stroke and an abnormal state of consciousness.

While headaches occur in up to one third of confirmed cases, anosmia or age shows a much more varied prevalence. In Italy, about one fifth of cases show this symptom, while almost 90% of patients in Germany have such symptoms.

The researchers said, “Given the reports of anosmia that appear as early symptoms of COVID-19, specific testing for anosmia can offer the potential for early detection of COVID-19 infection.”

Impaired consciousness can occur in up to 37% of patients, due to various mechanisms such as infection and direct brain injury, metabolic-toxic encephalopathy, and demyelinating disease. Encephalitis has not been documented as a result of COVID-19.

Toxic-metabolic encephalopathy can occur due to a number of disorders of metabolic and endocrine function. These include electrolyte and mineral imbalances, kidney disorders, and cytokine storms, hypo or hyperglycemia, and liver dysfunction. Patients who are elderly, ill, or already have symptoms of dementia, or are malnourished, are at higher risk for this condition.

Less common neurological complications include Guillain-Barre syndrome, which is a post-viral acute inflammatory demyelinating disease, and cerebrovascular events, including stroke.

Is COVID-19 Therapy Related to Neurological Manifestations?

Nowadays, many different drugs are used to treat this condition.

Chloroquine and hydroxychloroquine, for example, can cause psychosis, peripheral neuropathy, and the latter can worsen the symptoms of myasthenia gravis. Tocilizumab, an IL-6 blocker, is intended to reduce excessive cytokine release that occurs in severe inflammation. Although admission to CNS is limited, it can sometimes cause headaches and dizziness.

Precautions for COVID-19 Patients with Neurological Conditions

If a patient already has a neurological condition that requires special treatment, they tend to be at higher risk for COVID-19, due to existing lung, heart, or liver conditions, having kidney disease (dialysis), if they are overweight, or at immunosuppressive drugs. Also, it is likely that they may be in nursing homes, where many countries have reported severe outbreaks.

This study concludes: “Doctors must continue to monitor patients closely for neurological diseases. Early detection of neurological deficits can lead to improved clinical outcomes and better treatment algorithms. “

Journal reference:

  • Zubair, A. S. et al. (2020). Neuropathogenesis and Neurological Manifestations of Coronavirus in the Coronavirus Era 2019: Overview. JAMA Neurology. doi: 10.1001 / jamaneurol.2020.2065.

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