Tag Archives: Receptors

Worse problems with the SARS-CoV-2 variant may be occurring | Instant News


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease (COVID-19), continues to spread globally.

With this spread, new variants and strains have emerged, posing a threat to the newly developed and distributed SARS-CoV-2 vaccine. efficacy.

Researchers at the Department of Integrative Biomedical Sciences, University of Cape Town, South Africa, found evidence of significant changes in the selective power acting on immunologically important SARS-CoV-2 genes, such as N and S. This likely coincided with their appearance. of the 501Y lineage.

In the study, published on a pre-print server medRxiv*, the team examined patterns of mutations that appeared in the SARS-CoV-2 genome during the pandemic.

SARS-CoV-2 mutation

Between December 2019 and October 2020, worldwide viral evolution involved new, highly vulnerable host populations. D614G (Asp614-to-Gly) mutation in viruses spike protein accelerate the spread of the virus.

From there, only a few mutations were epidemiologically significant without affecting the pathogenesis of SARS-CoV-2. However, these mutations are characterized by a mutation pattern of slow and selectively neutral random genetic drift.

Since October 2020, SARS-CoV-2 has mutated several times. Currently, three variants are actively spreading – the British variant is called B.1.1.7 with multiple mutations in fall 2020, the South African variant is called B.1.351, and the Brazilian variant is called P.1.

SARS-CoV-2 genome map showing location and amino acid changes encoding of what we consider here to be the signature mutations of the V1, V2 and V3 sequences. Genes represented with light blue blocks encode non-structural proteins and genes in orange encode structural proteins: S encode spike protein, E envelope protein, M matrix protein, and N nucleocapsid protein. Within the S-gene, the receptor-binding domain (RBD) is shown in darker color and the site where the S protein is cleaved into two subunits during priming for receptor binding and cell entry is indicated by a dotted vertical line.

The British variant spreads faster and easier than the other variants. In January 2021, scientists said that the variant may be associated with an increased risk of death compared to other variants of the virus. It has spread to many countries around the world.

Variant B.1.351 is known to be resistant to the effects of vaccines and therapy against COVID-19. Meanwhile, the P.1 variant appeared on travelers from Brazil in early January. This variant contains an additional set of mutations that can affect their ability to be recognized by antibodies.

In the study, variants B.1.17 or 501Y.V1 were referred to as V1, B.1.351 or 501Y.V2 variants were V2, and variants P.1 or 501Y.V3 were referred to as V3.

To date, research has shown that antibodies produced by vaccination with approved vaccines recognize this variant, but further investigations are ongoing.

Amino acid locations encoded by codons evolved under positive selection and / or encoding convergent amino acid changes between lineages mapped to the 3D Spike structure (PDB 7DF4 structure; 47).  Human ACE2 receptors are shown in light blue color.  Signature mutations are not represented unless concluded to be under positive selection.  Site pairs detected coexisting in different lineages are connected by purple lines.

Amino acid locations encoded by codons evolved under positive selection and / or encoding convergent amino acid changes between lineages mapped to the 3D Spike structure (PDB 7DF4 structure; 47). Human ACE2 receptors are shown in light blue color. Signature mutations are not represented unless concluded to be under positive selection. Site pairs detected coexisting in different lineages are connected by purple lines.

Learning

This study aims to determine the evolutionary capacity of SARS-CoV-2 to adapt to increased population immunity and infection control measures such as social distancing and vaccinations.

The researchers examined the mutation patterns that appeared in the SARS-CoV-2 genome during the pandemic.

The team used a series of phylogenetic-based natural selection analysis techniques to examine positive selection patterns in the protein-coding sequences of the three lineages.

The study findings suggest the emergence of the 501Y lineage is consistent with substantial global changes in positive selection signals. This implies a general change in the selective environment in which SARS-CoV-2 thrives.

They also found significant changes in the selective power acting on the SARS-CoV-2 gene. Furthermore, the team revealed that the adaptive evolution of the 501Y lineage unites between lineages. This study highlights the essence of surveillance on how members of the 501Y lineage develop similar stages to ensure their survival and persistence.

The sudden appearance of the 501Y lineage

The team explained that in the first months of the pandemic no mutations had appeared. This is the sluggish pace of virus evolution. The start of the pandemic was like the pinnacle of a virus’ fitness in its ability to infect and transmit between people.

However, since October 2020, the sudden appearance of the 501Y lineage has caused cases to skyrocket around the world. V1, V2, and V3 caused faster virus transmission, which has now reached 192 countries and regions.

“Given the number of infections that occurred in October, all of these individual mutations, and even all pairs of mutations that could potentially interact epistatically, would have emerged independently,” the investigators explain.

To date, the number of cases has reached more than 117 million and 2.59 million deaths. The United States reports the highest number of infections, exceeding 29 million. Other countries whose cases have skyrocketed include India with 11.22 million cases; Brazil 11 million cases, Russia 4.28 million cases, and Britain 4.23 million cases.

* 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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The new N501 SARS-CoV-2 mutation may have been circulating in Italy since August 2020 | Instant News


A recent study published in Lancet Infectious Disease The journal suggests that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain mutated by substitution at position 501 may have been circulating unnoticed even before the end of September 2020, when the rapid emergence of the B.1.1.7 lineage (carrying the N501Y mutation) was initially reported.

On 14 December 2020, British authorities reported to the World Health Organization (WHO) that a new variant of SARS-CoV-2, the causative agent for the ongoing coronavirus disease 2019 (COVID-19) pandemic, was identified through the viral genome sequence.

This variant is often referred to as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, 2020, month 12, variant 01), was shown to spread more easily among people, although there was no significant association with symptom severity or vaccines efficacy.

However, the mutation is a viral spike type glycoproteins characteristics for this variant, with N501Y a major concern as it involves one of the six major amino acid residues which is responsible for the close contact between the SARS-CoV-2 receptor-binding domain (RBD) and cellular angiotensin-converting enzyme 2 (ACE2). receptors.

As a result, a group of researchers, led by Dr. Simona Fiorentini of the Department of Molecular and Translational Medicine at the University of Brescia in Italy, performed a detailed metagenomic sequencing and bioinformatic analysis to take an in-depth look at Italian isolates.

Detailed genetic characterization

In November 2020, a 59-year-old man with a history of SARS-CoV-2 infection continued to undergo molecular testing. After laboratory confirmation of the infection, genetic characterization of the virus in the November or MB61-Nov samples (but also the previous sample from August 2020, known as MB61-August) was carried out by metagenomic sequencing.

The two complete genomes obtained were then compared with the complete viral genomes freely available at GISAID platform, which is an open source of access to genome data for the influenza virus and SARS-CoV-2.

Strains with the N501Y mutation in spike RBD, recently characterized in Italy and Great Britain as belonging to the rapidly emerging B.1.1.7 lineage, were included in the analysis. Finally, sequence alignment and detailed editing are also carried out to get a complete picture.

The N501T variant arrived in early August

In summary, the bioinformatic analysis in this study revealed that the MB61-Aug SARS-CoV-2 isolate had accumulated ten amino acid changes compared to the initial Italian isolate; In addition, three more have appeared as it evolves until the end of November 2020.

It should be noted that the substitution of N501T was found in the MB61-Aug and MB61-Nov SARS-CoV-2 isolates, which leads to the conclusion that mutations in the key amino acid 501 residue have been spreading in Italy since August 2020..

Our maximum possible time scale tree shows that the N501T variant of this spike appeared in early August in northern Italy, and therefore the SARS-CoV-2 strain having a substitution at position 501 may have been circulating unnoticed even before the end of September 2020, when the Lineage A rapidly emerging B.1.1.7 (carrying the N501Y mutation) was first reported, “the study authors said.

The need for massive research efforts

Recent discoveries regarding the evolution of SARS-CoV-2, particularly in RBD, require massive scientific efforts to pinpoint new variants with the potential for increased spread of the virus, but also with a tendency to exhibit evasive behavior towards strains of infection or vaccines. induced neutralizing immunity.

This study is one step in that direction, and also compares the Wuhan reference strain with the two MB61 variants. The variant actually carries four mutations and one deletion to the glycoprotein spike – two of which are located within the RBD.

Nonetheless, more complex and lengthy studies requiring collaboration between different research groups will be needed in the future. In this regard, the recently established WHO SARS-CoV-2 Virus Evolution Working Group is a way to increase understanding of this timely problem.

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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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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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Heparin can stop host cells that infect SARS-CoV-2 | Instant News


Researcher at Sheffield University has developed a new test that can be used to assess the attachment of viruses to host cells and to test the potential inhibitors of viral infections.

Using the test, the team was able to demonstrate the binding of a spike protein in acute coronavirus 2 (SARS-CoV-2) respiratory syndrome to human cells expressing the angiotensin 2 converting enzyme (ACE2).

Spike proteins are the main structure used by SARS-CoV-2 to bind ACE2 receptors expressed on target cells, before infecting them and potentially causing coronavirus 2019 (COVID-19).

The SARS-CoV-2 virus binds to ACE-2 receptors in human cells, the initial stage of COVID-19 infection. Illustrated credit: Kateryna Kon / Shutterstock

The researchers also found that incubating cells with unfracted heparin stopped the surge of proteins that bind them.

The pre-printed version of paper can be accessed on the server bioRxiv*, while this paper underwent peer review.

SARS-CoV-2 infection mechanism

On binding to ACE2, the spike protein undergoes proteolytic division of the host cell into two subunits: S1, which contains receptor binding domains (RBD) and S2, which allow fusion with the host cell membrane and virus infusion.

“Serine host cell surface protein, TMPRSS2 [transmembrane serine proteinase 2]”It was also thought to be involved in virus entry and it was proposed to split S1 and S2, which led to the activation of the fusion machine,” wrote Peter Monk and colleagues.

The new test uses cells that express ACE2 and TMPRSS2

To investigate SARS-CoV-2 that binds to host cells, the team developed a new test using a transitional urinary bladder RT4 carcinoma cell line, which expresses ACE2 and TMPRSS2.

They found that the intact recombinant form of the viral surge protein containing both S1 and S2 (S1S2), but not only in the S1 domain, binds strongly to RT4 cells in a temperature-dependent manner.

The binding activity increased sharply at 37 ° C, indicating that proteolytic cleavage might be involved, the team said.

Are there other mechanisms for virus entry?

Monk and colleagues say that most cell types only express ACE2 levels that are low enough, suggesting that the surge protein might also interact with other receptor sites to get virus entry.

Certain viruses such as herpes simplex are known to bind to the host glycosaminoglycan called sulfuric deposits, the team said.

In addition, a study by one group suggested that soluble glycosaminoglycan heparin could inhibit the entry of SARS CoV-2 into “Vero” cells – cell lines derived from monkey kidney epithelium.

“These authors also demonstrated that heparin can interact with recombinant S1 RBD and cause conformational changes, leading to the suggestion that SARS-CoV-2 might use sulfate liver hosts as an additional site for attachment during infection,” the researchers wrote.

Unfracted heparin completely stops the bond

Given that the new test seems to mimic some features of SARS-CoV-2 infection, the researchers used it to test the effect of incubating RT4 cells with heparin at 37 ° C.

The team reports that unfrracted heparin (UFH) actually inhibits the binding of S1S2 cells to RT4.

Treating cells with two low molecular weight heparin (LMWHs) that has been used clinically also inhibits binding, but only partially and not as strongly.

“This shows that heparin, especially the non-diffracted form, can be considered to reduce the clinical manifestations of COVID-19 by inhibiting ongoing viral infections,” wrote Monk and the team.

Can spike proteins also bind to the host cell’s sulfate supply?

The authors say the interaction they observed between heparin and protein spike suggests that it might also bind to sulfate liver cells.

To test this hypothesis, they treated RT4 cells with a mixture of heparinase I and III, enzymes that degrade sulfate molecules, before testing the binding of S1S2.

Treatment did not result in a significant reduction in RT4 cell binding, indicating that sulfate exposure did not play a significant role in the attachment of the SARS-CoV-2 surge protein to host cells:

“Although our data support UFH inhibitory activity, it does not support the notion that sulfate deposits are very important for viral infections,” the team wrote.

What are the implications of this research?

The researchers say that LMWHs, which have been used to treat COVID-19 patients and have been shown to improve results, are much smaller than UFH and have a more predictable pharmacokinetics.

Monks and colleagues argue that their research shows that previous use of heparin should be considered when a viral infection is still an important factor in influencing the severity of the disease.

“The use of UFH rather than LMWH must also be considered, although we note that the administration and safety profile of UFH might prevent this in some cases,” they added.

Finally, the researchers said their newly developed flow cytometric test to assess the binding of SARS-CoV-2 spike protein to the host cell supports the previous findings that heparin can inhibit viral attachment to monkey kidney epithelial cells.

“Our new test could be the first screen to be useful for new inhibitors of coronavirus infection,” concluded the team.

* Important Notification

bioRxiv publishing initial scientific reports that are not reviewed by colleagues and, therefore, should not be considered conclusive, guide clinical practice / health-related behaviors, or be treated as pre-existing information.

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