Question: What is the protein structure of the SARS-CoV-2 spike?

SARS-CoV-2, the cause of Covid-19 pandemic, is a newly emerged β coronavirus with structural proteins including spike, nucleocapsid, membrane, and envelope. The spike protein facilitates attachment to ACE2 through its S1 subunit and membrane fusion through S2. The N protein, composed of N-terminal (NTD) and C-terminal (CTD), plays a role in viral

SARS-CoV-2, the virus causing Covid-19, is a newly emerged ß coronavirus with a positive RNA genome encoding structural and non-structural proteins. The structural proteins include spike (S), nucleocapsid (N), membrane (M), and envelope (E). The S protein facilitates attachment to ACE2 through its S1 subunit and membrane fusion through S2. The N protein, composed of

The passage discusses a study aimed at investigating the structural details of the complex between TMPRSS2, a human serine protease, and the spike protein of SARS-CoV-2, the virus causing COVID-19. The study used docking simulations to model the interaction between TMPRSS2 and the spike protein, revealing that TMPRSS2 interacts with two different loops of the spike protein, each containing a different cleav

This study explores how genetic variations in the human ACE2 receptor may impact its binding with the SARS-CoV-2 spike protein. Through molecular modeling, the authors found that while most ACE2 variants have similar binding affinity with the viral spike protein, certain alleles (rs73635825 and rs143936283) exhibit noticeable differences in their intermolecular interactions. These findings

Researchers used GNAT, a glycosylation network analysis tool, to reconstruct the N-glycan biosynthesis pathway of SARS-CoV-2's spike protein based on published mass spectrometric data. They identified 12 enzymes involved in glycosylation, and blocking certain enzymes led to significant modifications in the glycan profile. The study revealed an intricate enzymatic pathway for

The passage discusses how protein structures of the coronavirus SARS-CoV-2, specifically the spike protein, solved through cryo-electron microscopy and X-ray crystallography often lack the representation of sugar molecules or glycans on their surfaces. Researchers are now focusing on adding these missing sugars to gain a better understanding of the virus's biology and aid in the development of vaccines and treatments. Andrea Thorn, a structural

The SARS-CoV-2 spike protein, which mediates virion binding to human cells and is a prime immunization target, is heavily glycosylated with both O- and N-linked structures. A threonine (T678) near the furin cleavage site is O-glycosylated with core-1 and core-2 structures, and eight additional O-glycopeptides have been identified. All N-

A novel betacoronavirus, SARS-CoV-2, caused the Covid-19 outbreak in 2020, leading to over 120,000 deaths and 2 million documented infections. The virus's spike protein, S, is crucial for cellular entry and attaches to the host cell via the receptor-binding domain (RBD) and Angiotensin Converting Enzyme 2 (ACE

A novel betacoronavirus, SARS-CoV-2, caused COVID-19 outbreak in 2020 with over 120,000 deaths and 2 million documented infections. The virus's spike protein S, a structural protein, is critical for cellular entry and attaches to host cells via Angiotensin Converting Enzyme 2 (ACE2). The spike protein contains a receptor-binding

Researchers designed and produced over 100 variants of the SARS-CoV-2 spike protein based on a cryo-EM structure of the prefusion form. Through characterization, they identified several proline substitutions in the best variant, HexaPro, which increased yield and stability, allowing for high-yield production of a stabilized prefusion spike protein. This will expedite the development of vaccines and diagnostics for SARS-

The passage discusses the role of glycans in the SARS-CoV-2 spike protein, which is the focus of antibody development efforts for COVID-19. The spike protein utilizes a glycan shield to evade the host immune response. The authors built a full-length model of the glycosylated SARS-CoV-2 S protein and conducted molecular dynamics simulations to understand the glycan shield's structure,

A study was conducted to identify allosteric sites on the SARS-CoV-2 spike protein that can be targeted with allosteric drugs to weaken the spike-ACE2 interaction and reduce viral infectivity. Three computational methods - protein contact networks (PCNs), SEPAS, and perturbation response scanning (PRS) - were used to analyze the ACE2 complex with both SARS-CoV-2 and SARS-

A study was conducted to identify allosteric sites on the SARS-CoV-2 spike protein that could be targeted with allosteric drugs to weaken the spike-ACE2 interaction and reduce viral infectivity. Three computational methods - protein contact networks (PCNs), SEPAS, and perturbation response scanning (PRS) - were used to analyze the ACE2 complex with both SARS-CoV-2 and SARS-

The passage discusses the specific sequences and structures in the spike proteins of human SARS coronavirus-2 (SARS CoV-2) that enable it to recognize and infect human angiotensin converting enzyme-2 (ACE-2) receptors. Two regions in the N-terminal domain ("MESEFR" and "SYLTPG") and three regions in the receptor-binding domain ("VGGNY", "EI

CoV3D is a weekly updated database and molecular viewer of high resolution structures of SARS-CoV-2 and other coronavirus proteins. It annotates structures of coronavirus proteins and their complexes with antibodies, receptors, and small molecules. The database also provides information on spike glycoprotein sequence variability and polymorphisms, and maps these features onto the spike structure. Additionally, CoV3D includes

The passage discusses a study on the structural order-disorder propensity and evolution rates of SARS-CoV-2's spike and nucleocapsid proteins to identify their B cell and T cell epitopes. By comparing orthologs from seven human coronaviruses, the researchers found that most nucleocapsid protein epitopes overlap RNA-binding and dimerization domains with low rates of evolution. Spike protein epitopes are prefer

The passage discusses the specific sequences and structures in the spike proteins of human SARS coronavirus-2 (SARS CoV-2) that enable it to recognize and bind to the human angiotensin converting enzyme-2 (ACE-2) receptor, leading to COVID-19 infection. Two regions in the N-terminal domain ("MESEFR" and "SYLTPG") and two regions in the receptor binding domain

Researchers analyzed 2363 sequences of SARS-CoV-2's Spike protein and identified variability in 44 amino acid residues worldwide. They predicted conformational and linear epitopes for B-cells, T-Cytotoxic, and T-Helper cells, finding 45 epitopes with amino acid variations. The distribution of mutations within these epitopes can aid in developing more effective vaccines, therap

A study reveals that Fab-dimerized glycan-reactive HIV-1 broadly neutralizing antibodies (bnAbs), specifically 2G12, bind to the SARS-CoV-2 spike protein through a quaternary glycan epitope on the S2 domain. This new epitope is located at positions 709, 717, and 801 on the spike. The findings suggest a

The passage discusses the importance of understanding the 3D structures of SARS-CoV-2 proteins for developing diagnostic and therapeutic molecules. Through comparative analyses of SARS-CoV-2 and SARS-CoV Spike protein Receptor Binding Domains (RBDs), the study identifies structural and sequence differences that impact antibody recognition. The findings explain why some SARS-CoV RBD-specific monoc

The spike protein (S protein) of SARS-CoV-2 plays a crucial role in infecting cells by strongly binding to human angiotensin-converting enzyme 2 (ACE2). The S proteins of SARS-CoV-2 and SARS-CoV share a high sequence identity of 77%. The SARS-CoV-2 S protein is slightly more positively charged than SARS-Co

The spike protein of SARS-CoV-2 plays a crucial role in infecting cells by strongly binding to human angiotensin-converting enzyme 2 (ACE2). The similarity between SARS-CoV-2 and SARS-CoV spike proteins is 77%, with SARS-CoV-2 having a slightly more positive charge which may increase its affinity to bind to negatively charged regions.

The passage discusses the results of a molecular dynamics simulation study on the effect of temperature on the structure of the SARS-CoV-2 Spike protein. The study found that the solvent-exposed domain, S1, is more mobile and has optimally oriented charged residues at temperatures between 10-30°C. The receptor binding motif, present in the receptor binding domain of S1, begins to close around 40°C

The SARS-CoV-2 pandemic warrants molecular and structural studies to understand the dynamics of viral proteins involved in host cell adhesion. Comparative genomic studies have identified a Furin protease site in the SARS-CoV-2 spike glycoprotein, suggesting potential modifications and implications for virulence. This study structurally shows how Furin interacts with the SARS-CoV-2 spike gly

A mini-protein was engineered to interact with the Receptor Binding Domain (RBD) of the SARS-CoV-2 Spike protein, which is crucial for the virus's attachment to the human angiotensin-converting enzyme 2 (ACE2) receptor. The mini-protein, produced in high yields and with a stable α helical conformation, binds to the glycosylated Spike

The SARS-CoV-2 spike protein has a unique furin cleavage site (FCS) at its S1-S2 boundary due to the insertion of 12 nucleotides encoding four amino acids PRRA. This FCS is absent in related coronaviruses and is spatially located in a random coil loop region, mostly exposed to solvent with no structural proximity to other parts of the S protein. The insertion of

The passage discusses the role of the TMPRSS2 protein in SARS-CoV-2 infection and the impact of its genetic variants on COVID-19 severity. The authors used bioinformatics methods to analyze the prevalence and pathogenicity of TMPRSS2 variants, including a common variant p.V160M, and found that many rare variants cause structural destabilization and protein misfolding. They also discovered that

SARS-CoV-2 is a single-stranded RNA virus with a genome size of approximately 30 kb, belonging to the Coronavirus genus and Coronaviridae family. It has emerged recently and is of zoonotic origin, causing a pandemic. The virus has a similar structure to SARS-CoV, with viral proteins embedded in a lipid bilayer and a helical nucleocapsid. The genome consists

A study using computational simulations reveals the binding dynamics between the human Angiotensin converting enzyme 2 (ACE2) protein and the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. The SARS-CoV-2, identified as the cause of COVID-19, utilizes ACE2 as a receptor, similar to SARS-CoV. The researchers used homology modeling and molecular

The passage discusses the structural insights into the attachment, entry, and morphogenesis of SARS Coronavirus, focusing on the role of its large spike protein. The spike is a type 1 viral fusion protein responsible for host cell receptor recognition and membrane fusion. The binding of the spike to the viral receptor, angiotensin-converting enzyme 2 (ACE2), triggers conformational changes observable by cryo

A study analyzing 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 identified 483 unique variations, including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Twelve of these variations were located at the N-terminal domain and six at the receptor-binding domain, potentially altering the interaction of S protein with the host receptor angiot

A study analyzing 320 whole-genome sequences and spike protein sequences of SARS-CoV-2 identified 483 unique variations, including 25 nonsynonymous mutations and one deletion in the spike protein. Twelve of these variations were located at the N-terminal domain and six at the receptor-binding domain, potentially altering the interaction with the host receptor ACE2. Additionally, 22 amino acid

A new pipeline was developed to identify mutations that stabilize the thermodynamically unstable surface spike protein of SARS-CoV-2, which plays a crucial role in viral-host interaction and is the focus of vaccine development. The pipeline integrates bioinformatics analysis, molecular dynamics simulations, and structural analysis to identify stabilizing residues. The pipeline was validated through known stabilizing mutations and used to discover new ones.

The passage discusses the use of artificial intelligence and molecular dynamics simulation to analyze the structural flexibility of SARS-CoV-2's spike protein, revealing that certain regions in the S2 domain and the hinge connecting the S1 and S2 subunits lose their secondary structures without a stabilizing beta sheet. These findings, which include an immunodominant site in the S2 domain previously identified in SARS-CoV-1, may aid in the development

The passage discusses the investigation of the relationship between the spike glycoprotein of SARS-CoV-2, which is believed to have originated from bats, and that of a closely related bat virus, RaTG13. The study involved determining the crystal structures of RaTG13 S and both furin-cleaved and uncleaved SARS-CoV-2 S, and comparing them with previously reported structures for uncleaved SAR

The passage discusses the investigation of the relationship between the spike glycoprotein of SARS-CoV-2, which is believed to have originated from bats, and that of a closely related bat virus, RaTG13. Cryo-EM structures were determined for RaTG13 S and for both furin-cleaved and uncleaved SARS-CoV-2 S, and compared with recently reported structures for uncleaved SAR

This study explores carbohydrate-mediated interactions between the SARS-CoV-2 spike protein and host lectins, as well as the lung microbiota, to better understand the pathogenic mechanisms of COVID-19. The research revealed specific binding of the spike protein to DC-SIGN, MGL, Siglec-9, and Siglec-10, all expressed on myeloid immune cells. Additionally, the spike

The passage discusses the structural analysis of the SARS-CoV-2 spike protein and its interaction with the receptor angiotensin-converting enzyme 2 (ACE2). The study used X-ray crystallography and cryo-EM to examine the different conformational states of the SARS-CoV-2 receptor-binding domain (RBD). The results reveal that a κ-helix structure plays a key role in

A phylogenetic analysis of over 1,225 SARS-CoV-2 genomes identified the D614G mutation in the spike protein, which has become predominant in Europe and is spreading worldwide. The mutation emerged around mid-to-late January 2020 and in silico analyses suggest it is neutral to protein function regarding its interaction with the human ACE2 receptor. Clinical metadata is needed for further

A study was conducted to discover potential compounds from the Taiwan Database of Extracts and Compounds that could prevent SARS-CoV-2 spike proteins from binding to human angiotensin-converting enzyme 2 (ACE2) proteins, using structure-based virtual screening and molecular docking calculation with AutoDock Vina program. Thirty-nine potential compounds were identified, including natural products thioflexibilolide A from

The passage discusses new findings from molecular dynamics simulations that reveal the distal polybasic cleavage sites of the SARS-CoV-2 spike protein enhance its binding to the human cell receptor ACE2 through electrostatic interactions and hydration, despite being approximately 10 nm away from the receptor-binding domain (RBD). A negatively charged tetrapeptide was designed to neutralize the positively charged arginine on the poly

An antibody named EY6A, isolated from a late-stage COVID-19 patient, neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. The antibody binds tightly to the receptor binding domain (RBD) of the viral Spike glycoprotein, with a KD of 2 nM. A crystal structure of an RBD/EY6A Fab complex identified a highly

The passage discusses molecular dynamics simulations of the interface between the receptor binding domain of the spike protein of SARS-CoV-2 and SARS-CoV bound to ACE2 during the COVID-19 pandemic. Several dynamic contacts were formed, broke, and reformed, indicating unique strategies for stable binding to ACE2. Stable interactions included a salt bridge between Lys417 of SARS-CoV-2 and Asp30

The passage discusses the structural modeling of the envelope protein (E-protein) of the novel SARS-CoV-2 virus using bioinformatics and homology modeling. The E-protein shares sequence similarity with that of SARS-CoV-1 and is highly conserved in the N-terminal regions. Using computational methods, the most favorable structure of the E-protein was found to function as a gated proton channel.

The passage discusses the structural information available for the heptad repeat regions (HR1 and HR2) of the severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein, which plays a role in viral entry. While the post-fusion form of HR1 and HR2 has been determined by x-ray crystallography, there is no structural information for their prefusion conformations. In this study, the NMR structure of the

A study was conducted to understand the selective pressure driving mutations in SARS-CoV-2 isolates. The most common mutation sites were identified on the non-structural protein ORF1ab and the structural protein Spike. Mutations in cross-reactive epitopes between SARS-CoV-2 and seasonal coronavirus may help SARS-CoV-2 evade cellular immunity during large-scale transmission. Mutations on

The cryo-EM structure of SARS-CoV-2 spike protein reveals three composite binding pockets for the essential free fatty acid linoleic acid, providing a direct link between the spike protein and this key molecule involved in inflammation, immune modulation, and membrane fluidity.

The passage discusses a study on the interactions between the SARS-CoV-2 spike protein and the human ACE2 receptor, which plays a role in the COVID-19 virus's ability to invade human cells. The study used in silico comparative modeling analysis to gain insights into conformational changes in the spike protein and its interactions with ACE2. The findings provide a pipeline to identify existing antibodies that could prevent the virus from binding to

The SARS-CoV-2 coronavirus uses its spike (S) protein, a class I fusion protein, for host cell recognition, binding, and membrane fusion during viral entry. The S protein exists in a metastable state, which is cleaved by furin and TMPRSS2 for structural rearrangement and ACE2 binding. The protein is covered in N-linked glycans that impact its folding, processing, and immune

The passage discusses the similarities and differences in the binding of SARS-CoV-2 and SARS-CoV to the human receptor ACE2. Both viruses have similar binding conformations and free energies to ACE2, as shown by protein-protein interaction structure modeling and in vitro assays. However, existing SARS-CoV neutralizing antibodies have limited cross-neutralizing activities against SARS-CoV-

The passage discusses a study on the interactions between the SARS-CoV-2 spike protein and the human ACE2 receptor, which plays a role in the virus's ability to invade human cells. The study used in silico comparative modeling analysis to gain insights into the conformational changes in the spike protein and its interactions with ACE2. The findings provide a pipeline to identify existing antibodies that could prevent the virus from binding to ACE2

A study using computational methods identified 18,354 missense mutations in the SARS-CoV-2 spike protein, most of which destabilize the entire protein and its receptor-binding domain (RBD). Specifically, residues G431 and S514 in the RBD are important for stability. The dominant pandemic form, D614G, stabilizes the entire protein. N-linked glycosylation

The study analyzed available structures of the coronavirus spike protein to understand its mobility and found distinct configurations among different strains. Two soluble ectodomain constructs were developed, one with the receptor binding domain (RBD) in a locked down position and the other with a previously unobserved 2-RBDs 'up' configuration. These findings demonstrate the ability to control the spike protein's conformation through rational design, providing a framework for engineered

A study identified a new vulnerable epitope of the SARS-CoV-2 Spike protein through the isolation and characterization of monoclonal antibodies (mAbs) derived from convalescent COVID-19 patients. One mAb, named 4A8, targets the N-terminal domain (NTD) of the S protein and exhibits high neutralization potency against both authentic and pseudotyped SARS-CoV-

The study compares the genome composition and codon usage of SARS-CoV-2 with SARS, MERS, and a pangolin Beta-CoV. SARS-CoV-2 shows a preference for pyrimidine-rich codons and lower effective number of codons (ENc), indicating higher codon bias and gene expression efficiency for its structural proteins. SARS-CoV-2 also encodes the highest

This study compares the genome composition and codon usage of SARS-CoV-2 with SARS, MERS, and a pangolin Beta-CoV. SARS-CoV-2 shows a preference for pyrimidine-rich codons and lower effective number of codons (ENc), indicating higher codon bias and gene expression efficiency for its structural proteins. SARS-CoV-2 also encodes the highest

The SARS-CoV-2 spike protein's N-terminal domain (S1-NTD) was analyzed in this report for structural differences compared to SARS-CoV and other similar viruses. The SARS-CoV-2 S1-NTD contains a unique receptor-binding motif with insertions, including GTNGTKR, which have been found in other viruses' structural proteins. These motifs suggest potential

A study identified a genetic variant, rs12329760 in the TMPRSS2 gene and its mutant V160M, which may hinder SARS-CoV-2 viral entry. The researchers also found TMPRSS2 cleavage sites in the S2 domain of the spike glycoprotein and reported the structure of TMPRSS2 in complex with the spike glycoprotein. Additionally

A study analyzing 3090 SARS-CoV-2 isolates from the GenBank database revealed that the structural proteins, including envelope (E), membrane (M), nucleocapsid (N), and spike (S) glycoprotein, have undergone purifying selection during human-to-human transmission. However, strong positive selection pressure was identified at codon 614 of the S glycoprotein, resulting

The study aimed to understand the structural changes and binding interactions between the S-protein RBD of SARS-CoV 2 (nCoV) and the human ACE2 receptor, due to reported mutations. A total of 58 mutated residues in nCoV S-protein RBD resulted in structural changes, leading to 11 hydrogen bonds and 1 salt bridge in the binding interaction. Major hot spot amino acids in A

The passage describes a study using cryo-electron microscopy and tomography to determine the high-resolution structure, conformational flexibility, and distributions of SARS-CoV-2 spike (S) protein trimers on the surface of intact virions. Previous research focused on the structures and conformations of soluble, overexpressed, and purified S proteins, but the structure and distribution on the virion surface was unknown. The study found that

The passage discusses a study aiming to identify fusion inhibitors for the SARS-CoV-2 spike glycoprotein using virtual screening and molecular dynamics simulations. The authors used the cryo-electron microscopy structure of SARS-CoV-2 S trimer in the prefusion conformation to scan its inner cavity for strongly interacting drugs. The stability of the protein-drug complexes was tested through molecular dynamics simulations, and the

The passage discusses the global spread of the most invasive SARS-CoV-2 spike mutation, specifically the G clade variant with the A → G nucleotide change at genomic position 23,403 and D → G amino acid change at spike protein position 614. The study shows that this variant underwent significant demographic expansion in most countries, not explained by stochastic effects or enhanced pathogenicity. The

A study compared the structural and immunological analyses of spike proteins from Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2), focusing on their receptor-binding domains (RBDs). The results showed that RBDs from SARS-CoV and SARS-CoV-2 adopt a "standing" state, while

The passage discusses the findings of substitutions in the Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in Colombia. The study analyzed 43 patient samples and obtained genome sequences using Oxford Nanopore and Illumina MiSeq technologies. A total of 371 genome sequences from South America were included for comparison. The most frequent substitution in the Spike protein was D614G, found

The passage discusses the lack of research on enlightening Nigerians about the causes, drug development targets, and repositioning for COVID-19, caused by SARS-CoV-2. SARS-CoV-2 is a β coronavirus that causes symptoms like dry cough, sore throat, nasal congestion, tiredness, fever, loss of taste and smell. The virus targets the ACE2 receptor for entry and has structural proteins

The passage discusses the determination of the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, which is responsible for binding to the cell receptor ACE2. The binding mode of SARS-CoV-2 RBD to ACE2 is similar to that of SARS-CoV, indicating convergent evolution for improved binding. Essential residues for ACE2 binding in SARS

The SARS-CoV-2 genome undergoes frequent mutations as it spreads, and whole-genome sequencing data provides opportunities to study mutation dynamics, genome diversity, and their implications on protein stability and viral transmission. Through aligning over 600 SARS-CoV-2 genomes and validating in 10,000 datasets, researchers identified frequently mutated residues in the surface glycoprotein,

A study was conducted to assemble non-infectious SARS-CoV-2 virus like particles (VLPs) in mammalian cells by co-expressing the viral proteins S, M, and E. The resulting VLPs have a spike to spike size of 103 ± 6 nm and a membrane diameter of 63 ± 5 nm, with numerous S protein spikes. These particles retained their structural

A study was conducted on the SARS-CoV-2 spike protein, the causative agent of the 2019 novel coronavirus pandemic. The protein was identified as a Betacoronavirus closely related to SARS-CoV and bat coronaviruses, sharing the same receptor (ACE-2) with SARS-CoV. A structural model of the protein revealed an extended loop containing basic amino acids at the interface of the

The passage describes the use of cryo-electron tomography and subtomogram averaging to determine the molecular architecture of the authentic SARS-CoV-2 virus. Native structures of the S proteins in both pre- and postfusion conformations were obtained at average resolutions of 9-11 Å. The compositions of N-linked glycans from the native spikes were analyzed by mass spectrometry, revealing similarities to recombinant

The passage discusses the use of in silico modeling to study the flexibility and mobility of SARS-CoV-2 protein structures deposited in the Protein Databank, with a focus on identifying potential movements for drug docking studies. The authors employ a recent protein flexibility modeling approach to examine structures like the SARS-CoV-2 spike protein, revealing possible further movements and providing full results for over 200 related structures. This research aims to contribute to

A study used computational methods to identify B- and T-cell epitopes on the spike protein of SARS-CoV-2 by interacting with human leukocyte antigen alleles. Twenty-four conserved peptide stretches were identified, twenty of which are surface-exposed and have potential epitope binding efficiency. The findings could aid in understanding immunodominant regions in the surface protein and potentially help develop peptide-based

A study identified three neutralizing monoconal antibodies (mAbs) from ten COVID-19 patients, one of which, named 4A8, binds to the N-terminal domain (NTD) of the SARS-CoV-2 Spike protein. 4A8 exhibits high neutralization potency against both authentic and pseudotyped SARS-CoV-2 and does not bind the receptor binding domain (RBD

A study using Protein Contact Networks identified a specific region in the SARS-CoV spike protein that acts as an allosteric site, affecting its binding to angiotensin-converting enzyme 2 (ACE2). This finding could lead to the development of allosteric drugs to weaken the spike-ACE2 interface and reduce viral infectivity for both the 2003 SARS and the recent 2019

The passage discusses a study investigating the structural properties of ACE2 orthologs (versions of a gene in different species) bound to the SARS-CoV-2 spike protein to understand cross-species transmission. The study found that non-susceptible animal species have disruptive mutations in ACE2 amino acid residues, preventing polar and charged contacts with the viral spike protein. Predicted affinity-enhancing mutations could be

The Spike protein on the SARS-CoV-2 surface is the primary driver of its high infectivity due to its role in virus-host attachment, entry, and spread. The unique properties of the Spike's fusion peptides, including their hydrophobicity, rigidity from consecutive prolines, and synergistic organization, contribute to the virus's fusogenicity and infectivity, distinguishing it from other β-coronaviruses.

The passage discusses a study comparing the binding affinities of the spike proteins of SARS-CoV and SARS-CoV-2 to the ACE2 receptor using molecular dynamics simulations and Monte Carlo sampling. The results show that SARS-CoV-2 binds to ACE2 stronger than SARS-CoV by 7 kcal/mol due to enhanced electrostatic interactions. The major contributions to the electrostatic binding energies

The passage discusses the analysis of 3D structures of glycoforms of the SARS-CoV-2 spike protein, produced in HEK293 cells, and their impact on antigenicity. Molecular dynamics simulations were performed to determine the effect of glycan microheterogeneity. Identified peptides in the S protein were discussed in relation to their potential presentation in human leukocyte antigen complexes. The results showed that

A structural study of the cross-reactive antibody CR3022 reveals a conserved epitope on the receptor-binding domain of both SARS-CoV-2 and SARS-CoV.

The passage discusses a study on the interaction between the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein and Angiotensin-converting enzyme 2 (ACE2) as the host cell receptor. The study calculated binding energy scores and identified key amino acids (Q493 and P499) in SARS-CoV-2 RBD for binding to human ACE

The passage discusses a study on the interaction between the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein and Angiotensin-converting enzyme 2 (ACE2) as the host cell receptor. The study calculates binding energy scores and identifies key amino acids in the RBD for binding to human ACE2. The results suggest a higher affinity in SARS-CoV

SARS-CoV-2 infection is linked to delirium, a confusional state observed in 60-70% of severe cases. Delirium is also associated with orthopedic surgery. A study found that delirium-prone patients had lower CSF levels of phenethylamine (PEA) than blood, while controls had the opposite. PEA is metabolized by monoamine oxidase B (MAOB), which has

The passage discusses the results of a study on the SARS-Cov-2 Spike protein, which is responsible for the Covid-19 pandemic. The protein exists in both prefusion and fusion states, with each protomer in the prefusion state being in an Up or Down state based on the configuration of its receptor binding domain (RBD). The study performed all-atom energy mappings of the SARS-Cov-2 Spike protein in its static

SARS-CoV-2 infects human cardiomyocytes, leading to cytotoxic effects and cardiotoxicity. This was demonstrated through the detection of viral RNA and protein expression, as well as the confirmation of productive infections in cell lines. RNA sequencing revealed up-regulation of genes related to viral response, apoptosis, and reactive oxygen stress. The findings suggest that direct cardiotoxicity may contribute to the cardiac

The passage discusses the SARS-CoV-2 virus, the cause of the COVID-19 pandemic, and its structure. The spike protein is crucial for attachment, fusion, and entry into cells. However, other proteins like Orf3, Orf8, and Orf10, which have the least homology to SARS-CoV proteins, should be further studied for their potential roles in modulating antiviral and inflammatory

The COVID-19 pandemic is caused by SARS-CoV-2, a coronavirus that has resulted from interspecies transmission and poses a significant threat to global health. The virus's spike protein plays a crucial role in attachment, fusion, and entry. However, other structural and non-structural proteins, such as Orf3, Orf8, and Orf10, which have the least homology to SARS-CoV prote

Researchers are investigating the use of peptide-based binders to disrupt the binding between the receptor binding domain (RBD) of SARS-CoV-2's spike protein and angiotensin-converting enzyme 2 (ACE2) as a potential therapeutic intervention for COVID-19. Through molecular dynamics simulations and chemical synthesis, they identified a 23-mer peptide fragment (SBP1)

The passage discusses a study on the SARS-CoV-2 spike protein, focusing on its variability and potential drug target sites. The findings suggest that the S2 subunit of the spike protein, including HR1, CH, and CD domains, has low variability, low fluctuations, and forms a trimer cavity. In contrast, the receptor binding domain (RBD) is more variable and flexible. MD simulations indicate that the monomer form of the

A study analyzing SARS-CoV-2 and SARS genome sequences revealed that SARS-CoV-2 has a lower mutation rate than SARS. Minimum Evolution phylogeny analysis provided insights into the origin and early spread of SARS-CoV-2. A mutation in the receptor binding domain of a SARS-CoV-2 sample from India was identified, reducing its affinity for the human A

The study investigates conformational changes in the SARS-CoV spike when it binds to the viral receptor, angiotensin-converting enzyme 2 (ACE2), using cryo-electron microscopy and image processing on purified, irradiated SARS-CoV virions. The results reveal that ACE2 binding initiates structural changes leading to viral membrane fusion, and precisely locates the receptor

The passage discusses the properties of coronaviruses, specifically focusing on the seven known human coronaviruses, including SARS-CoV-2. Coronaviruses are spherical viruses with a positive sense, single stranded RNA enclosed in a helically symmetrical nucleocapsid and an envelope with club-shaped spikes. Human coronaviruses are classified under the α-CoV and β-CoV genera, with

The passage discusses the properties of coronaviruses, specifically focusing on the seven known human coronaviruses, including SARS-CoV-2. Coronaviruses are spherical, enveloped viruses with a positive sense, single stranded RNA genome. Human coronaviruses belong to the genera α-CoV and ß-CoV. SARS-CoV-2 is a ß-Co

A study analyzing 2952 SARS-CoV-2 genomes identified 1815 non-synonymous mutations in the S-protein, with six of these mutations located in the Receptor Binding Domain (RBD) region. These RBD mutations cluster into distinct phyletic clades, suggesting the emergence of new sublineages of the virus. Structure-guided analysis predicts altered virus-host interactions

The passage discusses two crystal structure models of the SARS-CoV-2 spike protein obtained through cryo-EM, representing the prefusion and postfusion conformations. The prefusion trimer has tightly packed receptor-binding domains, while the postfusion state is a rigid tower-like trimer decorated with N-linked glycans. The transition to the postfusion state occurs spontaneously under mild conditions, independent of target cells. These findings

The SARS-CoV-2 Spike protein variant D614G, which was not present in the initial SARS-CoV-2 genome but emerged in late January in Germany and China, has become the dominant variant worldwide. This variant is more infectious than the ancestral form on human lung and colon cell lines, as well as on other human cell lines, but does not affect the neutralization potency of monoclonal antibodies targeting

Eighteen Romanian patients' SARS-CoV-2 viral genomes were sequenced and analyzed to understand the impact of mutations on protein stability, particularly in the Spike glycoprotein. The findings were integrated into the European SARS-CoV-2 phylogenetic tree and provided an epidemiological overview of the patients' pre-existing conditions. Non-synonymous mutations in the Spike glycoprotein were modeled


Question: What is the result of phylogenetic analysis of SARS-CoV-2 genome sequence?

The Children's Hospital Los Angeles COVID-19 Analysis Research Database (CARD) is a genomic resource providing access to over 30,000 full-length SARS-CoV-2 viral genomes and associated metadata. It offers interactive online tools for phylogenetic analysis, including reference trees and a web-based Phylogenetic Tree Browser for flexible tree manipulation and advanced analysis. The Virus Genome Tracker compares

This study examines the quality of available SARS-CoV-2 full genome data, focusing on sampling bias and phylogenetic signals. Using data from GISAID, the researchers found that while the number of high-quality sequences is increasing, country-specific data sets still have limitations. The sequences from April 2020 contain sufficient phylogenetic information for reliable inference, but within-country studies should be considered preliminary. The authors

This study examines the quality of available SARS-CoV-2 full genome data, focusing on sampling bias and phylogenetic signals. While the number of sequences is growing and April 2020 data contains sufficient phylogenetic information, country-specific data sets have limitations and should be interpreted with caution. Studies on within-country spread or transmission clusters are currently preliminary and require more sequences for robust analysis.

A study analyzed 4,254 SARS-CoV-2 genomic sequences from the Global Initiative on Sharing all Influenza Data (GISAID). Phylogenetic analysis identified three major clades (S, V, and G) and two subclades (G.1 and G.2). There were 2,129 non-synonymous and 767 synonymous mutations. ORF1a,

The passage discusses the importance of large-scale genomic sequencing in addressing infectious diseases such as Severe Acute Respiratory Syndrome (SARS) and influenza. While large amounts of data are being generated, the ability to derive meaningful information from these datasets lags behind. The passage focuses on the computational challenges of comparative genomic analyses, specifically sequence alignment and phylogenetic tree reconstruction. SARS and influenza, both R

The passage describes an analysis of the SARS-CoV genome sequence (PUMC01) isolated at the Peking Union Medical College Hospital. The genome was sequenced and assembled using conventional methods, and variation and phylogenetic analysis were performed by comparing it to other SARS-CoV isolates. Ten variation sites were identified, and in phylogenetic analysis, two classes of SARS-CoV isolates were observed with different

The passage discusses the advantages of SARS-CoV-2 Whole Genome Sequencing (cWGS) for COVID-19 surveillance and control, including identifying cryptic virus origins and community transmissions. The study compares shotgun transcriptome sequencing and targeted SARS-CoV-2 full genome amplification and sequencing, showing significant improvements in data quality, viral detection, scalability, and cost-effectiveness with amplicon-

A study was conducted on SARS-CoV-2 genomes from India, sequencing and analyzing 64 new genomes along with 307 previously deposited ones. The results identified a distinct phylogenetic cluster (Clade I/A3i), which makes up 41% of Indian genomes and 3.5% of global genomes, characterized by specific genetic variants and a lower substitution rate. The cluster's common

This study aimed to characterize the SARS-CoV-2 sequences from three confirmed cases in India as of February 29, 2020. Throat and nasal swab specimens from 881 suspected cases were screened, and three cases with travel history from Wuhan, China, were identified as positive. Nearly complete genomes of cases 1 and 3, and a fragmented genome for case 2, were obtained

This study aimed to characterize the first two full-genome sequences of SARS-CoV-2 identified in India, obtained from three confirmed cases with a travel history from Wuhan, China. The sequences showed high identity (~99.98%) with the Wuhan seafood market pneumonia virus and belonged to different phylogenetic clusters. Predicted B-cell epitopes were concentrated in the S1 domain of the spike protein, and a

This study used phylogenetic and Bayesian phylodynamic analyses to trace the origin and diffusion pathways of SARS-CoV-2 in Spain and Europe. The results showed that most of the first 28 Spanish SARS-CoV-2 sequences belonged to the G and S clades, with two sequences in the V clade. Two monophyletic clusters, S-Spain and G-Spain, were identified, with

A study sequenced the genomes of SARS-CoV from three clinical specimens in Taiwan and found 19 genetic variations, two of which were linked to a specific genotype. Phylogenetic analysis revealed two major clusters of SARS patients in Taiwan, suggesting possible infection from two different origins. The researchers developed a rapid method to sequence the whole genome of SARS-CoV, which can help with molecular epidemiology and vaccine development.

The passage summarizes a genome analysis of SARS-CoV-2 isolates from India. The study found that Indian isolates are closely related to isolates from other countries, with most ORFs being highly conserved. However, mutations were identified in some ORFs, with key mutations at the 614th position of the S protein and 84th position of ORF 8, which are associated with high virulence and transmission rate

A phylogenetic analysis was conducted on 15,277 SARS-CoV-2 genomes, including the first 30 isolated in Turkey. The results suggest that the virus was introduced to Turkey earlier than the first reported case and is dispersed among various subtypes in the tree. Two subclusters were found to be enriched with Turkish isolates, indicating their widespread transmission within the country. The analysis also identified multiple independent international introductions and

A phylogenetic analysis was conducted on 15,277 SARS-CoV-2 genomes, including the first thirty isolated in Turkey. The results suggest that the virus was introduced to Turkey earlier than the first reported case and is dispersed among various types in the tree. Two sub-clusters with a high number of Turkish isolates were identified, indicating their widespread transmission in the country. The analysis also revealed multiple independent international introductions and a hub for

The passage discusses the specific sequences and structures in the spike proteins of human SARS coronavirus-2 (SARS CoV-2) that enable it to recognize and infect human angiotensin converting enzyme-2 (ACE-2) receptors. Two regions in the N-terminal domain ("MESEFR" and "SYLTPG") and three regions in the receptor-binding domain ("VGGNY", "EI

A study analyzed genome sequences of over 7,600 SARS-CoV-2 patients from the GISAID database using unsupervised cluster analysis. Instead of modeling mutation rates or using phylogenetic trees, they compared all pairs of sequences at all loci using the Jaccard index and principal component analysis. The results showed the geographic and chronological progression of the virus and identified distinct genetic subgroups, with ongoing research examining potential

The study examines SARS-CoV-2 sequences from Saudi Arabia and compares them to SARS-CoV, bat SARS-like CoVs, and MERS-CoV. Phylogenetic analysis reveals that Saudi SARS-CoV-2 sequences are closest to bat SARS-like CoVs and have undergone two recombination events with them. Positive selection pressure was detected between SARS-Co

The passage discusses the specific sequences and structures in the spike proteins of human SARS coronavirus-2 (SARS CoV-2) that enable it to recognize and bind to the human angiotensin converting enzyme-2 (ACE-2) receptor, leading to COVID-19 infection. Two regions in the N-terminal domain ("MESEFR" and "SYLTPG") and two regions in the receptor binding domain

Two SARS-CoV-2 sequences from Italian patients were analyzed with sequences from Europe and other regions. The Italian patient's sequence clustered with German sequences, while the tourist's sequence clustered with other European sequences in a phylogenetic tree. Additional European sequences were found outside these clusters, indicating multiple SARS-CoV-2 introductions in Europe or virus evolution during circulation.

Two SARS-CoV-2 sequences from Italian patients were analyzed with sequences from Europe and other regions. The Italian patient's sequence clustered with German sequences, while the tourist's sequence clustered with other European sequences in a phylogenetic tree. Some European sequences were found outside these clusters, indicating multiple SARS-CoV-2 introductions or virus evolution in Europe.

A study using genomic surveillance and phylogenetic analysis of SARS-CoV-2 in Dubai, UAE, a major international travel hub, revealed multiple introductions of the virus into the country from Asia, Europe, and the Middle East during the early phase of the pandemic. The research also identified early community-based transmission and new mutations in SARS-CoV-2 strains in the UAE, contributing to the understanding of the global transmission network

The passage discusses the investigation into unique features in the SARS-CoV-2 genome that contribute to its viral replication, host pathogenicity, and vulnerabilities. Unique sequence signatures were identified in the 3'-untranslated region (UTR) of betacoronavirus lineage B, which includes SARS-CoV-2, SARS-CoV, and various bat and animal coronaviruses. Genome

A study investigating the evolution of SARS-CoV-2 in Nigeria analyzed 39 complete genomes from the GISAID EpiFluTM database. The Maximum Likelihood method was used to construct a phylogenetic tree, revealing a monophyletic clade with a Wuhan sublineage and 100% similarity between strains. Comparative analysis showed 97.6% pairwise identity and 9

The UCSC SARS-CoV-2 Genome Browser is a tool that provides continuously updated access to molecular data of the SARS-CoV-2 genome and its proteins. It maps data from published studies and database submissions onto the viral genome, allowing for cross-referencing and comparison. The browser offers access to mutations in thousands of SARS-CoV-2 genomes, phylogenetic trees, alignments

The passage discusses an analysis pipeline for studying the Covid-19 virus (sars-cov-2) using machine intelligence. The pipeline includes phylogenetic analysis to trace the virus's evolutionary history and identify relationships between strains in different countries. Following this, a classification exercise is performed to determine the virulence of the strains. Important features are then extracted from the genetic material, which are used to predict mutations at specific sites using deep learning techniques.

This study aimed to characterize Indian SARS-CoV-2 genome variations, trace ancestries, and correlate state-wise distribution with mortality rates. A total of 305 whole genome sequences from 19 Indian states were analyzed, revealing 633 variants and 388 amino acid substitutions. The presence of low frequency variants and negative Tajima’s D values suggested population expansion. Two major clusters, clade

The passage discusses the results of a phylogenetic analysis of 95 SARS-CoV-2 sequences from the early stages of the pandemic, revealing insights into the evolution of the virus and the emergence of variants. Variants may pose challenges in diagnostics, immunology, and drug effectiveness. The analysis identified clusters with identical sequences and lineages with beginning diversification. Molecular epidemiological investigations can be conducted with the data, which includes

This study analyzed 46 Indian SARS-CoV-2 genome sequences from early 2020, assessing evolutionary dynamics and identifying co-evolving mutations in nine structural and non-structural genes. Phylogenetic analysis revealed the emergence of "genome-type clusters" and adaptive selection of "L" type strains with genetic similarity to bat coronaviruses. Two groups of mutations were identified: the "major

The manuscript describes a new method for acquiring a high-coverage SARS-CoV-2 genome sequence using target capture sequencing and enrichment probes. The approach significantly increases the number of mapped reads to the SARS-CoV-2 reference sequence compared to metagenomic sequencing technology. The method was tested using a culturing supernatant containing SARS-CoV-2 particles, resulting in a 93.47% fraction

A study was conducted to determine the complete genomic sequence of a Hong Kong Severe Acute Respiratory Syndrome (SARS) coronavirus (SARS-CoV) strain HK-39. The sequence, which is 29.7kb long, reveals that HK-39 is a distinct member of the Coronaviridae family. Six subgenomic transcripts were identified, and five open reading frames (ORFs

The Child Health Research Foundation in Bangladesh sequenced the first SARS-CoV-2 isolate from the country, revealing 9 single nucleotide variants compared to the Wuhan reference sequence. Most variants were in the ORF1ab gene and were also found in isolates from other countries. A sequence of three consecutive variants in the N protein gene was also identified and was observed in other isolates. Phylogenetic analysis showed the Bangladeshi isol

The passage discusses the results of a phylogenetic analysis of the full-length SARS-CoV sequences, which revealed that while the virus is mostly related to Group II coronaviruses for about 80% of its genome, there is no apparent similarity in three regions of the ORF1ab gene. The authors suggest that this discordant phylogenetic clustering could be due to ancient recombination events, altered evolutionary

A study sequenced 212 SARS-CoV-2 samples in Israel and used phylogenetic analysis to trace the origins and spread of the virus. Multiple independent introductions into Israel were identified, with returning travelers from the U.S. contributing significantly to viral spread. The basic reproduction number of the virus was initially around 2.0-2.6, but dropped by two-thirds after social distancing measures were implemented. The

The study aimed to analyze the evolution and variation of SARS-CoV-2 during the epidemic starting in late 2019. The researchers used bioinformatics software to construct a genomic evolution tree, infer the time evolution signal, calculate the tMRCA time, and analyze selection pressure. The results showed that SARS-CoV-2 belongs to the Sarbecovirus subgenus and had a weak time evolution signal with an average tMRCA

The study aimed to analyze the evolution and variation of SARS-CoV-2 during the epidemic that began at the end of 2019. The researchers downloaded full-length genome sequences of SARS-CoV-2 from GISAID and NCBI databases and used bioinformatics software to construct a genomic evolution tree, infer time evolution signals, calculate tMRCA time, and analyze selection pressure. The results showed that SAR

The passage discusses the limitations of current methods used to track the evolution of SARS-CoV-2 virus using consensus sequences and phylogenomic approaches. The introduction of a new framework called VERSO (Viral Evolution ReconStructiOn) addresses these limitations by accounting for clonal mutations and uncertainty in data, and exploiting intra-host variant frequency profiles to characterize sublineage similarity. The application of VERSO to RNA-sequencing

A study sequencing viral genomes from early COVID-19 patients in Connecticut found that the majority of these genomes were similar to those from Washington state, indicating that early SARS-CoV-2 transmission in Connecticut was likely due to domestic introductions. By March, the risk of domestic importation exceeded that of international importation, despite federal travel restrictions. The study reveals the widespread, sustained transmission of SARS-CoV-2 within the US and emphasizes

The SARS-CoV-2 pandemic has affected over 900,000 people and caused significant economic and societal distress. Many studies based on viral sequences have been published to investigate genetic heterogeneity and spatiotemporal dissemination. While the number of available full genomes is growing daily and contains sufficient phylogenetic information, country-specific datasets have limitations and should be interpreted with caution for within-country spread or transmission cluster studies.

A study analyzing 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 identified 483 unique variations, including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Twelve of these variations were located at the N-terminal domain and six at the receptor-binding domain, potentially altering the interaction of S protein with the host receptor angiot

A study analyzing 320 whole-genome sequences and spike protein sequences of SARS-CoV-2 identified 483 unique variations, including 25 nonsynonymous mutations and one deletion in the spike protein. Twelve of these variations were located at the N-terminal domain and six at the receptor-binding domain, potentially altering the interaction with the host receptor ACE2. Additionally, 22 amino acid

The first case of COVID-19 in Australia was a 58-year-old man from Wuhan, China who presented to Monash Medical Centre in Melbourne with fever, cough, and dyspnoea on January 24, 2020. A nasopharyngeal swab and sputum sample tested positive for SARS-CoV-2. The virus was isolated from the swab using Vero/hSLAM cells and confirmed

The first case of COVID-19 in Australia was identified in a 58-year-old man from Wuhan, China, who presented to Monash Medical Centre in Melbourne with fever, cough, and dyspnoea on January 24, 2020. A nasopharyngeal swab and sputum sample tested positive for SARS-CoV-2. The virus was isolated from the swab using Vero/hSLAM

The first case of SARS-CoV-2 in Mexico was identified in a patient who had traveled from Bergamo, Italy. The complete genome sequence of this virus was determined and shown to belong to subclade A2a (lineage G). It is closely related to isolates from Finland, Germany, and Brazil, all linked to travel history in Italy. This is the first report of the complete genome sequence of SARS-CoV-2 in Mexico.

A study was conducted to determine the phylogenetic relationship between Severe Acute Respiratory Syndrome Coronavirus (SARS CoV) and other coronaviruses using a large dataset and various methods. The results showed that all phylogenetic trees had an identical topology, supporting the hypothesis that SARS CoV and Group 2 CoVs have a monophyletic relationship. The relationships among all major coronavirus groups were

Twenty-five SARS-CoV-2 genome sequences from some of the first COVID-19 cases in eastern Ontario, Canada, were analyzed. The sequences belonged to the S-clade and G-clade, containing 45 polymorphic sites. Phylogenetic analysis traced the viral origin and potential transmission into and within Canada, suggesting at least thirteen unique infection events, including those from Europe and the USA. Four genomes were shared by

The passage discusses the objective of identifying the intermediate host and mechanisms of the interspecies jump of the novel coronavirus, SARS-CoV-2. Phylogenetic analysis of bat coronavirus complete genomes and those obtained from animals in Chinese markets was conducted. The results suggest that SARS-CoV-2 is closely related to bat CoV isolate RaTG13 and that pangolins may be possible intermediate hosts due to the formation of

The passage discusses a framework for efficiently identifying genetic subtypes of SARS-CoV-2, the virus causing COVID-19, through the use of Informative Subtype Markers (ISMs). ISMs are identified using an entropy measure and frequency analysis of available SARS-CoV-2 sequences. These markers define a compact set of nucleotide sites that characterize the most variable positions in the viral genome. ISMs reveal covarying

A novel coronavirus, named 2019-nCoV, was identified as the causative agent of viral pneumonia outbreak in Wuhan, China, in late December 2019. Genomic analysis of samples from nine patients revealed that 2019-nCoV was closely related to two bat-derived coronaviruses but distinct from SARS-CoV and MERS-CoV. Phylogenetic analysis placed

A study was conducted on the genomic variation of SARS-CoV-2 in Taiwan during the two waves of COVID-19 infections. A new ORF8-deletion mutant was discovered in a Taiwanese strain from a patient who had traveled to Wuhan. A new clade with ORF1ab-V378I mutation and some strains with travel history to Turkey and Iran was identified. The second wave was mainly caused by viruses

A study was conducted to investigate the genomic variation of SARS-CoV-2 in Taiwan during the two waves of COVID-19 infections. A new ORF8-deletion mutant was discovered in a Taiwanese strain from a patient who had traveled to Wuhan. A new clade with an ORF1ab-V378I mutation and some strains with travel history to Turkey and Iran was identified. The second wave was mainly caused by

A study of 15,487 whole genome sequences of SARS-CoV-2 from NCBI and GISAID archives revealed the existence of two major clades and six sub-clades of the virus, with convergent evolution occurring in several genome locations. The spike glycoprotein, which binds to the ACE2 receptor, showed evidence of selective pressure with a potentially critical mutation. Some mutations could also

Researchers analyzed 566 Indian SARS-CoV-2 genomes and identified 3,384 unique mutation points, including 933 substitutions, 2,449 deletions, and 2 insertions. The mutations were classified into three groups: 100 clusters of mutations, 1,609 point mutations, and 64 SNPs. The findings were visualized using BioCircos,

This study identified and characterized five coronaviruses (three Alpha-CoVs and two Beta-CoVs) from bats in Italy using next-generation sequencing and bioinformatics analysis. Two Beta-CoVs were closely related to MERS-CoV and formed a monophyletic group, while the three Alpha-CoVs were classified into two novel species due to their high divergence from human strains. The RBD structure

A study used ViReport, an automated tool for analyzing viral sequences and generating molecular epidemiological reports, to analyze over 4,000 full genome sequences of SARS-CoV-2 to trace its evolution and spread during the ongoing outbreak. The results can be accessed at the given link.

A study was conducted on SARS-CoV-2 in Colombia by sequencing the virus from 43 clinical samples and combining it with 73 existing sequences. The research revealed multiple introductions of the virus into the country, primarily from Europe, with at least 12 lineages identified. Phylogenetic analysis confirmed the linkage of epidemiologically-linked transmission chains. The study highlights the benefits of genome sequencing in COVID-19 investigation and emphas

A study analyzing 320 whole-genome sequences and spike protein sequences of SARS-CoV-2 identified 483 unique variations, including 25 non-synonymous mutations and one deletion in the spike protein. Twelve variations were located at the N-terminal domain and six at the receptor-binding domain, which might alter interaction with receptor molecules. Additionally, 22 amino acid insertions were identified in

A study comparing SARS-CoV-2 sequences to those of other viruses identified seven key miRNas (miR 8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) with significant links to KEGG pathways related to viral pathogenicity and host

A study comparing miR-like sequences in SARS-CoV-2 and other viruses identified seven key miRNas (miR 8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) with significant links to KEGG pathways related to viral pathogen

The Genome Detective Coronavirus Typing Tool is a web-based application that quickly and accurately identifies and characterizes SARS-related coronavirus (SARS-CoV-2) sequences from next generation sequencing datasets. It can process up to 2,000 sequences per submission and classify SARSr-CoV and SARS-CoV-2 with high accuracy. The tool allows tracking of new viral mutations and a

A study analyzing 116 genomes of SARS-CoV-2, including 10 new sequences, was used to investigate genetic variation and population demography. Results showed 80 haplotypes with 183 substitution sites, suggesting high mutation abundance and widespread adaptation. Phylogenetic analysis suggested a possible link to pangolins as an intermediate host, but this is controversial. One patient sample near the Huanan seafood

A study identified diverse alphacoronaviruses and a novel SARS-like coronavirus (LYRa11) from bat rectal swabs in Yunnan Province, China. LYRa11 was 29,805 nt long with 13 ORFs and shared high sequence identity with human/civet SARS CoVs and recently reported SARS-like CoVs in the S gene,

The passage discusses an analysis of 137 coronavirus genomes to understand the evolutionary history of SARS-CoV-2 and identify potential intermediate hosts. Phylogenetic analysis and structural reconstruction of spike glycoproteins revealed similarities between SARS-CoV-2 and bat betacoronavirus isolates HKU5 and HKU4. A yak betacoronavirus strain, YAK/HY24

The passage discusses an analysis of 137 coronavirus genomes to understand the evolutionary history of SARS-CoV-2 and identify potential animal hosts. Phylogenetic analysis and structural reconstruction of spike glycoproteins revealed similarities between SARS-CoV-2 and bat betacoronavirus isolates HKU5-related from Pipistrellus abramus and HKU4-related from Tylony

The study investigated the presence and infectiveness of SARS-CoV-2 in wastewater and rivers in the Milano Metropolitan Area, Italy. Raw wastewater samples tested positive for SARS-CoV-2 RNA, while treated water samples were negative. The positivity rate decreased after eight days, aligning with epidemiological trends. Virus infectiveness was not significant, indicating effective wastewater treatment or natural decay. River samples showed occasional positivity due to

A study was conducted to investigate the SARS-CoV-2 strains in seven Iranian COVID-19 patients using molecular and phylogenetic analysis. The results showed high similarity between Iranian and Chinese strains, with no significant polymorphisms identified in the assessed genes. Phylogenetic trees revealed no differences between Iranian isolates and those from other countries. The study concluded that Iranian SARS-CoV-2 isolates

A study was conducted to investigate the SARS-CoV-2 strains in seven Iranian COVID-19 patients using molecular and phylogenetic analysis. The results showed high similarity between Iranian and Chinese strains, with no significant polymorphisms identified in the assessed genes. Phylogenetic trees revealed no differences between Iranian isolates and those from other countries. The study concludes that Iranian SARS-CoV-2 isol

A study was conducted to identify human-adaptation related mutations in 4,894 SARS-CoV-2 complete genome sequences using phylogenetic and structural analysis. The virus's genetic diversity is low, but it can be divided into five clusters with low genetic distance and bootstrap support values. Eleven high-frequency substitutions were identified, four of which may be under positive selection. These mutations are located on the surface of prote

A study sequencing viral genomes from early COVID-19 patients in Connecticut found that the majority of these genomes were similar to those from Washington state, indicating that early SARS-CoV-2 transmission in Connecticut was likely due to domestic introductions. By March, the risk of domestic importation exceeded that of international importation, despite federal travel restrictions. The study highlights the importance of local surveillance as evidence of widespread sustained transmission of SARS-CoV-2

A cat in France, near Paris, was the first reported case of a natural SARS-CoV-2 infection in a cat. The animal showed mild respiratory and digestive signs and tested positive for the virus in rectal swabs, while nasopharyngeal swabs and serum samples were negative. The cat's SARS-CoV-2 genome sequence belonged to the A2a clade, similar to most human cases in France.

A study reported the first detection and genome sequencing of SARS-CoV-2 in a cat in France. Out of 22 cats and 11 dogs tested, one cat was positive for SARS-CoV-2 on rectal swab, but nasopharyngeal swabs were negative. The cat showed mild respiratory and digestive signs, and serological analysis confirmed the presence of antibodies against SARS-CoV

The passage discusses the origins of the novel coronavirus, SARS-CoV-2, and possible intermediate hosts based on phylogenetic analysis and mutation studies. The analysis suggests a close relationship between SARS-CoV-2 and bat CoV isolate RaTG13, and identifies pangolins as potential intermediate hosts due to the monophyletic cluster formed by SARS-CoV-2, bat RaTG

A study was conducted to compare the genome sequences of SARS-CoV-2, the virus causing COVID-19, with those of SARS-2003 and MERS-2012. As of May 27, 2020, there were 54,88,825 infected cases and 3,49,095 deaths from COVID-19 globally. The study found that the mort

A new coronavirus, SARS-CoV-2, was identified in December 2019 and has caused widespread disease and deaths. Phylogenetic analysis shows it clusters with SARS-CoV in the Sarbecovirus subgenus and relates to viruses found in bats and pangolins. The coding potential of SARS-CoV-2 is partially unknown, so researchers used data from related viruses to identify selective

A study was conducted to determine the selective events shaping the genome structure of SARS-CoV-2 and assess its coding potential using sequences of related viruses from bats and pangolins. Six genomic regions were identified with reduced variability at synonymous sites, including the E gene and two internal ORFs (ORF3h and ORF9a). ORF3h, a previously undescribed ORF, shares 90% identity

The Genome Detective Coronavirus Typing Tool is a web-based application that quickly and accurately identifies and characterizes SARS-related coronavirus (SARS-CoV-2) sequences from next-generation sequencing datasets. It can process up to 2000 sequences per submission and classify SARSr-CoV and SARS-CoV-2 with high accuracy. The tool allows tracking of new viral mutations and

In Guangdong Province, China, 1,388 SARS-CoV-2 infections were identified from 1.6 million molecular diagnostic tests by March 19, 2020. Genomic analyses of 53 virus isolates revealed multiple independent introductions of the virus into Guangdong, resulting in genetically distinct clusters. Effective large-scale epidemiological surveillance and intervention measures interrupted community transmission. However, continued

This study aims to identify the genetic diversity among Indian SARS-CoV-2 isolates by analyzing their phylogenetic data. The initial examination of 3123 viral genomes from different continents revealed multiple origins for Indian isolates. A more detailed analysis of 449 viral genomes revealed that most Indian samples were divided into two clusters, A and B. Cluster A showed more similarity to samples from Oceania and Kuwait

A study of the first four weeks of SARS-CoV-2 spread in Scotland identified at least 113 introductions of the virus, with 51% having no known international travel history. Most viral sequences were related to those in Europe, with travel-associated introductions occurring before restrictions. The first local transmission occurred three days after the first case, and community transmission began within 11 days. Earlier travel restrictions could have reduced introductions and cases,

A proposal is presented for a dynamic nomenclature system to name the expanding phylogenetic diversity of SARS-CoV-2 based on its contribution to active spread. The system uses a phylogenetic framework, limits hierarchical labels, and flags and declassifies inactive lineages. This nomenclature aims to assist in tracking and understanding the global spread of SARS-CoV-2 by focusing on active and spreading lineages.

A study retrieved 95 full-length genomic sequences of SARS-CoV-2 strains to establish a reference sequence and analyze sequence variations. The homology among all strains was high, with 99.99% identity at the nucleotide and amino acid levels. Thirteen variation sites were identified, with the highest mutation rates at positions nt28144 in ORF 8 (30.53%) and n

The passage discusses the relationship between SARS-coronavirus (SARS-CoV) and other groups of coronaviruses based on phylogenetic tree analyses and comparative genomic studies of their genes. The data suggests a monophyletic relationship between SARS-CoV and group 2 coronavirus, indicating a closer relationship between the two. However, further analysis is needed to increase our understanding of the origins and evolution of coronav

The passage discusses a study analyzing the genomic variation of twenty-eight SARS-CoV-2 strains isolated in Morocco from March 3, 2020, to May 15, 2020. The findings revealed 61 mutations in these Moroccan strains compared to the reference sequence Wuhan-Hu-1/2019, with 23 of these mutations present in two or more

The study analyzed the codon usage patterns of 13 SARS-CoV-2 isolates from different geo-locations, revealing a bias towards A/U content and CpU-ended codons. Eight common preferred codons, all A/U-ended, were identified. Cluster analysis based on Relative Synonymous Codon Usage (RSCU) values aligned with phylogenetic analysis. Natural selection and other factors may influence the

A phylogenetic analysis of over 1,225 SARS-CoV-2 genomes identified the D614G mutation in the spike protein, which has become predominant in Europe and is spreading worldwide. The mutation emerged around mid-to-late January 2020 and in silico analyses suggest it is neutral to protein function regarding its interaction with the human ACE2 receptor. Clinical metadata is needed for further

A new bioinformatic tool has been developed to analyze the genetic variability of SARS-CoV-2, specifically focusing on single mutations and minimal consensus sequence building for vaccine design. The analysis of the whole GISAID sequence dataset from April-June 2020 revealed limited mutational pressure on the viral genome. Focusing on the receptor-binding domain region of the spike protein, only a few variants associated with specific geographic

The passage compares three library preparation methods for SARS-CoV-2 amplicon sequencing on the Illumina MiSeq platform: Nextera XT and Nextera Flex using tagmentation, and KAPA HyperPrep using ligation. All methods allow for near-complete genome recovery with identical SNP calls. Nextera Flex and KAPA had better coverage than Nextera XT, which required more reads. K

A study analyzed SARS-CoV-2 genomes based on insights from SARS, focusing on non-coding RNAs, specifically miRNAs. The first approach identified 10 host miRNAs that could target both SARS-CoV-2 and SARS reference genomes, with a higher number targeting SARS-CoV-2. The second approach identified virus-encoded miRNAs that might regulate host

The passage discusses a study on the early outbreak of SARS-CoV-2 in Central Eastern Europe, specifically in Hungary. The researchers determined the full-length SARS-CoV-2 genomes from 32 clinical samples collected in Hungary during the first month of the disease. They compared these sequences to all available complete genomic sequences of SARS-CoV-2 from the GISAID database as of April 21, 2

A study was conducted to identify and characterize bat coronaviruses (BtCoV) in Pteropus medius and Rousettus species bats from different States in India. Rectal and throat swab specimens were screened using RT-PCR and next-generation sequencing (NGS). Eight Rousettus and 21 Pteropus bat specimens tested positive for the CoV RdRp gene. Phy

In February 2003, a new strain of coronavirus known as SARS-CoV emerged in Guangdong Province, China, causing a severe epidemic that affected public health, travel, and economic trade. Coronaviruses are highly infectious and genetically diverse, making them difficult to control. They can cause various diseases in animals and humans. SARS-CoV is believed to have originated from an animal reservoir, possibly bats

This study investigates the genetic diversity and epidemiology of SARS-CoV-2 in Morocco using 22 virus genomes reported from three laboratories and compares them to 40,366 genomes from around the world. Moroccan sequences had 62 mutations, with Spike_D614G and NSP12_P323L being the most common. Unique mutations included NSP1

A surveillance program for COVID-19 was initiated in France on January 10, 2020, and the first three cases of the disease in Europe were diagnosed there two weeks later. The study sequenced 97 SARS-CoV-2 genomes from infected patients between January 24 and March 24, 2020. Phylogenetic analysis revealed several early independent introductions of the virus without local transmission, indicating the effectiveness

This study used Whole Genome sequencing to determine the origin of SARS-CoV-2 in The Gambia from the first six confirmed cases. The sequencing was conducted using Illumina MiSeq and Nanopore GridION, and the results showed that three strains had European origin (from the UK and Spain), and two had Asian origin (from Japan). The study successfully identified the sources of SARS-CoV-2 infection in The Gamb

The passage reports on the first identified SARS-CoV-2 genomes from Venezuela and provides a snapshot of the epidemiologic landscape in the Colombian-Venezuelan border region. Three Venezuelan genomes were sequenced and analyzed, revealing they belonged to the B1 and B.1.13 lineages with the D614G mutation, associated with increased infectivity, and an additional three mutations in the N gene of one genome

A study identified bat-SARS-CoV, a coronavirus related to SARS-CoV, in 19% of Chinese horseshoe bats using RT-PCR. Genome sequencing and analysis showed that bat-SARS-CoV is a distinct group 2b coronavirus, with most differences in the spike gene. An insertion in ORF 8 suggests a common ancestor with civet SARS-CoV.