¿Cómo afectan las mutaciones en sars-cov-2 a su infectividad y antigenicidad?

(How do mutations in sars-cov-2 impact its infectivity and antigenicity?)

Primeras 5 respuestas:

Some mutations that break hydrogen bonds and/or salt bridges in antibody−antigen interactions will have a large impact.

These mutations lead to a significant decrease in the antigenicity of this epitope in the SARS-CoV-2 S protein.

This observed difference in genetic composition could possibly favor enhanced infectivity in target cells and accelerate [29] .

The observed mutations in HS binding motif (R682W and R685H) decreased the positive charge of the site and increased its hydrophobicity.

Mutation frequency is very high in RNA viruses, which enhances virulence and responsible for the formation of new species [19] .

Some mutations that break hydrogen bonds and/or salt bridges in antibody−antigen interactions will have a large impact.

... there are many mutations on the S proteins. The RBD is also prone to mutations. Some mutations that break hydrogen bonds and/or salt bridges in antibody−antigen interactions will have a large impact. However, silent mutations, such as those that replace hydrophobic residues with other hydrophobic residues, will ...

Ref: Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine [J Chem Inf Model, 2020-06-12]

These mutations lead to a significant decrease in the antigenicity of this epitope in the SARS-CoV-2 S protein.

... critical and conserved linear neutralization epitope (overlap with fusion peptide) around a sparsely glycosylated area. These mutations lead to a significant decrease in the antigenicity of this epitope in the SARS-CoV-2 S protein. In addition, 62 T-cell epitopes in the SARS-CoV-2 S protein were predicted in our study. ...

Ref: Immunoinformatic analysis of T-and B-cell epitopes for SARS-CoV-2 vaccine design [Vaccines, 2020]

This observed difference in genetic composition could possibly favor enhanced infectivity in target cells and accelerate [29] .

... with SARS-CoV-1 and MERS-CoV respectively [26] [27] [28] , acquired critical mutations within its genome. This observed difference in genetic composition could possibly favor enhanced infectivity in target cells and accelerate [29] . Notably, two-thirds of the viral RNA is housed within the first ORF (ORF1a/b) where translation ...

Ref: Immuno-epidemiology and pathophysiology of coronavirus disease 2019 (COVID-19) [J Mol Med (Berl), 2020-08-18]

The observed mutations in HS binding motif (R682W and R685H) decreased the positive charge of the site and increased its hydrophobicity.

... furin cleavage site PRRARS has a composition that overlaps with the HS binding motif XBBXBX. The observed mutations in HS binding motif (R682W and R685H) decreased the positive charge of the site and increased its hydrophobicity. To understand if the growth advantage was due to the loss of HS binding site ...

Ref: SARS-CoV-2 Quasispecies Mediate Rapid Virus Evolution and Adaptation [bioRxiv, 2020-08-10]

Mutation frequency is very high in RNA viruses, which enhances virulence and responsible for the formation of new species [19] .

... large genome size provides more plasticity in accommodating and modifying genes [36] [37] [38] . Mutation frequency is very high in RNA viruses, which enhances virulence and responsible for the formation of new species [19] . The high frequency of mutation within the viral genome at different geographical locations may be ...

Ref: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight [PLoS One, 2020-09-03]

Virus variants with S gene mutations generated smaller plaques and exhibited a more limited range of cell tropism compared to the wild-type strain.

... SARS-CoV-2 variants with mutations at the S protein cleavage site that undergo inefficient proteolytic cleavage. Virus variants with S gene mutations generated smaller plaques and exhibited a more limited range of cell tropism compared to the wild-type strain. These alterations were shown to result from their inability to utilize the entry pathway involving ...

Ref: SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells [bioRxiv, 2020-08-28]

The beneficial mutants can better evolve and adapt to host (9) , either strengthening or weakening the infectivity and pathogenicity.

... that viral mutations have important impact on the infection and pathogenicity of viruses (10) . The beneficial mutants can better evolve and adapt to host (9) , either strengthening or weakening the infectivity and pathogenicity. In addition, the variants may 10 generate drug resistance and shrink the efficacy of vaccine ...

Ref: Multi-site co-mutations and 5’UTR CpG immunity escape drive the evolution of SARS-CoV-2 [bioRxiv, 2020-07-27]

Our study provided evidence that the D614G mutation introduces an additional 327 elastase-2 cut site in the S protein,

... Our study provided evidence that the D614G mutation introduces an additional 327 elastase-2 cut site in the S protein, thereby promoting its cleavage and viral cell Table S1 ). All sera were tested positive using magnetic ...

Ref: D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity [bioRxiv, 2020-07-06]

some of these mutations may seriously undermine ongoing efforts on COVID-19 diagnostic testing, vaccine development, and drug discovery.

... spike protein, and papain-like protease are relatively the most non-conservative. We report an alarming fact that all of the SARS-CoV-2 proteins have undergone intensive mutations since January 5, 2020, and some of these mutations may seriously undermine ongoing efforts on COVID-19 diagnostic testing, vaccine development, and drug discovery. ...

Ref: Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine [bioRxiv, 2020-04-29]

Interesting correlation was observed between these mutations and travel or contact history of COVID-19 positive cases.

... the S 2domain, which is involved in triggering viral fusion with the host cell membrane. Interesting correlation was observed between these mutations and travel or contact history of COVID-19 positive cases. Consequent alterations of miRNA binding and structure were also predicted for these mutations. More importantly, ...

Ref: Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility [J. Biosci., 2020]

These mutations drive viral evolution and genome variability, thereby, facilitating viruses to have rapid antigenic shifting to evade host immunity and to develop drug resistance.

... the effective antivirals. SARS-CoV-2 is an RNA virus that has an inherent high mutation rate. These mutations drive viral evolution and genome variability, thereby, facilitating viruses to have rapid antigenic shifting to evade host immunity and to develop drug resistance. Viral RNA-dependent RNA polymerases (RdRp) perform viral genome duplication and RNA synthesis. Therefore, we compared ...

Ref: Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure [bioRxiv, 2020-05-11]

we show that most likely future mutations will make SARS-CoV-2 more infectious.

... a systematic evaluation of all possible 3686 future mutations on the S protein receptor-binding domain, we show that most likely future mutations will make SARS-CoV-2 more infectious. Combining sequence alignment, probability analysis, and binding free energy calculation, we predict that a few ...

Ref: Mutations Strengthened SARS-CoV-2 Infectivity [J Mol Biol, 2020]

This characterization of SARS-CoV-2 variants could lead to better therapeutics treatments, vaccines design and diagnostics approaches.

... We focused our study on SARS-CoV-2 mutations in order to assess if new viral variants were spreading across the Countries. This characterization of SARS-CoV-2 variants could lead to better therapeutics treatments, vaccines design and diagnostics approaches. ...

Ref: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant [J Transl Med, 2020-04-22]

Many of these mutations led to amino acid exchanges in replication-relevant viral proteins.

... mutations had been selected and found in up to > 80 % of viral genomes. Many of these mutations led to amino acid exchanges in replication-relevant viral proteins. Mutations in the SARS-CoV-2 genome would also impinge upon the secondary structure of the viral ...

Ref: Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world [Virus Res, 2020]

Differential effects of these mutations on CD8 T cell epitope generation by corresponding HLA alleles were observed.

... over the past few months identified three recurrent point mutations including L5F, D614G and G1124V. Differential effects of these mutations on CD8 T cell epitope generation by corresponding HLA alleles were observed. Finally, our multiple alignment analysis indicated the absence of seasonal CoV induced cross-reactive CD8 T ...

Ref: CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention [bioRxiv, 2020-09-10]

These mutations can cause a change in both conformational and linear antigenic determinants.

... as a result of mutations of the gene encoding this viral protein [29, 40] . These mutations can cause a change in both conformational and linear antigenic determinants. A thorough analysis of the variability of amino acids in different proteins of the SARS-CoV-2 ...

Ref: Change of Antigenic Determinants of SARS-CoV-2 Virus S-Protein as a Possible Cause of Antibody-Dependent Enhancement of Virus Infection and Cytokine Storm [Biophysics (Oxf), 2020-10-19]

From Figure 6 , a slightly increasing trend of binding free energy is observed such that the largest change is positive while the second largest change is negative.

... From Figure 6 , a slightly increasing trend of binding free energy is observed such that the largest change is positive while the second largest change is negative. Notice that mutation S477N is observed increasing of its frequency in Figure 3 . Interestingly, mutation T478I changes from amino acid with polar uncharged side chains, Threonine, to an amino ...

Ref: Mutations Strengthened SARS-CoV-2 Infectivity [J Mol Biol, 2020-07-23]

The mutations reported here might help this virus to evade the pharmacological agents that target Nsp10-Nsp16 complex activity.

... in SARS-CoV-2 Nsp10-Nsp16 complex which is a 2 ′ -O-methyltransferase required for viral RNA capping. The mutations reported here might help this virus to evade the pharmacological agents that target Nsp10-Nsp16 complex activity. Further, our study emphasizes the importance of variation studies to be conducted on emerging SARS-CoV-2 ...

Ref: Identification of novel mutations in the methyltransferase complex (Nsp10-Nsp16) of SARS-CoV-2 [Biochem Biophys Rep, 2020-10-10]

These mutations could also adversely affect the current efforts of drug repurposing because the binding mode of drugs may change in these cases.

... regions through international travel between various neighboring countries as most of these share land borders. These mutations could also adversely affect the current efforts of drug repurposing because the binding mode of drugs may change in these cases. These observations are important as the mutations discovered in the South Asian region pose a ...

Ref: Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis [Environmental Sustainability, 2020-09-18]

Some of these mutations are predicted to have impact on viral and host factors, which might affect transmission and disease severity.

... in the important regions of the viral genome including Spike, RdRP and nucleocapsid coding genes. Some of these mutations are predicted to have impact on viral and host factors, which might affect transmission and disease severity. This preliminary evidence of emergence of multiple subclones of SARS-CoV-2, which might have altered phenotypes, ...

Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness.

... virus is a recently-emerged zoonotic pathogen already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral ...

Ref: Implications of SARS-CoV-2 Mutations for Genomic RNA Structure and Host microRNA Targeting [J Biosci, 2020]

Mutations resulting in a mild disease could facilitate the spread of the virus and thereby maintain the outbreak.

... context, the most important question is to identify viral mutations leading to different patient outcomes. Mutations resulting in a mild disease could facilitate the spread of the virus and thereby maintain the outbreak. Other mutations leading to a more severe disease need immediate attention to prevent detrimental outcomes. ...

Ref: Different mutations in SARS-CoV-2 associate with severe and mild outcome [J Biosci, 2020-10-20]

Eighty-seven mutations across unique variants of ORF8 (SARS-CoV-2) are grouped into four classes based on their predicted effects.

... ORF8 of SARS-CoV-2 and Bat RaTG13-CoV are very much closer related than that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 (SARS-CoV-2) are grouped into four classes based on their predicted effects. Based on geolocations and timescale of collection, a possible flow of mutations was built. Furthermore, ...

Ref: A unique view of SARS-CoV-2 through the lens of ORF8 protein [bioRxiv, 2020-08-26]

we detected 14 substitution hotspots within 3,240 SARS-CoV-2 genome sequences,

... software, named BioAider, for quick sequence annotation and mutation analysis on large-scale genome-sequencing data Herein, we detected 14 substitution hotspots within 3,240 SARS-CoV-2 genome sequences, including 3 groups of potentially linked substitution NSP13-Y541C was crucial substitution which might affect the ...

Ref: BioAider: an efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission [Sustainable Cities and Society, 2020]

This could be the cause for the constant change and differed virulence with an increase in mortality and morbidity.

... we identified several hundreds of point mutations or SNPs in SARS-CoV-2 all across the genome. This could be the cause for the constant change and differed virulence with an increase in mortality and morbidity. Among the 12 different countries (one sequence from each country) with complete genome sequencing data, ...

Ref: Overwhelming mutations or SNPs of SARS-CoV-2: A point of caution [Gene, 2020]

The S2M of SARS-CoV-2 may promote its viability and infectivity.

Ref: Mutation in position of 32 (G>U) of S2M differentiate human SARS-CoV2 from Bat Coronavirus [bioRxiv, 2020-09-03]

This mutation was predicted to increase binding affinity to mACE2, potentially contributing to broad infectivity of the adapted MASCp6 strain in mice.

... of genes of this mouse-adapted SARS-CoV-2 showed five mutations absent in wild-type human SARS-CoV-2, one of which occurred at residue 501 (N501Y) of RBD in the S protein of SARS-CoV-2. This mutation was predicted to increase binding affinity to mACE2, potentially contributing to broad infectivity of the adapted MASCp6 strain in mice. ...

Ref: Rapid adaptation of SARS-CoV-2 in BALB/c mice: Novel mouse model for vaccine efficacy [bioRxiv, 2020-05-02]

The SARS-CoV-2 genomes from Moroccan patients revealed 62 mutations of which 30 were missense mutations.

... till the date 07/06/2020 as well as (40366) virus genomes from all around the world. The SARS-CoV-2 genomes from Moroccan patients revealed 62 mutations of which 30 were missense mutations. The mutations Spike_D614G and NSP12_P323L were present in all the 22 analyzed sequences, followed by ...

Ref: Genetic Diversity and Genomic Epidemiology of SARS-COV-2 in Morocco [bioRxiv, 2020-06-23]

The elevated synonymous mutations between SARS-CoV-2 and RaTG13, suggesting they underwent stronger purifying selection.

... RaTG13 was extensively higher than those from comparisons between other coronaviruses (range 1.29 - 4.81). The elevated synonymous mutations between SARS-CoV-2 and RaTG13, suggesting they underwent stronger purifying selection. Moreover, their nucleotide substitutions are enriched with T:C transition, which is consistent with the mutation ...

Ref: Comparative genomic analysis revealed specific mutation pattern between human coronavirus SARS-CoV-2 and Bat-SARSr-CoV RaTG13 [bioRxiv, 2020-03-02]

The lack of clinical metadata available prevented our investigation of association between viral clade and disease severity phenotype.

... neutral to protein function as it relates to its interaction with the human ACE2 receptor. The lack of clinical metadata available prevented our investigation of association between viral clade and disease severity phenotype. Future work that can leverage clinical outcome data with both viral and human genomic diversity ...

Ref: Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide [Sci Rep, 2020]

Comparison of scores with the original epitopes were done and thereby predicted the increase/decrease in binding affinity for class I MHC molecules due to mutations.

... across all 12 HLA subtypes. Their scores were recorded, and corresponding epitope-bearing mutations were analysed. Comparison of scores with the original epitopes were done and thereby predicted the increase/decrease in binding affinity for class I MHC molecules due to mutations. These eleven epitopes and mutational sequence-bearing epitopes were analysed using the IDEB tool to account ...

Ref: Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2 [bioRxiv, 2020-09-06]

Our data suggest that the mutations in SARS-CoV-2 lead to a greater binding affinity relative to SARS-CoV.

... alanine scanning mutagenesis on the “hotspot” residues at protein–protein interfaces using relative free energy calculations. Our data suggest that the mutations in SARS-CoV-2 lead to a greater binding affinity relative to SARS-CoV. In addition, our free energy calculations provide insight into the infectious ability of viruses on ...

Ref: Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations [J Chem Inf Model, 2020-07-28]

Amino acidic change stability analysis suggests both mutations could confer lower stability of the protein structures.

... affecting the Non-Structural Protein 6 (NSP6) and the Open Reding Frame10 (ORF 10) adjacent regions. Amino acidic change stability analysis suggests both mutations could confer lower stability of the protein structures. INTERPRETATION: One of the two mutations, likely developed within the genome during virus spread, could ...

Ref: Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy [J Infect, 2020]

Four types of mutations, which include synonymous, nonsynonymous, insertion and deletion, are detected.

... in SARS-CoV-2 and presents exemplified implications obtained from the analysis of these mutation pattern data. Four types of mutations, which include synonymous, nonsynonymous, insertion and deletion, are detected. We use 6,324 SARS-CoV-2 genome sequences collected in 45 countries and deposited to the NCBI ...

Ref: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) [bioRxiv, 2020-07-10]

We found that the distinctive mutations of S proteins could 98 impact potential effective epitopes of S proteins in different degree.

... changes of the likely epitope sites from dominant and 97 rare mutations of S protein. We found that the distinctive mutations of S proteins could 98 impact potential effective epitopes of S proteins in different degree. The exracellular domains divide into S1 and S2 subunits; S1 contains the N-terminal 137 domain ...

Ref: The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes [bioRxiv, 2020-08-24]

each mutation in the identical sequences causes a sharp increase in Shannon entropy, and also to omit biases in collection time and location in Shannon entropy analysis.

... of SARS-CoV-2 to be used for developing the current strategies of diagnosis, and treatment platforms. each mutation in the identical sequences causes a sharp increase in Shannon entropy, and also to omit biases in collection time and location in Shannon entropy analysis. [38] In a recent study, ten hotspot mutations including D614G (23403A>G) on S, L84S (28144T>C) ...

Ref: Genetics and genomics of SARS-CoV-2: A review of the literature with the special focus on genetic diversity and SARS-CoV-2 genome detection [Genomics, 2020-09-30]

These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules,

... the SARS-CoV-2 genome differs from those of RaTG13, the reconstructed common ancestor, and Pan-CoV-GD (Guangdong). These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results ...

Ref: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function [bioRxiv, 2020-09-22]

The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues,

... the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an "up" conformation ...

Ref: Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility [Res Sq, 2020]

Mutation entropy decreased between March and April of 2020 after steady increases at several sites,

... most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated ...

Ref: New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release [bioRxiv, 2020-07-31]

The mutation rate drives virus evolution and genome variability, which enables the virus to escape host immunity and to develop drug resistance.

... therapeutic strategies and vaccine development is in fact the high mutation rate of RNA viruses. The mutation rate drives virus evolution and genome variability, which enables the virus to escape host immunity and to develop drug resistance. To assess the genetic variation, an early study on eighty-six genomes of SARS-CoV-2 detected in ...

Ref: SARS‐CoV‐2 immunogenicity at the crossroads [Allergy, 2020-05-25]

The mutations might affect the severity and spread of the SARS-CoV-2.

... were 8782C>T in ORF1ab gene, 28144T>C in ORF8 gene and 29095C>T in the N gene. The mutations might affect the severity and spread of the SARS-CoV-2. The finding heavily supports an intense requirement for additional prompt, inclusive investigations that combine genomic ...

Ref: cord_uid mp3196kj Genomic characterization of a novel SARS-CoV-2 mp3196kj Genomic characterization of a novel SARS-CoV-2 Name: title, dtype: object [Allergy, cord_uid mp3196kj 2020 mp3196kj 2020 Name: publish_time, dtype: object]

mutations accumulated on the S protein of SARS-CoV-2, which may reduce the vaccine efficacy.

... S protein is one of the most popular surface proteins for the vaccine development. However, mutations accumulated on the S protein of SARS-CoV-2, which may reduce the vaccine efficacy. As we found in section 2, mutations are more likely to happen on the random ...

Ref: Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies [Allergy, 2020-10-13]

Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2.

... emerged independently multiple times (homoplasies), we identify 198 filtered recurrent mutations in the SARS-CoV-2 genome. Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2. Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the ...

Ref: Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 [Infect Genet Evol, 2020]

SARS CoV-2 induced severe and often lethal lung failure is caused due to its inhibition of ACE-2 expression [36] .

... to gain entry into human cells are the points also to be noted [35] . SARS CoV-2 induced severe and often lethal lung failure is caused due to its inhibition of ACE-2 expression [36] . So, keeping the ACE-2 normal functioning but blocking viral entry is the most challenging issue ...

Ref: Energetics based epitope screening in SARS CoV-2 (COVID 19) spike glycoprotein by Immuno-informatic analysis aiming to a suitable vaccine development [bioRxiv, 2020-04-05]

As viruses mutate 16 during replication,

... has been 15 the main practical approach to manage the emergency so far [7] . As viruses mutate 16 during replication, the emergence of SARS-CoV-2 sub-strains and the challenge of a 17 probable antigenic drift require ...

Ref: coronapp: A Web Application to Annotate and Monitor SARS-CoV-2 Mutations [bioRxiv, 2020-09-10]

These super-spreaders exhibit not only high transmission efficiency, but also high mutation rate without compromising infectivity,

... world, and that viruses without any signature mutation of the four super-spreaders appear to be transmitted much less efficiently. These super-spreaders exhibit not only high transmission efficiency, but also high mutation rate without compromising infectivity, posing enormous challenge to the control of future transmission of SARS-CoV-2. ...

Ref: Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries [Emerging microbes & infections, 2020-06-11]

the majority of which have a high predictive epitope and IEDB epitope mapping scores when compared to variant positions of other genes.

... It possesses the greatest number of residues across all SARS-CoV-2 genes with high-frequency non-synonymous mutations, the majority of which have a high predictive epitope and IEDB epitope mapping scores when compared to variant positions of other genes. This implies that there may be an inherent variability in dominant antibody responses to different ...

Ref: An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets [bioRxiv, 2020-05-12]

We confirmed that mutations in different genomic regions of SARS-CoV-2 have specific influence on virus reproductive adaptability,

... regions including the envelop, membrane, nucleocapsid, and spike glycoproteins to become a novel infectious agent. We confirmed that mutations in different genomic regions of SARS-CoV-2 have specific influence on virus reproductive adaptability, allowing for genotype adjustment and adaptations in rapidly changing environments. Moreover, for the first time ...

Ref: Evolutionary trajectory for the emergence of novel coronavirus SARS-CoV-2 [Pathogens, 2020]

These mutations drive viral evolution and genome variability, thereby facilitating viruses to have rapid antigenic shifting to evade host immunity and to develop drug resistance.

... for effective antivirals. SARS-CoV-2 is an RNA virus that has an inherently high mutation rate. These mutations drive viral evolution and genome variability, thereby facilitating viruses to have rapid antigenic shifting to evade host immunity and to develop drug resistance. Viral RNA-dependent RNA polymerases (RdRp) perform viral genome duplication and RNA synthesis. Therefore, we compared ...

Ref: Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure [PeerJ, 2020-07-03]

A total of 11 mutations in the United States has a frequency greater than 700.

... or top mutations that represent the most common characteristics of SARS-CoV-2 in the United States. A total of 11 mutations in the United States has a frequency greater than 700. Among them, 3 mutations are synonymous ones (i.e., 3037C>T-(F106F), 8782C>T-(S76S), Table 2 lists the frequencies ...

Ref: Characterizing SARS-CoV-2 mutations in the United States [Res Sq, 2020-08-11]

This mutation can increase infectivity of SARS-CoV-2 based on in vitro experiments [24] .

... originated in Europe, and further spread to North America and Oceania, then Asia [33] . This mutation can increase infectivity of SARS-CoV-2 based on in vitro experiments [24] . In Sweden, we found that on 14 May, the frequency of D614G on the S1 ...

Ref: Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic [Viruses, 2020-09-14]

A total of 18 354 mutations in S protein were analyzed,

... to quantify the systemic effects of missense mutations on SARS-CoV-2 S protein structure and function. A total of 18 354 mutations in S protein were analyzed, and we discovered that most of these mutations could destabilize the entire S protein and ...

Ref: Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity [Brief. bioinform, 2020]

The SARS-CoV-2 genome is accumulating mutations at a very high frequency.

... The SARS-CoV-2 genome is accumulating mutations at a very high frequency. As suggested 288 by the "mutation-selection balance" and the "speed-fidelity trade-off" theories [20, 21] , this 289 might be because it has concentrated its endeavours to hasten its replication for ...

Ref: Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: An endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations [bioRxiv, 2020-07-15]

Several reports have documented mutations in several SARS-CoV-2 encoded proteins,

... Several reports have documented mutations in several SARS-CoV-2 encoded proteins, in particular the Spike protein [7] which determines the infectivity of SARS-CoV-2 by binding to ACE2 [8, 9] . Other reports have described mutations in other proteins encoded by SARS-CoV-2, ...

Ref: Mutations in the phosphorylation sites of SARS-CoV-2 encoded nucleocapsid protein and structure model of sequestration by protein 14-3-3 [Biochem Biophys Res Commun, 2020-08-15]

SARS-CoV-2 antigens were detected using an anti-N polyclonal antibody (Fig. 1C) .

... ensure a) that the virus was SARS-CoV-2 and b) that all plaques could be identified. SARS-CoV-2 antigens were detected using an anti-N polyclonal antibody (Fig. 1C) . Variation in plaque size was observed for both strains and the immunoplaque assay was useful ...

Ref: SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected, hospitalized COVID-19 patients [bioRxiv, 2020-06-22]

This inherent feature often leads to altered virulence, infectivity and transmissibility as well as antigenic shift to escape host immunity,

... within the genome is the primary driving force for viral evolution within an endemic setting. This inherent feature often leads to altered virulence, infectivity and transmissibility as well as antigenic shift to escape host immunity, which might compromise the efficacy of vaccines and antiviral drugs. Therefore, we aimed at genome-wide ...

H93Y was particularly important,

... domain in SARS-CoV (6, 9) . We observed several mutations within this domain in SARS-CoV-2. H93Y was particularly important, previously being linked in SARS-CoV to the loss of the K ϩ channel and reduced ...

Ref: SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis [mSystems, 2020-05-05]

Distribution of SARS-CoV-2 mutations show variability among geographical locations, mainly due to founder effects, as well as various other epidemiological factors.

... Distribution of SARS-CoV-2 mutations show variability among geographical locations, mainly due to founder effects, as well as various other epidemiological factors. In order to compare the distribution of MoE among different geographic locations, Table 2 shows that there are statistically significant associations between the locations and MoE (p<0.001). The most frequently ...

Ref: RdRp mutations are associated with SARS-CoV-2 genome evolution [bioRxiv, 2020-05-20]

Mutations on most of these residues are likely to be deleterious, leading to less infectious virus strains that may suffer from negative selection.

... surface, we predicted many hot spot residues that make major contributions to the binding affinity. Mutations on most of these residues are likely to be deleterious, leading to less infectious virus strains that may suffer from negative selection. Meanwhile, several residues with mostly advantageous mutations have been predicted. It is more probable that ...

Ref: SARS-CoV-2 Spike Glycoprotein Receptor Binding Domain is Subject to Negative Selection with Predicted Positive Selection Mutations [bioRxiv, 2020-05-05]

These mutations are critical for vaccine development in disease control.

... pathogenic viruses in their gradual and local genetic variations. The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations. These mutations are critical for vaccine development in disease control. ...

Ref: Genotyping coronavirus SARS-CoV-2: methods and implications [bioRxiv, 2020-03-24]

The mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year.

... 634 mutation sites across the SARS-CoV-2 genome and 274 non-synonymous amino acid substitutions were detected. The mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year. Nine unique variants were detected based on non-anonymous amino acid substitutions in spike protein relative ...

Ref: The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh [bioRxiv, 2020-07-30]

These mutations negatively impact viral fitness through reducing the affinity to the host receptor (Tang et al. 2014 ).

... SARS-CoV S protein (T332I, F460C and L443R) were identified previously (Rockx et al. 2010 ). These mutations negatively impact viral fitness through reducing the affinity to the host receptor (Tang et al. 2014 ). The nonsynonymous mutations in the N protein, which have key roles in viral assembly, might ...

Ref: A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic [Int J Infect Dis, 2020-08-22]

SARS-CoV-2 S-protein is highly immunogenic,

... affinities in SARS-CoV-2 RBM mutants may account for global variations in COVID-19 transmission and outcome. SARS-CoV-2 S-protein is highly immunogenic, so recombinant vaccines and neutralizing antibodies that target the whole S-protein or RBD are currently ...

Ref: Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction [bioRxiv, 2020-10-01]

Among these, 99 missense mutations (90%) were predicted to destabilize protein structures.

... 180 mutations in the coding region of the genome, and 110 of these were missense. Among these, 99 missense mutations (90%) were predicted to destabilize protein structures. Remarkably, a mutation that leads to an I300F change in the nsp2 protein and a ...

Ref: In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh [bioRxiv, 2020-08-16]

Two mutations, 84S in orf8 protein and 251 V in orf3 protein, occurred coincidentally with human intervention.

... and ceased to increase afterwards, demonstrating the effectiveness of social distancing in preventing its spread. Two mutations, 84S in orf8 protein and 251 V in orf3 protein, occurred coincidentally with human intervention. The former first appeared on 1/5/2020 and plateaued around 1/23/2020. The latter rapidly increased in ...

Ref: The origin and underlying driving forces of the SARS-CoV-2 outbreak [J Biomed Sci, 2020-06-07]

Mutations in the viral binding proteins modulate infectivity and alter antigenicity leading to species specificity,

... mutations in the viral proteins to adapt to a new host and environment [26] . Mutations in the viral binding proteins modulate infectivity and alter antigenicity leading to species specificity, as in the case of SARS-CoV-2-RBD. The spike gene of the SARS-CoV-2 may be recombined ...

Ref: High Throughput Designing and Mutational Mapping of RBD-ACE2 Interface Guide Non-Conventional Therapeutic Strategies for COVID-19 [bioRxiv, 2020-05-19]

The d N /d S ratio is almost 14 times larger in the circulating SARS-CoV-2 strains than in the 11 outgroup lineage.

... The d N /d S ratio is almost 14 times larger in the circulating SARS-CoV-2 strains than in the 11 outgroup lineage. While some of this difference could possibly be explained by positive 12 selection acting at a higher rate after zoonotic transfer, it is perhaps more likely that a 13 substantial ...

Ref: Synonymous mutations and the molecular evolution of SARS-Cov-2 origins [bioRxiv, 2020-10-12]

the antigenicity of the predicted mutations inferred, and the epitopes were superimposed on the structure of the spike protein Results

... the mutations corresponding to the reported single nucleotide polymorphisms (SNPs) in the genomic study Further, the antigenicity of the predicted mutations inferred, and the epitopes were superimposed on the structure of the spike protein Results The sequence analysis resulted in high SNPs frequency The significant variations in the predicted epitopes ...

Ref: Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development [J Lab Physicians, 2020]

This leads to the creation of virus variants with possible different virulence, infectivity, and transmissibility [25] .

... the virus may have mutated over time to circumvent responses of the human immune system. This leads to the creation of virus variants with possible different virulence, infectivity, and transmissibility [25] . This paper reports all point mutations occurring so far in SARS-CoV-2 and presents exemplified implications ...

Ref: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) [bioRxiv, 2020-07-10]

For the C-to-U mutations, the context of the upstream uracil and downstream guanine from mutated position was found to be most prevalent.

... We also found the point mutations which are consistent with other RNA editing enzymes, ADARs. For the C-to-U mutations, the context of the upstream uracil and downstream guanine from mutated position was found to be most prevalent. Further, the degree of increase of U in SARS-CoV-2 variants correlates with enhanced production of ...

Ref: Point mutation bias in SARS-CoV-2 variants results in increased ability to stimulate inflammatory responses [Sci Rep, 2020-10-20]

its transcriptomic genetic polymorphisms at inter-host level and the viral gene expression level based on each Open Reading Frame (ORF) remains unclear.

... of the COVID-19 pandemic. Despite the genetic mutations across the SARS-CoV-2 genome being recently investigated, its transcriptomic genetic polymorphisms at inter-host level and the viral gene expression level based on each Open Reading Frame (ORF) remains unclear. Using available High Throughput Sequencing (HTS) data and based on SARS-CoV-2 infected human transcriptomic data, ...

Ref: Quasi-species nature and differential gene expression of severe acute respiratory syndrome coronavirus 2 and phylogenetic analysis of a novel Iranian strain [Infect Genet Evol, 2020]

Some mutations may lead the virus to be less pathogenic than the other countries.

... of the missense mutations in Bangladeshi isolates found to have weak effects on the pathogenesis. Some mutations may lead the virus to be less pathogenic than the other countries. Molecular docking analysis to evaluate the effect of the mutations on the interaction between the ...

Ref: Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism [bioRxiv, 2020-06-07]

Adaptive mutations in the SiA-binding domains increase the virus avidity for host and intercellular expansion processes which leads to increased infectivity and pathogenicity.

... which facilitating infection and supporting the intercellular expansion of virus through the cellular syncytial formation. Adaptive mutations in the SiA-binding domains increase the virus avidity for host and intercellular expansion processes which leads to increased infectivity and pathogenicity. Findings raise the idea that the lectinlike properties of zoonotic viruses contribute to facile crossspecies ...

Ref: Molecular Basis for Pathogenicity of Human Coronaviruses [Infect Drug Resist, 2020-07-17]

These mutations, together with additional mutations on the S protein, suggest that SARS-CoV-2 has become more infectious in the United States.

... nutshell, we analyze the characteristics of SARS-CoV-2 substrains and prevalent mutations in the United States. These mutations, together with additional mutations on the S protein, suggest that SARS-CoV-2 has become more infectious in the United States. Figure 1 : Pie chart plot of four clusters in the United States as of ...

Ref: Characterizing SARS-CoV-2 mutations in the United States [Infect Drug Resist, 2020-07-24]

Our results revealed that the furin cleavage site might not be required for SARS-CoV-2 to enter human cells in vivo.

... deletion, and six gains of premature stop codon that may affect the furin cleavage site. Our results revealed that the furin cleavage site might not be required for SARS-CoV-2 to enter human cells in vivo. The identified mutants may represent a new subgroup of SARS-CoV-2 coronavirus with reduced tropism and ...

Ref: Natural Polymorphisms Are Present in the Furin Cleavage Site of the SARS-CoV-2 Spike Glycoprotein [Front Genet, 2020-07-17]

Without these genetic mutations to enhance evolutionary adaptation, species recognition, host receptor affinity, and pathogenicity, it would not survive.

... of SARS-CoV-2 associated with host receptor affinity are derived from several mutations in its genes. Without these genetic mutations to enhance evolutionary adaptation, species recognition, host receptor affinity, and pathogenicity, it would not survive. It is expected that our results could provide an important clue in understanding the genomic ...

Ref: Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome [Osong Public Health Res Perspect, 2020-06-22]

the SARS-CoV-2 is evolving at an unprecedented rate, demanding advanced and specified analytic pipeline to capture the mutational spectra.

... Infecting millions of people, the SARS-CoV-2 is evolving at an unprecedented rate, demanding advanced and specified analytic pipeline to capture the mutational spectra. In order to explore mutations and deletions in the spike (S) protein - the most-discussed protein of SARS-CoV-2 - we comprehensively analyzed 35,750 complete S protein-coding ...

Ref: Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline [Transbound. emerg. dis. (Internet), 2020]

accumulations of further mutations at the S-protein receptor-binding domain could enhance the infectivity and pathogenicity of the virus.

... a substantial number of mutations, especially in the S-protein. With the advancement of the pandemic, accumulations of further mutations at the S-protein receptor-binding domain could enhance the infectivity and pathogenicity of the virus. Prediction and evaluation of such mutations are essential for understanding the potential development of more ...

Ref: Can SARS-CoV-2 Accumulate Mutations in the S-Protein to Increase Pathogenicity? [ACS Pharm. Transl. Sci., 2020]

23 point mutations were predicted to significantly influence the affinity and stability of the spike protein (Fig. 5) ,

... all mutationson the S gene and their binding capacity with ACE2 receptor in human beings. 23 point mutations were predicted to significantly influence the affinity and stability of the spike protein (Fig. 5) , among which 9 polymorphisms exhibited increased affinity and stability while 14 ones showed decreased affinity ...

Ref: Binding Ability Prediction between Spike Protein and Human ACE2 Reveals the Adaptive Strategy of SARS-CoV-2 in Humans [bioRxiv, 2020-06-25]

These mutations may have significant impact on the antigenic and immunogenic changes responsible for differences in the severity of the outbreak in different geographical regions.

... . Going well with the expectations from a rapidly transmitting pandemic virus, in our analysis, we observed various mutations located in the regions associated with immune response (Table S2) . These mutations may have significant impact on the antigenic and immunogenic changes responsible for differences in the severity of the outbreak in different geographical regions. ...

Ref: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis [bioRxiv, 2020-03-21]

a mutation in the SARS-CoV-2 3’-UTR leads to a weakened host immune response.

... involving the Influenza A H1N1 virus. This interaction also suggests a possible survival mechanism, whereby a mutation in the SARS-CoV-2 3’-UTR leads to a weakened host immune response. The potential roles of host microRNAs in SARS-CoV-2 replication and infection, and the exploitation of ...

Ref: CONSERVED GENOMIC TERMINALS OF SARS-COV-2 AS CO-EVOLVING FUNCTIONAL ELEMENTS AND POTENTIAL THERAPEUTIC TARGETS [bioRxiv, 2020-07-06]

These observations provided evidence of the genetic diversity and rapid evolution of this novel coronavirus.

... SARS-CoV-2 outbreak a global public health emergency. We performed genetic analyses of eighty-six complete or near-complete genomes of SARS-CoV-2 and revealed many mutations and deletions on coding and non-coding regions. These observations provided evidence of the genetic diversity and rapid evolution of this novel coronavirus. ...

Ref: Genetic diversity and evolution of SARS-CoV-2 [Infect Genet Evol, 2020-02-21]

result in a very prominent phenotypic change in plaque assays.

... pressure to acquire adaptive mutations in its spike protein gene. These mutations change or delete a putative ‘furin-like cleavage site’ in the region connecting the S1 and S2 domains and result in a very prominent phenotypic change in plaque assays. ...

Ref: SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology [bioRxiv, 2020-04-20]

SARS-Cov-2 S neighbor residues G496 and F497 introduce the most significant effects on RBD-ACE2 binding.

... SARS-Cov-2 S neighbor residues G496 and F497 introduce the most significant effects on RBD-ACE2 binding. Of 19 mutations in residue G496 (ΔΔΔG mean = 4.694 kcal/mol), 15 mutations can highly reduce the RBD-ACE2 binding affinity (ΔΔΔG > 2.5 kcal/mol), 3 mutations have the moderate destabilizing ...

Ref: Systemic Effects of Missense Mutations on SARS-CoV-2 Spike Glycoprotein Stability and Receptor Binding Affinity [bioRxiv, 2020-05-23]

This database incorporated 39920 mutations over 3990 unique positions.

... data available to the public includes mutations from 5688 SARS-CoV-2 sequences curated from 91 regions. This database incorporated 39920 mutations over 3990 unique positions. According to the translational impact, these mutations include 11829 synonymous mutations including 681 synonymous frameshifts ...

Ref: COVID-19 Variants Database: A repository for Human SARS-CoV-2 Polymorphism Data [bioRxiv, 2020-06-11]

the virus evolves at a rapid pace that helps them to survive better inside the host

... is an RNA virus that has inherent high rate of mutation Due to the mutations, the virus evolves at a rapid pace that helps them to survive better inside the host One of the hotspots of pharmacological interventions is to inhibit binding of virus with the ...

Ref: Identification of twenty-five mutations in surface glycoprotein (Spike) of SARS-CoV-2 among Indian isolates and their impact on protein dynamics [Gene Reports, 2020]

Nine of them cause structural alterations in the S protein, nsp2, nsp3, nsp4 and nsp12 regions.

... China. In this study, we identified 11 unique mutations in viral SARS-COV-2 isolates from Turkey. Nine of them cause structural alterations in the S protein, nsp2, nsp3, nsp4 and nsp12 regions. The mutations identified here might have significant functional implications that need to be addressed in ...

Ref: Identification of novel mutations in SARS-COV-2 isolates from Turkey [Arch Virol, 2020-10-06]

These additional mutations may cause changes in structural conformations and cause a higher binding affinity.

... receptors, there are several mutations that may have strengthened the binding affinity of the surface glycoprotein. Both the predictions and the 3D models reveal additional beta strands and hydrogen bonds. These additional mutations may cause changes in structural conformations and cause a higher binding affinity. ...

Ref: A comparative analysis for SARS-CoV-2 [Arch Virol, 2020-04-08]

single mutation might be significant enough to confer resistance to neutralizing antibodies against those viruses.

... et al., 2014) the close relatives of SARS-CoV-2 Zhou et al., 2020) , showed that single mutation might be significant enough to confer resistance to neutralizing antibodies against those viruses. Meanwhile, during the rampant spread of SARS-CoV-2 around the world, it has undergone multiple antigenic ...

Ref: Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh [bioRxiv, 2020-08-21]

recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness.

... already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral ...

Ref: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting [bioRxiv, 2020-05-16]

four types of mutations caused dramatic changes in protein structures (RMSD ≥5 0 Å),

... September 1st, 2020, then modeled and analyzed the mutant protein structures The results showed that four types of mutations caused dramatic changes in protein structures (RMSD ≥5 0 Å), which were Q57H and G251V in open reading frames 3a (ORF3a), S194L and R203K/G204R in ...

Ref: Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions [Journal of Medical Virology, 2020]

Quantitative analysis showed that viral particles carrying 614-G mutation had significantly higher infectivity titer than the corresponding 614-D mutation,

... . The research team also proposed that D614G mutation pseudovirus was associated with higher infectivity. Quantitative analysis showed that viral particles carrying 614-G mutation had significantly higher infectivity titer than the corresponding 614-D mutation, which increased by 2.6 to 9.3 times, and was confirmed in a variety of cell ...

Ref: Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020 [Biosaf Health, 2020-09-02]

The SARS-CoV-2 spike protein receptor-binding domain (RBD) is the critical determinant of viral tropism and infectivity.

... The current global pandemic of COVID-19 is caused by a novel coronavirus SARS-CoV-2. The SARS-CoV-2 spike protein receptor-binding domain (RBD) is the critical determinant of viral tropism and infectivity. To investigate whether naturally occurring mutations in the RBD have altered the receptor binding affinity and infectivity, ...

Ref: Emergence of SARS-CoV-2 spike RBD mutants that enhance viral infectivity through increased human ACE2 receptor binding affinity [bioRxiv, 2020-09-12]

A total of 11,627 (34.38%) genomes included single mutations affecting annealing of any PCR assay.

... included in the alignment, and accumulated genetic variability affecting any oligonucleotide annealing was annotated. RESULTS: A total of 11,627 (34.38%) genomes included single mutations affecting annealing of any PCR assay. Variations in 8,773 (25.94%) genomes were considered as high risk, whereas additional 2,854 (8.43%) genomes ...

Ref: Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak [Int J Infect Dis, 2020]

a single mutation P384A fully determines the affinity difference CR3022 does not neutralize SARS-CoV-2,

... illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency ...

Ref: A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody [bioRxiv, 2020]

Ultimately mutations help the virus to evolve into a better version of itself that fit best in its host environment.

... lead to emergence of mutants or variants which have elaborate cellular tropism or altered virulence. Ultimately mutations help the virus to evolve into a better version of itself that fit best in its host environment. Since, Spike protein is one of the major targets for drug and vaccine designing, sequence ...

Ref: A virus that has gone viral: amino acid mutation in S protein of Indian isolate of Coronavirus COVID-19 might impact receptor binding, and thus, infectivity [Biosci Rep, 2020-05-15]

Our results show that the protein surface of the ACE2 at the receptor binding domain (RBD) exhibits negative electrostatic potential,

... compare the binding affinities of the S proteins of SARS-CoV and SARS-CoV-2 to the ACE2. Our results show that the protein surface of the ACE2 at the receptor binding domain (RBD) exhibits negative electrostatic potential, while a positive potential is observed for the S proteins of SARS-CoV/SARS-CoV-2. In addition, the ...

Ref: Comparing the Binding Interactions in the Receptor Binding Domains of SARS-CoV-2 and SARS-CoV [J Phys Chem Lett, 2020]

These mutations may impact the diagnostic sensitivity and specialty,

... identify and analyze the SARS-CoV-2 mutation positions, frequencies, and encoded proteins in the global setting. These mutations may impact the diagnostic sensitivity and specialty, and therefore, they should be considered in designing new testing kits as the current effort ...

Ref: Mutations on COVID-19 diagnostic targets [Genomics, 2020-09-20]

These mutations can also influence the binding efficiency of PCR primers or probes during the molecular diagnosis of clinical samples.

... nonstructural proteins of SARS-CoV-2 might affect molecular recognition and specificity of antivirals or vaccigenic candidates. These mutations can also influence the binding efficiency of PCR primers or probes during the molecular diagnosis of clinical samples. Consequently, evidence of such mutation hotspots could explain how SARS-CoV-2 has a mechanism for disease ...

Ref: Genomics insights of SARS-CoV-2 (COVID-19) into target-based drug discovery [Med Chem Res, 2020-07-31]

There is a strong, nearly linear increase of frequency of missense mutations with synonymous mutations remaining at the approximately constant level ( Figure 3A ).

... their increasing solvent exposure following known trend observed in many protein families from different organisms. There is a strong, nearly linear increase of frequency of missense mutations with synonymous mutations remaining at the approximately constant level ( Figure 3A ). This can be explained by tightly packed cores presenting strong constraints for amino acid residue ...

Ref: The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins [bioRxiv, 2020-08-10]