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Last updated: 2021 Sep 7
Total hit(s): 798
Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay
We report a single-nucleotide variant (SNV) in the nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., G29179T. This SNV impairs the diagnostic sensitivity of the Xpert Xpress SARS-Cov-2 assay (Cepheid, Sunnyvale, CA, USA)
Ann Lab Med
2022 Jan 1
Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis
Study the dynamics of SARS-CoV-2 in patients with high confidence.Analyze intra-host population diversity.Consider a positive selection analysis of the SARS-CoV-2 genome.
Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation
A common mutation has occurred in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), known as D614G. There are discrepancies in the impact of this mutation on the virus's infectivity. The whole genome sequencings are expensive and time-consuming.
Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein
Phylogenicity of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 surface glycoproteins reported from Europe to the National Center for Biotechnology Information (NCBI) virus database by the mid-April 2021 is analyzed. Novel function for computing phylogenetic distance is proposed for that purpose. Proposed distance function resulted in better-fitted clusters than Jaccard and Sorensen-Dice.
Isolation of SARS-CoV-2 strains carrying a nucleotide mutation, leading to a stop codon in the ORF 6 protein
Study the genome sequences of two Italian COVID-19 patients.Understand the role of IFN in SARS-CoV-2 infected patients.
Emerg Microbes Infect
Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations
Identify the SARS-CoV-2 B.1.1.7 lineage.Determine the S:D178H mutation in the NTD of the S protein.
Emerg Microbes Infect
A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions
SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K have been associated with enhanced transmissibility and immune escape. A one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94 % and a linear range of over 5 log(10) copies/Reaction.
J Virol Methods
Genomic characterization of SARS-CoV-2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins
The characterization of full-length SARS-CoV-2 genomes is critical for understanding the origin and transmission pathways of the virus. A total of 293 distinct mutations were identified, of which 152 missense, 124 synonymous, 12 noncoding, and 5 deletions. Novel mutations were found in nsp12 (V111A, H133R, Y453C, M626K) and ORF2/S (R995G, V1068L)
J Med Virol
Revealing the Threat of Emerging SARS-CoV-2 Mutations to Antibody Therapies
Rapidly growing SARS-CoV-2 variants might compromise existing vaccines and monoclonal antibody (mAb) therapies. High-frequency mutations R346K/S, N439K, G446V, L455F, V483F/A, F486L, F490L /S, Q493L, and S494P might compromise some of mAbs in clinical trials.
J Mol Biol
2021 Sep 3
SARS-CoV-2 Variants Are Selecting for Spike Protein Mutations That Increase Protein Stability
The emergence of variants of SARS-CoV-2 with mutations in their spike protein are a major cause for concern for the efficacy of vaccines and control of the pandemic. We suggest that the computationally efficient analysis of mutational stability may aid in early screening of variants.
J Chem Inf Model
2021 Sep 2
Association of E484K spike protein mutation with SARS-CoV-2 infection in vaccinated persons---Maryland, January - May 2021
SARS-CoV-2 viruses carrying the spike protein mutation E484K were disproportionately prevalent among persons infected after full vaccination against COVID-19 as compared to infected persons who were not fully vaccinated (aOR 1.96, 95% CI, 1.36 to 2.83)
Clin Infect Dis
2021 Sep 2
A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees
As of June 9, 2021, our SARS-CoV-2 MAT consists of 834,521 sequences and provides a comprehensive view of the virus' evolutionary history using public data. We also present matUtils-a command-line utility for rapidly querying, interpreting and manipulating the MATs.
Mol Biol Evol
2021 Sep 1
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern
The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments.
J Chem Inf Model
2021 Sep 1
Phylogenomic analysis of SARS-CoV-2 from third wave clusters in Malaysia reveals dominant local lineage B.1.524 and persistent spike mutation A701V
96.2% of registered COVID-19 cases and 88.5% of confirmed deaths in Malaysia occurred during this third wave of infection. A phylogenomic study on 258 SARS-CoV-2 full genomes from February 2020-February 2021 has led to the discovery of a novel Malaysian lineage B.1.524. This lineage contains another spike mutation A701V that co-exists with the D614G spike mutation that was predominant in most of the third-wave clusters.
2021 Sep 1
Multiplex sequencing of SARS-Cov-2 genome directly from clinical samples using the Ion Personal Genome Machine (PGM)
SARS-CoV-2 genomic RNA was extracted from human nasopharyngeal swabs using the Ion Personal Genome Machine (PGM) This protocol involves concomitant amplification of 237 gene fragments. Five complete and one near-complete genome sequences were generated with a single Ion PGM sequencing run. Sequence coverage analysis revealed two amplicons (positions 13 751-13 965 and 23 941-24 106), which consistently gave low sequencing read coverage in all isolates except 4Apr20-64- Hu. The possible impact of other genome nucleotide variations warrants further investigation, and an improved version of the Ion AmpliSeq™ SARS CoV 2 Research Panel should be considered.
2021 Sep 1
Concise Update on Genomics of COVID-19: Approach to Its latest Mutations, Escalated Contagiousness, and Vaccine Resistance
The novel coronavirus disease 2019 (COVID-19) that started to invade the world from the Chinese fish market, causes an acute respiratory distress syndrome. In this new species with a positive, single-strand RNA genome and a huge size, from the proteomics point view, there are no changes in sequences of amino acids in NSP7, 13, matrix, or envelope or other proteins including 8b and p6. P6 is a multifunctional golgi-endoplasmic reticulum membrane-associated protein. This complex has a key duty to increase the replication rate of the virus and also causes intrinsic immune system responses by suppressing the signal transducer and activator of transcription factor 1 (STAT 1)
Glob Med Genet
Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population
SARS-CoV-2 is the causative agent of the ongoing viral pandemic of COVID-19. Mexico is currently in the third position in the number of deaths due to this virus. In the Mexican population, two variants of the spike protein (S-protein) are found, localized at H49Y and D614G. Energetic and structural analysis showed that the differences in infectivity can be explained by differences in affinity of the protein-protein interface between the wild-type and mutant S-protein with ACE2.
J Mol Graph Model
CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers
CoVrimer uses mutation data obtained from an online platform established by NGDC-CNCB (12 May 2021) to identify genomic regions, either conserved or with low levels of mutations. From which potential primer pairs are designed and provided to the user for filtering based on SARS-CoV-2 specific parameters. Alignments of primers and probes can be visualized with respect to the reference genome, indicating variant details and the level of conservation.
Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany
Monoclonal antibodies (mAb) have been introduced as a promising new therapeutic approach against SARS-CoV-2. At present, there is little experience regarding their clinical effects in patient populations underrepresented in clinical trials. Viral clearance was not achieved in five of six immunocompromised patients treated with bamlanivimab. Instead, viral replication increased again over the course of the following one to two weeks.
Lancet Reg Health Eur
Computational predictions for protein sequences of COVID-19 virus via machine learning algorithms
The rapid spread of coronavirus disease (COVID-19) has become a worldwide pandemic and affected more than 15 million patients reported in 27 countries. Machine learning algorithms are used to discover different protein sequences in the last stage. The obtained results demonstrate 100% accuracy, 100% sensitivity, and 90% specificity via the country-based binary labeling method with a linear support vector machine (SVM) classifier.
Med Biol Eng Comput
SARS-CoV-2 mutations altering regulatory properties: Deciphering host's and virus's perspectives
SARS-CoV-2 has acquired several mutations in its genome while spreading throughout the globe. Five host miRNAs lost their affinity for targeting the viral genome, and another five can target the mutated viral genome. Remarkably, we detected that three particular mutations in the IRES can disrupt its secondary structure which can consequently make the virus less functional.
Computational repurposing of tamibarotene against triple mutant variant of SARS-CoV-2
The triple mutant strain of severe acute respiratory syndrome coronavirus-2 (SARS-COV-2) was more virulent and pathogenic than its original strain. The reported genomic mutations are responsible for the alterations in the viral functional and structural proteins, causing the ineffectiveness of existing antiviral therapy targeting these proteins.
Comput Biol Med
2021 Aug 8
Comparative sequence analysis of the accessory and nucleocapsid genes of feline coronavirus strains isolated from cats diagnosed with effusive feline infectious peritonitis
Feline infectious peritonitis (FIP) is a lethal infectious disease of domestic cats caused by feline coronavirus (FCoV) infection. There have been numerous studies on FIP worldwide, whereas information about this disease in Thailand is still limited. The accessory gene sequence divergence may be responsible for driving the periodic emergence and continued persistence of FCoVs in Thai domestic cat populations.
2021 Aug 7
Deleterious single nucleotide polymorphisms (SNPs) of human IFNAR2 gene facilitate COVID-19 severity in patients: a comprehensive in silico approach
In humans, the dimeric receptor complex IFNAR2-IFNAR1 accelerates cellular response triggered by type I interferon (IFN) family proteins. P136R mutant may destabilize crucial binding with the IFN molecule in response to COVID-19 patients.
J Biomol Struct Dyn
2021 Aug 6
Enabling Artificial Intelligence for Genome Sequence Analysis of COVID-19 and Alike Viruses
Genome sequence analysis of COVID-19 is crucial to understand the virus's origin, behavior, and structure. System achieves good classification results with accuracy of 97% for COV-19, 96%, SARS, and 95% for MERS and Ebola genome sequences.
2021 Aug 6