scholarly journals Omicron variant of SARS-CoV-2 harbors a unique insertion mutation of putative viral or human genomic origin

2021 ◽  
Author(s):  
AJ Venkatakrishnan ◽  
Praveen Anand ◽  
Patrick Lenehan ◽  
Rohit Suratekar ◽  
Bharathwaj Raghunathan ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Infected Individual ◽  
Host Cells ◽  
Insertion Mutation ◽  
Template Switching ◽  
Global Public Health ◽  
Sequencing Data ◽  
Initial Discovery ◽  
Human Genomic ◽  
Amino Acid Mutations

The emergence of a heavily mutated SARS-CoV-2 variant (B.1.1.529, Omicron) and it’s spread to 6 continents within a week of initial discovery has set off a global public health alarm. Characterizing the mutational profile of Omicron is necessary to interpret its shared or distinctive clinical phenotypes with other SARS-CoV-2 variants. We compared the mutations of Omicron with prior variants of concern (Alpha, Beta, Gamma, Delta), variants of interest (Lambda, Mu, Eta, Iota and Kappa), and all 1523 SARS-CoV-2 lineages constituting 5.4 million SARS-CoV-2 genomes. Omicron’s Spike protein has 26 amino acid mutations (23 substitutions, two deletions and one insertion) that are distinct compared to other variants of concern. Whereas the substitution and deletion mutations have appeared in previous SARS-CoV-2 lineages, the insertion mutation (ins214EPE) has not been previously observed in any SARS-CoV-2 lineage other than Omicron. The nucleotide sequence encoding for ins214EPE could have been acquired by template switching involving the genomes of other viruses that infect the same host cells as SARS-CoV-2 or the human transcriptome of host cells infected with SARS-CoV-2. For instance, given recent clinical reports of co-infections in COVID-19 patients with seasonal coronaviruses (e.g. HCoV-229E), single cell RNA-sequencing data showing co-expression of the SARS-CoV-2 and HCoV-229E entry receptors (ACE2 and ANPEP) in respiratory and gastrointestinal cells, and HCoV genomes harboring sequences homologous to the nucleotide sequence that encodes ins214EPE, it is plausible that the Omicron insertion could have evolved in a co-infected individual. There is a need to understand the function of the Omicron insertion and whether human host cells are being exploited by SARS-CoV-2 as an ‘evolutionary sandbox’ for host-virus and inter-viral genomic interplay.

MOLECULAR GENETIC CHARACTERISTICS OF COMPONENTS OF THE COMPLEMENT SYSTEM IN SEVERE ACNE

2021 ◽  
Vol 100 (2) ◽  
pp. 40-48
Author(s):  
A.G. Rumyantsev ◽  
◽  
A.G. Rumyantsev ◽  
O.M. Demina ◽  
◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complement System ◽  
Molecular Genetic ◽  
Factor H ◽  
Host Cells ◽  
Pathophysiological Mechanism ◽  
Genetic Characteristics ◽  
Severe Acne ◽  
C3 Gene ◽  
The Complement System

It has been shown that the inflammatory response in acne develops at the early subclinical stages of the disease, sometimes before the formation of comedones. It is known that an important component of the innate immune system is the complement system, which includes more than 60 components, including 9 basic proteins (C1-C9), a variety of activation products (C3a, C3b, iC3b, C3d and C3dg), regulatory and inhibitory molecules [factor H, fH-like protein 1 (FHL1), CR1 (CD35), C4b-binding protein (C4BP), C1inh and vitronectin], proteases and secreted enzymes (factor B, factor D, C3bBb and C4bC2b), as well as receptors for effector molecules [C3aR, C5aR, C5L2 and C1q receptor (C1qR)]. The compliment is the central part of innate immunity, which is the first line of protection against alien and altered host cells. The objectives of this study were to determine and analyze the variants of the nucleotide sequence of the genes of the complement system C1QA, C1S, C2, C3, C5, C6, C7, C8A, C8B, C8G, C9 in patients with severe acne. Materials and methods of research: To achieve the target a prospective open non-randomized one-center study was carried out in 2017–2020. Under our supervision in the clinical setting at the Department of Skin Diseases and Cosmetology of the Pirogov Russian National Research Medical University, there were 50 patients in the main group and 20 participants in the comparison group (70 people in total) (42/60% men and 28/40% women) aged 15 to 46 years (median – 22,1 years). Molecular genetic diagnostics was performed in all 70 patients of the main and control groups by the method of high-throughput DNA sequencing – next-generation sequencing (NGS). Results: when analyzing the nucleotide sequence variants of the complement system genes identified in our study, it is shown that the severe form of acne probably has an association (4 SNPs of the C8A gene, 1 SNPs of the C8B gene, 2 SNPs of the C1S gene, 3 SNPs of the C3 gene, 2 SNPs of the C9 gene, 1 SNPs of the C7 gene, 1 SNPs of the C6 gene, 1 SNPs of the C2 gene, 2 SNPs of the C5 gene, 2 SNPs of the C8G gene), 13 SNPs of the complement system genes in introns (1 SNPs of the C8A gene, 1 SNPs of the C8B gene, 2 SNPs of the C1S gene, 1 SNPs of the C3 gene, 1 SNPs of the C7 gene, 2 SNPs of the C6 gene, 4 SNPs of the C5 gene, 1 SNPs of C8G gene), 6 SNPs of the complement system genes (2 SNPs of the C8B gene: one SNPs each in the 3'UTR and 5'UTR zones; 3 SNPs of the C3 gene in the 5'UTR zone, 1 SNPs of the C7 gene in the 3'UTR zone). Two mutations of the frame shift of the C2 gene (frameshift deletion) and the C9 gene (rs748464075, frameshift insertion) seem to have a protective effect in the development of acne. Conclusion: the obtained variants of the nucleotide sequence of the genes of the complement system C1QA, C1S, C2, C3, C5, C6, C7, C8A, C8B, C8G, C9, apparently, are associated with the formation of severe acne and cause an imbalance of the components of the complement system. It can cause a defect in chemotactic and phagocytic reactions, and as a result a disturbance of the regulation of the inflammatory reaction with chronization of the skin process occures. Thus, results of studies carried out, revealed – for the first time – polymorphic loci of genes of components of the complement system, the imbalance of which is the pathophysiological mechanism of acne.

scholarly journals CX3CR1 Engagement by Respiratory Syncytial Virus Leads to Induction of Nucleolin and Dysregulation of Cilia-related Genes

2020 ◽  
Author(s):  
Christopher S. Anderson ◽  
Tatiana Chirkova ◽  
Christopher G. Slaunwhite ◽  
Xing Qiu ◽  
Edward E. Walsh ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Epithelial Cells ◽  
G Protein ◽  
Infected Individual ◽  
The Elderly ◽  
Lung Epithelial Cells ◽  
Host Cells ◽  
Ciliated Cells ◽  
Transcriptional Changes ◽  
Syncytial Virus

AbstractRespiratory syncytial virus (RSV) contains a conserved CX3C motif on the ectodomain of the G-protein. The motif has been indicated as facilitating attachment of the virus to the host initiating infection via the human CX3CR1 receptor. The natural CX3CR1 ligand, CX3CL1, has been shown to induce signaling pathways resulting in transcriptional changes in the host cells. We hypothesize that binding of RSV to CX3CR1 via CX3C leads to transcriptional changes in host epithelial cells. Using transcriptomic analysis, the effect of CX3CR1 engagement by RSV was investigated. Normal human bronchial epithelial (NHBE) cells were infected with RSV virus containing either wildtype G-protein, or a mutant virus containing a CX4C mutation in the G-protein. RNA sequencing was performed on mock and 4-days-post-infected cultures. NHBE cultures were also treated with purified recombinant wild-type A2 G-protein. Here we report that RSV infection resulted in significant changes in the levels 766 transcripts. Many nuclear associated proteins were upregulated in the WT group, including Nucleolin. Alternatively, cilia-associated genes, including CC2D2A and CFAP221 (PCDP1), were downregulated. The addition of recombinant G-protein to the culture lead to the suppression of cilia-related genes while also inducing Nucleolin. Mutation of the CX3C motif (CX4C) reversed these effects on transcription decreasing nucleolin induction and lessening the suppression of cilia-related transcripts in culture. Furthermore, immunohistochemical staining demonstrated decreases in in ciliated cells and altered morphology. Therefore, it appears that engagement of CX3CR1 leads to induction of genes necessary for RSV entry as well as dysregulation of genes associated with cilia function.ImportanceRespiratory Syncytial Virus (RSV) has an enormous impact on infants and the elderly including increased fatality rates and potential for causing lifelong lung problems. Humans become infected with RSV through the inhalation of viral particles exhaled from an infected individual. These virus particles contain specific proteins that the virus uses to attach to human ciliated lung epithelial cells, initiating infection. Two viral proteins, G-protein and F-protein, have been shown to bind to human CX3CR1and Nucleolin, respectively. Here we show that the G-protein induces Nucleolin and suppresses gene transcripts specific to ciliated cells. Furthermore, we show that mutation of the CX3C-motif on the G-protein, CX4C, reverses these transcriptional changes.

scholarly journals Analysis of fragment ends in plasma DNA from patients with cancer

2021 ◽  
Author(s):  
Karan K. Budhraja ◽  
Bradon R. McDonald ◽  
Michelle D. Stephens ◽  
Tania Contente-Cuomo ◽  
Havell Markus ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Characteristic Curve ◽  
Cost Effective ◽  
Cancer Diagnostics ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Plasma Dna ◽  
Patients With Cancer ◽  
Fragmentation Patterns ◽  
Tumor Dna

AbstractFragmentation patterns observed in plasma DNA reflect chromatin accessibility in contributing cells. Since DNA shed from cancer cells and blood cells may differ in fragmentation patterns, we investigated whether analysis of genomic positioning and nucleotide sequence at fragment ends can reveal the presence of tumor DNA in blood and aid cancer diagnostics. We analyzed whole genome sequencing data from >2700 plasma DNA samples including healthy individuals and patients with 11 different cancer types. We observed higher fractions of fragments with aberrantly positioned ends in patients with cancer, driven by contribution of tumor DNA into plasma. Genomewide analysis of fragment ends using machine learning showed overall area under the receiver operative characteristic curve of 0.96 for detection of cancer. Our findings remained robust with as few as 1 million fragments analyzed per sample, suggesting that analysis of fragment ends can become a cost-effective and accessible approach for cancer detection and monitoring.One-sentence summaryAnalyzing the positioning and nucleotide sequence at fragment ends in plasma DNA may enable cancer diagnostics.

scholarly journals The Impact of Cellular Proliferation on the HIV-1 Reservoir

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 127
Author(s):  
Maria C. Virgilio ◽  
Kathleen L. Collins
Keyword(s):  
Cellular Proliferation ◽  
Integration Site ◽  
Infected Individual ◽  
Host Cells ◽  
Viral Reservoir ◽  
Proliferative Potential ◽  
Proliferation And Differentiation ◽  
Latently Infected ◽  
Infected Cells ◽  
The Impact

Human immunodeficiency virus (HIV) is a chronic infection that destroys the immune system in infected individuals. Although antiretroviral therapy is effective at preventing infection of new cells, it is not curative. The inability to clear infection is due to the presence of a rare, but long-lasting latent cellular reservoir. These cells harboring silent integrated proviral genomes have the potential to become activated at any moment, making therapy necessary for life. Latently-infected cells can also proliferate and expand the viral reservoir through several methods including homeostatic proliferation and differentiation. The chromosomal location of HIV proviruses within cells influences the survival and proliferative potential of host cells. Proliferating, latently-infected cells can harbor proviruses that are both replication-competent and defective. Replication-competent proviral genomes contribute to viral rebound in an infected individual. The majority of available techniques can only assess the integration site or the proviral genome, but not both, preventing reliable evaluation of HIV reservoirs.

scholarly journals Doratoxylon apetalum, an Indigenous Medicinal Plant from Mascarene Islands, Is a Potent Inhibitor of Zika and Dengue Virus Infection in Human Cells

2019 ◽  
Vol 20 (10) ◽  
pp. 2382 ◽  
Author(s):  
Juliano G. Haddad ◽  
Andrea Cristine Koishi ◽  
Arnaud Gaudry ◽  
Claudia Nunes Duarte dos Santos ◽  
Wildriss Viranaicken ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Medicinal Plant ◽  
Dengue Virus ◽  
Denv Infection ◽  
Antiviral Drugs ◽  
Human Cells ◽  
Host Cells ◽  
Global Public Health ◽  
Denv Serotypes ◽  
Mascarene Islands

Zika virus (ZIKV) and Dengue virus (DENV) are mosquito-borne viruses of the Flavivirus genus that could cause congenital microcephaly and hemorrhage, respectively, in humans, and thus present a risk to global public health. A preventive vaccine against ZIKV remains unavailable, and no specific antiviral drugs against ZIKV and DENV are licensed. Medicinal plants may be a source of natural antiviral drugs which mostly target viral entry. In this study, we evaluate the antiviral activity of Doratoxylum apetalum, an indigenous medicinal plant from the Mascarene Islands, against ZIKV and DENV infection. Our data indicated that D. apetalum exhibited potent antiviral activity against a contemporary epidemic strain of ZIKV and clinical isolates of four DENV serotypes at non-cytotoxic concentrations in human cells. Time-of-drug-addition assays revealed that D. apetalum extract acts on ZIKV entry by preventing the internalisation of virus particles into the host cells. Our data suggest that D. apetalum-mediated ZIKV inhibition relates to virus particle inactivation. We suggest that D. apetalum could be a promising natural source for the development of potential antivirals against medically important flaviviruses.

scholarly journals The nucleotide sequence of the region ofsrcgene deletion in transformation-defective Rous sarcoma virus adapted to semi-permissive host cells

1989 ◽  
Vol 17 (8) ◽  
pp. 3294-3294 ◽  
Author(s):  
V.I. Kashuba ◽  
S.V. Zubak ◽  
A.V. Rynditch ◽  
V.M. Kavsan ◽  
I. Hlozanek ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Rous Sarcoma Virus ◽  
Host Cells ◽  
Permissive Host ◽  
Rous Sarcoma ◽  
Sarcoma Virus

scholarly journals Dynamics of the Type III Secretion System Activity of Enteropathogenic Escherichia coli

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
Erez Mills ◽  
Kobi Baruch ◽  
Gili Aviv ◽  
Mor Nitzan ◽  
Ilan Rosenshine
Keyword(s):  
Escherichia Coli ◽  
Type Iii Secretion ◽  
Public Health Problem ◽  
Effector Proteins ◽  
Host Cells ◽  
Global Public Health ◽  
Secretion Systems ◽  
Comprehensive Description ◽  
Content Type ◽  
Type Iii

ABSTRACT Type III secretion systems (TTSSs) are employed by pathogens to translocate host cells with effector proteins, which are crucial for virulence. The dynamics of effector translocation, behavior of the translocating bacteria, translocation temporal order, and relative amounts of each of the translocated effectors are all poorly characterized. To address these issues, we developed a microscopy-based assay that tracks effector translocation. We used this assay alongside a previously described real-time population-based translocation assay, focusing mainly on enteropathogenic Escherichia coli (EPEC) and partly comparing it to Salmonella. We found that the two pathogens exhibit different translocation behaviors: in EPEC, a subpopulation that formed microcolonies carried out most of the translocation activity, while Salmonella executed protein translocation as planktonic bacteria. We also noted variability in host cell susceptibility, with some cells highly resistant to translocation. We next extended the study to determine the translocation dynamics of twenty EPEC effectors and found that all exhibited distinct levels of translocation efficiency. Further, we mapped the global effects of key TTSS-related components on TTSS activity. Our results provide a comprehensive description of the dynamics of the TTSS activity of EPEC and new insights into the mechanisms that control the dynamics. IMPORTANCE EPEC and the closely related enterohemorrhagic Escherichia coli (EHEC) represent a global public health problem. New strategies to combat EPEC and EHEC infections are needed, and development of such strategies requires better understanding of their virulence machinery. The TTSS is a critical virulence mechanism employed by these pathogens, and by others, including Salmonella. In this study, we aimed at elucidating new aspects of TTSS function. The results obtained provide a comprehensive description of the dynamics of TTSS activity of EPEC and new insights into the mechanisms that control these changes. This knowledge sets the stage for further analysis of the system and may accelerate the development of new ways to treat EPEC and EHEC infections. Further, the newly described microscopy-based assay can be readily adapted to study the dynamics of TTSS activity in other pathogens.

scholarly journals Cell adherence-promoted activity of Plesiomonas shigelloides GroEL

2007 ◽  
Vol 56 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Hitoshi Tsugawa ◽  
Humie Ito ◽  
Miho Ohshima ◽  
Yoshio Okawa
Keyword(s):  
Cell Death ◽  
Nucleotide Sequence ◽  
Apoptotic Cell ◽  
Positive Influence ◽  
Host Cells ◽  
Cell Fractionation ◽  
Apoptosis Induction ◽  
Cell Adherence ◽  
Plesiomonas Shigelloides ◽  
Facscalibur Flow Cytometer

Previously, it has been demonstrated that the invasion of Caco-2 cells by Plesiomonas shigelloides induces apoptotic cell death. Therefore, the attachment to and colonization of eukaryotic intestinal host cells by P. shigelloides are important steps in causing pathogenicity. In this study, the participation of P. shigelloides GroEL in the attachment of P. shigelloides was examined. The groESL operon of P. shigelloides was isolated by PCR. The nucleotide sequence of the groESL operon of P. shigelloides revealed two ORFs of 294 nucleotides for groES and 1647 nucleotides for groEL. Cell fractionation and immunostaining experiments suggested that the GroEL of P. shigelloides was associated with the bacterial cell surface. The expression of the groEL gene was upregulated during the attachment and apoptosis-induction stages, and the expression of the protein was also induced during the attachment stage. Furthermore, GroEL efficiently promoted the attachment of P. shigelloides to Caco-2 cells, as measured by a FACSCalibur flow cytometer. These results demonstrated that GroEL has a positive influence on the attachment of P. shigelloides to Caco-2 cells.

Cloning and molecular analysis of the human citrate synthase gene

Genome ◽  
1998 ◽  
Vol 41 (5) ◽  
pp. 733-738 ◽  
Author(s):  
Michael J Goldenthal ◽  
Jose Marin-Garcia ◽  
Radha Ananthakrishnan
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Human Heart ◽  
Citrate Synthase ◽  
Krebs Cycle ◽  
Chromosome 12 ◽  
Primary Sequence ◽  
Key Words Human ◽  
Human Genomic ◽  
Sequence Encoding

The nucleotide sequence encoding the citrate synthase (CS) gene was determined from the sequencing of the CS cDNA isolated from a human heart cDNA library. The primary sequence of CS deduced from its nucleotide sequence reveals a highly conserved, albeit slightly larger, protein of 466 amino acids, with 95% homology to its pig homologue. The data also indicate that the human genomic CS gene contains no introns, and confirms the location of the human CS gene on chromosome 12.Key words: human, citrate synthase, Krebs' cycle.

scholarly journals 1,2,3,4,6-Pentagalloyl Glucose, a RBD-ACE2 Binding Inhibitor to Prevent SARS-CoV-2 Infection

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Hong Chen ◽  
Li Jun Yang ◽  
Sami Hamdoun ◽  
Sookja Kim Chung ◽  
Christopher Wai-kei Lam ◽  
...  
Keyword(s):  
Antiviral Agent ◽  
Face Mask ◽  
Storage Condition ◽  
Cellular Level ◽  
Host Cells ◽  
Hek293 Cells ◽  
Global Public Health ◽  
Angiotensin Converting Enzyme 2 ◽  
Novel Drugs ◽  
Pentagalloyl Glucose

The outbreak of SARS-CoV-2 virus caused more than 80,155,187 confirmed COVID-19 cases worldwide, which has posed a serious threat to global public health and the economy. The development of vaccines and discovery of novel drugs for COVID-19 are urgently needed. Although the FDA-approved SARS-CoV-2 vaccines has been launched in many countries recently, the strength of safety, stringent storage condition and the possibly short-term immunized efficacy remain as the major challenges in the popularity and recognition of using vaccines against SARS-CoV-2. With the spike-receptor binding domain (RBD) of SARS-CoV-2 being responsible for binding to human angiotensin-converting enzyme 2 receptor (hACE2), ACE2 is identified as the receptor for the entry and viral infection of SARS-CoV-2. In this study, molecular docking and biolayer interferometry (BLI) binding assay were adopted to determine the direct molecular interactions between natural small-molecule, 1,2,3,4,6-Pentagalloyl glucose (PGG) and the spike-RBD of the SARS-CoV-2. Our results showed that PGG preferentially binds to a pocket that contains residues Glu 340 to Lys 356 of spike-RBD with a relatively low binding energy of -8 kcal/mol. BLI assay further confirmed that PGG exhibits a relatively strong binding affinity to SARS-CoV-2-RBD protein in comparison to hACE2. In addition, both ELISA and immunocytochemistry assay proved that PGG blocks SARS-CoV-2-RBD binding to hACE2 dose dependently in cellular level. Notably, PGG was confirmed to abolish the infectious property of RBD-pseudotyped lentivirus in hACE2 overexpressing HEK293 cells, which mimicked the entry of wild type SARS-CoV-2 virus in human host cells. Finally, maximal tolerated dose (MTD) studies revealed that up to 200 mg/kg/day of PGG was confirmed orally safe in mice. Our findings suggest that PGG may be a safe and potential antiviral agent against the COVID-19 by blockade the fusion of SARS-CoV-2 spike-RBD to hACE2 receptors. Therefore, PGG may be considered as a safe and natural antiviral agent for its possible preventive application in daily anti-virus hygienic products such as a disinfectant spray or face mask.

Sign in / Sign up

Export Citation Format

Share Document