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1.
Phys Chem Chem Phys ; 24(15): 8724-8737, 2022 Apr 13.
Article in English | MEDLINE | ID: covidwho-1774006

ABSTRACT

The continuous spread of the newly emerged SARS-CoV-2 Omicron variant (B.1.1.529) has become an important reason for the surge in COVID-19 infections. Its numerous mutated residues containing key sites on the receptor-binding domain (RBD) undoubtedly pose new challenges for epidemic control. Although the preventive measures are becoming more sophisticated, the effects of mutations on the binding of the virus to the receptor protein remain to be elucidated. Here, we used molecular dynamics (MD) simulations to investigate the differences in the binding mode between the Omicron variant and the angiotensin-converting enzyme 2 (ACE2) compared to the wild-type strain (WT). Multi-point mutations in the Omicron variant RBD could cause the conformation shift in the large Loop (where T478K and E484A are located), which makes it easier to wrap the N-terminal helix of ACE2 and form tighter contacts. The stronger electrostatic interaction was the main reason for its enhanced binding affinity as compared to WT. This was due to the large number of positively charged patches (N440K, T478K, Q493R, Q498R, and Y505H) formed by the substitution of neutral amino acids at multiple sites. The appearance of these highly polar hydrophilic amino acids may cause local perturbations and affect the electrostatic complementarity of RBD with the ACE2, and further mediate conformational changes. Thus, a more extensive interaction network was found in the mutation system and the complex interaction cluster was formed near E37@ACE2, which was essential for the stable binding of the two. In addition, we speculated that these mutations may affect the electrostatic complementarity with the four potential antibodies to reduce the sensitivity of the virus to antibodies. This study reveals the key details of the Omicron variant binding to ACE2 and provides important theoretical views for the enhanced infectivity of this variant. We hope that these observations can provide timely molecular insights for responding to the Omicron variant pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Angiotensin-Converting Enzyme 2/genetics , Binding Sites , COVID-19/genetics , Humans , Mutation , Point Mutation , Protein Binding , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism
2.
Viruses ; 14(3)2022 03 09.
Article in English | MEDLINE | ID: covidwho-1732252

ABSTRACT

The spread of the newly emerged severe acute respiratory syndrome (SARS-CoV-2) virus has led to more than 430 million confirmed cases, including more than 5.9 million deaths, reported worldwide as of 24 February 2022. Conservation of viral genomes is important for pathogen identification and diagnosis, therapeutics development and epidemiological surveillance to detect the emergence of new viral variants. An intense surveillance of virus variants has led to the identification of Variants of Interest and Variants of Concern. Although these classifications dynamically change as the pandemic evolves, they have been useful to guide public health efforts on containment and mitigation. In this work, we present CovDif, a tool to detect conserved regions between groups of viral genomes. CovDif creates a conservation landscape for each group of genomes of interest and a differential landscape able to highlight differences in the conservation level between groups. CovDif is able to identify loss in conservation due to point mutations, deletions, inversions and chromosomal rearrangements. In this work, we applied CovDif to SARS-CoV-2 clades (G, GH, GR, GV, L, O, S and G) and variants. We identified all regions for any defining SNPs. We also applied CovDif to a group of population genomes and evaluated the conservation of primer regions for current SARS-CoV-2 detection and diagnostic protocols. We found that some of these protocols should be applied with caution as few of the primer-template regions are no longer conserved in some SARS-CoV-2 variants. We conclude that CovDif is a tool that could be widely applied to study the conservation of any group of viral genomes as long as whole genomes exist.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Genome, Viral , Humans , Point Mutation , SARS-CoV-2/genetics
3.
Viruses ; 14(3)2022 02 28.
Article in English | MEDLINE | ID: covidwho-1715783

ABSTRACT

We describe a flight-associated infection scenario of seven individuals with a B.1.617.2 (Delta) lineage, harbouring an S:E484Q point mutation. In Sweden, at least 10% of all positive SARS-CoV-2 samples were sequenced in each county; the B.1.717.2 + S:E484Q combination was not detected in Sweden before and was imported within the scenario described in this report. The high transmission rate of the delta lineage combined with the S:E484Q mutation, associated with immune escape in other lineages, makes this specific genetic combination a possible threat to the global fight against the COVID-19 pandemic. Even within the Omicron wave, the B.1.617.2 + S:E484Q variant appeared in community samples in Sweden, as it seems that this combination has an evolutionary gain compared to other B.1.617.2 lineages. The here described genomic combination was not detectable with the common fasta file-based Pango-lineage analysis, hence increasing the probability of the true global prevalence to be higher.


Subject(s)
COVID-19 , Pandemics , COVID-19/epidemiology , Humans , Point Mutation , SARS-CoV-2/genetics
4.
Microbiol Spectr ; 10(1): e0068121, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1691411

ABSTRACT

The N501Y amino acid mutation caused by a single point substitution A23063T in the spike gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is possessed by three variants of concern (VOCs), B.1.1.7, B.1.351, and P.1. A rapid screening tool using this mutation is important for surveillance during the coronavirus disease 2019 (COVID-19) pandemic. We developed and validated a single nucleotide polymorphism real-time reverse transcription PCR assay using allelic discrimination of the spike gene N501Y mutation to screen for potential variants of concern and differentiate them from SARS-CoV-2 lineages without the N501Y mutation. A total of 160 clinical specimens positive for SARS-CoV-2 were characterized as mutant (N501Y) or N501 wild type by Sanger sequencing and were subsequently tested with the N501Y single nucleotide polymorphism real-time reverse transcriptase PCR assay. Our assay, compared to Sanger sequencing for single nucleotide polymorphism detection, demonstrated positive percent agreement of 100% for all 57 specimens displaying the N501Y mutation, which were confirmed by Sanger sequencing to be typed as A23063T, including one specimen with mixed signal for wild type and mutant. Negative percent agreement was 100% in all 103 specimens typed as N501 wild type, with A23063 identified as wild type by Sanger sequencing. The identification of circulating SARS-CoV-2 lineages carrying an N501Y mutation is critical for surveillance purposes. Current identification methods rely primarily on Sanger sequencing or whole-genome sequencing, which are time consuming, labor intensive, and costly. The assay described herein is an efficient tool for high-volume specimen screening for SARS-CoV-2 VOCs and for selecting specimens for confirmatory Sanger or whole-genome sequencing. IMPORTANCE During the coronavirus disease 2019 (COVID-19) pandemic, several variants of concern (VOCs) have been detected, for example, B.1.1.7, B.1.351, P.1, and B.1.617.2. The VOCs pose a threat to public health efforts to control the spread of the virus. As such, surveillance and monitoring of these VOCs is of the utmost importance. Our real-time RT-PCR assay helps with surveillance by providing an easy method to quickly survey SARS-CoV-2 specimens for VOCs carrying the N501Y single nucleotide polymorphism (SNP). Samples that test positive for the N501Y mutation in the spike gene with our assay can be sequenced to identify the lineage. Thus, our assay helps to focus surveillance efforts and decrease turnaround times.


Subject(s)
COVID-19/diagnosis , Mutation, Missense , Point Mutation , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Alleles , Amino Acid Substitution , COVID-19/epidemiology , COVID-19/virology , Genes, Viral , Humans , Mass Screening , Ontario/epidemiology , Polymorphism, Single Nucleotide , Population Surveillance , Prevalence , Reproducibility of Results , Sensitivity and Specificity
5.
Proc Natl Acad Sci U S A ; 119(6)2022 02 08.
Article in English | MEDLINE | ID: covidwho-1642083

ABSTRACT

Adenosine deaminases acting on RNA (ADAR) are RNA-editing enzymes that may restrict viral infection. We have utilized deep sequencing to determine adenosine to guanine (A→G) mutations, signifying ADAR activity, in clinical samples retrieved from 93 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients in the early phase of the COVID-19 pandemic. A→G mutations were detected in 0.035% (median) of RNA residues and were predominantly nonsynonymous. These mutations were rarely detected in the major viral population but were abundant in minor viral populations in which A→G was more prevalent than any other mutation (P < 0.001). The A→G substitutions accumulated in the spike protein gene at positions corresponding to amino acids 505 to 510 in the receptor binding motif and at amino acids 650 to 655. The frequency of A→G mutations in minor viral populations was significantly associated with low viral load (P < 0.001). We additionally analyzed A→G mutations in 288,247 SARS-CoV-2 major (consensus) sequences representing the dominant viral population. The A→G mutations observed in minor viral populations in the initial patient cohort were increasingly detected in European consensus sequences between March and June 2020 (P < 0.001) followed by a decline of these mutations in autumn and early winter (P < 0.001). We propose that ADAR-induced deamination of RNA is a significant source of mutated SARS-CoV-2 and hypothesize that the degree of RNA deamination may determine or reflect viral fitness and infectivity.


Subject(s)
Adenosine Deaminase/genetics , COVID-19/epidemiology , Point Mutation , RNA Editing , RNA, Viral/genetics , RNA-Binding Proteins/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Adenosine/metabolism , Adenosine Deaminase/metabolism , Adult , Aged , Aged, 80 and over , Amino Acid Substitution , COVID-19/genetics , COVID-19/transmission , COVID-19/virology , Deamination , Female , Genetic Fitness , Genome, Viral , Guanine/metabolism , Host-Pathogen Interactions/genetics , Humans , Male , Middle Aged , RNA, Viral/metabolism , RNA-Binding Proteins/metabolism , SARS-CoV-2/growth & development , SARS-CoV-2/pathogenicity , Signal Transduction , Spike Glycoprotein, Coronavirus/metabolism , Sweden/epidemiology , Viral Load , Virulence
6.
Microbiol Spectr ; 10(1): e0222321, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1622006

ABSTRACT

Rapid onsite whole-genome sequencing of two suspected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) N gene diagnostic escape samples revealed a previously unreported N gene point mutation at genome position 29195. Because the G29195T mutation occurs within a region probed by a commonly referenced U.S. CDC N gene reverse transcription (RT)-PCR assay, we hypothesize that the G29195T mutation rendered the N gene target of a proprietary commercial assay undetectable. The putative diagnostic escape G29195T mutation demonstrates the need for nearly real-time surveillance, as emergence of a novel SARS-CoV-2 variant with the potential to escape diagnostic tests continues to be a threat. IMPORTANCE Accurate diagnostic detection of SARS-CoV-2 currently depends on the large-scale deployment of RT-PCR assays. SARS-CoV-2 RT-PCR assays target predetermined regions in the viral genomes by complementary binding of primers and probes to nucleic acid sequences in the clinical samples. Potential diagnostic escapes, such as those of clinical samples harboring the G29195T mutation, may result in false-negative SARS-CoV-2 RT-PCR results. The rapid detection and sharing of potential diagnostic escapes are essential for diagnostic laboratories and manufacturers around the world, to optimize their assays as SARS-CoV-2 continues to evolve.


Subject(s)
COVID-19/diagnosis , Point Mutation , SARS-CoV-2/genetics , Reverse Transcriptase Polymerase Chain Reaction
7.
J Cell Biochem ; 123(2): 417-430, 2022 02.
Article in English | MEDLINE | ID: covidwho-1525444

ABSTRACT

Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a large number of mutations in its genome have been reported. Some of the mutations occur in noncoding regions without affecting the pathobiology of the virus, while mutations in coding regions are significant. One of the regions where a mutation can occur, affecting the function of the virus is at the receptor-binding domain (RBD) of the spike protein. RBD interacts with angiotensin-converting enzyme 2 (ACE2) and facilitates the entry of the virus into the host cells. There is a lot of focus on RBD mutations, especially the displacement of N501Y which is observed in the UK/Kent, South Africa, and Brazilian lineages of SARS-CoV-2. Our group utilizes computational biology approaches such as immunoinformatics, protein-protein interaction analysis, molecular dynamics, free energy computation, and tertiary structure analysis to disclose the consequences of N501Y mutation at the molecular level. Surprisingly, we discovered that this mutation reduces the immunogenicity of the spike protein; also, displacement of Asn with Tyr reduces protein compactness and significantly increases the stability of the spike protein and its affinity to ACE2. Moreover, following the N501Y mutation secondary structure and folding of the spike protein changed dramatically.


Subject(s)
COVID-19/virology , Mutation, Missense , Pandemics , Point Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Amino Acid Substitution , Angiotensin-Converting Enzyme 2/metabolism , Antigens, Viral/chemistry , Antigens, Viral/immunology , Binding Sites , Computational Biology/methods , Energy Transfer , Epitopes/chemistry , Epitopes/immunology , Evolution, Molecular , Humans , Molecular Docking Simulation , Protein Binding , Protein Conformation , Protein Stability , Receptors, Virus/metabolism , SARS-CoV-2/immunology , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/metabolism , Structure-Activity Relationship
8.
Microbiol Spectr ; 9(3): e0149421, 2021 12 22.
Article in English | MEDLINE | ID: covidwho-1522929

ABSTRACT

Accurate and rapid diagnostic tests are a critical component for the early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and of the overall control strategy for the current pandemic. Nucleic acid amplification tests are the gold standard for diagnosis of acute SARS-CoV-2 infection, and many real-time PCR diagnostic assays have been developed. Mutations that occur within the primer/probe binding regions of the SARS-CoV-2 genome can negatively impact the performance of diagnostic assays. Here, we report two single-point mutations in the N gene of SARS-CoV-2 associated with N gene target detection failures in the Cepheid Xpert Xpress SARS-CoV-2 assay, the first a C to T mutation at position 29197, found in five patients, and the second a C to T mutation at position 29200, found in eight patients. By sequencing the Xpert amplicons, we showed both mutations to be located within the amplified region of the Xpert N gene target. This report highlights the necessity for multiple genetic targets and the continual monitoring and evaluation of diagnostic assay performance. IMPORTANCE This paper reports the identification of single-point mutations in the N gene of SARS-CoV-2 associated with a gene target failure by the Cepheid Xpert commercial system. In order to determine the mutation(s) responsible for the N gene detection failures, the genomic products from the Cepheid Xpert system were sequenced and compared to whole genomes of SARS-CoV-2 from clinical cases. This report is the first to our knowledge which characterizes the amplified PCR products of the Xpert system, confirming the mutations associated with the gene target failure. The mutations identified have previously been reported.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Coronavirus Nucleocapsid Proteins/genetics , Phosphoproteins/genetics , Point Mutation , SARS-CoV-2/isolation & purification , Diagnostic Tests, Routine , Humans , Indans , Molecular Diagnostic Techniques/methods , Phylogeny , SARS-CoV-2/classification , Sensitivity and Specificity , Whole Genome Sequencing
9.
Nucleic Acids Res ; 50(D1): D858-D866, 2022 01 07.
Article in English | MEDLINE | ID: covidwho-1511005

ABSTRACT

SCoV2-MD (www.scov2-md.org) is a new online resource that systematically organizes atomistic simulations of the SARS-CoV-2 proteome. The database includes simulations produced by leading groups using molecular dynamics (MD) methods to investigate the structure-dynamics-function relationships of viral proteins. SCoV2-MD cross-references the molecular data with the pandemic evolution by tracking all available variants sequenced during the pandemic and deposited in the GISAID resource. SCoV2-MD enables the interactive analysis of the deposited trajectories through a web interface, which enables users to search by viral protein, isolate, phylogenetic attributes, or specific point mutation. Each mutation can then be analyzed interactively combining static (e.g. a variety of amino acid substitution penalties) and dynamic (time-dependent data derived from the dynamics of the local geometry) scores. Dynamic scores can be computed on the basis of nine non-covalent interaction types, including steric properties, solvent accessibility, hydrogen bonding, and other types of chemical interactions. Where available, experimental data such as antibody escape and change in binding affinities from deep mutational scanning experiments are also made available. All metrics can be combined to build predefined or custom scores to interrogate the impact of evolving variants on protein structure and function.


Subject(s)
COVID-19/virology , Databases, Genetic , Molecular Dynamics Simulation , SARS-CoV-2/genetics , Software , Viral Proteins/genetics , Evolution, Molecular , Gene Expression Regulation, Viral , Genome, Viral , Humans , Hydrogen Bonding , Internet , Models, Molecular , Phylogeny , Point Mutation , Protein Binding , Protein Interaction Mapping , SARS-CoV-2/growth & development , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , Structure-Activity Relationship , Viral Proteins/chemistry , Viral Proteins/metabolism
10.
Sci Rep ; 11(1): 13464, 2021 06 29.
Article in English | MEDLINE | ID: covidwho-1500743

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19) that emerged in human populations recently. Severely ill COVID-19 patients exhibit the elevation of proinflammatory cytokines, and such an unbalanced production of proinflammatory cytokines is linked to acute respiratory distress syndrome with high mortality in COVID-19 patients. Our study provides evidence that the ORF3a, M, ORF7a, and N proteins of SARS-CoV-2 were NF-κB activators. The viral sequence from infected zoo lions belonged to clade V, and a single mutation of G251V is found for ORF3a gene compared to all other clades. No significant functional difference was found for clade V ORF3a, indicating the NF-κB activation is conserved among COVID-19 variants. Of the four viral proteins, the ORF7a protein induced the NF-κB dictated proinflammatory cytokines including IL-1α, IL-1ß, IL-6, IL-8, IL-10, TNF-α, and IFNß. The ORF7a protein also induced IL-3, IL-4, IL-7, IL-23. Of 15 different chemokines examined in the study, CCL11, CCL17, CCL19, CCL20, CCL21, CCL22, CCL25, CCL26, CCL27, and CXCL9 were significantly upregulated by ORF7. These cytokines and chemokines were frequently elevated in severely ill COVID-19 patients. Our data provide an insight into how SARS-CoV-2 modulates NF-κB signaling and inflammatory cytokine expressions. The ORF7a protein may be a desirable target for strategic developments to minimize uncontrolled inflammation in COVID-19 patients.


Subject(s)
Cytokines/metabolism , NF-kappa B/metabolism , SARS-CoV-2/metabolism , Viral Proteins/metabolism , Amino Acid Sequence , COVID-19/pathology , COVID-19/virology , Chemokines/genetics , Chemokines/metabolism , Cytokines/genetics , HeLa Cells , Humans , Point Mutation , SARS-CoV-2/isolation & purification , Sequence Alignment , Severity of Illness Index , Up-Regulation , Viral Matrix Proteins/genetics , Viral Proteins/genetics , Viroporin Proteins/chemistry , Viroporin Proteins/genetics , Viroporin Proteins/metabolism
11.
J Biol Chem ; 297(6): 101371, 2021 12.
Article in English | MEDLINE | ID: covidwho-1487811

ABSTRACT

The emergence of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and the subsequent COVID-19 pandemic have visited a terrible cost on the world in the forms of disease, death, and economic turmoil. The rapid development and deployment of extremely effective vaccines against SARS-CoV-2 have seemingly brought within reach the end of the pandemic. However, the virus has acquired mutations. and emerging variants of concern are more infectious and reduce the efficacy of existing vaccines. Although promising efforts to combat these variants are underway, the evolutionary pressures leading to these variants are poorly understood. To that end, here we have studied the effects on the structure and function of the SARS-CoV-2 spike glycoprotein receptor-binding domain of three amino-acid substitutions found in several variants of concern, including alpha (B.1.1.7), beta (B.1.351), and gamma (P.1). We found that these substitutions alter the receptor-binding domain structure, stability, and ability to bind to angiotensin converting enzyme 2, in such a way as to possibly have opposing and compensatory effects. These findings provide new insights into how these variants of concern may have been selected for infectivity while maintaining the structure and stability of the receptor binding domain.


Subject(s)
Amino Acid Substitution , COVID-19/virology , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Angiotensin-Converting Enzyme 2/metabolism , COVID-19/metabolism , Humans , Models, Molecular , Point Mutation , Protein Binding , Protein Domains , Protein Stability , SARS-CoV-2/chemistry , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism
12.
Cell Rep ; 37(3): 109841, 2021 10 19.
Article in English | MEDLINE | ID: covidwho-1439922

ABSTRACT

Nonstructural protein 1 (nsp1) is a coronavirus (CoV) virulence factor that restricts cellular gene expression by inhibiting translation through blocking the mRNA entry channel of the 40S ribosomal subunit and by promoting mRNA degradation. We perform a detailed structure-guided mutational analysis of severe acute respiratory syndrome (SARS)-CoV-2 nsp1, revealing insights into how it coordinates these activities against host but not viral mRNA. We find that residues in the N-terminal and central regions of nsp1 not involved in docking into the 40S mRNA entry channel nonetheless stabilize its association with the ribosome and mRNA, both enhancing its restriction of host gene expression and enabling mRNA containing the SARS-CoV-2 leader sequence to escape translational repression. These data support a model in which viral mRNA binding functionally alters the association of nsp1 with the ribosome, which has implications for drug targeting and understanding how engineered or emerging mutations in SARS-CoV-2 nsp1 could attenuate the virus.


Subject(s)
COVID-19/genetics , Gene Expression Regulation, Viral , SARS-CoV-2/genetics , Viral Nonstructural Proteins/metabolism , Anisotropy , COVID-19/immunology , DNA Mutational Analysis , Female , Gene Expression Profiling , Green Fluorescent Proteins/metabolism , HEK293 Cells , Humans , Kinetics , Mutation , Phenotype , Point Mutation , Protein Biosynthesis , Protein Domains , RNA Stability , Ribosome Subunits, Small, Eukaryotic/metabolism , Ribosomes/metabolism
13.
Diagn Microbiol Infect Dis ; 102(1): 115540, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1415358

ABSTRACT

Five SARS-CoV-2-positive samples showed N-gene drop-out with a RT-PCR multiplex test. WGS found all samples to harbor a deletion in the same region of the N gene, which is likely to impair the efficiency of amplification. This highlights the need for a continued surveillance of viral evolution and diagnostic test performance.


Subject(s)
COVID-19 Testing , COVID-19/virology , SARS-CoV-2/genetics , COVID-19/diagnosis , Diagnostic Tests, Routine , Genome, Viral , Humans , Multiplex Polymerase Chain Reaction , Point Mutation , Whole Genome Sequencing
15.
Euro Surveill ; 25(13)2020 04.
Article in English | MEDLINE | ID: covidwho-1389098

ABSTRACT

Whole genome sequences of SARS-CoV-2 obtained from two patients, a Chinese tourist visiting Rome and an Italian, were compared with sequences from Europe and elsewhere. In a phylogenetic tree, the Italian patient's sequence clustered with sequences from Germany while the tourist's sequence clustered with other European sequences. Some additional European sequences in the tree segregated outside the two clusters containing the patients' sequences. This suggests multiple SARS-CoV-2 introductions in Europe or virus evolution during circulation.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Coronavirus/genetics , Genome, Viral/genetics , Pneumonia, Viral/diagnosis , RNA, Viral/genetics , Severe Acute Respiratory Syndrome/diagnosis , Travel , Whole Genome Sequencing/methods , Betacoronavirus/isolation & purification , COVID-19 , China , Coronavirus/classification , Coronavirus/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Germany , Humans , Italy , Molecular Epidemiology , Pandemics , Phylogeny , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Point Mutation , RNA, Viral/isolation & purification , SARS-CoV-2 , Severe Acute Respiratory Syndrome/virology
16.
Am J Hematol ; 96(12): 1580-1586, 2021 12 01.
Article in English | MEDLINE | ID: covidwho-1375592

ABSTRACT

The recent association of cerebral venous thrombosis (CVT) with COVID-19 vaccinations prompted the current retrospective review of 74 cases of CVT (median age = 44 years, range 15-85; 61% females) associated with myeloproliferative neoplasms (MPNs), seen at the Mayo Clinic, Catholic University of Rome, and University of Florence, between 1991 and 2021. Disease-specific frequencies were 1.3% (39/2893), 1.2% (21/1811) and 0.2% (3/1888) for essential thrombocythemia, polycythemia vera and primary myelofibrosis, respectively. Cerebral venous thrombosis occurred either prior to (n = 20, 27%), at (n = 32, 44%) or after (n = 22) MPN diagnosis. A total of 72% of patients presented with headaches. Transverse (51%), sagittal (43%) and sigmoid sinuses (35%) were involved with central nervous system hemorrhage noted in 10 (14%) patients. In all, 91% of tested patients harbored JAK2V617F. An underlying thrombophilic condition was identified in 19 (31%) cases and history of thrombosis in 10 (14%). Treatment for CVT included systemic anticoagulation alone (n = 27) or in conjunction with aspirin (n = 24), cytoreductive therapy (n = 14), or both (n = 9). At a median follow-up of 5.1 years (range 0.1-28.6), recurrent CVT was documented in three (4%) patients while recurrent arterial and venous thromboses and major hemorrhage were recorded in 11%, 9% and 14%, respectively. Follow-up neurological assessment revealed headaches (n = 9), vision loss (n = 1) and cognitive impairment (n = 1). The current study lends clarity to MPN-associated CVT and highlights its close association with JAK2V617F, younger age and female gender. Clinical features that distinguish COVID vaccine-related CVT from MPN-associated CVT include, in the latter, lower likelihood of concurrent venous thromboses and intracerebral hemorrhage; as a result, MPN-associated CVT was not fatal.


Subject(s)
COVID-19 Vaccines/adverse effects , COVID-19/prevention & control , Intracranial Thrombosis/etiology , Myeloproliferative Disorders/complications , Venous Thrombosis/etiology , Adolescent , Adult , Aged , Aged, 80 and over , Female , Humans , Intracranial Thrombosis/genetics , Janus Kinase 2/genetics , Male , Middle Aged , Myeloproliferative Disorders/genetics , Point Mutation , Polycythemia Vera/complications , Polycythemia Vera/genetics , Primary Myelofibrosis/complications , Primary Myelofibrosis/genetics , Retrospective Studies , Thrombocythemia, Essential/complications , Thrombocythemia, Essential/genetics , Venous Thrombosis/genetics , Young Adult
17.
FEBS Lett ; 595(18): 2366-2382, 2021 09.
Article in English | MEDLINE | ID: covidwho-1363633

ABSTRACT

Favipiravir is a broad-spectrum inhibitor of viral RNA-dependent RNA polymerase (RdRp) currently being used to manage COVID-19. Accumulation of mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp may facilitate antigenic drift, generating favipiravir resistance. Focussing on the chain-termination mechanism utilized by favipiravir, we used high-throughput interface-based protein design to generate > 100 000 designs of the favipiravir-binding site of RdRp and identify mutational hotspots. We identified several single-point mutants and designs having a sequence identity of 97%-98% with wild-type RdRp, suggesting that SARS-CoV-2 can develop favipiravir resistance with few mutations. Out of 134 mutations documented in the CoV-GLUE database, 63 specific mutations were already predicted as resistant in our calculations, thus attaining ˜ 47% correlation with the sequencing data. These findings improve our understanding of the potential signatures of adaptation in SARS-CoV-2 against favipiravir.


Subject(s)
Amides/pharmacology , Antiviral Agents/pharmacology , Pyrazines/pharmacology , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , SARS-CoV-2/drug effects , SARS-CoV-2/genetics , Drug Resistance, Viral/genetics , Mutation/genetics , Point Mutation/genetics
18.
J Hematol Oncol ; 14(1): 123, 2021 08 16.
Article in English | MEDLINE | ID: covidwho-1365373

ABSTRACT

Thromboembolism is a frequent cause of severity and mortality in COVID-19. However, the etiology of this phenomenon is not well understood. A cohort of 1186 subjects, from the GEN-COVID consortium, infected by SARS-CoV-2 with different severity was stratified by sex and adjusted by age. Then, common coding variants from whole exome sequencing were mined by LASSO logistic regression. The homozygosity of the cell adhesion molecule P-selectin gene (SELP) rs6127 (c.1807G > A; p.Asp603Asn) which has been already associated with thrombotic risk is found to be associated with severity in the male subcohort of 513 subjects (odds ratio = 2.27, 95% Confidence Interval 1.54-3.36). As the SELP gene is downregulated by testosterone, the odd ratio is increased in males older than 50 (OR 2.42, 95% CI 1.53-3.82). Asn/Asn homozygotes have increased D-dimers values especially when associated with poly Q ≥ 23 in the androgen receptor (OR 3.26, 95% CI 1.41-7.52). These results provide a rationale for the repurposing of antibodies against P-selectin as adjuvant therapy in rs6127 male homozygotes especially if older than 50 or with an impaired androgen receptor.


Subject(s)
COVID-19/genetics , P-Selectin/genetics , Thrombosis/genetics , COVID-19/complications , Down-Regulation , Female , Humans , Male , Middle Aged , Point Mutation , SARS-CoV-2/isolation & purification , Thrombosis/etiology
19.
J Hematol Oncol ; 14(1): 123, 2021 08 16.
Article in English | MEDLINE | ID: covidwho-1357037

ABSTRACT

Thromboembolism is a frequent cause of severity and mortality in COVID-19. However, the etiology of this phenomenon is not well understood. A cohort of 1186 subjects, from the GEN-COVID consortium, infected by SARS-CoV-2 with different severity was stratified by sex and adjusted by age. Then, common coding variants from whole exome sequencing were mined by LASSO logistic regression. The homozygosity of the cell adhesion molecule P-selectin gene (SELP) rs6127 (c.1807G > A; p.Asp603Asn) which has been already associated with thrombotic risk is found to be associated with severity in the male subcohort of 513 subjects (odds ratio = 2.27, 95% Confidence Interval 1.54-3.36). As the SELP gene is downregulated by testosterone, the odd ratio is increased in males older than 50 (OR 2.42, 95% CI 1.53-3.82). Asn/Asn homozygotes have increased D-dimers values especially when associated with poly Q ≥ 23 in the androgen receptor (OR 3.26, 95% CI 1.41-7.52). These results provide a rationale for the repurposing of antibodies against P-selectin as adjuvant therapy in rs6127 male homozygotes especially if older than 50 or with an impaired androgen receptor.


Subject(s)
COVID-19/genetics , P-Selectin/genetics , Thrombosis/genetics , COVID-19/complications , Down-Regulation , Female , Humans , Male , Middle Aged , Point Mutation , SARS-CoV-2/isolation & purification , Thrombosis/etiology
20.
PLoS Comput Biol ; 17(8): e1009284, 2021 08.
Article in English | MEDLINE | ID: covidwho-1341479

ABSTRACT

Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial role in protein engineering and drug design. In this study, we develop GeoPPI, a novel structure-based deep-learning framework to predict the change of binding affinity upon mutations. Based on the three-dimensional structure of a protein, GeoPPI first learns a geometric representation that encodes topology features of the protein structure via a self-supervised learning scheme. These representations are then used as features for training gradient-boosting trees to predict the changes of protein-protein binding affinity upon mutations. We find that GeoPPI is able to learn meaningful features that characterize interactions between atoms in protein structures. In addition, through extensive experiments, we show that GeoPPI achieves new state-of-the-art performance in predicting the binding affinity changes upon both single- and multi-point mutations on six benchmark datasets. Moreover, we show that GeoPPI can accurately estimate the difference of binding affinities between a few recently identified SARS-CoV-2 antibodies and the receptor-binding domain (RBD) of the S protein. These results demonstrate the potential of GeoPPI as a powerful and useful computational tool in protein design and engineering. Our code and datasets are available at: https://github.com/Liuxg16/GeoPPI.


Subject(s)
Amino Acid Substitution , Models, Chemical , Proteins/metabolism , Point Mutation , Protein Binding , Proteins/chemistry , Proteins/genetics
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