Updated SARS-CoV-2 Single Nucleotide Variants and Mortality Association

AbstractSince its outbreak in December 2019, COVID-19 has caused 100,5844,555 cases and 2,167,313 deaths as of Jan 27, 2021. Comparing our previous study of SARS-CoV-2 single nucleotide variants (SNVs) before June 2020, we found out that the SNV clustering had changed considerably since June 2020. Apart from that the group SNVs represented by two non-synonymous mutations A23403G (S: D614G) and C14408T (ORF1ab: P4715L) became dominant and carried by over 95% genomes, a few emerging groups of SNVs were recognized with sharply increased monthly occurrence ratios up to 70% in November 2020. Further investigation revealed that several SNVs were strongly associated with the mortality, but they presented distinct distribution in specific countries, e.g., Brazil, USA, Saudi Arabia, India, and Italy. SNVs including G25088T, T25A, G29861T and G29864A were adopted in a regularized logistic regression model to predict the mortality status in Brazil with the AUC of 0.84. Protein structure analysis showed that the emerging subgroups of non-synonymous SNVs and those mortality-related ones in Brazil were located on protein surface area. The clashes in protein structure introduced by these mutations might in turn affect virus pathogenesis through conformation changes, leading to the difference in transmission and virulence. Particularly, we found that SNVs tended to occur in intrinsic disordered regions (IDRs) of Spike (S) and ORF1ab, suggesting a critical role of SNVs in protein IDRs to determine protein folding and immune evasion.

Download Full-text

Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology

npj Precision Oncology ◽

10.1038/s41698-021-00155-6 ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

Ianthe A. E. M. van Belzen ◽

Alexander Schönhuth ◽

Patrick Kemmeren ◽

Jayne Y. Hehir-Kwa

Keyword(s):

Intratumor Heterogeneity ◽

Precision Oncology ◽

Single Nucleotide Variants ◽

Full Spectrum ◽

Single Nucleotide ◽

Sequencing Technologies ◽

Cancer Genomes ◽

Genomic Aberrations

AbstractCancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a known pathogenic SV used in diagnosis or treatment stratification. However, research into the role of SVs in cancer has been limited due to difficulties in detection. Biological and computational challenges confound SV detection in cancer samples, including intratumor heterogeneity, polyploidy, and distinguishing tumor-specific SVs from germline and somatic variants present in healthy cells. Classification of tumor-specific SVs is challenging due to inconsistencies in detected breakpoints, derived variant types and biological complexity of some rearrangements. Full-spectrum SV detection with high recall and precision requires integration of multiple algorithms and sequencing technologies to rescue variants that are difficult to resolve through individual methods. Here, we explore current strategies for integrating SV callsets and to enable the use of tumor-specific SVs in precision oncology.

Download Full-text

Genetics of Schizophrenia and Bipolar Disorder

10.1093/med/9780190681425.003.0013 ◽

2017 ◽

Author(s):

Alexander Charney ◽

Pamela Sklar

Keyword(s):

Bipolar Disorder ◽

Copy Number ◽

Psychotic Disorders ◽

Copy Number Variants ◽

Nucleotide Polymorphisms ◽

Common Variants ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Number Variation

Schizophrenia and bipolar disorder are the classic psychotic disorders. Both diseases are strongly familial, but have proven recalcitrant to genetic methodologies for identifying the etiology until recently. There is now convincing genetic evidence that indicates a contribution of many DNA changes to the risk of becoming ill. For schizophrenia, there are large contributions of rare copy number variants and common single nucleotide variants, with an overall highly polygenic genetic architecture. For bipolar disorder, the role of copy number variation appears to be much less pronounced. Specific common single nucleotide polymorphisms are associated, and there is evidence for polygenicity. Several surprises have emerged from the genetic data that indicate there is significantly more molecular overlap in copy number variants between autism and schizophrenia, and in common variants between schizophrenia and bipolar disorder.

Download Full-text

2466. What’s Lurking in the Drain? Serial transmission of NDM-1Klebsiella pneumoniae to patients admitted 9 months apart to the same ICU room

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.2144 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S854-S854

Author(s):

Becky A Smith ◽

Amy Mathers ◽

Shireen Kotay ◽

Hardik Parikh ◽

Katie E Barry ◽

...

Keyword(s):

Environmental Samples ◽

Index Patient ◽

Point Prevalence ◽

Secondary Case ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Environmental Investigation ◽

Long Duration ◽

Rectal Colonization

Abstract Background We evaluated the role of an in-room sink in NDM-1 K. pneumoniae (NDMKP) transmission. Methods In October 2017, Infection Prevention (IP) initiated weekly point prevalence rectal screening cultures in 4 ICUs. In 3/2018, IP launched an epidemiologic and environmental investigation following identification of a patient with NDMKP rectal colonization. Environmental samples including swabs of biofilm from drains and water from p-traps were obtained from the in-room sink. Illumina whole-genome sequencing (WGS) was performed on all NDMKP patient and environmental isolates. Single nucleotide variants (SNVs) were identified against the reference Klebsiella pneumoniae strain MLST15 (NZ_CP022127), and isolates within 150 SNVs of each other were considered to be genomically related. Results Two patients were identified with NDMKP infection or colonization between July 2017 and March 2018. The index patient had prolonged hospitalization and developed NDMKP bacteremia on hospital day (HD) 30. Approximately 9 months later, the second patient was admitted to the same ICU room that had been occupied by the index patient for 13 days and was identified to have NDMKP rectal colonization on HD 5. Environmental samples from the in-room sink of the ICU room grew NDMKP. WGS demonstrated relatedness between NDMKP isolates from the 2 patients (112 SNV), the index patient and the sink (52 SNV), and the second patient and the sink (80 SNV). The in-room sink was replaced in 4/18 and no further cases of NDMKP infection or colonization have been identified at DUH in over 12 months. Conclusion We report an NDM-1 K. pneumoniae transmission event possibly related to a contaminated in-room sink drain. Remarkably, 9 months elapsed between the index case and the second case, with no additional interim cases detected on weekly point-prevalence screening or clinical cultures. The long duration of time between and the index patient, secondary case, and sink culture may explain why WGS showed relatedness but not identical clones. Education around sink use, design, and more effective cleaning strategies are needed to mitigate environment-to-patient transmission of CRO. Disclosures All authors: No reported disclosures.

Download Full-text

Implementing the Team Approach in Higher Education

Industry and Higher Education ◽

10.5367/000000008785201775 ◽

2008 ◽

Vol 22 (4) ◽

pp. 245-251 ◽

Cited By ~ 1

Author(s):

Tracy M. Lara ◽

Aaron W. Hughey

Keyword(s):

Higher Education ◽

Needs Assessment ◽

Higher Education Administration ◽

Critical Role ◽

Education Administration ◽

Team Approach ◽

Academic Environment ◽

Team Efficacy ◽

The Difference

Many companies have implemented the team approach as a way to empower their employees in an effort to enhance productivity, quality and overall profitability. While application of the concept to higher education administration has been limited, colleges and universities could benefit from the team approach if implemented appropriately and conscientiously. The authors discuss some of the issues and concerns that are relevant to implementing the team approach in an academic environment. Suggestions for implementing teams in higher education are provided, including the difference between the team approach and traditional administration, the importance of a preliminary needs assessment, the development of an implementation plan, the critical role of leadership, dealing with issues of assessment and accountability, and the concept of team efficacy.

Download Full-text

The role of single-nucleotide variants of the energy metabolism-linked genes SIRT3, PPARGC1A and APOE in amyotrophic lateral sclerosis risk

Genes & Genetic Systems ◽

10.1266/ggs.16-00023 ◽

2016 ◽

Vol 91 (6) ◽

pp. 301-309 ◽

Cited By ~ 2

Author(s):

Diego Albani ◽

Elisabetta Pupillo ◽

Elisa Bianchi ◽

Armando Chierchia ◽

Rosalba Martines ◽

...

Keyword(s):

Amyotrophic Lateral Sclerosis ◽

Energy Metabolism ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Lateral Sclerosis

Download Full-text

Critical Negatively Charged Residues Are Important for the Activity of SARS-CoV-1 and SARS-CoV-2 Fusion Peptides

10.1101/2021.11.03.467161 ◽

2021 ◽

Author(s):

Alex L. Lai ◽

Jack H. Freed

Keyword(s):

Critical Role ◽

Binding Energies ◽

Host Cells ◽

Topological Model ◽

Pseudotyped Virus ◽

Fusion Peptides ◽

Human Pathogens ◽

Charged Residues ◽

The Difference

AbstractCoronaviruses are a major infectious disease threat, and include the human pathogens of zoonotic origin SARS-CoV (“SARS-1”), SARS-CoV-2 (“SARS-2”) and MERS-CoV (“MERS”). Entry of coronaviruses into host cells is mediated by the viral spike (S) protein. Previously, we identified that the domain immediately downstream of the S2’ cleavage site is the bona fide FP (amino acids 798-835) for SARS-1 using ESR spectroscopy technology. We also found that the SARS-1 FP induces membrane ordering in a Ca2+ dependent fashion. In this study, we want to know which residues are involved in this Ca2+ binding, to build a topological model and to understand the role of the Ca2+. We performed a systematic mutation study on the negatively charged residues on the SARS-1 FP. While all six negatively charged residues contributes to the membrane ordering activity of the FP to some extent, D812 is the most important residue. We provided a topological model of how the FP binds Ca2+ ions: both FP1 and FP2 bind one Ca2+ ion, and there are two binding sites in FP1 and three in FP2. We also found that the corresponding residue D830 in the SARS-2 FP plays a similar critical role. ITC experiments show that the binding energies between the FP and Ca2+ as well as between the FP and membranes also decreases for all mutants. The binding of Ca2+, the folding of FP and the ordering activity correlated very well across the mutants, suggesting that the function of the Ca2+ is to help to folding of FP in membranes to enhance its activity. Using a novel pseudotyped virus particle (PP)-liposome methodology, we monitored the membrane ordering induced by the FPs in the whole S proteins in its trimer form in real time. We found that the SARS-1 and SARS-2 PPs also induce membrane ordering as the separate FPs do, and the mutations of the negatively charged residues also greatly reduce the membrane ordering activity. However, the difference in kinetic between the PP and FP indicates a possible role of FP trimerization. This finding could lead to therapeutic solutions that either target the FP-calcium interaction or block the Ca2+ channel to combat the ongoing COVID-19 pandemic.

Download Full-text

Role of a genetic variation in the microRNA-4421 binding site of ERP29 regarding risk of oropharynx cancer and prognosis

Scientific Reports ◽

10.1038/s41598-020-73675-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Juliana Carron ◽

Ana Paula Dalla Costa ◽

José Augusto Rinck-Junior ◽

Fernanda Viviane Mariano ◽

Benilton de Sá Carvalho ◽

...

Keyword(s):

Binding Site ◽

Luciferase Reporter ◽

Data Validation ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Kaplan Meier ◽

Genome Wide ◽

Variant Genotype ◽

Stage 1

Abstract We conducted a two-stage association study on patients with oropharynx (OP) squamous cell carcinoma (SCC) and healthy controls to identify single nucleotide variants (SNVs) located at the microRNA (miR)-binding sites of carcinogenesis genes associated with risk and prognosis of the disease. In stage 1, 49 patients and 49 controls were analyzed using Genome-Wide Human SNV Arrays to identify variants in the 3′-untranslated region (3′-UTR) of carcinogenesis-related genes, and one SNV was selected for data validation in stage 2 by TaqMan assays in 250 OPSCC patients and 250 controls. The ERP29 c.*293A > G (rs7114) SNV located at miR-4421 binding site was selected for data validation among 46 SNVs. The ERp29 and miR-4421 levels were evaluated by quantitative-PCR and Western blotting. Interaction between miR-4421 with 3′-UTR of ERP29 was evaluated by luciferase reporter assay. Event-free survival (EFS) was calculated by Kaplan–Meier and Cox methods. ERP29 GG variant genotype was more common in OPSCC patients than in controls (6.4% vs 3.6%, p = 0.02; odds ratio: 5.67; 95% confidence interval (CI) 1.27–25.26). Shorter EFS were seen in the base of tongue (BT) SCC patients with GG genotype (0.0% vs 36.2%, p = 0.01; hazard ratio: 2.31; 95% CI: 1.03–5.15). Individuals with ERP29 AG or GG genotypes featured lower levels of ERP29 mRNA (p = 0.005), ERp29 protein (p < 0.001) and higher levels of miR-4421 (p = 0.02). The miR-4421 showed more efficient binding with 3′-UTR of the variant G allele when compared with wild-type allele A (p = 0.001). Our data suggest that ERP29 rs7114 SNV may alter the risk and prognosis of OPSCC due to variation in the ERp29 production possibly modulated by miR-4421.

Download Full-text

A Critical Role of Non-active Site Residues on Cyclooxygenase Helices 5 and 6 in the Control of Prostaglandin Stereochemistry at Carbon 15

Journal of Biological Chemistry ◽

10.1074/jbc.m704950200 ◽

2007 ◽

Vol 282 (38) ◽

pp. 28157-28163 ◽

Cited By ~ 3

Author(s):

Karin Valmsen ◽

William E. Boeglin ◽

Reet Järving ◽

Ivar Järving ◽

Külliki Varvas ◽

...

Keyword(s):

Amino Acid ◽

Active Site ◽

Amino Acid Sequence Identity ◽

Critical Role ◽

Site Directed Mutagenesis ◽

Single Amino Acid ◽

Active Site Residues ◽

The Core ◽

The Difference

The correct stereochemistry of prostaglandins is a prerequisite of their biological activity and thus is under a strict enzymatic control. Recently, we cloned and characterized two cyclooxygenase (COX) isoforms in the coral Plexaura homomalla that share 97% amino acid sequence identity, yet form prostaglandins with opposite stereochemistry at carbon 15. The difference in oxygenation specificity is only partially accounted for by the single amino acid substitution in the active site (Ile or Val at position 349). For further elucidation of residues involved in the C-15 stereocontrol, a series of sequence swapping and site-directed mutagenesis experiments between 15R- and 15S-COX were performed. Our results show that the change in stereochemistry at carbon 15 of prostaglandins relates mainly to five amino acid substitutions on helices 5 and 6 of the coral COX. In COX proteins, these helices form a helix-turn-helix motif that traverses through the entire protein, contributing to the second shell of residues around the oxygenase active site; it constitutes the most highly conserved region where even slight changes result in loss of catalytic activity. The finding that this region is among the least conserved between the P. homomalla 15S- and 15R-specific COX further supports its significance in maintaining the desired prostaglandin stereochemistry at C-15. The results are particularly remarkable because, based on its strong conservation, the conserved middle of helix 5 is considered as central to the core structure of peroxidases, of which COX proteins are derivatives. Now we show that the same parts of the protein are involved in the control of oxygenation with 15R or 15S stereospecificity in the dioxygenase active site.

Download Full-text

A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome

PLoS ONE ◽

10.1371/journal.pone.0261014 ◽

2022 ◽

Vol 17 (1) ◽

pp. e0261014

Author(s):

Carlos Arana ◽

Chaoying Liang ◽

Matthew Brock ◽

Bo Zhang ◽

Jinchun Zhou ◽

...

Keyword(s):

Virus Genome ◽

Positive Control ◽

Nasopharyngeal Swab ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Spike Gene ◽

Synonymous Mutations ◽

Variant Detection ◽

Variant Analysis ◽

New Mutations

High viral transmission in the COVID-19 pandemic has enabled SARS‐CoV‐2 to acquire new mutations that may impact genome sequencing methods. The ARTIC.v3 primer pool that amplifies short amplicons in a multiplex-PCR reaction is one of the most widely used methods for sequencing the SARS-CoV-2 genome. We observed that some genomic intervals are poorly captured with ARTIC primers. To improve the genomic coverage and variant detection across these intervals, we designed long amplicon primers and evaluated the performance of a short (ARTIC) plus long amplicon (MRL) sequencing approach. Sequencing assays were optimized on VR-1986D-ATCC RNA followed by sequencing of nasopharyngeal swab specimens from fifteen COVID-19 positive patients. ARTIC data covered 94.47% of the virus genome fraction in the positive control and patient samples. Variant analysis in the ARTIC data detected 217 mutations, including 209 single nucleotide variants (SNVs) and eight insertions & deletions. On the other hand, long-amplicon data detected 156 mutations, of which 80% were concordant with ARTIC data. Combined analysis of ARTIC + MRL data improved the genomic coverage to 97.03% and identified 214 high confidence mutations. The combined final set of 214 mutations included 203 SNVs, 8 deletions and 3 insertions. Analysis showed 26 SARS-CoV-2 lineage defining mutations including 4 known variants of concern K417N, E484K, N501Y, P618H in spike gene. Hybrid analysis identified 7 nonsynonymous and 5 synonymous mutations across the genome that were either ambiguous or not called in ARTIC data. For example, G172V mutation in the ORF3a protein and A2A mutation in Membrane protein were missed by the ARTIC assay. Thus, we show that while the short amplicon (ARTIC) assay provides good genomic coverage with high throughput, complementation of poorly captured intervals with long amplicon data can significantly improve SARS-CoV-2 genomic coverage and variant detection.

Download Full-text

Intra-host evolution provides for continuous emergence of SARS-CoV-2 variants

10.1101/2021.05.08.21256775 ◽

2021 ◽

Author(s):

Justin Landis ◽

Razia Moorad ◽

Linda J. Pluta ◽

Carolina Caro-Vegas ◽

Ryan P. McNamara ◽

...

Keyword(s):

Public Health ◽

Sequence Evolution ◽

Clinical Progression ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Viral Genomes ◽

Synonymous Mutations ◽

Health Measures ◽

Broad Public Health ◽

Host Evolution

Variants of concern (VOC) in SARS-CoV-2 refer to viral genomes that differ significantly from the ancestor virus and that show the potential for higher transmissibility and/or worse clinical progression. VOC have the potential to disrupt ongoing public health measures and vaccine efforts. Yet, little is known regarding how frequently different viral variants emerge and under what circumstances. We report a longitudinal study to determine the degree of SARS-CoV-2 sequence evolution in 94 COVID-19 cases and to estimate the frequency at which highly diverse variants emerge. 2 cases accumulated 9 single-nucleotide variants (SNVs) over a two-week period and 1 case accumulated 23 SNVs over a three-week period, including three non-synonymous mutations in the Spike protein (D138H, E554D, D614G). We estimate that in 2% of COVID cases, viral variants with multiple mutations, including in the Spike glycoprotein, can become the dominant strains in as little as one month of persistent in patient virus replication. This suggests the continued local emergence of VOC independent of travel patterns. Surveillance by sequencing for (i) viremic COVID-19 patients, (ii) patients suspected of re-infection, and (iii) patients with diminished immune function may offer broad public health benefits.

Download Full-text