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Background. Using a computational approach, NL-CVX1 was developed by Neoleukin Therapeutics, Inc. to create a de novo protein that both blocks SARS-CoV-2 infection and is highly resilient to viral escape. In this study we evaluated the efficacy of NL-CVX1 against variants of the original SARS-CoV-2 strain, including important viral variants of concern (VOC) such as B.1.1.7, B.1.351, and P.1. Methods. The relative binding affinity of NL-CVX1 to the SARS-CoV-2 viral spike protein of VOC was measured using biolayer interferometry (Octet). A competitive ELISA measured the ability of NL-CVX1 to compete with hACE2 for binding to the receptor binding domain (RBD) of the SARS-CoV-2 S protein from the original strain and VOC. The activity of NL-CVX1 in preventing viral infection was assessed by evaluating the cytopathic effects (CPE) of SARS-CoV-2 in a transmembrane protease, serine 2-expressing Vero E6 cell line (Vero E6/TMPRSS2) and determining the viral load using quantitative real-time reverse transcriptase polymerase chain reaction in infected cells. A K18hACE2 mouse model of SARS CoV-2 infection was used to study the dose-response of NL-CVX1 anti-viral activity in vivo. Results. NL-CVX1 binds the RBD of different VOC of SARS-CoV-2 at low nanomolar concentrations (Fig 1;Kd < 1-~5 nM). When competing with hACE2, NL-CVX1 achieved 100% inhibition against hACE2 binding to the RBD of different VOC with IC50s values ranging from 0.7-53 nM (Fig 2). NL-CVX1 neutralized the B.1.1.7 variant as efficiently as the original strain in Vero E6/TMPRSS2 cells, with EC50 values of 16 nM and 101. 2 nM, respectively (Fig 3). In mice, we found that a single intranasal dose of 100 μg NL-CVX1 prevented clinically significant SARS-CoV-2 infection and protected mice from succumbing to infection. Results from additional in vitro and in vivo experiments to be conducted this summer will be presented. Figure 1. NL-CVX1 binds the RBD from multiple strains of SARS-CoV-2 at low nanomolar concentrations. Figure 2. NL-CVX1 achieves 100% inhibition against all strains tested, including SARS-CoV-2 VOC. Figure 3. NL-CVX1 neutralizes the B.1.1.7 variant as efficiently as the original SARSCoV-2 strain. Conclusion. In vitro and in vivo data (Fig 4) demonstrate that NL-CVX1 is a promising drug candidate for the prevention and treatment of COVID-19. As a hACE2 mimetic, it is resilient to antibody escape mutations found in SARS-CoV-2 VOC. NL-CVX1 further demonstrates the power and utility of de novo protein design for developing proteins as human therapeutics. Figure 4. NL-CVX1 is effective in preventing clinically significant SARS-CoV-2 viral infection in a K18hACE2 mouse model.
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Background. Over 600,000 COVID-19 cases, including >7000 deaths reported to MN Dept of Health (MDH) by June 1, 2021. Clinical trials demonstrated high effectiveness of COVID vaccines. We assessed COVID-19 cases among fully vaccinated residents [vaccine breakthrough (VB) cases]. Methods. COVID-19 VB cases were MN residents with completed COVID-19 vaccination series ≥14 days prior to symptom onset or positive for SARS-CoV-2 by nucleic acid amplification or antigen test. COVID-19 cases were reported to MDH and COVID-19 vaccinations reported to the MN Immunization Information Connection (MIIC). COVID-19 cases were matched to MIIC to identify VB and interviewed;medical records of hospitalized cases were reviewed. Available VB case specimens underwent whole genome sequencing (WGS) at MDH or collaborating lab. Results. Jan 19 - June 1, 2021, 2765 VB cases were reported among >2.45 million fully vaccinated residents and 147,445 COVID-19 cases. VB case median (MED) age was 52 y (IQR 38, 68), 83% white, 65% female;MED age of fully vaccinated was 55 y (IQR 30, 68), 77% white, 54% female. Of VB cases, 273 (10%) were hospitalized and 32 (1%) died (MED age 74 y;IQR 66, 85). 2212 (80%) VB cases were interviewed;60% reported symptoms;most common were fatigue (53%), rhinorrhea (49%), cough (42%), headache (41%). 35% reported a comorbidity. Of hospitalized VB cases, 120 had completed record reviews. 64 were admitted for COVID-19 related illness (MED age 74 y, IQR:65, 83) including 27 admitted to ICU (MED age 71 y, IQR: 65, 83). 90% (108) reported a comorbidity, most common being chronic metabolic conditions (46%), obesity (45%), renal disease (31%) and chronic lung disease (26%);27 were immunocompromised (not mutually exclusive), including immunosuppressive therapy (15), hematological malignancy (9), other cancer (11), and organ transplant recipients (8). Of 604 VB case specimens, 79% were B.1.1.7, 9% B.1.427/429, 3% P.1, and 2% B.1.351;lineage distribution was similar to overall 24,157 MN SARS-CoV2 WGS data. Conclusion. Identified VB cases were 0.1% of those vaccinated and < 2% of total cases reported in the time period. COVID-19 vaccines are an important tool in preventing COVID-19. Additional surveillance, including WGS and case characteristics will be useful to monitor VB.
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Background. In December 2020, B.1.1.7 lineage of SARS-CoV-2 was first detected in the United States and has since become the dominant lineage. Previous investigations involving B.1.1.7 suggested higher rates of transmission relative to non-B.1.1.7 lineages. We conducted a household transmission investigation to determine the secondary infection rates (SIR) of B.1.1.7 and non-B.1.1.7 SARS-CoV-2 lineages. Methods. From January-April 2021, we enrolled members of households in San Diego County, CA, and Denver, CO metropolitan area (Tri-County), with a confirmed SARS-CoV-2 infection in a household member with illness onset date in the previous 10 days. CDC investigators visited households at enrollment and 14 days later at closeout to obtain demographic and clinical data and nasopharyngeal (NP) samples on all consenting household members. Interim visits, with collection of NP swabs, occurred if a participant became symptomatic during follow-up. NP samples were tested for SARS-CoV-2 using TaqPath™ RT-PCR test, where failure to amplify the spike protein results in S-Gene target failure (SGTF) may indicate B.1.1.7 lineage. Demographic characteristics and SIR were compared among SGTF and non-SGTF households using two-sided p-values with chi-square tests;95% confidence intervals (CI) were calculated with Wilson score intervals. Results. 552 persons from 151 households were enrolled. 91 (60%) households were classified as SGTF, 57 (38%) non-SGTF, and 3 (2%) indeterminant. SGTF and non-SGTF households had similar sex distribution (49% female and 52% female, respectively;P=0.54) and age (median 30 years, interquartile range (IQR 14-47) and 31 years (IQR 15-45), respectively). Hispanic people accounted for 24% and 32% of enrolled members of SGTF and non-SGTF households, respectively (p=0.04). At least one secondary case occurred in 61% of SGTF and 58% of non-SGTF households (P=0.66). SIR was 52% (95%[CI] 46%-59%) for SGTF and 45% (95% CI 37%-53%) for non-SGTF households (P=0.18). Conclusion. SIRs were high in both SGTF and non-SGTF households;our findings did not support an increase in SIR for SGTF relative to non-SGTF households in this setting. Sequence confirmed SARS-CoV-2 samples will provide further information on lineage specific SIRs.
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Background. Molnupiravir (MOV, MK-4482, EIDD-2801) is an orally administered prodrug of N-hydroxycytidine (NHC, EIDD-1931), a nucleoside with broad antiviral activity against a range of RNA viruses. MOV acts by driving viral error catastrophe following its incorporation by the viral RdRp into the viral genome. Given its mechanism of action, MOV activity should not be affected by substitutions in the spike protein present in SARS-CoV-2 variants of concern which impact efficacy of therapeutic neutralizing antibodies and vaccine induced immunity. We characterized MOV activity against variants by assessing antiviral activity in vitro and virologic response from the Phase 2/3 clinical trials (MOVe-In, MOVe-Out) for treatment of COVID-19. Methods. MOV activity against several SARS-CoV-2 variants, was evaluated in an in vitro infection assay. Antiviral potency of NHC (IC50) was determined in Vero E6 cells infected with virus at MOI ~0.1 by monitoring CPE. Longitudinal SARSCoV-2 RNA viral load measures in participants enrolled in MOVe-In and MOVe-Out were analyzed based on SARS-CoV-2 genotype. Sequences of SARS-CoV-2 from study participants were amplified from nasal swabs by PCR and NGS was performed on samples with viral genome RNA of >22,000 copies/ml amplified by primers covering full length genome with Ion Torrent sequencing to identify clades represented in trial participants. SARS-CoV-2 clades were assigned using clade.nextstrain.org. Results. In vitro, NHC was equally effective against SARS-CoV-2 variants B.1.1.7 (20I), B.1351 (20H), and P1 (20J), compared with the original WA1 (19B) isolate. In clinical trials, no discernable difference was observed in magnitude of viral response measured by change from baseline in RNA titer over time across all clades represented including 20A through 20E and 20G to 20I. No participants at the time of the study presented with 20F, 20J, or 21A. Conclusion. Distribution of clades in participants in MOVe-In and MOVe-Out was representative of those circulating globally at the time of collection (Oct 2020 -Jan 2021). Both in vitro and clinical data suggest that spike protein substitutions do not impact antiviral activity of MOV and suggest its potential use for the treatment of SARS-CoV-2 variants.
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Background. Nucleic acid amplification testing (NAAT) is an essential tool both for biomedical research and for clinical molecular diagnostics. Currently, there are multiple NAAT platforms available, each offering certain performance and utility advantages and disadvantages as compared to each other. Next generation NAAT platforms aim to deliver increased target detection sensitivity and specificity, low limits of target detection, quantitative high multiplex target capacity, rapid time to results, and simple sample-to-answer workflow. Methods. Here we describe the Torus Synestia System, a NAAT platform capable of rapid, highly multiplexed amplification and detection of both DNA and RNA targets. The platform comprises a small, portable (~ 2kg) amplification and detection device and a disposable single-use cartridge housing a PCR amplification chamber with an integrated label-free microarray for real-time data acquisition and interpretation. The platform offers a 30-min turnaround time with a detection limit of 10 DNA/RNA molecules per assay and single nucleotide discrimination. Results. We demonstrate the Synestia System performance and utility with three distinct molecular applications: 1) detection of 20 genetic loci and 30 single nucleotide polymorphisms in human genomic DNA;2) detection and genotyping of 43 unique bacterial species associated with human urinary tract infections;and 3) detection and profiling human respiratory viral pathogens including SARS-CoV-1/2, seasonal coronaviruses, Influenza A/B, and human respiratory syncytial viruses. In addition, the single-nucleotide specificity of our label-free microarray probes allowed for robust identification and discrimination of newly emerging SARS-CoV-2 lineages, such as B.1.1.7 (a.k.a. UK), B.1.351 (a.k.a. South African), P.1 (a.k.a. Brazilian), and B.1.617 (a.k.a. Indian). Conclusion. The Torus Synestia System has broad applicability in both clinical and research environments. We are confident that the Torus Synestia System will revolutionize syndromic diagnostics at the point of care (PoC) and lead to improved response times during future epidemic and pandemic pathogen outbreaks.
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Background. In a Phase 3 trial, the Janssen COVID-19 vaccine, Ad26.COV2.S, showed robust efficacy against severe-critical COVID-19 in countries where different SARS-CoV-2 variants were circulating. We evaluated Ad26.COV2.S-elicited antibody neutralizing activity against variants of concern (VOC) B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta) in sera from participants in clinical trials following a single dose of Ad26.COV2.S. Methods. Neutralizing activities of Ad26.COV2.S (given at a dose level of 5 x 1010 viral particles [vp]) against VOC were assessed by wild-type virus neutralizing (wtVNA) and pseudovirion neutralization (psVNA) assays in sera from participants in Phase 1/2a and Phase 3 clinical trials, respectively. Geometric mean titers (GMTs) were determined at Days 29 and 71 after vaccination. Results. In serum samples from Phase 1/2a participants (n = 6), at Day 29 after 1 dose of Ad26.COV2.S, wtVNA titers against VOC were lower than for the original strain (GMT = 573), with GMT = 65, 14, and 15 for Alpha, Beta, and Delta, respectively, representing 8.8-, 40.9-, and 37.7-fold decreases. By Day 71 after vaccination (n = 14), fold differences between the original strain (GMT = 375) and VOC (GMT = 113, 27, and 28) were smaller (3.3-, 13.9-, and 13.4-fold) than at Day 29, suggestive of B-cell maturation (Figure 1). Day 71 titers against the Delta variant were maintained for at least 8 months following a single dose of Ad26.COV2.S (5 x 1010 vp). In serum samples from Phase 3 participants (n = 8), psVNA titers against VOC were lower than the original strain at Day 71 after vaccination, with the lowest titers observed for the Beta variant (3.6-fold decrease vs original strain). Smaller reductions in Nab titers for VOC were observed in the psVNA assay compared to wtVNA. Conclusion. Ad26.COV2.S-elicited serum neutralizing activity against VOC showed an overall decrease in titers relative to the original strain that was largest for the Beta variant, even though vaccine efficacy against severe-critical COVID-19 was maintained in countries where these variants were circulating versus in countries where they were not circulating. Over time, titers against variants increased, suggesting B-cell affinity maturation leading to increasing coverage of VOC.
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Myelodysplastic syndromes (MDS) represent a spectrum of clonal bone marrow neoplasms from low risk disease through to those transforming into acute myeloid leukaemia. The COVID-19 pandemic has presented a great risk to those with hematological malignancies who are at higher risk of severe disease and death than the general population. Previous studies looking at the immune response to influenza vaccination in those with MDS had shown promising results, with immune responses not differing from those of healthy family members. Whilst some data exist to reassure the MDS community that majority of patients show seroconversion following Covid-19 vaccination, little data exists on their neutralizing capacity or post vaccination T-cell responses in this cohort. In addition, the majority of patients in these studies received BNT162b2 and there is little published data on vaccine response to the ChAdOx1 nCoV-19 vaccine. We have investigated the humoral and T-cell response of 39 patients with MDS two to four weeks following Covid-19 booster vaccination with BNT162b2 or ChAdOx1 nCoV-19 through the SOAP study (Sars-cov-2 fOr cAncer Patients, IRAS project ID:282337). Plasma and PBMCs from MDS cases and healthy controls have been collected, and are being assessed for both humoral and cellular responses to SARS_CoV_2, the alpha (B.1.1.7) and delta (B.1.617.2) variants. Humoral responses will be assessed using ELISA (peptide binding) and functional viral neutralization assays. Cellular responses will be assessed using IFNy ELISPOT and flow cytometry (CD25 and CD69 expression) after 24h peptide stimulation. All data at time point 1 (2 - 4 weeks following booster vaccination) have been collected and will subsequently be collected at 6 months and 12 months post-vaccination. We also report on the safety data for these vaccines within this patient population. Of this cohort 64% were male with a median age of 65 years (range 21-84). 54% received vaccination with ChAdOx1 nCoV-19 and 44% received BNT162b2 (2% unrecorded). The vaccines were well tolerated with no serious adverse events to date. The mean interval between doses was 70.7 days (range 50 - 90 days). 71% of the cohort were receiving no disease modifying therapy at the time of vaccination, half of whom were receiving supportive therapy and the other half no intervention for their MDS. Of those receiving disease modifying therapy;5 were receiving azacitidine, (1 in conjunction with low-dose cytarabine) and 3 ciclosporin. We will report the largest study of the humoral and T-cell mediated response to the Covid-19 vaccine in MDS patients to date. This will include cellular response to the delta variant and immunogenicity of both the BNT162b2 and ChAdOx1 nCoV-19 vaccines. Given the vulnerability of these patients to severe disease, investigating the immune response to the vaccines begins to build an evidence base for advising MDS patients on their ongoing risk of infection during the pandemic and going forward. The SOAP study will reassess the immune response at 6 and 12 months post-vaccination to continue to investigate post-vaccine immunity in this cohort. Disclosures: Kulasekararaj: F. Hoffmann-La Roche Ltd.: Consultancy, Honoraria, Speakers Bureau;Apellis: Consultancy;Akari: Consultancy, Honoraria, Speakers Bureau;Biocryst: Consultancy, Honoraria, Speakers Bureau;Achilleon: Consultancy, Honoraria, Speakers Bureau;Alexion: Consultancy, Honoraria, Speakers Bureau;Ra Pharma: Consultancy, Honoraria, Speakers Bureau;Amgen: Consultancy, Honoraria, Speakers Bureau;Novartis: Consultancy, Honoraria, Speakers Bureau;Celgene: Consultancy, Honoraria, Research Funding, Speakers Bureau;Alexion, AstraZeneca Rare Disease Inc.: Consultancy, Honoraria, Other: Travel support. Patten: JANSSEN: Honoraria;NOVARTIS: Honoraria;GILEAD SCIENCES: Honoraria, Research Funding;ROCHE: Research Funding;ASTRA ZENECA: Honoraria;ABBVIE: Honoraria.
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The current global pandemic (COVID-19) caused by the new Betacoronavirus SARS-CoV-2 is characterized by successive waves of infection due to new variants that include mutations in the gene encoding the Spike protein, the main target of the nucleic acidbased vaccines. In fact, as of autumn 2020, several countries have reported the detection of SARS-CoV-2 variants that have spread more efficiently (referred to as variants of concern by WHO). Such variants include the Alpha variant (English variant, B.1.1.7), the Beta variant (South African variant, B.1.351), the Gamma variant (Brazilian variant, P.1), and the more recent Delta variant (Indian variant, B.1.617. 2). Therefore, it is pivotal to monitor the virus and the onset of SARSCoV-2 variants characterized by high transmissibility or reduced susceptibility to neutralizing antibodies induced by vaccination.Surveillance of genomic variants is currently based on sequencing of viral genomes performed on a random fraction of samples positive by molecular test. The sequencing of 228 SARS-CoV-2 positive samples by ASUR Marche Area Vasta 1 (Fano-Pesaro-Urbino) from February to June 2021 highlighted the progressive increase of variants (mainly B.1.1.7 and to a lesser extent P.1) from early February until March 18th. From March 18th onwards, only variants B.1.1.7 and P.1 were detected. DNA sequencing involves high costs and extended analysis time compared to a PCR-based diagnostic test. To rapidly identify the samples containing virus variants to be sequenced for complete characterization, in synergy with the University of Urbino, five rapid tests based on real-time PCR and high-resolution melting (HRM) were designed on the gene encoding the Spike protein. Preliminary results indicated that the sensitivity of the assays was not significantly different from that of commercial molecular tests. Furthermore, through HRM analysis, it was possible to discriminate amplicons with mutation 1709 C > A causing the amino acid substitution A570D, specific for the alpha variant.
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Purpose of Study Despite the tremendous success of SARSCoV- 2 vaccines, breakthrough infections occur and are being recognized with increasing frequency. It is unclear whether breakthrough infections are the result of host and/or viral factors. We examined clinical and viral genomic data from patients with SARS-CoV-2 infection after vaccination to elucidate factors contributing to breakthrough. Methods Used This study was conducted in the Emory Healthcare (EHC) System. Patients with vaccine breakthrough infection, defined as a positive PCR test ≥14 days after the final dose of an FDA approved vaccine, were identified by both routine surveillance and notification by treating clinicians. Vaccination status was obtained from the Georgia Registry of Immunization Transactions and Services records by the Georgia Emerging Infections Program. Clinical information was derived from electronic medical records and was compared to data from 2-3 matched controls per case. Residual SARS-CoV-2 positive nasopharyngeal (NP) samples were collected and underwent RNA extraction. SARSCoV- 2 genome sequencing was performed using random-primer cDNA synthesis, Nextera XT library preparation, and Illumina sequencing. Summary of Results Forty vaccine breakthrough cases were identified between March 22 and July 16, 2021. The median time from final vaccine dose to positive COVID-19 test was 91 days (range 15-163). Compared to 94 controls, vaccine breakthrough cases were significantly older (median 57.5 years vs 42.0 years, p<.0001). Individuals over 60 accounted for half of all breakthrough cases, and individuals over 40 accounted for 80%. Immunosuppressed individuals represented 37.5% of breakthrough cases compared to 25% of unvaccinated controls. Rates of symptomatic infection and severe disease leading to hospitalization were similar between cases and controls. There was no difference in SARS-CoV-2 RT-PCR cycle threshold (Ct) between cases (n=32, median Ct=20.7, interquartile range (IQR)- 10.3) and controls (n=94, median Ct=24.0, IQR= 7.0;p=0.34). SARS-CoV-2 genome sequences from 24 cases were compared to 116 baseline surveillance sequences from unvaccinated EHC patients. There was no distinct phylogenetic clustering of vaccine breakthrough cases, and their sequences belonged to the predominant lineage of the time. From March 22-June 19, B.1.1.7 (alpha) accounted for 78% of breakthrough infections and 77% of surveillance sequences. From June 20-July 16, B.1.617.2 (delta) accounted for 86% of breakthrough infections and 72% of surveillance sequences. No spike mutations or deletions were associated with vaccine breakthrough infections. Conclusions Overall, our findings suggest that host factors, such as older age and immunosuppression, play a more important role than viral factors in SARS-CoV-2 vaccine breakthrough infections. Further studies are needed to understand the potential impacts of waning immunity or poor immunogenicity in individuals who experience vaccine breakthrough infections.
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Emergence of novel SARS-CoV-2 variants has been an important source of concern since the onset of the COVID-19 pandemic. Variants of Concern (VoC) carry important mutations especially in the SARS-CoV-2 Spike protein that render the virus more transmissible. The N501Y mutation was first defined in the B.1.1.7. lineage that was identified in the UK and is also shared with other VoCs including P.1 and B.1.351 lineages from Brazil and South Africa. Variants of SARS-CoV-2 have been reported to affect transmissibility of the virus, have an impact on vaccine effectiveness and evade viral diagnostic tests. In this context, monitoring of the circulating SARS-CoV-2 variants bearing mutations represents a major requirement for a public health response in a country. We aimed to investigate the prevalence of SARS-CoV-2 positive samples bearing the N501Y mutation in Northern Cyprus between November 2020 and March 2021. All samples that were identified as SARS-CoV-2 positive between these dates were screened for the presence of N501Y mutation by reverse transcription quantitative PCR (RT-qPCR) technique. Our results indicate that while no samples that contain the N501Y mutation was detected in November and December 2020, the proportion of N501Y bearing variants significantly increased from January through March 2021 (45.2%-69.2%) and became the dominant lineage in Northern Cyprus. These results highlight an alarming situation that require strict governmental measures to minimize COVID-19 transmission, morbidity, and mortality in the country.
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Background: The SARS-CoV-2 B.1.1.7 variant, also known as the UK or alpha variant, carries the spike 69/70 deletion mutation and has been reported to be more contagious and possibly more virulent than other variants. This study examines follow-up cardiovascular outcomes for patients infected with deletion-carrying SARS-CoV-2 alpha variant. Methods: From October 2020 to May 2021, all positive SARS-CoV-2 samples at Intermountain Healthcare were tested for the 69/70 deletion (n=92822). Patient characteristics, COVID-19 treatments, and follow-up outcomes were extracted from Intermountain records. Cox hazard regression analysis with multivariable adjustment was used to determine risk of subsequent major cardiovascular adverse event outcomes (MACE), which included all-cause death, heart failure (HF), and hospitalization for coronary artery disease (CAD) or atrial fibrillation (AF). Results: Overall, 4.2% of patients testing positive for the SARS-CoV-2 virus carried the deletion mutation with prevalence increasing with time, ranging from 1.3% in October to 61.0% in May. Baseline characteristics, treatments, and outcomes stratified by non-mutant and deletion mutation status are shown in the Table. While the mutation did result in higher rates of COVID hospitalization (adjusted OR=1.68, p<0.001), there was no difference in overall MACE after adjustment by baselinecharacteristics and risk factors. There was a non-significant trend toward an increased rate of allcause death in patients carrying the mutant variant (adjusted HR=1.90, p=0.12). Conclusions: The SARS-CoV-2 deletion mutant, while resulting in an increased risk of COVID hospitalization and a trend toward increased death, did not increase the risk of subsequent CVD. Because of the recent emergence of the variant the long-term effects are not known. Thus, it remains important to minimize risk of exposure. Moreover, long-term surveillance of subsequent CVD risk is warranted.
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The new COVID-19 variants are triggering a fresh panic all around. Scientists still have not found any closely related identification of these variants in the context of their evolution. The scrupulous deletion/mutations recognized inside the spike protein of the variants are emerging with an amplified pace and are observed to be associated with the alterations in the receptor-binding region (RBD) of the spike protein. This paper highlights the reported mechanistic studies conducted on SARS-CoV-2 mutant variants;the mutant virus's ability in response to the antibody recognition to evade the immune system in humans. The role of cellular immunity in response to its interaction with SARS-CoV-2 variants and importantly the discussion on the antibody-dependent enhancement (ADE) of SARS-CoV-2 disease with therapeutic antibodies and vaccines has been highlighted. It is expected that this may likely be interesting and helpful for readers in clearing all their presumptions related to the spreading severity of the mutant virus strains and more importantly the effectiveness of current and upcoming vaccines for its possible control.
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Introduction During the course of coronavirus disease-2019 (COVID-19) pandemic, many neuropsychiatric manifestations of the disease have been observed while the precise pathophysiology remains unknown [1]. New variants of coronavirus such as the 501.V2 and B.1.1.7 have emerged and obscurities in pathogenesis have increased even further with these variants. Here, we describe a patient with long-term effects of COVID-19, manifesting first episode psychosis accompanied by Cotard's Syndrome (CS) after infection with the B.1.1.7 variant of SARS-CoV-2. Case A 41-year-old female with no adverse medical history was admitted to the emergency department with symptoms of loss of smell, myalgia and sore throat and COVID-19 infection was confirmed by a positive RT-PCR test result for the B.1.1.7 variant of coronavirus. Two months after the completion of treatment for COVID-19, the patient started to have thoughts of being annihilated by viral occupation of her body and of her nervous system getting decomposed. The patient's family brought her to the psychiatric emergency department. The patient was found to have strong suicidal ideations, referential thoughts, belief of being physically dead and her children being in danger of obliteration by COVID-19. Clinical evaluation of the mental state of the patient was significant for decreased speech output and speed as well as psychomotor activity. Nihilistic, persecutory and referential delusions with no insight were recorded. Upon hospitalization and treatment with olanzapine 20mg/day orally and electroconvulsive therapy, her psychiatric symptoms and suicidal ideation ameliorated. The patient was discharged from the hospital with olanzapine 20mg/day orally and she is currently being followed-up in our outpatient clinic. Discussion To the best of our knowledge, this is the first report of a patient who developed CS and psychotic symptoms associated with COVID-19 following infection with a new variant of coronavirus. CS is a rare self-perceptual anomaly with the presentation of nihilistic delusions. While the exact pathogenesis of CS remains unexplained, defective mechanisms of proprioception or interoception may lead to a self-misattribution following a perceptual dysfunction which might trigger CS [2]. Although blood tests indicated no systemic inflammation for the index patient, an indistinct neuroinflammatory process may lead to neurotoxicity that might result in perceptual disruption and CS or psychotic features, as suggested in previous reports [3]. Considering well-described anosmia and ageusia with COVÍD-19 and our case's symptoms after the infection, new variants of SARS-CoV-2 might affect the perceptual pathways. The angiotensin-converting enzyme-2 (ACE-2) receptor which might modulate smell and taste perception, has been identified as a potential viral receptor. Such interaction may disrupt chemosensory perception. Overall, COVID-19 may cause abnormal processing of perceptions. This in turn can lead to anosmia, ageusia and defective proprioception, resulting in self-misattributions as seen in the patient in the current case report who was diagnosed with CS. Clinicians should keep in mind that infections with the rapidly spreading B.1.1.7 variant of SARS-CoV-2 might result in more severe symptoms or long-term consequences of COVID-19 compared to other strains. No conflict of interest
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Objective: SARS-CoV-2 causes the coronavirus disease 2019 (COVID-19) and has spawned a global health crisis. Virus infection can lead to elevated markers of cardiac injury and inflammation associated with a higher risk of mortality. However, it is so far unclear whether cardiovascular damage is caused by direct virus infection or is mainly secondary due to inflammation. Recently, additional novel SARS-CoV-2 variants have emerged accounting for more than 70% of all cases in Germany. To what extend these variants differ from the original strain in their pathology remains to be elucidated. Here, we investigated the effect of the novel SARS-CoV-2 variants on cardiovascular cells. Results: To study whether cardiovascular cells are permissive for SARSCoV-2, we inoculated human iPS-derived cardiomyocytes and endothelial cells from five different origins, including umbilical vein endothelial cells, coronary artery endothelial cells (HCAEC), cardiac and lung microvascular endothelial cells, or pulmonary arterial cells, in vitro with SARS-CoV-2 isolates (G614 (original strain), B.1.1.7 (British variant), B.1.351 (South African variant) and P.1 (Brazilian variant)). While the original virus strain infected iPS-cardiomyocytes and induced cell toxicity 96h post infection (290±10 cells vs. 130±10 cells;p=0.00045), preliminary data suggest a more severe infection by the novel variants. To what extend the response to the novel variants differ from the original strain is currently investigated by phosphoproteom analysis. Of the five endothelial cells studied, only human coronary artery EC took up the original virus strain, without showing viral replication and cell toxicity. Spike protein was only detected in the perinuclear region and was co-localized with calnexin-positive endosomes, which was accompanied by elevated ER-stress marker genes, such as EDEM1 (1.5±0.2-fold change;p=0.04). Infection with the novel SARS-CoV-2 variants resulted in significant higher levels of viral spike compared to the current strain. Surprisingly, viral up-take was also seen in other endothelial cell types (e.g. HUVEC). Although no viral replication was observed (850±158 viral RNA copies at day 0 vs. 197±43 viral RNA copies at day 3;p=0.01), the British SARS-CoV-2 variant B.1.1.7 reduced endothelial cell numbers (0.63±0.03-fold change;p=0.0001). Conclusion: Endothelial cells and cardiomyocytes showed a distinct response to SARS-CoV-2. Whereas cardiomyocytes were permissively infected, endothelial cells took up the virus, but were resistant to viral replication. However, both cell types showed signs of increased toxicity induced by the British SARS-CoV-2 variant. These data suggest that cardiac complications observed in COVID-19 patients might at least in part be based on direct infection of cardiovascular cells. The more severe cytotoxic effects of the novel variants implicate that patients infected with the new variants should be even more closely monitored.
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Context: SARS-CoV-2, a member of family Coronaviridae and the causative agent of COVID-19, is a virus which is transmitted to human and other mammals. Aims: To analyze the B-cell epitope conserved region and viroinformatics-based study of the SARS-CoV-2 lineage from Indonesian B.1.1.7 isolates to invent a vaccine nominee for overcoming COVID-19. Methods: The sequences of seven Indonesian B.1.1.7 isolates, Wuhan-Hu- 1 isolate, and WIV04 isolate were extracted from the GISAID EpiCoV and GenBank, NCBI. MEGA X was employed to understand the transformations of amino acid in the S protein and to develop a molecular phylogenetic tree. The IEDB was implemented to reveal the linear B-cell epitopes. In addition, PEP-FOLD3 web server was utilized to perform peptide modeling, while docking was performed using PatchDock, FireDock, and the PyMOL software. Moreover, in silico cloning was developed by using SnapGene v.3.2.1 software. Results: In this study, the changes of amino acid in all seven Indonesian B.1.1.7 isolates were uncovered. Furthermore, various peptides based on the B-cell epitope prediction, allergenicity prediction, toxicity prediction from S protein to generate a vaccine contrary to SARS-CoV-2 were identified. Furthermore, the development of in silico cloning using pET plasmid was successfully achieved. Conclusions: This study exhibits the transformations of amino acid in Indonesian B.1.1.7 isolates, and proposes four peptides ("LTPGDSSSGWTAG", "VRQIAPGQTGKIAD", "ILPDPSKPSKRS", and "KNHTSPDVDLG") from S protein as the candidate for a peptide-based vaccine. However, further advance trials such as in vitro and in vivo testing are involved for validation.