scholarly journals Early Computational Detection of Potential High Risk SARS-CoV-2 Variants

2021 ◽  
Author(s):  
Karim Beguir ◽  
Marcin J Skwark ◽  
Yunguan Fu ◽  
Thomas Pierrot ◽  
Santiago Nicolas Lopez Carranza ◽  
...  

The ongoing COVID-19 pandemic is leading to the discovery of hundreds of novel SARS-CoV-2 variants on a daily basis. While most variants do not impact the course of the pandemic, some variants pose significantly increased risk when the acquired mutations allow better evasion of antibody neutralisation in previously infected or vaccinated subjects, or increased transmissibility. Early detection of such high risk variants (HRVs) is paramount for the proper management of the pandemic. However, experimental assays to determine immune evasion and transmissibility characteristics of new variants are resource-intensive and time-consuming, potentially leading to delayed appropriate responses by decision makers. Here we present a novel in silico approach combining Spike protein structure modelling and large protein transformer language models on Spike protein sequences, to accurately rank SARS-CoV-2 variants for immune escape and fitness potential. We validate our immune escape and fitness metrics with in vitro pVNT and binding assays. These metrics can be combined into an automated Early Warning System (EWS) capable of evaluating new variants in minutes and risk monitoring variant lineages in near real-time. The EWS flagged 12 out of 13 variants, designated by the World Health Organisation (WHO, Alpha-Omicron) as potentially dangerous, on average two months ahead of them being designated as such, demonstrating its ability to help increase preparedness against future variants. Omicron was flagged by the EWS on the day its sequence was made available, with immune evasion and binding metrics subsequently confirmed through our in vitro experiments.

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1076
Author(s):  
Anne Gégout Petit ◽  
Hélène Jeulin ◽  
Karine Legrand ◽  
Nicolas Jay ◽  
Agathe Bochnakian ◽  
...  

The World Health Organisation recommends monitoring the circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We investigated anti–SARS-CoV-2 total immunoglobulin (IgT) antibody seroprevalence and in vitro sero-neutralization in Nancy, France, in spring 2020. Individuals were randomly sampled from electoral lists and invited with household members over 5 years old to be tested for anti–SARS-CoV-2 (IgT, i.e., IgA/IgG/IgM) antibodies by ELISA (Bio-rad); the sero-neutralization activity was evaluated on Vero CCL-81 cells. Among 2006 individuals, the raw seroprevalence was 2.1% (95% confidence interval 1.5 to 2.9), was highest for 20- to 34-year-old participants (4.7% (2.3 to 8.4)), within than out of socially deprived area (2.5% vs. 1%, p = 0.02) and with than without intra-family infection (p < 10−6). Moreover, 25% of participants presented at least one COVID-19 symptom associated with SARS-CoV-2 positivity (p < 10−13), with highly discriminant anosmia or ageusia (odds ratio 27.8 [13.9 to 54.5]); 16.3% (6.8 to 30.7) of seropositive individuals were asymptomatic. Positive sero-neutralization was demonstrated in vitro for 31/43 seropositive subjects. Regarding the very low seroprevalence, a preventive effect of the lockdown in March 2020 can be assumed for the summer, but a second COVID-19 wave, as expected, could be subsequently observed in this poorly immunized population.


2021 ◽  
Author(s):  
Daniel Morgan Foulkes ◽  
Keri McLean ◽  
Marta Sloniecka ◽  
Dominic Byrne ◽  
Atikah S Haneef ◽  
...  

Infection from the opportunistic pathogen Pseudomonas aeruginosa is one of leading causes of disability and mortality worldwide and the world health organisation has listed it with the highest priority for the need of new antimicrobial therapies. P. aeruginosa strains responsible for the poorest clinical outcomes express either ExoS or ExoU, which are injected into target host cells via the type III secretion system (T3SS). ExoS is a bifunctional cytotoxin that promotes intracellular survival of invasive P. aeruginosa by preventing targeting of the bacteria to acidified intracellular compartments and lysosomal degradation. ExoU is a potent phospholipase which causes rapid destruction of host cell plasma membranes, leading to acute tissue damage and bacterial dissemination. Fluoroquinolones are usually employed as a first line of therapy as they have been shown to be more active against P. aeruginosa in vitro than other antimicrobial classes. However, their overuse over the past decade has caused alarming rates of antibiotic resistance to emerge. In certain clinical situations, aminoglycosides have been shown to be more effective then fluoroquinolones, despite their reduced potency towards P. aeruginosa in vitro. In this study, we evaluated the effects of fluoroquinolones (moxifloxacin and ciprofloxacin) and aminoglycosides (tobramycin and gentamycin) on T3SS expression and toxicity, in corneal epithelial cell infection models. We discovered tobramycin disrupted T3SS expression and inhibited both ExoS and ExoU mediated cytotoxicity, protecting infected HCE-T cells even at concentrations below the minimal inhibitory concentrations (MIC). Fluoroquinolones moxifloxacin and ciprofloxacin, however, upregulated the T3SS and in particular did not subvert the cytotoxic effects of ExoS and ExoU.


2021 ◽  
Author(s):  
Daniele Focosi ◽  
Fabrizio Maggi ◽  
Massimo Franchini ◽  
Scott McConnell ◽  
Arturo Casadevall

Accelerated SARS-CoV-2 evolution under selective pressure by massive deployment of neutralizing antibody-based therapeutics is a concern with potentially severe implications for public health. We review here reports of documented immune escape after treatment with monoclonal antibodies and COVID19 convalescent plasma (CCP). While the former is mainly associated with specific single amino acid mutations at residues within the receptor-binding domain (e.g., E484K/Q, Q493R, and S494P), the few cases of immune evasion after CCP were associated with recurrent deletions within the N-terminal domain of Spike protein (e.g, delHV69-70, delLGVY141-144 and delAL243-244). Continuous genomic monitoring of non-responders is needed to better understand immune escape frequencies and fitness of emerging variants.


2020 ◽  
Author(s):  
Mahdi Rezaei ◽  
Mohsen Azarmi

Abstract Social distancing is a recommended solution by the World Health Organisation (WHO) to minimise the spread of COVID-19 in public places. The majority of governments and national health authorities have set the 2-meter physical distancing as a mandatory safety measure in shopping centres, schools and other covered areas. In this research, we develop a generic Deep Neural Network-Based model for automated people detection, tracking, and inter-people distances estimation in the crowd, using common CCTV security cameras. The proposed model includes a YOLOv4-based framework and inverse perspective mapping for accurate people detection and social distancing monitoring in challenging conditions, including people occlusion, partial visibility, and lighting variations. We also provide an online risk assessment scheme by statistical analysis of the Spatio-temporal data from the moving trajectories and the rate of social distancing violations. We identify high-risk zones with the highest possibility of virus spread and infection. This may help authorities to redesign the layout of a public place or to take precaution actions to mitigate high-risk zones. The efficiency of the proposed methodology is evaluated on the Oxford Town Centre dataset, with superior performance in terms of accuracy and speed compared to three state-of-the-art methods.


Author(s):  
Mahdi Rezaei ◽  
Mohsen Azarmi

Social distancing is a recommended solution by the World Health Organisation (WHO) to minimise the spread of COVID-19 in public places. The majority of governments and national health authorities have set the 2-meter physical distancing as a mandatory safety measure in shopping centres, schools and other covered areas. In this research, we develop a Deep Neural Network-based Model for automated people detection, tracking, and inter-people distances estimation in the crowd, using common CCTV security cameras. The proposed DNN model along with an inverse perspective mapping technique leads to a very accurate people detection and social distancing monitoring in challenging conditions, including people occlusion, partial visibility, and lighting variations. We also provide an online infection risk assessment scheme by statistical analysis of the Spatio-temporal data from the moving trajectories and the rate of social distancing violations. We identify high-risk zones with the highest possibility of virus spread and infection. This may help authorities to redesign the layout of a public place or to take precaution actions to mitigate high-risk zones. The efficiency of the proposed methodology is evaluated on the Oxford Town Centre dataset, with superior performance in terms of accuracy and speed compared to three state-of-the-art methods.


2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Grace Sum ◽  
Gerald Choon-Huat Koh ◽  
Stewart W. Mercer ◽  
Lim Yee Wei ◽  
Azeem Majeed ◽  
...  

Abstract Background The burden of non-communicable diseases (NCDs) is rising rapidly in middle-income countries (MICs), where NCDs are often undiagnosed, untreated and uncontrolled. How comorbidity impacts diagnosis, treatment, and control of NCDs is an emerging area of research inquiry and have important clinical implications as highlighted in the recent National Institute for Health and Care Excellence guidelines for treating patients suffering from multiple NCDs. This is the first study to examine the association between increasing numbers of comorbidities with being undiagnosed, untreated, and uncontrolled for NCDs, in 6 large MICs. Methods Cross-sectional analysis of the World Health Organisation Study of Global Ageing and Adult Health (WHO SAGE) Wave 1 (2007–10), which consisted of adults aged ≥18 years from 6 populous MICs, including China, Ghana, India, Mexico, Russia and South Africa (overall n = 41, 557). Results A higher number of comorbidities was associated with better odds of diagnosis for hypertension, angina, and arthritis, and higher odds of having treatment for hypertension and angina. However, more comorbidities were associated with increased odds of uncontrolled hypertension, angina, arthritis, and asthma. Comorbidity with concordant conditions was associated with improved diagnosis and treatment of hypertension and angina. Conclusion Patients with more comorbidities have better diagnosis of chronic conditions, but this does not translate into better management and control of these conditions. Patients with multiple NCDs are high users of health services and are at an increased risk of adverse health outcomes. Hence, improving their access to care is a priority for healthcare systems.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 5621-5621
Author(s):  
Ricardo Amaru ◽  
Ariel Amaru ◽  
Hortensia Miguez ◽  
Gina Torres ◽  
Josue Mamani ◽  
...  

Abstract Background Polycythemia Vera (PV) is a clonal myeloproliferative neoplasm, characterized by the JAK2V617F mutation. The main goal of current therapies for PV is to prevent thrombotic events and delay transformation to Myelofibrosis (MF) or Acute Myeloid Leukemia (AML).Treatment for PV to keep an hematocrit (Hct) level <45 %, has been associated with a reduction in cardiovascular deaths and thrombotic events (Marchioli, R et al. NEJM 2013). Currently, low-risk PV patients (<60 years and no previous thrombotic events) are treated with aspirin and phlebotomy while high-risk patients require additional cytoreductive therapy, usually with Hydroxyurea (HU). Resistance to HU is associated with an increased risk of transformation and reduced survival. This is why for HU-refractory patients, second line treatments with interferon alpha, anagrelide or even ruxolitinib are recommended. In Latin America, because of high cost and drugs availability, this last group reflects difficulties to be treated. Because statins have been reported to modulate the erythroid clonogenic activity of normal BM erythroid colonies we performed a pilot study to investigate in vitro and in vivo the biologic and clinical activity of atorvastatin in PV patients Patients and Methods Ten high risk PV patients with a median age of 64.3 years (range 58-73) entered into this study. The diagnosis of PV was done according to the 2008 World Health Organization diagnostic criteria and patients were stratified according to an algorithm proposal provided by Griesshammer et al. (Ann Hematol, 2015). The definition of HU resistance (Barosi, G et al.: BJH 2009) was applicable to five patients (median age 63.9 years) failing to achieve a satisfactory hematologic response upon treatment with more than 2 g of HU, 100 mg of Aspirin and phlebotomies. The assessment of the JAK2V617F mutation was performed as previously described (Guerini et al.: Leukemia 2009). Colony assay, proliferation and apoptosis tests were performed with or without Simvastatin (3.5 uM), as previously described (Amaru, A, Experimental Hematology 2012), on cell lines (UKE1 and K562) and bone marrow mononuclear cells obtained from PV patients and healthy donors. Patients with HU refractory PV (n=5) and high risk PV with hypercholesterolemia (n=5) were eligible to receive Atorvastatin (20 mg/day) added on the top of the ongoing treatment with phlebotomies, Aspirin (100 mg/day) and cytoreductive HU therapy (500 mg/day). All treated patients were high altitude residents (> 3.600 m.a.s.l.) of La Paz (Bolivia) where the normal Hct level of healthy subjects is 48-57% for men and 44-54% for women. This pilot study was approved by the Review Board of the Hospital and the University of San Andres, La Paz. Results In a preliminary set of in vitro proliferation cell assays, simvastatin (3.5 uM), added for 5 days, induced a 33% inhibition of cell proliferation of UKE-1 (JAK2V617F mutated) as compared to 5 % of K562 (BCR/ABL positive). A comparable result was obtained in a 7-day clonogenic cell assay where the colony inhibition was 50 % for UKE-1 and 10 % for K562. On the basis of these results similar experiments were also performed using BM mononuclear cells derived from PV patients and healthy donors. In these experiments performed with the addition of simvastatin, it induced a 41% of inhibition in BFU-E colonies of PV patients and a 25% of inhibition in healthy donors. Furthermore, BFU-E colonies inhibited by simvastatin presented a decrease in hemoglobinization and the size of colonies. HU refractory PV patients and High-risk PV patients with hypercholesterolemia treated with the addition of Atorvastatin, Aspirin, cytoreductive HU and phlebotomies; after a follow-up of 2.6 years (1-7 years), induced a decrease of WBC from 16.500 to 9.270/ul, Hct 61.1 to 52.3% and PLT 457.900,000 to 324.7000/ul. The number of required phlebotomies is reduced in comparison to the required at starting treatment. None of the patients presented thrombotic or cardiopulmonary event. One patient died within two years of starting treatment, due to complications of diabetes mellitus. Conclusions In vitro and in vivo, statins showed some evidence of inhibitory activity of the hematopoiesis of PV patients. These preliminary results might indicate the opportunity to further investigate the potential clinical value of these molecules in the treatment of PV. Disclosures Off Label Use: Atorvastatin was used for its antiproliferative activity on myeloid progenitor cells shown by in vitro experiments.


2019 ◽  
Vol 37 (4_suppl) ◽  
pp. 246-246
Author(s):  
Yun-Fan Sun ◽  
Xin-Rong Yang ◽  
Fan Jia

246 Background: The transcriptional heterogeneity and immune evasion mechanisms of CTCs during systemic circulation are not well defined. Methods: Blood was drawn from 4 different vascular sites, including hepatic vein (HV), peripheral artery (PA), peripheral vein (PV) and portal vein (PoV) of 10 localized HCC patients. Single CTCs were isolated by negative enrichment and robotic micromanipulator, followed by single-cell RNA-sequencing (sc-RNAseq). After filtering, 113 CTCs with qualified data remained were subjected to further bioinformatics analysis. The scRNA-seq results were further validated in three independent cohorts of HCC patients. Results: Our scRNA-seq data revealed remarkable intra- and inter-vascular heterogeneity among CTCs from four vascular sites. We determined CTC transcriptional dynamics during transportation through consecutive vascular compartments and revealed their adaptation mechanisms under biomechanical stress during circulation. We further classified CTCs from different vascular sites into two subsets, namely dormant CTCs and activated CTCs. Dormant CTCs were associated with a non-cycling state and upregulation of EMT/angiogenic signatures and showed stronger prognostic ability for early recurrence than activated CTCs did. Furthermore, we discovered an immune escape mechanism by which CTCs recruited regulatory T cells (Tregs) via expression of CCL5, consequently promoting the formation of an immunosuppressive microenvironment favorable for their survival in the bloodstream and seeding in secondary organs. We proved that MAX, activated through the p38 pathway, was the key transcriptional factor regulating CCL5 overexpression, which was validated by ChIP, luciferase reporter gene and in vitro/vivo knockdown assays. And we further determined that Tregs-derived TGF-β1 can heighten MAX expression, thus amplifying the CCL5 expression. Conclusions: Collectively, our results reveal a previously unappreciated spatial heterogeneity of CTCs and a CTC immune-escape mechanism, which may aid in designing new anti-metastasis therapeutic strategies in HCC.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11196
Author(s):  
Eden Mannix-Fisher ◽  
Samantha McLean

Background The increasing prevalence of bacterial infections that are resistant to antibiotic treatment has caused the scientific and medical communities to look for alternate remedies aimed at prevention and treatment. In addition to researching novel antimicrobials, there has also been much interest in revisiting some of the earliest therapies used by man. One such antimicrobial is silver; its use stretches back to the ancient Greeks but interest in its medicinal properties has increased in recent years due to the rise in antibiotic resistance. Currently antimicrobial silver is found in everything from lunch boxes to medical device implants. Though much is claimed about the antimicrobial efficacy of silver salts the research in this area is mixed. Methods Herein we investigated the efficacy of silver acetate against a carbapenem resistant strain of Acinetobacter baumannii to determine the in vitro activity of this silver salt against a World Health Organisation designated category I critical pathogen. Furthermore, we use the Galleria mellonella larvae model to assess toxicity of the compound and its efficacy in treating infections in a live host. Results We found that silver acetate can be delivered safely to Galleria at medically relevant and antimicrobial levels without detriment to the larvae and that administration of silver acetate to an infection model significantly improved survival. This demonstrates the selective toxicity of silver acetate for bacterial pathogens but also highlights the need for administration of well-defined doses of the antimicrobial to provide an efficacious treatment.


PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248838
Author(s):  
Winstone Mokaya Nyandiko ◽  
Paul Kiptoon ◽  
Florence Ajaya Lubuya

Neonatal hypothermia is a great concern with near epidemic levels globally. In Kenya, its prevalence is as high as 87% with limited local data on the associated factors such as adherence to warm chain guidelines as recommended by the World Health Organisation (WHO) is limited. This study aimed to determine the prevalence of hypothermia and level of adherence to the WHO thermal care guidelines among newborns admitted at Moi Teaching and Referral Hospital (MTRH). It adopted a prospective study design of following up neonates for the first 24 hours of admission to the MTRH newborn unit. Thermometry, interview of mothers and observation of thermal care practices was done. Descriptive and inferential statistical techniques were adopted. Specifically, Pearson’s chi-square test of associations between predictors of neonatal hypothermia and management outcomes was conducted with their corresponding risk estimates at 95% confidence interval. Among the 372 participants, 64.5% (n = 240) were born at MTRH, 47.6% (177) were preterm and 53.2% (198) had birth weights below 2500 grams. Admission hypothermia was noted among 73.7% (274) and 13% (49) died on the first day of admission. Only 7.8% (29) newborns accessed optimal thermal care. Prematurity, day one mortality and adherence to the warm chain were significantly (p<0.001) associated with admission hypothermia. Inappropriate thermal appliance, inadequate clothing and late breastfeeding significantly increased the risk of neonatal hypothermia. Absence of admission hypothermia increased the likelihood of neonatal survival more than twenty-fold (AOR = 20.91, 95% CI: 2.15–153.62). Three out four neonates enrolled had admission hypothermia which was significantly associated with prematurity, lack of adherence to warm chain and increased risk of neonatal mortality on the first day of life. There was low adherence to the WHO thermal care guidelines. This should be optimized among preterm neonates to improve likelihood of survival.


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