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Yousef M, Rob M, Varghese S, Rao S, Zamir F, Paul P, Chaari A. The effect of microbiome therapy on COVID-19-induced gut dysbiosis: A narrative and systematic review. Life Sci 2024; 342:122535. [PMID: 38408636 DOI: 10.1016/j.lfs.2024.122535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
AIMS Emerging evidence highlights the role of COVID-19 in instigating gut dysbiosis, with repercussions on disease severity and bidirectional gut-organ communication involving the lung, heart, brain, and liver. This study aims to evaluate the efficacy of probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) in addressing gut dysbiosis associated with COVID-19, as well as their impact on related disease severity and clinical outcomes. MATERIALS AND METHODS We systematically review 27 studies exploring the efficacy of different microbiome-modulating therapies: probiotics, prebiotics, synbiotics, and fecal microbiota transplantation as potential interventions for COVID-19. KEY FINDINGS The probiotics and synbiotics investigated encompassed a spectrum of eight bacterial and fungal genera, namely Lactobacillus, Bifidobacterium, Streptococcus, Enterococcus, Pediococcus, Bacillus, Saccharomyces, and Kluyveromyces. Noteworthy prebiotics employed in these studies included chestnut tannin, galactooligosaccharides, fructooligosaccharides, xylooligosaccharide, and resistant dextrin. The majority of the investigated biotics exhibited positive effects on COVID-19 patients, manifesting in symptom alleviation, inflammation reduction, and notable decreases in mortality rates. Five studies reported death rates, showing an average mortality ranging from 0 % to 11 % in the intervention groups, as compared to 3 % to 30 % in the control groups. Specifically, probiotics, prebiotics, and synbiotics demonstrated efficacy in diminishing the duration and severity of symptoms while significantly accelerating viral and symptomatic remission. FMT emerged as a particularly effective strategy, successfully restoring gut microbiota and ameliorating gastrointestinal disorders. SIGNIFICANCE The insights gleaned from this review significantly contribute to our broader comprehension of the therapeutic potential of biotics in addressing COVID-19-related gut dysbiosis and mitigating secondary multi-organ complications.
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Affiliation(s)
- Mahmoud Yousef
- Weill Cornell Medicine-Qatar, Qatar Foundation-Education City, P.O. Box 24144, Doha, Qatar
| | - Mlaak Rob
- Weill Cornell Medicine-Qatar, Qatar Foundation-Education City, P.O. Box 24144, Doha, Qatar
| | - Sanish Varghese
- Weill Cornell Medicine-Qatar, Qatar Foundation-Education City, P.O. Box 24144, Doha, Qatar
| | - Shrinidhi Rao
- Weill Cornell Medicine-Qatar, Qatar Foundation-Education City, P.O. Box 24144, Doha, Qatar
| | - Fahad Zamir
- Weill Cornell Medicine-Qatar, Qatar Foundation-Education City, P.O. Box 24144, Doha, Qatar
| | - Pradipta Paul
- Weill Cornell Medicine-Qatar, Qatar Foundation-Education City, P.O. Box 24144, Doha, Qatar
| | - Ali Chaari
- Weill Cornell Medicine-Qatar, Qatar Foundation-Education City, P.O. Box 24144, Doha, Qatar.
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2
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Saviano M, Fierro A, Liccardo A. A deterministic compartmental model for the transition between variants in the spread of Covid-19 in Italy. PLoS One 2023; 18:e0293416. [PMID: 37963148 PMCID: PMC10645303 DOI: 10.1371/journal.pone.0293416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/08/2023] [Indexed: 11/16/2023] Open
Abstract
We propose a deterministic epidemic model to describe the transition between two variants of the same virus, through the combination of a series of realistic mechanisms such as partial cross immunity, waning immunity for vaccinated individuals and a novel data-based algorithm to describe the average immunological status of the population. The model is validated on the evolution of Covid-19 in Italy, during the period in which the transition between Delta and Omicron variant occurred, with very satisfactory agreement with the experimental data. According to our model, if the vaccine efficacy had been equal against Delta and Omicron variant infections, the transition would have been smoothed and the epidemic would have gone extinct. This circumstance confirms the fundamental role of vaccines in combating the epidemic, and the importance of identifying vaccines capable of intercepting new variants.
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Affiliation(s)
- Mario Saviano
- Physics Department, Università degli Studi di Napoli ‘Federico II’, Napoli, Italy
| | - Annalisa Fierro
- Consiglio Nazionale delle Ricerche (CNR), Institute Superconductors, Oxides and other Innovative Materials and Devices (SPIN), Napoli, Italy
| | - Antonella Liccardo
- Physics Department, Università degli Studi di Napoli ‘Federico II’, Napoli, Italy
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3
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Ahmed R, Saba AA, Paul A, Nur J, Alam MS, Chakraborty S, Howlader MZH, Islam LN, Nabi AHMN. Intronic Variants of the Angiotensin-Converting Enzyme 2 Gene Modulate Plasma ACE2 Levels and Possibly Confer Protection against Severe COVID-19. BIOMED RESEARCH INTERNATIONAL 2023; 2023:5705076. [PMID: 37929242 PMCID: PMC10622595 DOI: 10.1155/2023/5705076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/24/2023] [Accepted: 10/07/2023] [Indexed: 11/07/2023]
Abstract
Membrane-bound angiotensin-converting enzyme 2 (ACE2) receptor acts as the entry point for the novel coronavirus, SARS-CoV-2. Polymorphisms in the ACE2 gene may alter viral binding, regulate the expression of ACE2, and thus, affect disease severity. In this study, 68 COVID-19 patients with varying degrees of severity and 40 healthy controls were enrolled. The genetic landscape of the ACE2 gene was explored by whole exome sequencing of 29 individuals, and specific regions of ACE2 were analyzed for the rest of the participants via PCR, followed by barcode-tagged sequencing. The mean soluble ACE2 level in the plasma of healthy controls and patients did not vary significantly but was higher in the patient group (3.77 ± 1.55 ng/mL vs. 3.94 ± 1.42 ng/mL). Analysis of exon 1, exon 2, and exon 8 of the ACE2 gene revealed that these regions are highly conserved in our population. Investigation of exon 11 and its flanking intronic region revealed that deletions in a stretch of 18T nucleotides in the noncoding region significantly decrease ACE2 levels in plasma, as individuals harboring wild-type variants had higher plasma ACE2 levels compared to those harboring T1del, T2del, and T3del variants. However, the intronic variants were not found to be significantly associated with disease severity.
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Affiliation(s)
- Rubaiat Ahmed
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Abdullah Al Saba
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Anik Paul
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Jasmin Nur
- Department of Immunology, Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders, Shahbag, Dhaka, Bangladesh
| | - Md Sohrab Alam
- Department of Immunology, Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders, Shahbag, Dhaka, Bangladesh
| | - Sajib Chakraborty
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Md. Zakir Hossain Howlader
- Laboratory of Nutrition and Health Research, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Laila N. Islam
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - A. H. M. Nurun Nabi
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
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4
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Häring C, Jungwirth J, Schroeder J, Löffler B, Engert B, Ehrhardt C. The Local Anaesthetic Procaine Prodrugs ProcCluster ® and Procaine Hydrochloride Impair SARS-CoV-2 Replication and Egress In Vitro. Int J Mol Sci 2023; 24:14584. [PMID: 37834031 PMCID: PMC10572566 DOI: 10.3390/ijms241914584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
As vaccination efforts against SARS-CoV-2 progress in many countries, there is still an urgent need for efficient antiviral treatment strategies for those with severer disease courses, and lately, considerable efforts have been undertaken to repurpose existing drugs as antivirals. The local anaesthetic procaine has been investigated for antiviral properties against several viruses over the past decades. Here, we present data on the inhibitory effect of the procaine prodrugs ProcCluster® and procaine hydrochloride on SARS-CoV-2 infection in vitro. Both procaine prodrugs limit SARS-CoV-2 progeny virus titres as well as reduce interferon and cytokine responses in a proportional manner to the virus load. The addition of procaine during the early stages of the SARS-CoV-2 replication cycle in a cell culture first limits the production of subgenomic RNA transcripts, and later affects the replication of the viral genomic RNA. Interestingly, procaine additionally exerts a prominent effect on SARS-CoV-2 progeny virus release when added late during the replication cycle, when viral RNA production and protein production are already largely completed.
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Affiliation(s)
- Clio Häring
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Johannes Jungwirth
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Josefine Schroeder
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany;
| | | | - Christina Ehrhardt
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
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5
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Jeican II, Gheban D, Mariș A, Albu S, Aluaș M, Siserman CV, Gheban BA. Flurona: The First Autopsied Case. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1616. [PMID: 37763736 PMCID: PMC10537609 DOI: 10.3390/medicina59091616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
COVID-19-associated coinfections increase the patient's risk of developing a severe form of the disease and, consequently, the risk of death. The term "flurona" was proposed to describe the coinfection of the influenza virus and SARS-CoV-2. This report is about a case of a 7-month-old female infant who died due to flurona coinfection. A histopathological exam showed activation of microglia (becoming CD45 positive), bronchial inflammation, diffuse alveolar damage in proliferative phase with vasculitis, a peribronchial infiltrate that was predominantly CD20-positive, and a vascular wall infiltrate that was predominantly CD3-positive. The aggressiveness of the two respiratory viruses added up and they caused extensive lung inflammation, which led to respiratory failure, multiple organ failure, and death. Tissues injuries caused by both the influenza virus and SARS-CoV-2 could be observed, without the ability to certify the dominance of the aggression of one of the two viruses.
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Affiliation(s)
- Ionuț Isaia Jeican
- Department of Anatomy and Embryology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Dan Gheban
- Department of Pathology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
- Department of Pathology, Emergency Clinical Hospital for Children, 400370 Cluj-Napoca, Romania
| | - Alexandra Mariș
- Intensive Care Unit, Emergency Clinical Hospital for Children, 400370 Cluj-Napoca, Romania;
| | - Silviu Albu
- Department of Head and Neck Surgery and Otorhinolaryngology, University Clinical Hospital of Railway Company, Iuliu Hatieganu University of Medicine and Pharmacy, 400015 Cluj-Napoca, Romania
| | - Maria Aluaș
- Department of Oral Health, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Costel Vasile Siserman
- Institute of Legal Medicine, 400006 Cluj-Napoca, Romania
- Department of Legal Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Bogdan Alexandru Gheban
- Department of Histology, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
- Department of Pathology, Emergency Clinical County Hospital, 400347 Cluj-Napoca, Romania
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6
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Gerardi V, Rohaim MA, Naggar RFE, Atasoy MO, Munir M. Deep Structural Analysis of Myriads of Omicron Sub-Variants Revealed Hotspot for Vaccine Escape Immunity. Vaccines (Basel) 2023; 11:vaccines11030668. [PMID: 36992252 DOI: 10.3390/vaccines11030668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The emergence of the Omicron variant has reinforced the importance of continued SARS-CoV-2 evolution and its possible impact on vaccine effectiveness. Specifically, mutations in the receptor-binding domain (RBD) are critical to comprehend the flexibility and dynamicity of the viral interaction with the human agniotensin-converting enzyme 2 (hACE2) receptor. To this end, we have applied a string of deep structural and genetic analysis tools to map the substitution patterns in the S protein of major Omicron sub-variants (n = 51) with a primary focus on the RBD mutations. This head-to-head comparison of Omicron sub-variants revealed multiple simultaneous mutations that are attributed to antibody escape, and increased affinity and binding to hACE2. Our deep mapping of the substitution matrix indicated a high level of diversity at the N-terminal and RBD domains compared with other regions of the S protein, highlighting the importance of these two domains in a matched vaccination approach. Structural mapping identified highly variable mutations in the up confirmation of the S protein and at sites that critically define the function of the S protein in the virus pathobiology. These substitutional trends offer support in tracking mutations along the evolutionary trajectories of SAR-CoV-2. Collectively, the findings highlight critical areas of mutations across the major Omicron sub-variants and propose several hotspots in the S proteins of SARS-CoV-2 sub-variants to train the future design and development of COVID-19 vaccines.
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Affiliation(s)
- Valeria Gerardi
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
| | - Mohammed A Rohaim
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Rania F El Naggar
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
- Department of Virology, Faculty of Veterinary Medicine, University of Sadat City, Sadat 32897, Egypt
| | - Mustafa O Atasoy
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
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7
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Möhler R, Jenetzky E, Schwarz S, Gwiasda M, Rathjens L, Martin DD. Children’s Symptoms with a Febrile Illness and a Positive or Negative Test of SARS-CoV-2 during the Omicron Wave. CHILDREN 2023; 10:children10030419. [PMID: 36979977 PMCID: PMC10047075 DOI: 10.3390/children10030419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Febrile infections are common in childhood. Children can be infected with SARS-CoV-2, but their course is milder than in adults. So far, a comparison between febrile infections with a positive or negative Corona test with the Omicron variant is missing. The data used are from the FeverApp registry, which collects parent-reported data on febrile infections in children and informs about fever management. A comparison of symptomatic differences between episodes with a positive or negative Corona test was performed using Χ2-tests. During the Omicron wave, reported tests doubled and positive test results nearly 12-folded. In episodes with positive Corona saliva tests, more cough, fatigue, disturbed smell/taste, limb pain, sore throat, signs of serious sickness, and touch sensitivity were reported. Children with a negative Corona test show more tonsillitis, teething, any pain symptoms, earaches, and rashes. Thus, there are some significant differences between febrile infections with a positive or negative Corona test, but symptoms are present on both sides. The omicron variant seems to be more infectious than the alpha or delta variants in children, but the symptoms remain mild and do not differ much from other febrile infections.
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Affiliation(s)
- Ricarda Möhler
- Faculty of Health, School of Medicine, 58448 Witten, Germany
| | - Ekkehart Jenetzky
- Faculty of Health, School of Medicine, 58448 Witten, Germany
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Center of the Johannes-Gutenberg-University Mainz, 55131 Mainz, Germany
- Correspondence:
| | - Silke Schwarz
- Faculty of Health, School of Medicine, 58448 Witten, Germany
| | - Moritz Gwiasda
- Faculty of Health, School of Medicine, 58448 Witten, Germany
| | - Larisa Rathjens
- Faculty of Health, School of Medicine, 58448 Witten, Germany
| | - David D. Martin
- Faculty of Health, School of Medicine, 58448 Witten, Germany
- Department of Pediatrics, Eberhard-Karls University Tübingen, 72076 Tübingen, Germany
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8
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Fericean RM, Oancea C, Reddyreddy AR, Rosca O, Bratosin F, Bloanca V, Citu C, Alambaram S, Vasamsetti NG, Dumitru C. Outcomes of Elderly Patients Hospitalized with the SARS-CoV-2 Omicron B.1.1.529 Variant: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2150. [PMID: 36767517 PMCID: PMC9915911 DOI: 10.3390/ijerph20032150] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/12/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The Omicron (B.1.1.529) variant of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) had an increased rate of spreading among the general population. Although this virus mutation resulted in milder symptoms, those on the vulnerable side of the population are still in danger of developing severe symptoms. Thus, this systematic review focused on identifying the clinical outcomes of older age patients (>65) that are hospitalized with the SARS-CoV-2 Omicron variant. The research was conducted using four electronic databases (PubMed, Scopus, Web of Science, and ProQuest Central), with a search query in December 2022 that comprised the duration of the COVID-19 pandemic. The inclusion criteria comprised (1) a population of patients older than 65 years, (2) a history of hospitalization for SARS-CoV-2 infection, and (3) infection with Omicron B.1.1.529 variant. The initial search generated 295 articles, out of which six were included in the systematic review, and a total of 7398 patients. The main findings were that when looking at the elderly population, the mortality and hospitalization rates remained high. This is because older people are more vulnerable and have more comorbidities that interfere with the virus's progress. However, there is inconsistency in mortality rates, since the data reported by the included studies had different selection criteria based on the severity of the COVID-19 infection. Although no statistically significant differences were found between the unvaccinated and vaccinated groups, patients who got booster doses of vaccination had a lower likelihood of developing severe symptoms, serving as a protective factor for this population.
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Affiliation(s)
- Roxana Manuela Fericean
- Department XIII, Discipline of Infectious Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Cristian Oancea
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Akash Reddy Reddyreddy
- School of General Medicine, Bhaskar Medical College, Amdapur Road 156-162, Hyderabad 500075, India
| | - Ovidiu Rosca
- Department XIII, Discipline of Infectious Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Felix Bratosin
- Department XIII, Discipline of Infectious Diseases, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
- Doctoral School, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Vlad Bloanca
- Department of Plastic Surgery, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Cosmin Citu
- Department of Obstetrics and Gynecology, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Satish Alambaram
- School of General Medicine, Bhaskar Medical College, Amdapur Road 156-162, Hyderabad 500075, India
| | - Neeharika Gayatri Vasamsetti
- Faculty of General Medicine, Kaloji Narayana Rao University of Health Sciences, Nizampura, Warangal 506007, India
| | - Catalin Dumitru
- Department of Obstetrics and Gynecology, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania
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9
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D3AI-Spike: A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2. Comput Biol Med 2022; 151:106212. [PMID: 36327885 PMCID: PMC9597563 DOI: 10.1016/j.compbiomed.2022.106212] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 12/27/2022]
Abstract
The number of SARS-CoV-2 spike Receptor Binding Domain (RBD) with multiple amino acid mutations is huge due to random mutations and combinatorial explosions, making it almost impossible to experimentally determine their binding affinities to human angiotensin-converting enzyme 2 (hACE2). Although computational prediction is an alternative way, there is still no online platform to predict the mutation effect of RBD on the hACE2 binding affinity until now. In this study, we developed a free online platform based on deep learning models, namely D3AI-Spike, for quickly predicting binding affinity between spike RBD mutants and hACE2. The models based on CNN and CNN-RNN methods have the concordance index of around 0.8. Overall, the test results of the models are in agreement with the experimental data. To further evaluate the prediction power of D3AI-Spike, we predicted and experimentally determined the binding affinity of a VUM (variants under monitoring) variant IHU (B.1.640.2), which has fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions located in the spike protein. The predicted average affinity score for wild-type RBD and IHU to hACE2 are 0.483 and 0.438, while the determined Kaff values are 5.39 ± 0.38 × 107 L/mol and 1.02 ± 0.47 × 107 L/mol, respectively, demonstrating the strong predictive power of D3AI-Spike. We think D3AI-Spike will be helpful to the viral transmission prediction for the new emerging SARS-CoV-2 variants. D3AI-Spike is now available free of charge at https://www.d3pharma.com/D3Targets-2019-nCoV/D3AI-Spike/index.php.
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10
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Rangu R, Wander PL, Zraika S. Does diabetes risk after SARS-CoV-2 infection depend on the viral variant? Diabetes Res Clin Pract 2022; 191:110054. [PMID: 36038088 PMCID: PMC9420316 DOI: 10.1016/j.diabres.2022.110054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022]
Abstract
SARS-CoV-2 infection is associated with an elevated risk of new-onset diabetes. With infections forecast to rise in the coming months, this may exacerbate an existing public health crisis by increasing rates of diabetes worldwide. Much remains to be learned about a causal link between SARS-CoV-2 and incident diabetes. This is complicated by the rapid evolution of new SARS-CoV-2 variants that may have differential effects on development of diabetes. It is possible that some variants confer an increased risk, while others carry little to no risk. Distinguishing between these possibilities could be key in preventing or screening for new-onset diabetes, and could inform care of at-risk individuals with recent SARS-CoV-2 infection.
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Affiliation(s)
- Rohita Rangu
- Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, United States; Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, University of Washington, Seattle, WA 98195, United States
| | - Pandora L Wander
- Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, United States; Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, WA 98195, United States
| | - Sakeneh Zraika
- Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, United States; Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, University of Washington, Seattle, WA 98195, United States.
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11
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Smallman-Raynor MR, Cliff AD. Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021. Epidemiol Infect 2022; 150:e145. [PMID: 35855577 PMCID: PMC9353238 DOI: 10.1017/s0950268822001285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/04/2022] [Accepted: 07/14/2022] [Indexed: 11/05/2022] Open
Abstract
This paper uses a robust method of spatial epidemiological analysis to assess the spatial growth rate of multiple lineages of SARS-CoV-2 in the local authority areas of England, September 2020-December 2021. Using the genomic surveillance records of the COVID-19 Genomics UK (COG-UK) Consortium, the analysis identifies a substantial (7.6-fold) difference in the average rate of spatial growth of 37 sample lineages, from the slowest (Delta AY.4.3) to the fastest (Omicron BA.1). Spatial growth of the Omicron (B.1.1.529 and BA) variant was found to be 2.81× faster than the Delta (B.1.617.2 and AY) variant and 3.76× faster than the Alpha (B.1.1.7 and Q) variant. In addition to AY.4.2 (a designated variant under investigation, VUI-21OCT-01), three Delta sublineages (AY.43, AY.98 and AY.120) were found to display a statistically faster rate of spatial growth than the parent lineage and would seem to merit further investigation. We suggest that the monitoring of spatial growth rates is a potentially valuable adjunct to outbreak response procedures for emerging SARS-CoV-2 variants in a defined population.
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Affiliation(s)
| | - A. D. Cliff
- Department of Geography, University of Cambridge, Cambridge, UK
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Müller-Hilke B, Mai F, Müller M, Volzke J, Reisinger EC. Higher SARS-CoV-2 Spike Binding Antibody Levels and Neutralization Capacity 6 Months after Heterologous Vaccination with AZD1222 and BNT162b2. Vaccines (Basel) 2022; 10:vaccines10020322. [PMID: 35214780 PMCID: PMC8880180 DOI: 10.3390/vaccines10020322] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
Within a year after the emergence of SARS-CoV-2, several vaccines had been developed, clinically evaluated, proven to be efficacious in preventing symptomatic disease, and licensed for global use. The remaining questions about the vaccines concern the duration of protection offered by vaccination and its efficacy against variants of concern. Therefore, we set out to analyze the humoral and cellular immune responses 6 months into homologous and heterologous prime-boost vaccinations. We recruited 190 health care workers and measured their anti-spike IgG levels, their neutralizing capacities against the Wuhan-Hu-1 strain and the Delta variant using a surrogate viral neutralization test, and their IFNγ-responses towards SARS-CoV-2-derived spike peptides. We here show that IFNγ secretion in response to peptide stimulation was significantly enhanced in all three vaccination groups and comparable in magnitude. In contrast, the heterologous prime-boost regimen using AZD1222 and BNT162b2 yielded the highest anti-spike IgG levels, which were 3–4.5 times more than the levels resulting from homologous AZD1222 and BNT162b2 vaccination, respectively. Likewise, the neutralizing capacity against both the wild type as well as the Delta receptor binding domains was significantly higher following the heterologous prime-boost regimen. In conclusion, our results suggest that mixing different SARS-CoV-2 vaccines might lead to more efficacious and longer-lasting humoral protection against breakthrough infections.
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Affiliation(s)
- Brigitte Müller-Hilke
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, 18055 Rostock, Germany; (F.M.); (M.M.).; (J.V.)
- Correspondence: ; Tel.: +49-381-4945883
| | - Franz Mai
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, 18055 Rostock, Germany; (F.M.); (M.M.).; (J.V.)
| | - Michael Müller
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, 18055 Rostock, Germany; (F.M.); (M.M.).; (J.V.)
| | - Johann Volzke
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, 18055 Rostock, Germany; (F.M.); (M.M.).; (J.V.)
| | - Emil C. Reisinger
- Division of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, Rostock University Medical Center, 18055 Rostock, Germany;
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da Silva SJR, de Lima SC, da Silva RC, Kohl A, Pena L. Viral Load in COVID-19 Patients: Implications for Prognosis and Vaccine Efficacy in the Context of Emerging SARS-CoV-2 Variants. Front Med (Lausanne) 2022; 8:836826. [PMID: 35174189 PMCID: PMC8841511 DOI: 10.3389/fmed.2021.836826] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022] Open
Abstract
The worldwide spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an unprecedented public health crisis in the 21st century. As the pandemic evolves, the emergence of SARS-CoV-2 has been characterized by the emergence of new variants of concern (VOCs), which resulted in a catastrophic impact on SARS-CoV-2 infection. In light of this, research groups around the world are unraveling key aspects of the associated illness, coronavirus disease 2019 (COVID-19). A cumulative body of data has indicated that the SARS-CoV-2 viral load may be a determinant of the COVID-19 severity. Here we summarize the main characteristics of the emerging variants of SARS-CoV-2, discussing their impact on viral transmissibility, viral load, disease severity, vaccine breakthrough, and lethality among COVID-19 patients. We also provide a rundown of the rapidly expanding scientific evidence from clinical studies and animal models that indicate how viral load could be linked to COVID-19 prognosis and vaccine efficacy among vaccinated individuals, highlighting the differences compared to unvaccinated individuals.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Suelen Cristina de Lima
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
| | - Ronaldo Celerino da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
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