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Angulo-Aguado M, Carrillo-Martinez JC, Contreras-Bravo NC, Morel A, Parra-Abaunza K, Usaquén W, Fonseca-Mendoza DJ, Ortega-Recalde O. Next-generation sequencing of host genetics risk factors associated with COVID-19 severity and long-COVID in Colombian population. Sci Rep 2024; 14:8497. [PMID: 38605121 PMCID: PMC11009356 DOI: 10.1038/s41598-024-57982-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 03/24/2024] [Indexed: 04/13/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) was considered a major public health burden worldwide. Multiple studies have shown that susceptibility to severe infections and the development of long-term symptoms is significantly influenced by viral and host factors. These findings have highlighted the potential of host genetic markers to identify high-risk individuals and develop target interventions to reduce morbimortality. Despite its importance, genetic host factors remain largely understudied in Latin-American populations. Using a case-control design and a custom next-generation sequencing (NGS) panel encompassing 81 genetic variants and 74 genes previously associated with COVID-19 severity and long-COVID, we analyzed 56 individuals with asymptomatic or mild COVID-19 and 56 severe and critical cases. In agreement with previous studies, our results support the association between several clinical variables, including male sex, obesity and common symptoms like cough and dyspnea, and severe COVID-19. Remarkably, thirteen genetic variants showed an association with COVID-19 severity. Among these variants, rs11385942 (p < 0.01; OR = 10.88; 95% CI = 1.36-86.51) located in the LZTFL1 gene, and rs35775079 (p = 0.02; OR = 8.53; 95% CI = 1.05-69.45) located in CCR3 showed the strongest associations. Various respiratory and systemic symptoms, along with the rs8178521 variant (p < 0.01; OR = 2.51; 95% CI = 1.27-4.94) in the IL10RB gene, were significantly associated with the presence of long-COVID. The results of the predictive model comparison showed that the mixed model, which incorporates genetic and non-genetic variables, outperforms clinical and genetic models. To our knowledge, this is the first study in Colombia and Latin-America proposing a predictive model for COVID-19 severity and long-COVID based on genomic analysis. Our study highlights the usefulness of genomic approaches to studying host genetic risk factors in specific populations. The methodology used allowed us to validate several genetic variants previously associated with COVID-19 severity and long-COVID. Finally, the integrated model illustrates the importance of considering genetic factors in precision medicine of infectious diseases.
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Affiliation(s)
- Mariana Angulo-Aguado
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Juan Camilo Carrillo-Martinez
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Nora Constanza Contreras-Bravo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Adrien Morel
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | | | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, D.C, Colombia
| | - Dora Janeth Fonseca-Mendoza
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Oscar Ortega-Recalde
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia.
- Departamento de Morfología, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Bogotá, D.C, Colombia.
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2
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Godin R, Hejazi S, Reuel NF. Advancements in Airborne Viral Nucleic Acid Detection with Wearable Devices. ADVANCED SENSOR RESEARCH 2024; 3:2300061. [PMID: 38764891 PMCID: PMC11101210 DOI: 10.1002/adsr.202300061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Indexed: 05/21/2024]
Abstract
Wearable health sensors for an expanding range of physiological parameters have experienced rapid development in recent years and are poised to disrupt the way healthcare is tracked and administered. The monitoring of environmental contaminants with wearable technologies is an additional layer of personal and public healthcare and is also receiving increased focus. Wearable sensors that detect exposure to airborne viruses could alert wearers of viral exposure and prompt proactive testing and minimization of viral spread, benefitting their own health and decreasing community risk. With the high levels of asymptomatic spread of COVID-19 observed during the pandemic, such devices could dramatically enhance our pandemic response capabilities in the future. To facilitate advancements in this area, this review summarizes recent research on airborne viral detection using wearable sensing devices as well as technologies suitable for wearables. Since the low concentration of viral particles in the air poses significant challenges to detection, methods for airborne viral particle collection and viral sensing are discussed in detail. A special focus is placed on nucleic acid-based viral sensing mechanisms due to their enhanced ability to discriminate between viral subtypes. Important considerations for integrating airborne viral collection and sensing on a single wearable device are also discussed.
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Affiliation(s)
- Ryan Godin
- Department of Chemical and Biological Engineering, Iowa State University
| | - Sepehr Hejazi
- Department of Chemical and Biological Engineering, Iowa State University
| | - Nigel F. Reuel
- Department of Chemical and Biological Engineering, Iowa State University
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3
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Gerashchenko GV, Hryshchenko NV, Melnichuk NS, Marchyshak TV, Chernushyn SY, Demchyshina IV, Chernenko LM, Kuzin IV, Tkachuk ZY, Kashuba VI, Tukalo MA. Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021-January 2022. Heliyon 2024; 10:e25618. [PMID: 38380034 PMCID: PMC10877268 DOI: 10.1016/j.heliyon.2024.e25618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
The aim of our study was to identify and characterize the SARS-CoV-2 variants in COVID-19 patients' samples collected from different regions of Ukraine to determine the relationship between SARS-CoV-2 phylogenetics and COVID-19 epidemiology. Patients and methods Samples were collected from COVID-19 patients during 2021 and the beginning of 2022 (401 patients). The SARS-CoV-2 genotyping was performed by parallel whole genome sequencing. Results The obtained SARS-CoV-2 genotypes showed that three waves of the COVID-19 pandemic in Ukraine were represented by three main variants of concern (VOC), named Alpha, Delta and Omicron; each VOC successfully replaced the earlier variant. The VOC Alpha strain was presented by one B.1.1.7 lineage, while VOC Delta showed a spectrum of 25 lineages that had different prevalence in 19 investigated regions of Ukraine. The VOC Omicron in the first half of the pandemic was represented by 13 lines that belonged to two different clades representing B.1 and B.2 Omicron strains. Each of the three epidemic waves (VOC Alpha, Delta, and Omicron) demonstrated their own course of disease, associated with genetic changes in the SARS-CoV-2 genome. The observed epidemiological features are associated with the genetic characteristics of the different VOCs, such as point mutations, deletions and insertions in the viral genome. A phylogenetic and transmission analysis showed the different mutation rates; there were multiple virus sources with a limited distribution between regions. Conclusions The evolution of SARS-CoV-2 virus and high levels of morbidity due to COVID-19 are still registered in the world. Observed multiple virus sourses with the limited distribution between regions indicates the high efficiency of the anti-epidemic policy pursued by the Ministry of Health of Ukraine to prevent the spread of the epidemic, despite the low level of vaccination of the Ukrainian population.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zenovii Yu Tkachuk
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Mykhailo A. Tukalo
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
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4
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Brugger SW, Grose JH, Decker CH, Pickett BE, Davis MF. Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive Importance. Viruses 2024; 16:276. [PMID: 38400051 PMCID: PMC10891864 DOI: 10.3390/v16020276] [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: 12/06/2023] [Revised: 01/20/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 has fueled its global proliferation since its discovery in 2019, with several notable variants having been responsible for increases in cases of coronavirus disease 2019 (COVID-19). Analyses of codon bias and usage in these variants between phylogenetic clades or lineages may grant insights into the evolution of SARS-CoV-2 and identify target codons indicative of evolutionary or mutative trends that may prove useful in tracking or defending oneself against emerging strains. We processed a cohort of 120 SARS-CoV-2 genome sequences through a statistical and bioinformatic pipeline to identify codons presenting evidence of selective pressure as well as codon coevolution. We report the identification of two codon sites in the orf8 and N genes demonstrating such evidence with real-world impacts on pathogenicity and transmissivity.
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Affiliation(s)
| | | | | | | | - Mary F. Davis
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA (J.H.G.); (B.E.P.)
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5
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He S, Gou H, Zhou Y, Wu C, Ren X, Wu X, Guan G, Jin B, Huang J, Jin Z, Zhao T. The SARS-CoV-2 nucleocapsid protein suppresses innate immunity by remodeling stress granules to atypical foci. FASEB J 2023; 37:e23269. [PMID: 37889852 DOI: 10.1096/fj.202201973rr] [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: 11/25/2022] [Revised: 08/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023]
Abstract
Viruses deploy multiple strategies to suppress the host innate immune response to facilitate viral replication and pathogenesis. Typical G3BP1+ stress granules (SGs) are usually formed in host cells after virus infection to restrain viral translation and to stimulate innate immunity. Thus, viruses have evolved various mechanisms to inhibit SGs or to repurpose SG components such as G3BP1. Previous studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection inhibited host immunity during the early stage of COVID-19. However, the precise mechanism is not yet well understood. Here we showed that the SARS-CoV-2 nucleocapsid (SARS2-N) protein suppressed the double-stranded RNA (dsRNA)-induced innate immune response, concomitant with inhibition of SGs and the induction of atypical SARS2-N+ /G3BP1+ foci (N+ foci). The SARS2-N protein-induced formation of N+ foci was dependent on the ability of its ITFG motif to hijack G3BP1, which contributed to suppress the innate immune response. Importantly, SARS2-N protein facilitated viral replication by inducing the formation of N+ foci. Viral mutations within SARS2-N protein that impair the formation of N+ foci are associated with the inability of the SARS2-N protein to suppress the immune response. Taken together, our study has revealed a novel mechanism by which SARS-CoV-2 suppresses the innate immune response via induction of atypical N+ foci. We think that this is a critical strategy for viral pathogenesis and has potential therapeutic implications.
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Affiliation(s)
- Su He
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Hongwei Gou
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yulin Zhou
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Chunxiu Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Xinxin Ren
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Xiajunpeng Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Guanwen Guan
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Boxing Jin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jinhua Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Zhigang Jin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Tiejun Zhao
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
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6
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Giardina F, Ferrari G, Zavaglio F, Paolucci S, Rovida F, Campanini G, Pellegrinelli L, Galli C, Pariani E, Bergami F, Nava A, Matarazzo E, Renica S, Fanti D, Cento V, Alteri C, Scaglione F, Vismara C, Perno CF, Piralla A, Baldanti F. An overview of SARS-CoV-2 variants circulating in the 2020-2022 period in Lombardy. Diagn Microbiol Infect Dis 2023; 107:116070. [PMID: 37714081 DOI: 10.1016/j.diagmicrobio.2023.116070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
Since the beginning of the pandemic, SARS-CoV-2 has shown genetic variability. All the variants that have sustained pandemic waves have shown several mutations, especially in the Spike protein that could affect viral pathogenesis. A total of 15,729 respiratory samples, collected between December 2020 and August 2022, have been included in this study. We report the circulation of SARS-CoV-2 variants in the Lombardy region, Italy, in a 2-year study period. Alpha, Delta, and Omicron variants became predominant causing the majority of cases whereas Beta or Gamma variants mostly caused local outbreaks. Next-generation sequencing revealed several mutations and few deletions in all of the main variants. For example, 147 mutations were observed in the Spike protein of Omicron sublineages; 20% of these mutations occurred in the receptor-binding domain region.
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Affiliation(s)
- Federica Giardina
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Guglielmo Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Zavaglio
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefania Paolucci
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesca Rovida
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giulia Campanini
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Federica Bergami
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alice Nava
- Microbiological Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Elisa Matarazzo
- Microbiological Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Silvia Renica
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Diana Fanti
- Microbiological Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Valeria Cento
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Claudia Alteri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Francesco Scaglione
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Chiara Vismara
- Microbiological Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Carlo Federico Perno
- Multimodal Research Area, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - Fausto Baldanti
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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7
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Liu LT, Chiou SS, Chen PC, Chen CH, Lin PC, Tsai CY, Chuang WL, Hwang SJ, Chong IW, Tsai JJ. Epidemiology and analysis of SARS-CoV-2 Omicron subvariants BA.1 and 2 in Taiwan. Sci Rep 2023; 13:16583. [PMID: 37789031 PMCID: PMC10547678 DOI: 10.1038/s41598-023-43357-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first detected in October 2021, possessed many mutations compared to previous variants. We aimed to identify and analyze SARS-CoV-2 Omicron subvariants among coronavirus disease 2019 (COVID-19) patients between January 2022 and September 2022 in Taiwan. The results revealed that BA.2.3.7, featuring K97E and G1251V in the spike protein compared with BA.2, emerged in March 2022 and persistently dominated between April 2022 and August 2022, resulting in the largest COVID-19 outbreak since 2020. The accumulation of amino acid (AA) variations, mainly AA substitution, in the spike protein was accompanied by increasing severity in Omicron-related COVID-19 between April 2022 and January 2023. Older patients were more likely to have severe COVID-19, and comorbidity was a risk factor for COVID-19-related mortality. The accumulated case fatality rate (CFR) dropped drastically after Omicron variants, mainly BA.2.3.7, entered Taiwan after April 2022, and the CFR was 0.16% in Taiwan, which was lower than that worldwide (0.31%) between April 2021 and January 2023. The relatively low CFR in Omicron-related COVID-19 patients can be attributed to adjustments to public health policies, promotion of vaccination programs, effective antiviral drugs, and the lower severity of the Omicron variant.
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Affiliation(s)
- Li-Teh Liu
- Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, Tainan City, Taiwan
| | - Shyh-Shin Chiou
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Po-Chih Chen
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Chun-Hong Chen
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Ping-Chang Lin
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Ching-Yi Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Wan-Long Chuang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Shang-Jyh Hwang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Inn-Wen Chong
- Department of Internal Medicine and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Department of Pulmonary Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Jih-Jin Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan.
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan.
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, No. 100, Tzyou 1st Road, Kaohsiung City, 80756, Taiwan.
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8
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Li C, Ma L, Zou D, Zhang R, Bai X, Li L, Wu G, Huang T, Zhao W, Jin E, Bao Y, Song S. RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1066-1079. [PMID: 37898309 PMCID: PMC10928372 DOI: 10.1016/j.gpb.2023.10.004] [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: 06/09/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
The Resource for Coronavirus 2019 (RCoV19) is an open-access information resource dedicated to providing valuable data on the genomes, mutations, and variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this updated implementation of RCoV19, we have made significant improvements and advancements over the previous version. Firstly, we have implemented a highly refined genome data curation model. This model now features an automated integration pipeline and optimized curation rules, enabling efficient daily updates of data in RCoV19. Secondly, we have developed a global and regional lineage evolution monitoring platform, alongside an outbreak risk pre-warning system. These additions provide a comprehensive understanding of SARS-CoV-2 evolution and transmission patterns, enabling better preparedness and response strategies. Thirdly, we have developed a powerful interactive mutation spectrum comparison module. This module allows users to compare and analyze mutation patterns, assisting in the detection of potential new lineages. Furthermore, we have incorporated a comprehensive knowledgebase on mutation effects. This knowledgebase serves as a valuable resource for retrieving information on the functional implications of specific mutations. In summary, RCoV19 serves as a vital scientific resource, providing access to valuable data, relevant information, and technical support in the global fight against COVID-19. The complete contents of RCoV19 are available to the public at https://ngdc.cncb.ac.cn/ncov/.
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Affiliation(s)
- Cuiping Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lina Ma
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Rongqin Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Bai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lun Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Gangao Wu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianhao Huang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Enhui Jin
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shuhui Song
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Stracci F, Gili A, Caruso E, Polosa R, Ambrosio G. Value of hospital datasets of COVID-19 patients across different pandemic periods: challenges and opportunities. Intern Emerg Med 2023; 18:969-971. [PMID: 36592272 PMCID: PMC9807090 DOI: 10.1007/s11739-022-03162-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 01/03/2023]
Affiliation(s)
- Fabrizio Stracci
- Department of Medicine and Surgery, Public Health Section, University of Perugia, Perugia, Italy
| | - Alessio Gili
- Department of Medicine and Surgery, Public Health Section, University of Perugia, Perugia, Italy
| | - Enza Caruso
- Department of Political Sciences, University of Perugia, Perugia, Italy
| | - Riccardo Polosa
- Center of Excellence for the Acceleration of HArm Reduction (CoEHAR), University of Catania, Catania, Italy
- Department of Clinical & Experimental Medicine, University of Catania, Catania, Italy
- ECLAT Srl, Spin-off of the University of Catania, Catania, Italy
| | - Giuseppe Ambrosio
- Department of Medicine and Surgery, Cardiology and Cardiovascular Pathophysiology Section, University of Perugia, Perugia, Italy.
- CERICLET-Centro Ricerca Clinica E Traslazionale, University of Perugia, Perugia, Italy.
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10
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Alquraan L, Alzoubi KH, Rababa'h SY. Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity. INFORMATICS IN MEDICINE UNLOCKED 2023; 39:101256. [PMID: 37131549 PMCID: PMC10127666 DOI: 10.1016/j.imu.2023.101256] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/04/2023] Open
Abstract
Numerous variations of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), including D614G, B.1.1.7 (United Kingdom), B.1.1.28 (Brazil P1, P2), CAL.20C (Southern California), B.1.351 (South Africa), B.1.617 (B.1.617.1 Kappa & Delta B.1.617.2) and B.1.1.529, have been reported worldwide. The receptor-binding domain (RBD) of the spike (S) protein is involved in virus-cell binding, where virus-neutralizing antibodies (NAbs) react. Novel variants in the S-protein could maximize viral affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor and increase virus transmission. Molecular detection with false-negative results may refer to mutations in the part of the virus's genome used for virus diagnosis. Furthermore, these changes in S-protein structure alter the neutralizing ability of NAbs, resulting in a reduction in vaccine efficiency. Further information is needed to evaluate how new mutations may affect vaccine efficacy.
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Affiliation(s)
- Laiali Alquraan
- Department of Biology, Faculty of Science, Yarmouk University, Irbid, Jordan
| | - Karem H Alzoubi
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Suzie Y Rababa'h
- Department of Medical Science, Irbid Faculty, Al-Balqa Applied University (BAU), Irbid, Jordan
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11
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Bacorn M, Romero-Soto HN, Levy S, Chen Q, Hourigan SK. The Gut Microbiome of Children during the COVID-19 Pandemic. Microorganisms 2022; 10:microorganisms10122460. [PMID: 36557713 PMCID: PMC9783902 DOI: 10.3390/microorganisms10122460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
The gut microbiome has been shown to play a critical role in maintaining a healthy state. Dysbiosis of the gut microbiome is involved in modulating disease severity and potentially contributes to long-term outcomes in adults with COVID-19. Due to children having a significantly lower risk of severe illness and limited sample availability, much less is known about the role of the gut microbiome in children with COVID-19. It is well recognized that the developing gut microbiome of children differs from that of adults, but it is unclear if this difference contributes to the different clinical presentations and complications. In this review, we discuss the current knowledge of the gut microbiome in children with COVID-19, with gut microbiome dysbiosis being found in pediatric COVID-19 but specific taxa change often differing from those described in adults. Additionally, we discuss possible mechanisms of how the gut microbiome may mediate the presentation and complications of COVID-19 in children and the potential role for microbial therapeutics.
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12
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La Torre G, Moretti L, Vezza F. Prevention and Epidemiological, Clinical, and Economic Issues of COVID-19: Far More Than a Respiratory Disease. J Clin Med 2022; 11:jcm11237218. [PMID: 36498792 PMCID: PMC9736616 DOI: 10.3390/jcm11237218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The Journal of Clinical Medicine has published many papers on coronavirus disease 2019 (COVID-19), and it is now clear that this is not simply a respiratory disease [...].
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13
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Gusdon AM, Faraday N, Aita JS, Kumar S, Mehta I, Choi HA, Cleland JL, Robinson K, McCullough LD, Ng DK, Kannan RM, Kannan S. Dendrimer nanotherapy for severe COVID-19 attenuates inflammation and neurological injury markers and improves outcomes in a phase2a clinical trial. Sci Transl Med 2022; 14:eabo2652. [PMID: 35857827 DOI: 10.1126/scitranslmed.abo2652] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hyperinflammation triggered by SARS-CoV-2 is a major cause of disease severity, with activated macrophages implicated in this response. OP-101, a hydroxyl-polyamidoamine dendrimer-N-acetylcysteine conjugate that specifically targets activated macrophages, improves outcomes in preclinical models of systemic inflammation and neuroinflammation. In this multicenter, randomized, double-blind, placebo-controlled, adaptive phase 2a trial, we evaluated safety and preliminary efficacy of OP-101 in patients with severe COVID-19. Twenty-four patients classified as having severe COVID-19 with a baseline World Health Organization seven-point ordinal scale of ≥5 were randomized to receive a single intravenous dose of placebo (n = 7 patients) or OP-101 at 2 (n = 6), 4 (n = 6), or 8 mg/kg (n = 5 patients). All study participants received standard of care, including corticosteroids. OP-101 at 4 mg/kg was better than placebo at decreasing inflammatory markers; OP-101 at 4 and 8 mg/kg was better than placebo at reducing neurological injury markers, (neurofilament light chain and glial fibrillary acidic protein). Risk for the composite outcome of mechanical ventilation or death at 30 and 60 days after treatment was 71% (95% CI: 29%, 96%) for placebo and 18% (95% CI: 4%, 43%; P = 0.021) for the pooled OP-101 treatment arms. At 60 days, 3 of 7 patients given placebo and 14 of 17 OP-101-treated patients were surviving. No drug-related adverse events were reported. These data show that OP-101 was well tolerated and may have potential to treat systemic inflammation and neuronal injury, reducing morbidity and mortality in hospitalized patients with severe COVID-19.
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Affiliation(s)
- Aaron M Gusdon
- Department of Neurosurgery, The University of Texas, McGovern Medical School, Memorial Hermann Hospital, Houston, TX, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John S Aita
- Avera McKennan Hospital and University Health Center, Sioux Falls, SD, USA
| | - Sunil Kumar
- Broward Health Medical Center, Fort Lauderdale, FL, USA
| | - Ishan Mehta
- Emory University School of Medicine, Atlanta, GA, USA
| | - HuiMahn A Choi
- Department of Neurosurgery, The University of Texas, McGovern Medical School, Memorial Hermann Hospital, Houston, TX, USA
| | | | | | - Louise D McCullough
- Department of Neurology, The University of Texas, McGovern Medical School, Memorial Hermann Hospital, Houston, TX, USA
| | - Derek K Ng
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rangaramanujam M Kannan
- Department of Ophthalmology, Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University SOM, Baltimore, MD, USA
| | - Sujatha Kannan
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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14
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Berengua C, López M, Esteban M, Marín P, Ramos P, Cuerpo MD, Gich I, Navarro F, Miró E, Rabella N. Viral culture and immunofluorescence for the detection of SARS-CoV-2 infectivity in RT-PCR positive respiratory samples. J Clin Virol 2022; 152:105167. [PMID: 35523105 PMCID: PMC9046102 DOI: 10.1016/j.jcv.2022.105167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/06/2022] [Accepted: 04/20/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Knowing how long SARS-CoV-2-positive individuals can remain infective is crucial for the design of infection prevention and control strategies. Viral culture is the gold standard for detecting an active-replicative virus and evaluating its infectious potential. OBJECTIVE To assess the correlation of SARS-CoV-2 infectivity with the number of days from symptom onset and the Ct value, using culture as a reference method. Also, to describe a detailed protocol for SARS-CoV-2 culture and immunofluorescence confirmation based on our experience with other respiratory viruses. STUDY DESIGN 100 consecutive respiratory samples positive for SARS-CoV-2 by RT-PCR from different subjects were inoculated into VERO E6 cells. RESULTS Viral isolation was successful in 58% of samples. The median number of days from symptom onset for culture-positive samples was 2, and 15 for culture-negative samples. Six positive cultures were obtained in patients ≥14 days after symptom onset, all of whom were immunocompromised or with severe COVID-19. The mean Ct value was 12.64 units higher in culture-negative than in culture-positive samples. The probability of successfully isolating SARS-CoV-2 in samples with a Ct value <22 was 100%, decreasing to 3.1% when >27. CONCLUSIONS Our findings show a significant positive correlation between the probability of isolating SARS-CoV-2 in culture, fewer days of symptoms and a lower RT-PCR Ct value. SARS-CoV-2 infectivity lasts no more than 14 days from symptom onset in immunocompetent individuals. In contrast, in immunocompromised patients or those with severe COVID-19 infectivity may remain after 14 days. Ct value <22 always indicates infectivity.
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Affiliation(s)
- Carla Berengua
- Microbiology Department. Hospital de la Santa Creu i Sant Pau. Universitat Autónoma de Barcelona (UAB). Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain,Corresponding author at: Microbiology Department, Hospital de la Santa Creu i Sant Pau, Sant Quintí Street, 89, Barcelona, 08041, Spain
| | - Marina López
- Microbiology Department. Hospital de la Santa Creu i Sant Pau. Universitat Autónoma de Barcelona (UAB). Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain
| | - Montserrat Esteban
- Microbiology Department. Hospital de la Santa Creu i Sant Pau. Universitat Autónoma de Barcelona (UAB). Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain
| | - Pilar Marín
- Microbiology Department. Hospital de la Santa Creu i Sant Pau. Universitat Autónoma de Barcelona (UAB). Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain
| | - Paula Ramos
- Microbiology Department. Hospital de la Santa Creu i Sant Pau. Universitat Autónoma de Barcelona (UAB). Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain
| | - Margarita del Cuerpo
- Microbiology Department. Hospital de la Santa Creu i Sant Pau. Universitat Autónoma de Barcelona (UAB). Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain
| | - Ignasi Gich
- CIBER Epidemiología y Salud Pública (CIBERESP). Clinical Epidemiology and Public Health Department. Hospital de la Santa Creu i Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain
| | - Ferran Navarro
- Microbiology Department. Hospital de la Santa Creu i Sant Pau. Universitat Autónoma de Barcelona (UAB). Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain
| | - Elisenda Miró
- Microbiology Department. Hospital de la Santa Creu i Sant Pau. Universitat Autónoma de Barcelona (UAB). Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain
| | - Núria Rabella
- Microbiology Department. Hospital de la Santa Creu i Sant Pau. Universitat Autónoma de Barcelona (UAB). Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona. Spain
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15
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Abdullaev A, Abdurakhimov A, Mirakbarova Z, Ibragimova S, Tsoy V, Nuriddinov S, Dalimova D, Turdikulova S, Abdurakhmonov I. Genome sequence diversity of SARS-CoV-2 obtained from clinical samples in Uzbekistan. PLoS One 2022; 17:e0270314. [PMID: 35759503 PMCID: PMC9236271 DOI: 10.1371/journal.pone.0270314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/07/2022] [Indexed: 11/27/2022] Open
Abstract
Tracking temporal and spatial genomic changes and evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are among the most urgent research topics worldwide, which help to elucidate the coronavirus disease 2019 (COVID-19) pathogenesis and the effect of deleterious variants. Our current study concentrates genetic diversity of SARS-CoV-2 variants in Uzbekistan and their associations with COVID-19 severity. Thirty-nine whole genome sequences (WGS) of SARS-CoV-2 isolated from PCR-positive patients from Tashkent, Uzbekistan for the period of July-August 2021, were generated and further subjected to further genomic analysis. Genome-wide annotations of clinical isolates from our study have revealed a total of 223 nucleotide-level variations including SNPs and 34 deletions at different positions throughout the entire genome of SARS-CoV-2. These changes included two novel mutations at the Nonstructural protein (Nsp) 13: A85P and Nsp12: Y479N, which were unreported previously. There were two groups of co-occurred substitution patterns: the missense mutations in the Spike (S): D614G, Open Reading Frame (ORF) 1b: P314L, Nsp3: F924, 5`UTR:C241T; Nsp3:P2046L and Nsp3:P2287S, and the synonymous mutations in the Nsp4:D2907 (C8986T), Nsp6:T3646A and Nsp14:A1918V regions, respectively. The “Nextstrain” clustered the largest number of SARS-CoV-2 strains into the Delta clade (n = 32; 82%), followed by two Alpha-originated (n = 4; 10,3%) and 20A (n = 3; 7,7%) clades. Geographically the Delta clade sample sequences were grouped into several clusters with the SARS-CoV genotypes from Russia, Denmark, USA, Egypt and Bangladesh. Phylogenetically, the Delta isolates in our study belong to the two main subclades 21A (56%) and 21J (44%). We found that females were more affected by 21A, whereas males by 21J variant (χ2 = 4.57; p ≤ 0.05, n = 32). The amino acid substitution ORF7a:P45L in the Delta isolates found to be significantly associated with disease severity. In conclusion, this study evidenced that Identified novel substitutions Nsp13: A85P and Nsp12: Y479N, have a destabilizing effect, while missense substitution ORF7a: P45L significantly associated with disease severity.
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Affiliation(s)
| | | | | | | | - Vladimir Tsoy
- Center for Advanced Technologies, Tashkent, Uzbekistan
| | | | | | | | - Ibrokhim Abdurakhmonov
- Center for Advanced Technologies, Tashkent, Uzbekistan
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Qibray Region, Tashkent, Republic of Uzbekistan
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16
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Broad neutralization against SARS-CoV-2 variants induced by ancestral and B.1.351 AS03-Adjuvanted recombinant Plant-Derived Virus-Like particle vaccines. Vaccine 2022; 40:4017-4025. [PMID: 35654621 PMCID: PMC9135691 DOI: 10.1016/j.vaccine.2022.05.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 01/08/2023]
Abstract
Since 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection resulting in the coronavirus disease 2019 (COVID-19) has afflicted hundreds of millions of people in a worldwide pandemic. Several safe and effective COVID-19 vaccines are now available. However, the rapid emergence of variants and risk of viral escape from vaccine-induced immunity emphasize the need to develop broadly protective vaccines. A recombinant plant-derived virus-like particle vaccine for the ancestral COVID-19 (CoVLP) recently authorized by Canadian Health Authorities and a modified CoVLP.B1351 targeting the B.1.351 variant (both formulated with the adjuvant AS03) were assessed in homologous and heterologous prime-boost regimen in mice. Both strategies induced strong and broadly cross-reactive neutralizing antibody (NAb) responses against several Variants of Concern (VOCs), including B.1.351/Beta, B.1.1.7/Alpha, P.1/Gamma, B.1.617.2/Delta and B.1.1.529/Omicron strains. The neutralizing antibody (NAb) response was robust with both primary vaccination strategies and tended to be higher for almost all VOCs following the heterologous prime-boost regimen.
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17
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SARS-CoV-2 Omicron variant causes mild pathology in the upper and lower respiratory tract of hamsters. Nat Commun 2022; 13:3519. [PMID: 35725735 PMCID: PMC9207884 DOI: 10.1038/s41467-022-31200-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Since its discovery in 2019, multiple variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have been identified. This study investigates virus spread and associated pathology in the upper and lower respiratory tracts of Syrian golden hamsters at 4 days post intranasal SARS-CoV-2 Omicron infection, in comparison to infection with variants of concern (VOCs) Gamma and Delta as well as ancestral strain 614 G. Pathological changes in the upper and lower respiratory tract of VOC Omicron infected hamsters are milder than those caused by other investigated strains. VOC Omicron infection causes a mild rhinitis with little involvement of the olfactory epithelium and minimal lesions in the lung, with frequent sparing of the alveolar compartment. Similarly, viral antigen, RNA and infectious virus titers are lower in respiratory tissues of VOC Omicron infected hamsters. These findings demonstrate that the variant has a decreased pathogenicity for the upper and lower respiratory tract of hamsters. Since the emergence of SARS-CoV-2 several variants of concerns have been identified, with altered disease progression and transmission dynamics. Here, Armando et al. compare virus spread and pathology in the upper and lower respiratory tracts of Syrian golden hamster after 4 days post infection for VOCs Gamma, Delta and Omicron and find milder pathology for Omicron.
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18
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Delandre O, Gendrot M, Jardot P, Le Bideau M, Boxberger M, Boschi C, Fonta I, Mosnier J, Hutter S, Levasseur A, La Scola B, Pradines B. Antiviral Activity of Repurposing Ivermectin against a Panel of 30 Clinical SARS-CoV-2 Strains Belonging to 14 Variants. Pharmaceuticals (Basel) 2022; 15:445. [PMID: 35455442 PMCID: PMC9024598 DOI: 10.3390/ph15040445] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/05/2023] Open
Abstract
Over the past two years, several variants of SARS-CoV-2 have emerged and spread all over the world. However, infectivity, clinical severity, re-infection, virulence, transmissibility, vaccine responses and escape, and epidemiological aspects have differed between SARS-CoV-2 variants. Currently, very few treatments are recommended against SARS-CoV-2. Identification of effective drugs among repurposing FDA-approved drugs is a rapid, efficient and low-cost strategy against SARS-CoV-2. One of those drugs is ivermectin. Ivermectin is an antihelminthic agent that previously showed in vitro effects against a SARS-CoV-2 isolate (Australia/VI01/2020 isolate) with an IC50 of around 2 µM. We evaluated the in vitro activity of ivermectin on Vero E6 cells infected with 30 clinically isolated SARS-CoV-2 strains belonging to 14 different variants, and particularly 17 strains belonging to six variants of concern (VOC) (variants related to Wuhan, alpha, beta, gamma, delta and omicron). The in vitro activity of ivermectin was compared to those of chloroquine and remdesivir. Unlike chloroquine (EC50 from 4.3 ± 2.5 to 29.3 ± 5.2 µM) or remdesivir (EC50 from 0.4 ± 0.3 to 25.2 ± 9.4 µM), ivermectin showed a relatively homogeneous in vitro activity against SARS-CoV-2 regardless of the strains or variants (EC50 from 5.1 ± 0.5 to 6.7 ± 0.4 µM), except for one omicron strain (EC50 = 1.3 ± 0.5 µM). Ivermectin (No. EC50 = 219, mean EC50 = 5.7 ± 1.0 µM) was, overall, more potent in vitro than chloroquine (No. EC50 = 214, mean EC50 = 16.1 ± 9.0 µM) (p = 1.3 × 10-34) and remdesivir (No. EC50 = 201, mean EC50 = 11.9 ± 10.0 µM) (p = 1.6 × 10-13). These results should be interpreted with caution regarding the potential use of ivermectin in SARS-CoV-2-infected patients: it is difficult to translate in vitro study results into actual clinical treatment in patients.
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Affiliation(s)
- Océane Delandre
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Mathieu Gendrot
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Priscilla Jardot
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Marion Le Bideau
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Manon Boxberger
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Sébastien Hutter
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Anthony Levasseur
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
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19
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Giraud-Gatineau A, Kaba L, Boschi C, Devaux C, Casalta JP, Gautret P, Chaudet H, Colson P, Raoult D. Control of common viral epidemics but not of SARS-CoV-2 through the application of hygiene and distancing measures. J Clin Virol 2022; 150-151:105163. [PMID: 35472752 PMCID: PMC9013017 DOI: 10.1016/j.jcv.2022.105163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 03/12/2022] [Accepted: 04/13/2022] [Indexed: 12/21/2022]
Abstract
Background We systematically survey respiratory and gastrointestinal infections of viral origin in samples sent to our university hospital institute in Marseille, southern France. Here, we evaluated whether the measures implemented to fight COVID-19 had an effect on the dynamics of viral respiratory or gastrointestinal infections. Methods We analysed PCR performed and positive for the diagnoses of viral respiratory and gastrointestinal infections over five years (January 2017-February 2021). Data were collected from our epidemiological surveillance system (MIDaS). Dates and contents of French measures against SARS-CoV-2 were collected from: https://www.gouvernement.fr/info-coronavirus/les-actions-du-gouvernement. Results Over the 2017-2021 period, 990,364 analyses were carried out for respiratory infections not including SARS-CoV-2, 510,671 for SARS-CoV-2 and 27,719 for gastrointestinal infections. During winter 2020–2021, when the most restrictive lockdown measures were in place in France, a marked decrease of infections with influenza viruses (one case versus 1,839-1,850 cases during 2017-2020 cold seasons) and with the RSV (56 cases versus 988-1,196 cases during 2017-2020 cold seasons) was observed, demonstrating the relative effectiveness of these measures on their occurrence. SARS-CoV-2 incidence seemed far less affected. Rhinoviruses, parainfluenza 3 virus, and the coronavirus NL63 remained at comparable levels. Also, the norovirus winter season positivity rates decreased continuously and significantly over time from 9.3% in 2017–2018 to 2.0% in 2020–2021. Conclusion The measures taken to control COVID-19 were effective against lower respiratory tract infections viruses and gastroenteritis agents, but not on the agents of the common winter cold and SARS-CoV-2. This suggests that more specific measures to prevent COVID-19 and upper respiratory tract infections need to be discovered to limit the spread of this epidemic.
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Affiliation(s)
- Audrey Giraud-Gatineau
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France;; French Armed Forces Center for Epidemiology and Public Health (CESPA), Service de Santé des Armées (SSA), camp de Sainte Marthe, BP 40026, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Lancei Kaba
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France;; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France; Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | - Jean-Paul Casalta
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France;; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France;; French Armed Forces Center for Epidemiology and Public Health (CESPA), Service de Santé des Armées (SSA), camp de Sainte Marthe, BP 40026, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.
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20
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Clinical Significance of COVID-19 and Diabetes: In the Pandemic Situation of SARS-CoV-2 Variants including Omicron (B.1.1.529). BIOLOGY 2022; 11:biology11030400. [PMID: 35336774 PMCID: PMC8945151 DOI: 10.3390/biology11030400] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023]
Abstract
Simple Summary Amidst the dual pandemics of diabetes and coronavirus disease 2019 (COVID-19), with the constant emergence of novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a vicious cycle has been created, i.e., a hyperglycemic state contributes to the severe clinical course of COVID-19, which in turn has deleterious effects on glycometabolism and in some cases causes new-onset diabetes. Here, we present a comprehensive review of the current literature on the clinical and experimental findings associated with the interrelationship between diabetes and COVID-19. To control disease outcomes and glucometabolic complications in COVID-19, this issue is still being investigated. Abstract The coronavirus disease 2019 (COVID-19) global pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains uncontrolled, with the spread of emerging variants. According to accumulating evidence, diabetes is one of the leading risk factors for a severe COVID-19 clinical course, depending on the glycemic state before admission and during COVID-19 hospitalization. Multiple factors are thought to be responsible, including an altered immune response, coexisting comorbidity, and disruption of the renin-angiotensin system through the virus–host interaction. However, the precise underlying mechanisms remain under investigation. Alternatively, the focus is currently on the diabetogenic and ketosis-prone potential of SARS-CoV-2 itself, even for probable triggers of stress and steroid-induced hyperglycemia in COVID-19. In this article, we present a comprehensive review of the recent literature on the clinical and experimental findings associated with diabetes and COVID-19, and we discuss their bidirectional relationship, i.e., the risk for an adverse prognosis and the deleterious effects on glycometabolism. Accurate assessments of the incidence of new-onset diabetes induced by COVID-19 and its pathogenicity are still unknown, especially in the context of the circulation of SARS-CoV-2 variants, such as Omicron (B.1.1.529), which is a major challenge for the future.
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21
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Hoang VT, Assoumani L, Delerce J, Houhamdi L, Bedotto M, Lagier JC, Million M, Levasseur A, Fournier PE, La Scola B, Raoult D, Gautret P, Colson P. Introduction of the SARS-CoV-2 Beta variant from Comoros into the Marseille geographical area. Travel Med Infect Dis 2022; 46:102277. [PMID: 35158042 PMCID: PMC8837475 DOI: 10.1016/j.tmaid.2022.102277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/26/2022] [Accepted: 02/08/2022] [Indexed: 10/28/2022]
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22
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Chu DT, Vu Ngoc SM, Vu Thi H, Nguyen Thi YV, Ho TT, Hoang VT, Singh V, Al-Tawfiq JA. COVID-19 in Southeast Asia: current status and perspectives. Bioengineered 2022; 13:3797-3809. [PMID: 35081861 PMCID: PMC8974206 DOI: 10.1080/21655979.2022.2031417] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Coronavirus Disease-2019 (COVID-19) has spread globally with catastrophic damages to the public health, social and economy since the beginning of the outbreak. In 2020, Southeast Asia proved that it could prevent the worst effects of a pandemic through the closure of activities and borders and movement restriction, as well as social distancing. Nevertheless, with the occurrence of the common variants of concern (VOCs), especially Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), Southeast Asia is facing a significant increase in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections. Now, the area also has the threats of the spreading out of the dangerous variant – Omicron (B.1.1.529) from other close countries or regions. COVID-19 countermeasures such as closures and social distancing seem to be insufficient. Moreover, Southeast Asia is being held back by a shortage of vaccines and other medical resources. This work focuses on describing the COVID-19 situation, the virus variants, and the coverage of COVID-19 vaccination in the area. We also provide perspectives on the COVID-19 vaccine distribution, protecting the economic capitals, developing the green zone, and the importance of finding more vaccine supplies in Southeast Asia.
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Affiliation(s)
- Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.,Department of Natural Science and Technology, International School, Vietnam National University, Hanoi, Vietnam
| | - Suong-Mai Vu Ngoc
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Yen-Vy Nguyen Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Thuy-Tien Ho
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Van-Thuan Hoang
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, India
| | - Jaffar A Al-Tawfiq
- Infectious Disease Unit, Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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23
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Harirugsakul K, Wainipitapong S, Phannajit J, Paitoonpong L, Tantiwongse K. Erectile dysfunction among Thai patients with COVID-19 infection. Transl Androl Urol 2022; 10:4376-4383. [PMID: 35070819 PMCID: PMC8749063 DOI: 10.21037/tau-21-807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2021] [Indexed: 02/06/2023] Open
Abstract
Background Erectile dysfunction (ED) is suspected to be the symptom manifestation of COVID-19. However, scarce data was presented this day. Our study was conducted to determine the prevalence of ED and its associated factors among Thai patients with COVID-19. Methods Sexually active males with COVID-19, hospitalized between May and July 2021 at one university hospital in Bangkok, were screened for erectile dysfunction by the International Index of Erectile Function 5 (IIEF-5). Demographic data and COVID-19 treatment history were collected. Mental health status, including depression and anxiety, was evaluated with the Thai Patient Health Questionnaire 9 (PHQ-9) and the Generalized Anxiety Disorder Scale (GAD-7), respectively. The sample size was calculated, and logistic regression was used to analyze the association. Results One hundred fifty-three men with COVID-19 were recruited. ED prevalence was 64.7%, of which severity was mostly mild. Logistic regression, adjusted for age, BMI, and medical comorbidities, portrayed a significant association between ED and mental health status. Higher risk of ED was found in participants with major depression [adjusted OR 8.45, 95% CI: 1.01–70.96, P=0.049] and higher GAD-7 total score [adjusted OR 1.15, 95% CI: 1.01–1.31, P=0.039]. Conclusions Thai patients with COVID-19 had high prevalence of ED, which was associated with mental disorders. Thus, screening for mental problems is recommended in individuals with COVID-19 and ED.
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Affiliation(s)
- Kawintharat Harirugsakul
- Division of Urology, Department of Surgery, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Sorawit Wainipitapong
- Department of Psychiatry and Center of Excellence in Transgender Health (CETH), Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Jeerath Phannajit
- Division of Clinical Epidemiology and Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Leilani Paitoonpong
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Kavirach Tantiwongse
- Division of Urology, Department of Surgery, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
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24
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Zhang L, Chen J, He M, Su X. Molecular dynamics simulation‐guided toehold mediated strand displacement probe for single‐nucleotide variants detection. EXPLORATION 2022; 2:20210265. [PMCID: PMC10190925 DOI: 10.1002/exp.20210265] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/03/2021] [Indexed: 06/16/2023]
Abstract
Single nucleotide variant (SNV) has become an emerging biomarker for various diseases such as cancers and infectious diseases. Toehold‐mediated strand displacement (TMSD), the core reaction of DNA nanotechnology, has been widely leveraged to identify SNVs. However, inappropriate choice of mismatch location results in poor discrimination ability. Here, we comprehensively investigate the effect of mismatch location on TMSD kinetics by molecular dynamic simulation tool oxDNA through umbrella sampling and forward flux sampling disclosing that mismatches at the border of the toehold and branch migration domain yield the lowest TMSD reaction rate. Nine disease‐related SNVs (SARS‐CoV‐2‐D614G, EGFR‐L858R, EGFR‐T790M, KRAS‐G12R, etc.) were tested experimentally showing a good agreement with simulation. The best choice of mismatch location enables high discrimination factor with a median of 124 for SNV and wild type. Coupling with a probe‐sink system, a low variant allele frequency of 0.1% was detected with 3 S/N. We successfully used the probes to detect SNVs with high confidence in the PCR clones of constructed plasmids. This work provides mechanistic insights into TMSD process at the single‐nucleotide level and can be a guidance for the design of TMSD system with fine‐tuning kinetics for various applications in biosensors and nanotechnology.
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Affiliation(s)
- Linghao Zhang
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Jing Chen
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Mengya He
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Xin Su
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
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25
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Zhang M, Liang Y, Yu D, Du B, Cheng W, Li L, Yu Z, Luo S, Zhang Y, Wang H, Zhang X, Zhang W. A systematic review of Vaccine Breakthrough Infections by SARS-CoV-2 Delta Variant. Int J Biol Sci 2022; 18:889-900. [PMID: 35002532 PMCID: PMC8741840 DOI: 10.7150/ijbs.68973] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022] Open
Abstract
Vaccines are proving to be highly effective in controlling hospitalization and deaths associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as shown by clinical trials and real-world evidence. However, a deadly second wave of coronavirus disease 2019 (COVID-19), infected by SARS-CoV-2 variants, especially the Delta (B.1.617.2) variant, with an increased number of post-vaccination breakthrough infections were reported in the world recently. Actually, Delta variant not only resulted in a severe surge of vaccine breakthrough infections which was accompanied with high viral load and transmissibility, but also challenged the development of effective vaccines. Therefore, the biological characteristics and epidemiological profile of Delta variant, the current status of Delta variant vaccine breakthrough infections and the mechanism of vaccine breakthrough infections were discussed in this article. In addition, the significant role of the Delta variant spike (S) protein in the mechanism of immune escape of SARS-CoV-2 was highlighted in this article. In particular, we further discussed key points on the future SARS-CoV-2 vaccine research and development, hoping to make a contribution to the early, accurate and rapid control of the COVID-19 epidemic.
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Affiliation(s)
- Mengxin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Ying Liang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Bang Du
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Shuying Luo
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Huanmin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Xianwei Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
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26
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Jalil M, Pietras J, Ahmed SN, Daniels P, Hostoffer R. COVID-19 Infection in Patients with Humoral Immunodeficiency: A Case Series and Literature Review. ALLERGY & RHINOLOGY 2022; 13:21526575221096044. [PMID: 35496893 PMCID: PMC9047039 DOI: 10.1177/21526575221096044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background The coronavirus 2019 disease (COVID-19) has infected many individuals worldwide and continues to pose a significant threat to those with weakened immune systems. The data evaluating the clinical outcomes of patients with humoral immunodeficiencies that contract COVID-19 is limited and conflicting. Objective To describe the clinical outcomes of COVID-19 infections in patients with primary humoral immunodeficiency and compare results to current literature. Methods We conducted a retrospective cohort review on 15 patients with a humoral immunodeficiency defined as Common Variable Immunodeficiency, Specific Antibody Deficiency, or unspecified hypogammaglobulinemia, who contracted COVID-19. Severity scores were determined to evaluate the clinical outcomes of these patients. Results Of our 15-patient cohort, 33% of individuals with a humoral immunodeficiency infected with COVID-19 had moderate to severe disease, requiring hospitalization or resulting in death. COVID-19 mortality rate was found to be 7%. All 5 of our patients with severe COVID-19 infection had at least 1 comorbidity or risk factor. Conclusion Within our cohort of humoral immunodeficient patients infected with COVID-19, we found a higher rate of moderate to severe COVID-19 infection and worse clinical outcomes, particularly in patients with comorbidities or risk factors.
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Affiliation(s)
- Maaz Jalil
- Cleveland Medical Center, University Hospitals, Cleveland, Ohio, USA
| | - Julianne Pietras
- Lake Erie College of Osteopathic Medicine, Erie, Pennsylvania, USA
| | - Syed N. Ahmed
- Lake Erie College of Osteopathic Medicine, Erie, Pennsylvania, USA
| | - Phuong Daniels
- Lake Erie College of Osteopathic Medicine, Erie, Pennsylvania, USA
| | - Robert Hostoffer
- Cleveland Medical Center, University Hospitals, Cleveland, Ohio, USA
- Allergy/Immunology Associates Inc., Mayfield Heights, Ohio, USA
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27
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Power H, Wu J, Turville S, Aggarwal A, Valtchev P, Schindeler A, Dehghani F. Virtual screening and in vitro validation of natural compound inhibitors against SARS-CoV-2 spike protein. Bioorg Chem 2021; 119:105574. [PMID: 34971947 PMCID: PMC8693770 DOI: 10.1016/j.bioorg.2021.105574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/24/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus has led to a major public health burden and has resulted in millions of deaths worldwide. As effective treatments are limited, there is a significant requirement for high-throughput, low resource methods for the discovery of novel antivirals. The SARS-CoV-2 spike protein plays a key role in viral entry and has been identified as a therapeutic target. Using the available spike crystal structure, we performed a virtual screen with a library of 527 209 natural compounds against the receptor binding domain of this protein. Top hits from this screen were subjected to a second, more comprehensive molecular docking experiment and filtered for favourable ADMET properties. The in vitro activity of 10 highly ranked compounds was assessed using a virus neutralisation assay designed to facilitate viral entry in a physiologically relevant manner via the plasma membrane route. Subsequently, four compounds ZINC02111387, ZINC02122196, SN00074072 and ZINC04090608 were identified to possess antiviral activity in the µM range. These findings validate the virtual screening method as a tool for identifying novel antivirals and provide a basis for future drug development against SARS-CoV-2.
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Affiliation(s)
- Helen Power
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia,Bioengineering and Molecular Medicine Laboratory, The Children’s Hospital at Westmead and Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Jiadai Wu
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Stuart Turville
- The Kirby Institute, University of NSW, Kensington, NSW 2052, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of NSW, Kensington, NSW 2052, Australia
| | - Peter Valtchev
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Aaron Schindeler
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia,Bioengineering and Molecular Medicine Laboratory, The Children’s Hospital at Westmead and Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia,Corresponding author
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28
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Poudel S, Ishak A, Perez-Fernandez J, Garcia E, León-Figueroa DA, Romaní L, Bonilla-Aldana DK, Rodriguez-Morales AJ. Highly mutated SARS-CoV-2 Omicron variant sparks significant concern among global experts - What is known so far? Travel Med Infect Dis 2021; 45:102234. [PMID: 34896326 PMCID: PMC8666662 DOI: 10.1016/j.tmaid.2021.102234] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Sujan Poudel
- Division of Research and Academic Affairs, Larkin Community Hospital, South Miami, USA
| | - Angela Ishak
- Division of Research and Academic Affairs, Larkin Community Hospital, South Miami, USA
| | - Javier Perez-Fernandez
- Program Director, Pulmonary and Critical Care Fellowship Training Program, Larkin University, Miami, USA
| | - Efrain Garcia
- Program Director, Infectious Disease Fellowship Training Program, Larkin Community Hospital, Miami, USA
| | - Darwin A León-Figueroa
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Chiclayo, Peru; Sociedad Científica Médico Estudiantil Peruana, Lima, Peru; Sociedad Científica de Estudiantes de Medicina Veritas (SCIEMVE), Chiclayo, Peru; Emerge, Unidad de Investigación en Enfermedades Emergentes y Cambio Climático, Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia. Lima, Peru
| | - Luccio Romaní
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Chiclayo, Peru; Sociedad Científica de Estudiantes de Medicina Veritas (SCIEMVE), Chiclayo, Peru; Emerge, Unidad de Investigación en Enfermedades Emergentes y Cambio Climático, Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia. Lima, Peru
| | - D Katterine Bonilla-Aldana
- Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación GISCA, Fundación Universitaria Autónoma de Las Américas, Pereira, Risaralda, Colombia; Latin American Network of Coronavirus Disease 2019 Research (LANCOVID), Pereira, 660003, Colombia; Institución Universitaria Visión de las Américas, Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Latin American Network of Coronavirus Disease 2019 Research (LANCOVID), Pereira, 660003, Colombia; Grupo de Investigacion Biomedicina, Faculty of Medicine, Fundacion Universitaria Autonoma de Las Americas, Pereira, Risaralda, Colombia; Universidad Cientifica Del Sur, Lima, Peru; School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia; Institución Universitaria Visión de las Américas, Pereira, Risaralda, Colombia.
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Bayarri-Olmos R, Johnsen LB, Idorn M, Reinert LS, Rosbjerg A, Vang S, Hansen CB, Helgstrand C, Bjelke JR, Bak-Thomsen T, Paludan SR, Garred P, Skjoedt MO. The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. eLife 2021; 10:e70002. [PMID: 34821555 PMCID: PMC8635972 DOI: 10.7554/elife.70002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/24/2021] [Indexed: 12/26/2022] Open
Abstract
The alpha/B.1.1.7 SARS-CoV-2 lineage emerged in autumn 2020 in the United Kingdom and transmitted rapidly until winter 2021 when it was responsible for most new COVID-19 cases in many European countries. The incidence domination was likely due to a fitness advantage that could be driven by the receptor-binding domain (RBD) residue change (N501Y), which also emerged independently in other variants of concern such as the beta/B.1.351 and gamma/P.1 strains. Here, we present a functional characterization of the alpha/B.1.1.7 variant and show an eightfold affinity increase towards human angiotensin-converting enzyme-2 (ACE-2). In accordance with this, transgenic hACE2 mice showed a faster disease progression and severity after infection with a low dose of B.1.1.7, compared to an early 2020 SARS-CoV-2 isolate. When challenged with sera from convalescent individuals or anti-RBD monoclonal antibodies, the N501Y variant showed a minor, but significant elevated evasion potential of ACE-2/RBD antibody neutralization. The data suggest that the single asparagine to tyrosine substitution remarkable rise in affinity may be responsible for the higher transmission rate and severity of the B.1.1.7 variant.
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Affiliation(s)
- Rafael Bayarri-Olmos
- Recombinant Protein and Antibody Laboratory, Copenhagen University HospitalCopenhagenDenmark
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet Copenhagen University HospitalCopenhagenDenmark
| | | | - Manja Idorn
- Department of Biomedicine, Aarhus UniversityÅrhusDenmark
| | - Line S Reinert
- Department of Biomedicine, Aarhus UniversityÅrhusDenmark
| | - Anne Rosbjerg
- Recombinant Protein and Antibody Laboratory, Copenhagen University HospitalCopenhagenDenmark
- Institute of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University HospitalAarhusDenmark
| | - Cecilie Bo Hansen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet Copenhagen University HospitalCopenhagenDenmark
| | | | | | | | | | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet Copenhagen University HospitalCopenhagenDenmark
| | - Mikkel-Ole Skjoedt
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet Copenhagen University HospitalCopenhagenDenmark
- Institute of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
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von Bartheld CS, Hagen MM, Butowt R. The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. ACS Chem Neurosci 2021; 12:3535-3549. [PMID: 34533304 PMCID: PMC8482322 DOI: 10.1021/acschemneuro.1c00542] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
The prevalence of chemosensory dysfunction in patients with COVID-19 varies greatly between populations. It is unclear whether such differences are due to factors at the level of the human host, or at the level of the coronavirus, or both. At the host level, the entry proteins which allow virus binding and entry have variants with distinct properties, and the frequency of such variants differs between ethnicities. At the level of the virus, the D614G mutation enhances virus entry to the host cell. Since the two virus strains (D614 and G614) coexisted in the first six months of the pandemic in most populations, it has been difficult to distinguish between contributions of the virus and contributions of the host for anosmia. To answer this question, we conducted a systematic review and meta-analysis of studies in South Asian populations when either the D614 or the G614 virus was dominant. We show that populations infected predominantly with the G614 virus had a much higher prevalence of anosmia (pooled prevalence of 31.8%) compared with the same ethnic populations infected mostly with the D614 virus strain (pooled anosmia prevalence of 5.3%). We conclude that the D614G mutation is a major contributing factor that increases the prevalence of anosmia in COVID-19, and that this enhanced effect on olfaction constitutes a previously unrecognized phenotype of the D614G mutation. The new virus strains that have additional mutations on the background of the D614G mutation can be expected to cause a similarly increased prevalence of chemosensory dysfunctions.
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Affiliation(s)
- Christopher S. von Bartheld
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Molly M. Hagen
- School of Public Health, University of Nevada, Reno, Nevada 89557, USA
| | - Rafal Butowt
- L. Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094 Bydgoszcz, Poland
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31
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Hoang VT, Colson P, Levasseur A, Delerce J, Lagier JC, Parola P, Million M, Fournier PE, Raoult D, Gautret P. Clinical outcomes in patients infected with different SARS-CoV-2 variants at one hospital during three phases of the COVID-19 epidemic in Marseille, France. INFECTION GENETICS AND EVOLUTION 2021; 95:105092. [PMID: 34571275 PMCID: PMC8462069 DOI: 10.1016/j.meegid.2021.105092] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 02/07/2023]
Abstract
Objectives To compare the demographics, clinical characteristics and severity of patients infected with nine different SARS-CoV-2 variants, during three phases of the COVID-19 epidemic in Marseille. Methods A single centre retrospective cohort study was conducted in 1760 patients infected with SARS-CoV-2 of Nextstrain clades 20A, 20B, and 20C (first phase, February–May 2020), Pangolin lineages B.1.177 (we named Marseille-2) and B.1.160 (Marseille-4) variants (second phase, June–December 2020), and B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and A.27 (Marseille-501) variants (third phase, January 2021-today). Outcomes were the occurrence of clinical failures, including hospitalisation, transfer to the intensive-care unit, and death. Results During each phase, no major differences were observed with regards to age and gender distribution, the prevalence of chronic diseases, and clinical symptoms between variants circulating in a given phase. The B.1.177 and B.1.160 variants were associated with more severe outcomes. Infections occurring during the second phase were associated with a higher rate of death as compared to infections during the first and third phases. Patients in the second phase were more likely to be hospitalised than those in the third phase. Patients infected during the third phase were more frequently obese than others. Conclusion: A large cohort study is recommended to evaluate the transmissibility and to better characterise the clinical severity of emerging variants.
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Affiliation(s)
- Van-Thuan Hoang
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Anthony Levasseur
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | | | - Jean-Christophe Lagier
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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