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Liu Z, Petinrin OO, Chen N, Toseef M, Liu F, Zhu Z, Qi F, Wong KC. Identification and evaluation of candidate COVID-19 critical genes and medicinal drugs related to plasma cells. BMC Infect Dis 2024; 24:1099. [PMID: 39363208 PMCID: PMC11451256 DOI: 10.1186/s12879-024-10000-3] [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: 12/25/2023] [Accepted: 09/25/2024] [Indexed: 10/05/2024] Open
Abstract
The ongoing COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents one of the most significant global health crises in recent history. Despite extensive research into the immune mechanisms and therapeutic options for COVID-19, there remains a paucity of studies focusing on plasma cells. In this study, we utilized the DESeq2 package to identify differentially expressed genes (DEGs) between COVID-19 patients and controls using datasets GSE157103 and GSE152641. We employed the xCell algorithm to perform immune infiltration analyses, revealing notably elevated levels of plasma cells in COVID-19 patients compared to healthy individuals. Subsequently, we applied the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm to identify COVID-19 related plasma cell module genes. Further, positive cluster biomarker genes for plasma cells were extracted from single-cell RNA sequencing data (GSE171524), leading to the identification of 122 shared genes implicated in critical biological processes such as cell cycle regulation and viral infection pathways. We constructed a robust protein-protein interaction (PPI) network comprising 89 genes using Cytoscape, and identified 20 hub genes through cytoHubba. These genes were validated in external datasets (GSE152418 and GSE179627). Additionally, we identified three potential small molecules (GSK-1070916, BRD-K89997465, and idarubicin) that target key hub genes in the network, suggesting a novel therapeutic approach. These compounds were characterized by their ability to down-regulate AURKB, KIF11, and TOP2A effectively, as evidenced by their low free binding energies determined through computational analyses using cMAP and AutoDock. This study marks the first comprehensive exploration of plasma cells' role in COVID-19, offering new insights and potential therapeutic targets. It underscores the importance of a systematic approach to understanding and treating COVID-19, expanding the current body of knowledge and providing a foundation for future research.
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Affiliation(s)
- Zhe Liu
- Institute for Hepatology, The Second Affiliated Hospital, School of Medicine, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | | | - Nanjun Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Muhammad Toseef
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Fang Liu
- Rocgene (Beijing) Technology Co., Ltd, Beijing, Beijing, 102200, China
| | - Zhongxu Zhu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
| | - Furong Qi
- Institute for Hepatology, The Second Affiliated Hospital, School of Medicine, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China.
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China.
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China.
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2
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Hotowy A, Strojny-Cieślak B, Ostrowska A, Zielińska-Górska M, Kutwin M, Wierzbicki M, Sosnowska M, Jaworski S, Chwalibóg A, Kotela I, Sawosz Chwalibóg E. Silver and Carbon Nanomaterials/Nanocomplexes as Safe and Effective ACE2-S Binding Blockers on Human Skin Cell Lines. Molecules 2024; 29:3581. [PMID: 39124987 PMCID: PMC11313757 DOI: 10.3390/molecules29153581] [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: 06/28/2024] [Revised: 07/19/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
(1) Background: Angiotensin-converting enzyme 2 (ACE2) is a crucial functional receptor of the SARS-CoV-2 virus. Although the scale of infections is no longer at pandemic levels, there are still fatal cases. The potential of the virus to infect the skin raises questions about new preventive measures. In the context of anti-SARS-CoV-2 applications, the interactions of antimicrobial nanomaterials (silver, Ag; diamond, D; graphene oxide, GO and their complexes) were examined to assess their ability to affect whether ACE2 binds with the virus. (2) Methods: ACE2 inhibition competitive tests and in vitro treatments of primary human adult epidermal keratinocytes (HEKa) and primary human adult dermal fibroblasts (HDFa) were performed to assess the blocking capacity of nanomaterials/nanocomplexes and their toxicity to cells. (3) Results: The nanocomplexes exerted a synergistic effect compared to individual nanomaterials. HEKa cells were more sensitive than HDFa cells to Ag treatments and high concentrations of GO. Cytotoxic effects were not observed with D. In the complexes, both carbonic nanomaterials had a soothing effect against Ag. (4) Conclusions: The Ag5D10 and Ag5GO10 nanocomplexes seem to be most effective and safe for skin applications to combat SARS-CoV-2 infection by blocking ACE2-S binding. These nanocomplexes should be evaluated through prolonged in vivo exposure. The expected low specificity enables wider applications.
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Affiliation(s)
- Anna Hotowy
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland; (B.S.-C.); (A.O.); (M.Z.-G.); (M.K.); (M.W.); (M.S.); (S.J.); (E.S.C.)
| | - Barbara Strojny-Cieślak
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland; (B.S.-C.); (A.O.); (M.Z.-G.); (M.K.); (M.W.); (M.S.); (S.J.); (E.S.C.)
| | - Agnieszka Ostrowska
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland; (B.S.-C.); (A.O.); (M.Z.-G.); (M.K.); (M.W.); (M.S.); (S.J.); (E.S.C.)
| | - Marlena Zielińska-Górska
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland; (B.S.-C.); (A.O.); (M.Z.-G.); (M.K.); (M.W.); (M.S.); (S.J.); (E.S.C.)
| | - Marta Kutwin
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland; (B.S.-C.); (A.O.); (M.Z.-G.); (M.K.); (M.W.); (M.S.); (S.J.); (E.S.C.)
| | - Mateusz Wierzbicki
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland; (B.S.-C.); (A.O.); (M.Z.-G.); (M.K.); (M.W.); (M.S.); (S.J.); (E.S.C.)
| | - Malwina Sosnowska
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland; (B.S.-C.); (A.O.); (M.Z.-G.); (M.K.); (M.W.); (M.S.); (S.J.); (E.S.C.)
| | - Sławomir Jaworski
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland; (B.S.-C.); (A.O.); (M.Z.-G.); (M.K.); (M.W.); (M.S.); (S.J.); (E.S.C.)
| | - André Chwalibóg
- Section of Production, Nutrition and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark
| | - Ireneusz Kotela
- Department of Orthopaedics, National Medical Institute of the Ministry of the Interior and Administration, 02-507 Warsaw, Poland;
- Collegium Medicum, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland
| | - Ewa Sawosz Chwalibóg
- Department of Nanobiotechnology, Warsaw University of Life Sciences, 02-786 Warsaw, Poland; (B.S.-C.); (A.O.); (M.Z.-G.); (M.K.); (M.W.); (M.S.); (S.J.); (E.S.C.)
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Huang Y, Chen J, Chen S, Huang C, Li B, Li J, Jin Z, Zhang Q, Pan P, Du W, Liu L, Liu Z. Molecular characterization of SARS-CoV-2 nucleocapsid protein. Front Cell Infect Microbiol 2024; 14:1415885. [PMID: 38846351 PMCID: PMC11153676 DOI: 10.3389/fcimb.2024.1415885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 06/09/2024] Open
Abstract
Corona Virus Disease 2019 (COVID-19) is a highly prevalent and potent infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Until now, the world is still endeavoring to develop new ways to diagnose and treat COVID-19. At present, the clinical prevention and treatment of COVID-19 mainly targets the spike protein on the surface of SRAS-CoV-2. However, with the continuous emergence of SARS-CoV-2 Variants of concern (VOC), targeting the spike protein therapy shows a high degree of limitation. The Nucleocapsid Protein (N protein) of SARS-CoV-2 is highly conserved in virus evolution and is involved in the key process of viral infection and assembly. It is the most expressed viral structural protein after SARS-CoV-2 infection in humans and has high immunogenicity. Therefore, N protein as the key factor of virus infection and replication in basic research and clinical application has great potential research value. This article reviews the research progress on the structure and biological function of SARS-CoV-2 N protein, the diagnosis and drug research of targeting N protein, in order to promote researchers' further understanding of SARS-CoV-2 N protein, and lay a theoretical foundation for the possible outbreak of new and sudden coronavirus infectious diseases in the future.
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Affiliation(s)
- Yanping Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Junkai Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Siwei Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Congcong Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Bei Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixiong Jin
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Qiwei Zhang
- Central Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Pan Pan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [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: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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5
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Hong SM, Kim SJ, An SH, Kim J, Ha EJ, Kim H, Kwon HJ, Choi KS. Receptor binding motif surrounding sites in the spike 1 protein of infectious bronchitis virus have high susceptibility to mutation related to selective pressure. J Vet Sci 2023; 24:e51. [PMID: 37532296 PMCID: PMC10404704 DOI: 10.4142/jvs.23039] [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: 02/03/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND To date, various genotypes of infectious bronchitis virus (IBV) have co-circulated and in Korea, GI-15 and GI-19 lineages were prevailing. The spike protein, particularly S1 subunit, is responsible for receptor binding, contains hypervariable regions and is also responsible for the emerging of novel variants. OBJECTIVE This study aims to investigate the putative major amino acid substitutions for the variants in GI-19. METHODS The S1 sequence data of IBV isolated from 1986 to 2021 in Korea (n = 188) were analyzed. Sequence alignments were carried out using Multiple alignment using Fast Fourier Transform of Geneious prime. The phylogenetic tree was generated using MEGA-11 (ver. 11.0.10) and Bayesian analysis was performed by BEAST v1.10.4. Selective pressure was analyzed via online server Datamonkey. Highlights and visualization of putative critical amino acid were conducted by using PyMol software (version 2.3). RESULTS Most (93.5%) belonged to the GI-19 lineage in Korea, and the GI-19 lineage was further divided into seven subgroups: KM91-like (Clade A and B), K40/09-like, QX-like (I-IV). Positive selection was identified at nine and six residues in S1 for KM91-like and QX-like IBVs, respectively. In addition, several positive selection sites of S1-NTD were indicated to have mutations at common locations even when new clades were generated. They were all located on the lateral surface of the quaternary structure of the S1 subunits in close proximity to the receptor-binding motif (RBM), putative RBM motif and neutralizing antigenic sites in S1. CONCLUSIONS Our results suggest RBM surrounding sites in the S1 subunit of IBV are highly susceptible to mutation by selective pressure during evolution.
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Affiliation(s)
- Seung-Min Hong
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Rsearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Seung-Ji Kim
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Se-Hee An
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Jiye Kim
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Eun-Jin Ha
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Howon Kim
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Hyuk-Joon Kwon
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Rsearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Laboratory of Poultry Medicine, Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, Pyeongchang 25354, Korea
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Rsearch Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
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Kapten K, Orczyk K, Smolewska E. Immunity in SARS-CoV-2 Infection: Clarity or Mystery? A Broader Perspective in the Third Year of a Worldwide Pandemic. Arch Immunol Ther Exp (Warsz) 2023; 71:7. [PMID: 36810662 PMCID: PMC9943048 DOI: 10.1007/s00005-023-00673-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its mechanisms have been thoroughly studied by researchers all over the world with the hope of finding answers that may aid the discovery of new treatment options or effective means of prevention. Still, over 2 years into the pandemic that is an immense burden on health care and economic systems, there seem to be more questions than answers. The character and multitude of immune responses elicited in coronavirus disease 2019 (COVID-19) vary from uncontrollable activation of the inflammatory system, causing extensive tissue damage and consequently leading to severe or even fatal disease, to mild or asymptomatic infections in the majority of patients, resulting in the unpredictability of the current pandemic. The aim of the study was to systematize the available data regarding the immune response to SARS-CoV-2, to provide some clarification among the abundance of the knowledge available. The review contains concise and current information on the most significant immune reactions to COVID-19, including components of both innate and adaptive immunity, with an additional focus on utilizing humoral and cellular responses as effective diagnostic tools. Moreover, the authors discussed the present state of knowledge on SARS-CoV-2 vaccines and their efficacy in cases of immunodeficiency.
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Affiliation(s)
- Katarzyna Kapten
- Department of Pediatric Cardiology and Rheumatology, Central Teaching Hospital of Medical University of Lodz, Lodz, Poland
| | - Krzysztof Orczyk
- Department of Pediatric Cardiology and Rheumatology, Medical University of Lodz, Sporna 36/50, 91-738, Lodz, Poland
| | - Elzbieta Smolewska
- Department of Pediatric Cardiology and Rheumatology, Medical University of Lodz, Sporna 36/50, 91-738, Lodz, Poland.
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Rapid System to Detect Variants of SARS-CoV-2 in Nasopharyngeal Swabs. Viruses 2023; 15:v15020353. [PMID: 36851567 PMCID: PMC9966895 DOI: 10.3390/v15020353] [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: 09/24/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Currently, the reference method for identifying the presence of variants of SARS-CoV-2 is whole genome sequencing. Although it is less expensive than in the past, it is still time-consuming, and interpreting the results is difficult, requiring staff with specific skills who are not always available in diagnostic laboratories. The test presented in this study aimed to detect, using traditional real-time PCR, the presence of the main variants described for the spike protein of the SARS-CoV-2 genome. The primers and probes were designed to detect the main deletions that characterize the different variants. The amplification targets were deletions in the S gene: 25-27, 69-70, 241-243, and 157-158. In the ORF1a gene, the deletion 3675-3677 was chosen. Some of these mutations can be considered specific variants, while others can be identified by the simultaneous presence of one or more deletions. We avoided using point mutations in order to improve the speed of the test. Our test can help clinical and medical microbiologists quickly recognize the presence of variants in biological samples (particularly nasopharyngeal swabs). The test can also be used to identify variants of the virus that could potentially be more diffusive as well as not responsive to the vaccine.
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Varlas VN, Borș RG, Plotogea M, Iordache M, Mehedințu C, Cîrstoiu MM. Thromboprophylaxis in Pregnant Women with COVID-19: An Unsolved Issue. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1949. [PMID: 36767320 PMCID: PMC9915713 DOI: 10.3390/ijerph20031949] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
SARS-CoV-2 infection in pregnant women is of growing interest due to controversy over the use of antiplatelet and/or anticoagulant drugs during pregnancy and postpartum. Pregnant women are susceptible to develop severe forms of viral infections due to pregnancy-related immune alterations, changes in lung functions, and hypercoagulability. The association of pregnancy with SARS-CoV-2 infection can cause an increased incidence of thrombotic complications, especially in the case of patients with some genetic variants that favor inflammation and thrombosis. Compared to the general population, pregnant women may be at increased risk of thrombotic complications related to COVID-19. The lack of extensive clinical trials on thromboprophylaxis and extrapolating data from non-pregnant patients lead to major discrepancies in treating pregnant women with COVID-19. Currently, a multidisciplinary team should determine the dose and duration of prophylactic anticoagulant therapy for these patients, depending on the disease severity, the course of pregnancy, and the estimated due date. This narrative review aims to evaluate the protective effect of thromboprophylaxis in pregnant women with COVID-19. It is unknown at this time whether antiplatelet or anticoagulant therapy initiated at the beginning of pregnancy for various diseases (preeclampsia, intrauterine growth restriction, thrombophilia) offers a degree of protection. The optimal scheme for thromboprophylaxis in pregnant women with COVID-19 must be carefully established through an individualized decision concerning gestational age and the severity of the infection.
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Affiliation(s)
- Valentin Nicolae Varlas
- Department of Obstetrics and Gynecology, Filantropia Clinical Hospital, 011171 Bucharest, Romania
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu St., 050451 Bucharest, Romania
| | - Roxana Georgiana Borș
- Department of Obstetrics and Gynecology, Filantropia Clinical Hospital, 011171 Bucharest, Romania
| | - Mihaela Plotogea
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu St., 050451 Bucharest, Romania
- Department of Obstetrics and Gynecology, Nicolae Malaxa Clinical Hospital Bucharest, 022441 Bucharest, Romania
| | - Madalina Iordache
- Doctoral School, “Carol Davila”, University of Medicine and Pharmacy, 4192910 Bucharest, Romania
| | - Claudia Mehedințu
- Department of Obstetrics and Gynecology, Filantropia Clinical Hospital, 011171 Bucharest, Romania
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu St., 050451 Bucharest, Romania
| | - Monica Mihaela Cîrstoiu
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu St., 050451 Bucharest, Romania
- Department of Obstetrics and Gynecology, University Emergency Hospital Bucharest, 050098 Bucharest, Romania
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9
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Sokhansanj BA, Rosen GL. Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning. Comput Biol Med 2022; 149:105969. [PMID: 36041271 PMCID: PMC9384346 DOI: 10.1016/j.compbiomed.2022.105969] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/11/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Epidemiological studies show that COVID-19 variants-of-concern, like Delta and Omicron, pose different risks for severe disease, but they typically lack sequence-level information for the virus. Studies which do obtain viral genome sequences are generally limited in time, location, and population scope. Retrospective meta-analyses require time-consuming data extraction from heterogeneous formats and are limited to publicly available reports. Fortuitously, a subset of GISAID, the global SARS-CoV-2 sequence repository, includes "patient status" metadata that can indicate whether a sequence record is associated with mild or severe disease. While GISAID lacks data on comorbidities relevant to severity, such as obesity and chronic disease, it does include metadata for age and sex to use as additional attributes in modeling. With these caveats, previous efforts have demonstrated that genotype-patient status models can be fit to GISAID data, particularly when country-of-origin is used as an additional feature. But are these models robust and biologically meaningful? This paper shows that, in fact, temporal and geographic biases in sequences submitted to GISAID, as well as the evolving pandemic response, particularly reduction in severe disease due to vaccination, create complex issues for model development and interpretation. This paper poses a potential solution: efficient mixed effects machine learning using GPBoost, treating country as a random effect group. Training and validation using temporally split GISAID data and emerging Omicron variants demonstrates that GPBoost models are more predictive of the impact of spike protein mutations on patient outcomes than fixed effect XGBoost, LightGBM, random forests, and elastic net logistic regression models.
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Affiliation(s)
- Bahrad A Sokhansanj
- Ecological and Evolutionary Signal Processing & Informatics Laboratory, Drexel University, 3100 Chestnut St., Philadelphia, PA, 19104, United States of America.
| | - Gail L Rosen
- Ecological and Evolutionary Signal Processing & Informatics Laboratory, Drexel University, 3100 Chestnut St., Philadelphia, PA, 19104, United States of America.
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10
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Lin C, Wang W, Li M, Lin Y, Yang Z, Urbina AN, Assavalapsakul W, Thitithanyanont A, Chen K, Kuo C, Lin Y, Hsiao H, Lin K, Lin S, Chen Y, Yu M, Su L, Wang S. Boosting the detection performance of severe acute respiratory syndrome coronavirus 2 test through a sensitive optical biosensor with new superior antibody. Bioeng Transl Med 2022; 8:e10410. [PMID: 36248235 PMCID: PMC9538096 DOI: 10.1002/btm2.10410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus emerged in late 2019 leading to the COVID-19 disease pandemic that triggered socioeconomic turmoil worldwide. A precise, prompt, and affordable diagnostic assay is essential for the detection of SARS-CoV-2 as well as its variants. Antibody against SARS-CoV-2 spike (S) protein was reported as a suitable strategy for therapy and diagnosis of COVID-19. We, therefore, developed a quick and precise phase-sensitive surface plasmon resonance (PS-SPR) biosensor integrated with a novel generated anti-S monoclonal antibody (S-mAb). Our results indicated that the newly generated S-mAb could detect the original SARS-CoV-2 strain along with its variants. In addition, a SARS-CoV-2 pseudovirus, which could be processed in BSL-2 facility was generated for evaluation of sensitivity and specificity of the assays including PS-SPR, homemade target-captured ELISA, spike rapid antigen test (SRAT), and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Experimentally, PS-SPR exerted high sensitivity to detect SARS-CoV-2 pseudovirus at 589 copies/ml, with 7-fold and 70-fold increase in sensitivity when compared with the two conventional immunoassays, including homemade target-captured ELISA (4 × 103 copies/ml) and SRAT (4 × 104 copies/ml), using the identical antibody. Moreover, the PS-SPR was applied in the measurement of mimic clinical samples containing the SARS-CoV-2 pseudovirus mixed with nasal mucosa. The detection limit of PS-SPR is calculated to be 1725 copies/ml, which has higher accuracy than homemade target-captured ELISA (4 × 104 copies/ml) and SRAT (4 × 105 copies/ml) and is comparable with qRT-PCR (1250 copies/ml). Finally, the ability of PS-SPR to detect SARS-CoV-2 in real clinical specimens was further demonstrated, and the assay time was less than 10 min. Taken together, our results indicate that this novel S-mAb integrated into PS-SPR biosensor demonstrates high sensitivity and is time-saving in SARS-CoV-2 virus detection. This study suggests that incorporation of a high specific recognizer in SPR biosensor is an alternative strategy that could be applied in developing other emerging or re-emerging pathogenic detection platforms.
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Affiliation(s)
- Chih‐Yen Lin
- Department of Medical Laboratory Science and BiotechnologyKaohsiung Medical UniversityKaohsiungTaiwan
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
| | - Wen‐Hung Wang
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐Sen UniversityKaohsiungTaiwan
- Division of Infection Disease, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Meng‐Chi Li
- Thin Film Technology CenterNational Central UniversityTaoyuanTaiwan
- Optical Sciences CenterNational Central UniversityTaoyuanTaiwan
| | - Yu‐Ting Lin
- Department of Medical Laboratory Science and BiotechnologyKaohsiung Medical UniversityKaohsiungTaiwan
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
| | - Zih‐Syuan Yang
- Department of Medical Laboratory Science and BiotechnologyKaohsiung Medical UniversityKaohsiungTaiwan
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
| | - Aspiro Nayim Urbina
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
| | | | | | - Kai‐Ren Chen
- Department of Optics and PhotonicsNational Central UniversityTaoyuanTaiwan
| | - Chien‐Cheng Kuo
- Thin Film Technology CenterNational Central UniversityTaoyuanTaiwan
- Department of Optics and PhotonicsNational Central UniversityTaoyuanTaiwan
| | | | - Hui‐Hua Hsiao
- Division of Hematology and Oncology, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Kun‐Der Lin
- Division of Endocrinology and MetabolismKaohsiung Medical University Hospital, Kaohsiung Medical UniversityKaohsiungTaiwan
| | - Shang‐Yi Lin
- Division of Infection Disease, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
- Department of Laboratory MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Yen‐Hsu Chen
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐Sen UniversityKaohsiungTaiwan
- Division of Infection Disease, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Ming‐Lung Yu
- School of Medicine, College of MedicineNational Sun Yat‐Sen UniversityKaohsiungTaiwan
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis CenterKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Li‐Chen Su
- General Education CenterMing Chi University of TechnologyNew Taipei CityTaiwan
- Organic Electronics Research CenterMing Chi University of TechnologyNew Taipei CityTaiwan
| | - Sheng‐Fan Wang
- Department of Medical Laboratory Science and BiotechnologyKaohsiung Medical UniversityKaohsiungTaiwan
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
- Department of Medical ResearchKaohsiung Medical University HospitalKaohsiungTaiwan
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11
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Masud M, Islam MH, Kim BN. Understanding the Role of Environmental Transmission on COVID-19 Herd Immunity and Invasion Potential. Bull Math Biol 2022; 84:116. [PMID: 36088430 PMCID: PMC9464060 DOI: 10.1007/s11538-022-01070-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/18/2022] [Indexed: 11/28/2022]
Abstract
COVID-19 is caused by the SARS-CoV-2 virus, which is mainly transmitted directly between humans. However, it is observed that this disease can also be transmitted through an indirect route via environmental fomites. The development of appropriate and effective vaccines has allowed us to target and anticipate herd immunity. Understanding of the transmission dynamics and the persistence of the virus on environmental fomites and their resistive role on indirect transmission of the virus is an important scientific and public health challenge because it is essential to consider all possible transmission routes and route specific transmission strength to accurately quantify the herd immunity threshold. In this paper, we present a mathematical model that considers both direct and indirect transmission modes. Our analysis focuses on establishing the disease invasion threshold, investigating its sensitivity to both transmission routes and isolate route-specific transmission rate. Using the tau-leap algorithm, we perform a stochastic model simulation to address the invasion potential of both transmission routes. Our analysis shows that direct transmission has a higher invasion potential than that of the indirect transmission. As a proof of this concept, we fitted our model with early epidemic data from several countries to uniquely estimate the reproduction numbers associated with direct and indirect transmission upon confirming the identifiability of the parameters. As the indirect transmission possess lower invasion potential than direct transmission, proper estimation and necessary steps toward mitigating it would help reduce vaccination requirement.
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Affiliation(s)
- M.A Masud
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451 South Korea
| | - Md. Hamidul Islam
- Department of Applied Mathematics, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Byul Nim Kim
- Institute for Mathematical Convergence, Kyungpook National University, Daegu, 41566 South Korea
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12
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Barozi V, Edkins AL, Tastan Bishop Ö. Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins. Comput Struct Biotechnol J 2022; 20:4562-4578. [PMID: 35989699 PMCID: PMC9384468 DOI: 10.1016/j.csbj.2022.08.015] [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: 07/05/2022] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 11/23/2022] Open
Abstract
The interaction between the Spike (S) protein of SARS-CoV-2 and the human angiotensin converting enzyme 2 (hACE2) is essential for infection, and is a target for neutralizing antibodies. Consequently, selection of mutations in the S protein is expected to be driven by the impact on the interaction with hACE2 and antibody escape. Here, for the first time, we systematically characterized the collective effects of mutations in each of the Omicron sub-lineages (BA.1, BA.2, BA.3 and BA.4) on both the viral S protein receptor binding domain (RBD) and the hACE2 protein using post molecular dynamics studies and dynamic residue network (DRN) analysis. Our analysis suggested that Omicron sub-lineage mutations result in altered physicochemical properties that change conformational flexibility compared to the reference structure, and may contribute to antibody escape. We also observed changes in the hACE2 substrate binding groove in some sub-lineages. Notably, we identified unique allosteric communication paths in the reference protein complex formed by the DRN metrics betweenness centrality and eigencentrality hubs, originating from the RBD core traversing the receptor binding motif of the S protein and the N-terminal domain of the hACE2 to the active site. We showed allosteric changes in residue network paths in both the RBD and hACE2 proteins due to Omicron sub-lineage mutations. Taken together, these data suggest progressive evolution of the Omicron S protein RBD in sub-lineages towards a more efficient interaction with the hACE2 receptor which may account for the increased transmissibility of Omicron variants.
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Affiliation(s)
- Victor Barozi
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6139, South Africa
| | - Adrienne L. Edkins
- The Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6139, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6139, South Africa
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13
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Vitello GA, Federico C, Bruno F, Vinci M, Musumeci A, Ragalmuto A, Sturiale V, Brancato D, Calì F, Saccone S. Allelic Variations in the Human Genes TMPRSS2 and CCR5, and the Resistance to Viral Infection by SARS-CoV-2. Int J Mol Sci 2022; 23:ijms23169171. [PMID: 36012436 PMCID: PMC9409186 DOI: 10.3390/ijms23169171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/18/2022] [Accepted: 08/13/2022] [Indexed: 12/28/2022] Open
Abstract
During the first wave of COVID-19 infection in Italy, the number of cases and the mortality rates were among the highest compared to the rest of Europe and the world. Several studies demonstrated a severe clinical course of COVID-19 associated with old age, comorbidities, and male gender. However, there are cases of virus infection resistance in subjects living in close contact with infected subjects. Thus, to explain the predisposition to virus infection and to COVID-19 disease progression, we must consider, in addition to the genetic variability of the virus and other environmental or comorbidity conditions, the allelic variants of specific human genes, directly or indirectly related to the life cycle of the virus. Here, we analyzed three human genetic polymorphisms belonging to the TMPRSS2 and CCR5 genes in a sample population from Sicily (Italy) to investigate possible correlations with the resistance to viral infection and/or to COVID-19 disease progression as recently described in other human populations. Our results did not show any correlations of the rs35074065, rs12329760, and rs333 polymorphisms with SARS-CoV-2 infection or with COVID-19 disease severity. Further studies on other human genetic polymorphisms should be performed to identify the major human determinants of SARS-CoV-2 viral resistance.
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Affiliation(s)
| | - Concetta Federico
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Francesca Bruno
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Mirella Vinci
- Oasi Research Institute-IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy
| | - Antonino Musumeci
- Oasi Research Institute-IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy
| | - Alda Ragalmuto
- Oasi Research Institute-IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy
| | - Valentina Sturiale
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Desiree Brancato
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Francesco Calì
- Oasi Research Institute-IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy
| | - Salvatore Saccone
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
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14
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Flores-Vega VR, Monroy-Molina JV, Jiménez-Hernández LE, Torres AG, Santos-Preciado JI, Rosales-Reyes R. SARS-CoV-2: Evolution and Emergence of New Viral Variants. Viruses 2022; 14:653. [PMID: 35458383 PMCID: PMC9025907 DOI: 10.3390/v14040653] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent responsible for the coronavirus disease 2019 (COVID-19). The high rate of mutation of this virus is associated with a quick emergence of new viral variants that have been rapidly spreading worldwide. Several mutations have been documented in the receptor-binding domain (RBD) of the viral spike protein that increases the interaction between SARS-CoV-2 and its cellular receptor, the angiotensin-converting enzyme 2 (ACE2). Mutations in the spike can increase the viral spread rate, disease severity, and the ability of the virus to evade either the immune protective responses, monoclonal antibody treatments, or the efficacy of current licensed vaccines. This review aimed to highlight the functional virus classification used by the World Health Organization (WHO), Phylogenetic Assignment of Named Global Outbreak (PANGO), Global Initiative on Sharing All Influenza Data (GISAID), and Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data, the chronological emergence of viral variants of concern (VOCs) and variants of interest (VOIs), the major findings related to the rate of spread, and the mutations in the spike protein that are involved in the evasion of the host immune responses elicited by prior SARS-CoV-2 infections and by the protection induced by vaccination.
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Affiliation(s)
- Verónica Roxana Flores-Vega
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 06726, Mexico; (V.R.F.-V.); (J.V.M.-M.); (J.I.S.-P.)
- Escuela de Ciencias de la Salud, Campus Coyoacán, Universidad del Valle de México, Calzada de Tlalpan 3000, Alcaldía Coyoacán, Mexico City 04910, Mexico;
| | - Jessica Viridiana Monroy-Molina
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 06726, Mexico; (V.R.F.-V.); (J.V.M.-M.); (J.I.S.-P.)
- Escuela de Ciencias de la Salud, Campus Coyoacán, Universidad del Valle de México, Calzada de Tlalpan 3000, Alcaldía Coyoacán, Mexico City 04910, Mexico;
| | - Luis Enrique Jiménez-Hernández
- Escuela de Ciencias de la Salud, Campus Coyoacán, Universidad del Valle de México, Calzada de Tlalpan 3000, Alcaldía Coyoacán, Mexico City 04910, Mexico;
| | - Alfredo G. Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - José Ignacio Santos-Preciado
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 06726, Mexico; (V.R.F.-V.); (J.V.M.-M.); (J.I.S.-P.)
| | - Roberto Rosales-Reyes
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 06726, Mexico; (V.R.F.-V.); (J.V.M.-M.); (J.I.S.-P.)
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15
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Wurtzer S, Waldman P, Levert M, Cluzel N, Almayrac JL, Charpentier C, Masnada S, Gillon-Ritz M, Mouchel JM, Maday Y, Boni M, Marechal V, Moulin L. SARS-CoV-2 genome quantification in wastewaters at regional and city scale allows precise monitoring of the whole outbreaks dynamics and variants spreading in the population. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152213. [PMID: 34896511 PMCID: PMC8656174 DOI: 10.1016/j.scitotenv.2021.152213] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 05/19/2023]
Abstract
SARS-CoV-2 is a coronavirus causing a globalized outbreak called COVID-19. SARS-CoV-2 transmission is associated with inhalation of contaminated respiratory droplets and could causes severe complications. Until today several "waves" of infections have been observed despite implementation of strict health policies. Decisions for such sanitary measures are based on population health monitoring. Unfortunately, for COVID-19, a significant proportion of individuals are asymptomatic but play a role in the virus transmission. To overcome these limitations, several strategies were developed including genome quantification in wastewater that could allow monitoring of the health status of population, since shedding of SARS-CoV-2 in patient stool is frequent. Wastewater-based epidemiology (WBE) was established and several countries implemented this approach to allow COVID-19 outbreak monitoring. In France, the OBEPINE project performed a quantitative analysis of SARS-CoV-2 in raw wastewater samples collected from major wastewater treatment plants (WWTP) since March 2020. In the greater Paris area 1101 samples (507 for five WWTP and 594 for sewer) were collected. This 16 months monitoring allows us to observe the outbreak dynamics. Comparison of WBE indicators with health data lead to several important observation; the good level of correlation with incidence rates, the average 3 days lead time, and the sensitivity (WBE change when incidence is > to 7/100000 inhabitants). We also compared the local monitoring (city level) with the regional monitoring, to help cluster identification. Moreover, variants of concern (VOC) emerged due to the selection pressure. We developed a specific RT-qPCR method targeting the deletion H69-V70 in the spike protein, using this deletion as a proxy of the B.1.1.7 presence in the wastewater. With this data we demonstrate the predominant role played by this strain in the third wave. All these results allow a better description and understanding of the pandemic and highlight the role of such WBE indicators.
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Affiliation(s)
- S Wurtzer
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France
| | - P Waldman
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, Paris, France
| | - M Levert
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - N Cluzel
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - J L Almayrac
- SIAAP, Service process-laboratoire SIAAP site Seine Amont, Valenton, France
| | - C Charpentier
- Service de Virologie, Université de Paris, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - S Masnada
- SIAM - STV, Avenue de la courtiere, 77400 Saint Thibault des vignes, France
| | - M Gillon-Ritz
- Direction de la Propreté et de l'Eau - Service Technique de l'Eau et de l'Assainissement, rue du Commandeur, 75014 Paris, France
| | - J M Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, Paris, France
| | - Y Maday
- Sorbonne Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), et Institut Universitaire de France, Paris, France
| | - M Boni
- Institut de Recherche Biomédicale des Armées, 1 place Valérie André, F-91220 Brétigny sur Orge, France
| | - V Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine2, Paris, France
| | - L Moulin
- Eau de Paris, R&D Laboratory, DRDQE Ivry/Seine, France.
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16
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Gusev E, Sarapultsev A, Solomatina L, Chereshnev V. SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19. Int J Mol Sci 2022; 23:1716. [PMID: 35163638 PMCID: PMC8835786 DOI: 10.3390/ijms23031716] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
The review aims to consolidate research findings on the molecular mechanisms and virulence and pathogenicity characteristics of coronavirus disease (COVID-19) causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and their relevance to four typical stages in the development of acute viral infection. These four stages are invasion; primary blockade of antiviral innate immunity; engagement of the virus's protection mechanisms against the factors of adaptive immunity; and acute, long-term complications of COVID-19. The invasion stage entails the recognition of the spike protein (S) of SARS-CoV-2 target cell receptors, namely, the main receptor (angiotensin-converting enzyme 2, ACE2), its coreceptors, and potential alternative receptors. The presence of a diverse repertoire of receptors allows SARS-CoV-2 to infect various types of cells, including those not expressing ACE2. During the second stage, the majority of the polyfunctional structural, non-structural, and extra proteins SARS-CoV-2 synthesizes in infected cells are involved in the primary blockage of antiviral innate immunity. A high degree of redundancy and systemic action characterizing these pathogenic factors allows SARS-CoV-2 to overcome antiviral mechanisms at the initial stages of invasion. The third stage includes passive and active protection of the virus from factors of adaptive immunity, overcoming of the barrier function at the focus of inflammation, and generalization of SARS-CoV-2 in the body. The fourth stage is associated with the deployment of variants of acute and long-term complications of COVID-19. SARS-CoV-2's ability to induce autoimmune and autoinflammatory pathways of tissue invasion and development of both immunosuppressive and hyperergic mechanisms of systemic inflammation is critical at this stage of infection.
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Affiliation(s)
- Evgenii Gusev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| | - Alexey Sarapultsev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080 Chelyabinsk, Russia
| | - Liliya Solomatina
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| | - Valeriy Chereshnev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
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17
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Gálvez JM, Chaparro-Solano HM, Pinzón-Rondón ÁM, Albornoz LL, Pardo-Oviedo JM, Zapata-Gómez FA, Patiño-Aldana AF, Hernández-Rodríguez ADP, Díaz-Quiroz M, Ruiz-Sternberg ÁM. Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105192. [PMID: 34933126 PMCID: PMC8684288 DOI: 10.1016/j.meegid.2021.105192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/18/2021] [Accepted: 12/14/2021] [Indexed: 10/25/2022]
Abstract
The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is the etiopathogenic agent of COVID-19, a condition that has led to a formally recognized pandemic by March 2020 (World Health Organization -WHO). The SARS-CoV-2 genome is constituted of 29,903 base pairs, that code for four structural proteins (N, M, S, and E) and more than 20 non-structural proteins. Mutations in any of these regions, especially in those that encode for the structural proteins, have allowed the identification of diverse lineages around the world, some of them named as Variants of Concern (VOC) and Variants of Interest (VOI), according to the WHO and CDC. In this study, by using Next Generation Sequencing (NGS) technology, we sequenced the SARS-CoV-2 genome of 422 samples from Colombian residents, all of them collected between April 2020 and January 2021. We obtained genetic information from 386 samples, leading us to the identification of 14 new lineages circulating in Colombia, 13 of which were identified for the first time in South America. GH was the predominant GISAID clade in our sample. Most mutations were either missense (53.6%) or synonymous mutations (37.4%), and most genetic changes were located in the ORF1ab gene (63.9%), followed by the S gene (12.9%). In the latter, we identified mutations E484K, L18F, and D614G. Recent evidence suggests that these mutations concede important particularities to the virus, compromising host immunity, the diagnostic test performance, and the effectiveness of some vaccines. Some important lineages containing these mutations are the Alpha, Beta, and Gamma (WHO Label). Further genomic surveillance is important for the understanding of emerging genomic variants and their correlation with disease severity.
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Affiliation(s)
| | - Henry Mauricio Chaparro-Solano
- Genuino Research Group, Gencell Pharma, Colombia; Clinical Investigation Group, Universidad del Rosario, Colombia; Hospital Universitario Mayor - Méderi, Colombia
| | | | | | - Juan Mauricio Pardo-Oviedo
- Clinical Investigation Group, Universidad del Rosario, Colombia; Hospital Universitario Mayor - Méderi, Colombia
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18
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Dahal A, Sonju JJ, Kousoulas KG, Jois SD. Peptides and peptidomimetics as therapeutic agents for Covid-19. Pept Sci (Hoboken) 2022; 114:e24245. [PMID: 34901700 PMCID: PMC8646791 DOI: 10.1002/pep2.24245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/27/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Covid-19 pandemic has caused high morbidity and mortality rates worldwide. Virus entry into cells can be blocked using several strategies, including inhibition of protein-protein interactions (PPIs) between the viral spike glycoprotein and cellular receptors, as well as blocking of spike protein conformational changes that are required for cleavage/activation and fusogenicity. The spike-mediated viral attachment and entry into cells via fusion of the viral envelope with cellular membranes involve PPIs mediated by short peptide fragments exhibiting particular secondary structures. Thus, peptides that can inhibit these PPIs may be used as potential antiviral agents preventing virus entry and spread. This review is focused on peptides and peptidomimetics as PPI modulators and protease inhibitors against SARS-CoV-2.
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Affiliation(s)
- Achyut Dahal
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
| | - Jafrin Jobayer Sonju
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
| | - Konstantin G. Kousoulas
- Department of Pathobiological Sciences, School of Veterinary MedicineLouisiana State UniversityBaton RougeLouisianaUSA
| | - Seetharama D. Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
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19
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Paiardi G, Richter S, Oreste P, Urbinati C, Rusnati M, Wade RC. The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms. J Biol Chem 2021; 298:101507. [PMID: 34929169 PMCID: PMC8683219 DOI: 10.1016/j.jbc.2021.101507] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 01/03/2023] Open
Abstract
Heparin, a naturally occurring glycosaminoglycan, has been found to have antiviral activity against SARS-CoV-2, the causative virus of COVID-19. To elucidate the mechanistic basis for the antiviral activity of heparin, we investigated the binding of heparin to the SARS-CoV-2 spike glycoprotein by means of sliding window docking, molecular dynamics simulations, and biochemical assays. Our simulations show that heparin binds at long, positively-charged patches on the spike glycoprotein, thereby masking basic residues of both the receptor binding domain (RBD) and the multifunctional S1/S2 site. Biochemical experiments corroborated the simulation results, showing that heparin inhibits the furin-mediated cleavage of spike by binding to the S1/S2 site. Our simulations also showed that heparin can act on the hinge region responsible for motion of the RBD between the inactive closed and active open conformations of the spike glycoprotein. In simulations of the closed spike homotrimer, heparin binds the RBD and the N-terminal domain of two adjacent spike subunits and hinders opening. In simulations of open spike conformations, heparin induces stabilization of the hinge region and a change in RBD motion. Taken together, our results indicate that heparin can inhibit SARS-CoV-2 infection by three mechanisms: by allosterically hindering binding to the host cell receptor, by directly competing with binding to host heparan sulfate proteoglycan co-receptors, and by preventing spike cleavage by furin. Furthermore, these simulations provide insights into how host heparan sulfate proteoglycans can facilitate viral infection. Our results will aid the rational optimization of heparin derivatives for SARS-CoV-2 antiviral therapy.
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Affiliation(s)
- Giulia Paiardi
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; Macromolecular Interaction Analysis Unit, Section of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, 25123 Brescia, Italy.
| | - Stefan Richter
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
| | | | - Chiara Urbinati
- Macromolecular Interaction Analysis Unit, Section of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, 25123 Brescia, Italy
| | - Marco Rusnati
- Macromolecular Interaction Analysis Unit, Section of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, 25123 Brescia, Italy
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; Zentrum für Molekulare Biologie (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany.
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20
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Ruiz-Sternberg ÁM, Chaparro-Solano HM, Albornoz LLA, Pinzón-Rondón ÁM, Pardo-Oviedo JM, Molano-González N, Otero-Rodríguez DA, Zapata-Gómez FA, Gálvez-Bermúdez JM. GENOMIC CHARACTERIZATION OF SARS-CoV-2 AND ITS ASSOCIATION WITH CLINICAL OUTCOMES: A ONE-YEAR LONGITUDINAL STUDY OF THE PANDEMIC IN COLOMBIA. Int J Infect Dis 2021; 116:91-100. [PMID: 34920122 PMCID: PMC8673727 DOI: 10.1016/j.ijid.2021.12.326] [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: 08/23/2021] [Revised: 11/10/2021] [Accepted: 12/08/2021] [Indexed: 01/08/2023] Open
Abstract
Objectives This study aimed to explore associations between the molecular characterization of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and disease severity in ambulatory and hospitalized patients in two main Colombian epicentres during the first year of the coronavirus disease 2019 pandemic. Methods In total, 1000 patients with SARS-CoV-2 infection were included in this study. Clinical data were collected from 997 patients, and 678 whole-genome sequences were obtained by massively parallel sequencing. Bivariate, multi-variate, and classification and regression tree analyses were run between clinical and genomic variables. Results Age >88 years, and infection with lineages B.1.1, B.1.1.388, B.1.523 or B.1.621 for patients aged 71–88 years were associated with death [odds ratio (OR) 6.048036, 95% confidence interval (CI) 1.346567–32.92521; P=0.01718674]. The need for hospitalization was associated with higher age and comorbidities. The hospitalization rate increased significantly for patients aged 38–51 years infected with lineages A, B, B.1.1.388, B.1.1.434, B.1.153, B.1.36.10, B.1.411, B.1.471, B.1.558 or B.1.621 (OR 8.368427, 95% CI 2.573145–39.10672, P=0.00012). Associations between clades and clinical outcomes diverged from previously reported data. Conclusions Infection with lineage B.1.621 increased the hospitalization and mortality rates. These findings, plus the rapidly increasing prevalence in Colombia and other countries, suggest that lineage B.1.621 should be considered as a ‘variant of interest’. If associated disease severity is confirmed, possible designation as a ‘variant of concern’ should be considered.
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Affiliation(s)
| | - Henry Mauricio Chaparro-Solano
- Clinical Investigation Group, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia; Genuino Research Group, Gencell Pharma, Calle 82 # 18 - 12, Bogotá, Colombia; Hospital Universitario Mayor - Méderi, Calle 24 # 29 - 45, Bogotá, Colombia.
| | - Ludwig Luis Antonio Albornoz
- Departamento de Patología y Medicina de Laboratorio, Fundación Valle del Lili, Carrera 98 # 18 - 49, Cali, Colombia; Facultad de Ciencias de la Salud, Universidad ICESI, Calle 18 # 122 - 135, Cali, Colombia.
| | | | - Juan Mauricio Pardo-Oviedo
- Clinical Investigation Group, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia; Hospital Universitario Mayor - Méderi, Calle 24 # 29 - 45, Bogotá, Colombia.
| | - Nicolás Molano-González
- Clinical Investigation Group, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia.
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21
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Khan MI, Baig MH, Mondal T, Alorabi M, Sharma T, Dong JJ, Cho JY. Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. Viruses 2021; 13:2295. [PMID: 34835101 PMCID: PMC8625741 DOI: 10.3390/v13112295] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 01/08/2023] Open
Abstract
The recent emergence of novel SARS-CoV-2 variants has threatened the efforts to contain the COVID-19 pandemic. The emergence of these "variants of concern" has increased immune escape and has supplanted the ancestral strains. The novel variants harbored by the B.1.617 lineage (kappa and delta) carry mutations within the receptor-binding domain of spike (S) protein (L452R + E484Q and L452R + T478K), the region binding to the host receptor. The double mutations carried by these novel variants are primarily responsible for an upsurge number of COVID-19 cases in India. In this study, we thoroughly investigated the impact of these double mutations on the binding capability to the human host receptor. We performed several structural analyses and found that the studied double mutations increase the binding affinity of the spike protein to the human host receptor (ACE2). Furthermore, our study showed that these double mutants might be a dominant contributor enhancing the receptor-binding affinity of SARS-CoV-2 and consequently making it more stable. We also investigated the impact of these mutations on the binding affinity of two monoclonal antibodies (Abs) (2-15 and LY-CoV555) and found that the presence of the double mutations also hinders its binding with the studied Abs. The principal component analysis, free energy landscape, intermolecular interaction, and other investigations provided a deeper structural insight to better understand the molecular mechanism responsible for increased viral transmissibility of these variants.
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Affiliation(s)
- Mohd Imran Khan
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea;
| | - Mohammad Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea; (M.H.B.); (T.S.)
| | - Tanmoy Mondal
- Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, 41345 Gothenburg, Sweden;
| | - Mohammed Alorabi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Tanuj Sharma
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea; (M.H.B.); (T.S.)
| | - Jae-June Dong
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea; (M.H.B.); (T.S.)
| | - Jae Yong Cho
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea;
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22
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Abstract
Methods for detecting and dissecting the interactions of virally encoded proteins are essential for probing basic viral biology and providing a foundation for therapeutic advances. The dearth of targeted therapeutics for the treatment of coronavirus disease 2019 (COVID-19), an ongoing global health crisis, underscores the importance of gaining a deeper understanding of the interactions of proteins encoded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we describe the use of a convenient bacterial cell-based two-hybrid (B2H) system to analyze the SARS-CoV-2 proteome. We identified 16 distinct intraviral protein-protein interactions (PPIs), involving 16 proteins. We found that many of the identified proteins interact with more than one partner. Further, our system facilitates the genetic dissection of these interactions, enabling the identification of selectively disruptive mutations. We also describe a modified B2H system that permits the detection of disulfide bond-dependent PPIs in the normally reducing Escherichia coli cytoplasm, and we used this system to detect the interaction of the SARS-CoV-2 spike protein receptor-binding domain (RBD) with its cognate cell surface receptor ACE2. We then examined how the RBD-ACE2 interaction is perturbed by several RBD amino acid substitutions found in currently circulating SARS-CoV-2 variants. Our findings illustrate the utility of a genetically tractable bacterial system for probing the interactions of viral proteins and investigating the effects of emerging mutations. In principle, the system could also facilitate the identification of potential therapeutics that disrupt specific interactions of virally encoded proteins. More generally, our findings establish the feasibility of using a B2H system to detect and dissect disulfide bond-dependent interactions of eukaryotic proteins.
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23
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SARS-CoV-2 in Urine May Predict a Severe Evolution of COVID-19. J Clin Med 2021; 10:jcm10184061. [PMID: 34575171 PMCID: PMC8466152 DOI: 10.3390/jcm10184061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 02/05/2023] Open
Abstract
We hypothesized that the spread of SARS-CoV-2 in urine during a severe COVID-19 infection may be the expression of the worsening disease evolution. Therefore, the aim of this study was to verify if the COVID-19 disease severity is related to the viral presence in urine samples. We evaluated the clinical evolution in acute COVID-19 patients admitted in the sub-intensive care and intensive care units between 28 of December 2020 and 15th of February 2021 and being positive for SARS-CoV-2 RNA in the respiratory tract, including repeated endotracheal aspirates (ETA), sputum, nasopharyngeal swabs (NPS) and urine. We found that those subjects with SARS-COV-2 in the urine at admittance (8 out of 60 eligible patients) had a more severe disease than those with negative SARS-CoV-2 in urine. Further, they showed an increase in fibrinogen and (C-reactive Protein) CRP serum levels, requiring mechanic ventilation. Of those with positive SARS-CoV-2 in the urine, 50% died. According to our preliminary results, it seems that the presence of SARS-CoV-2 in the urine characterizes patients with a more severe disease and is also related to a higher death rate.
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24
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Patients Admitted for Variant Alpha COVID-19 Have Poorer Outcomes than Those Infected with the Old Strain. J Clin Med 2021; 10:jcm10163550. [PMID: 34441844 PMCID: PMC8396910 DOI: 10.3390/jcm10163550] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/23/2021] [Accepted: 08/10/2021] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVES The variant alpha COVID-19 rapidly spread across Europe in early 2021. While this variant's increased infectivity has been proven, little is known of its clinical presentation and outcomes compared to the old strain. METHODS We identified patients admitted to the Cannes General Hospital for variant alpha-related COVID-19 infection from January to April 2021. Their main demographic parameters, inflammatory markers and clinical characteristics were recorded. Patients admitted from October to December 2020 for 20E (EU1) COVID-19 were selected as controls. Differences between groups were analyzed. RESULTS We included 157 patients (mean age 73 years; 58% men; mean delay of symptoms 6.9 days). Comorbidities were present in 92% (mainly hypertension, diabetes and obesity or overweight). The prevalence of comorbidities did not differ between groups. In 28% of cases, patients either died or required transfer to the Intensive Care Unit (ICU). The cause of death or of transfer to the ICU was presumably associated with severe pneumonia. Variant alpha COVID-19 had 3.8-fold higher risk of death or transfer to the ICU compared to the old strain. DISCUSSION Patients infected with variant alpha COVID-19, despite similar background characteristics, had a higher risk of unfavorable outcomes than those infected with the old strain, suggesting increased virulence related to this variant.
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25
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Wang WH, Thitithanyanont A, Urbina AN, Wang SF. Emerging and Re-Emerging Diseases. Pathogens 2021; 10:827. [PMID: 34209374 PMCID: PMC8308756 DOI: 10.3390/pathogens10070827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
Throughout history, infectious diseases have vastly impacted human civilization [...].
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Affiliation(s)
- Wen-Hung Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (W.-H.W.); (A.N.U.)
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical, University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Arunee Thitithanyanont
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Aspiro Nayim Urbina
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (W.-H.W.); (A.N.U.)
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (W.-H.W.); (A.N.U.)
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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26
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Gerotziafas GT, Catalano M, Theodorou Y, Dreden PV, Marechal V, Spyropoulos AC, Carter C, Jabeen N, Harenberg J, Elalamy I, Falanga A, Fareed J, Agathaggelou P, Antic D, Antignani PL, Bosch MM, Brenner B, Chekhonin V, Colgan MP, Dimopoulos MA, Douketis J, Elnazar EA, Farkas K, Fazeli B, Fowkes G, Gu Y, Gligorov J, Ligocki MA, Indran T, Kannan M, Kantarcioglu B, Kasse AA, Konstantinidis K, Leivano F, Lewis J, Makatsariya A, Mbaye PM, Mahé I, Panovska-Stavridis I, Olinic DM, Papageorgiou C, Pecsvarady Z, Pillon S, Ramacciotti E, Abdel-Razeq H, Sabbah M, Sassi M, Schernthaner G, Siddiqui F, Shiomura J, Slama-Schwok A, Wautrecht JC, Tafur A, Taher A, Klein-Wegel P, Zhai Z, Zoubida TM. The COVID-19 Pandemic and the Need for an Integrated and Equitable Approach: An International Expert Consensus Paper. Thromb Haemost 2021; 121:992-1007. [PMID: 34169495 PMCID: PMC8322591 DOI: 10.1055/a-1535-8807] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND One year after the declaration of the coronavirus disease 2019 (COVID-19) pandemic by the World Health Organization (WHO) and despite the implementation of mandatory physical barriers and social distancing, humanity remains challenged by a long-lasting and devastating public health crisis. MANAGEMENT Non-pharmacological interventions (NPIs) are efficient mitigation strategies. The success of these NPIs is dependent on the approval and commitment of the population. The launch of a mass vaccination program in many countries in late December 2020 with mRNA vaccines, adenovirus-based vaccines, and inactivated virus vaccines has generated hope for the end of the pandemic. CURRENT ISSUES The continuous appearance of new pathogenic viral strains and the ability of vaccines to prevent infection and transmission raise important concerns as we try to achieve community immunity against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and its variants. The need of a second and even third generation of vaccines has already been acknowledged by the WHO and governments. PERSPECTIVES There is a critical and urgent need for a balanced and integrated strategy for the management of the COVID-19 outbreaks organized on three axes: (1) Prevention of the SARS-CoV-2 infection, (2) Detection and early diagnosis of patients at risk of disease worsening, and (3) Anticipation of medical care (PDA). CONCLUSION The "PDA strategy" integrated into state policy for the support and expansion of health systems and introduction of digital organizations (i.e., telemedicine, e-Health, artificial intelligence, and machine-learning technology) is of major importance for the preservation of citizens' health and life world-wide.
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Affiliation(s)
- Grigoris T Gerotziafas
- Sorbonne Université, INSERM, UMR_S 938, Research Group Cancer, Biology and Therapeutics, Centre de recherche Saint-Antoine (CRSA), Institut Universitaire de Cancérologie, Paris, France.,Thrombosis Center, Tenon-Saint Antoine, Hôpitaux Universitaires de l'Est Parisien, Assistance Publique Hôpitaux de Paris (APHP), France
| | - Mariella Catalano
- Research Center on Vascular Disease & Angiology Unit, Department of Biomedical Science, L Sacco Hospital, University of Milan, Milan, Italy
| | - Yiannis Theodorou
- Centre d'Immunologie et des Maladies Infectieuses UPMC UMRS CR7, Inserm U1135, CNRS ERL 8255, Paris, France
| | - Patrick Van Dreden
- Sorbonne Université, INSERM, UMR_S 938, Research Group Cancer, Biology and Therapeutics, Centre de recherche Saint-Antoine (CRSA), Institut Universitaire de Cancérologie, Paris, France
| | - Vincent Marechal
- Sorbonne Université, INSERM, UMR_S 938, Research Group Cancer, Biology and Therapeutics, Centre de recherche Saint-Antoine (CRSA), Institut Universitaire de Cancérologie, Paris, France
| | - Alex C Spyropoulos
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, United States.,Department of Obstetrics and Gynecology, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Charles Carter
- Department of Clinical Research, College of Pharmacy & Health Sciences, Campbell University, Buies Creek, North Carolina, United States
| | - Nusrat Jabeen
- Department of Microbiology, University of Karachi, Karachi, Pakistan
| | - Job Harenberg
- Department for Physical Chemistry, Heidelberg University, Heidelberg, Germany.,DOASENSE GmbH, Heidelberg, Germany
| | - Ismail Elalamy
- Sorbonne Université, INSERM, UMR_S 938, Research Group Cancer, Biology and Therapeutics, Centre de recherche Saint-Antoine (CRSA), Institut Universitaire de Cancérologie, Paris, France.,Thrombosis Center, Tenon-Saint Antoine, Hôpitaux Universitaires de l'Est Parisien, Assistance Publique Hôpitaux de Paris (APHP), France.,Department of Obstetrics and Gynecology, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Anna Falanga
- Immunohematology and Transfusion Medicine Department, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy.,School of Medicine, University of Milan Bicocca, Monza, Italy
| | - Jawed Fareed
- Department of Pathology and Laboratory Medicine, Cardiovascular Research Institute, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States.,Department of Pharmacology and Neuroscience, Cardiovascular Research Institute, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States
| | - Petros Agathaggelou
- Cyprus Department of Interventional Cardiology, American Heart Institute of Cyprus, Nicosia, Cyprus
| | - Darko Antic
- Clinic of Hematology, Clinical Center of Serbia, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Manuel Monreal Bosch
- Department of Internal Medicine, Hospital Universitario Germans Trias i Pujol de Badalona, Universidad Católica de Murcia, Murcia, Spain
| | - Benjamin Brenner
- Thrombosis and Hemostasis Unit, Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa, Israel.,Bruce Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Vladimir Chekhonin
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Mary-Paula Colgan
- Department of Vascular Surgery, St. James's Hospital/Trinity College Dublin, Dublin, Ireland
| | | | - Jim Douketis
- Division of Hematology and Thromboembolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Division of Thoracic Surgery, St. Joseph's Healthcare Hamilton, Firestone Institute for Respiratory Health, Hamilton, Ontario, Canada
| | | | - Katalin Farkas
- Department of Angiology, St. Imre University Teaching Hospital, Budapest, Hungary
| | - Bahare Fazeli
- Immunology Department, Avicenna (Bu-Ali) Research Institute, Mashhad University of Medical Sciences, Iran
| | - Gerry Fowkes
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Yongquan Gu
- Department of Vascular Surgery, Xuan Wu Hospital, Capital Medical University and Institute of Vascular Surgery, Capital Medical University, Beijing, China
| | - Joseph Gligorov
- Sorbonne Université, INSERM, UMR_S 938, Research Group Cancer, Biology and Therapeutics, Centre de recherche Saint-Antoine (CRSA), Institut Universitaire de Cancérologie, Paris, France.,Medical Oncology Department, CLIP(2) Galilée, Hôpital Tenon, Hôpitaux Universitaires de l'Est Parisien, Assistance Publique Hôpitaux de Paris (APHP), France
| | - Mark A Ligocki
- Department of Pathology and Laboratory Medicine, Cardiovascular Research Institute, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States.,Department of Pharmacology and Neuroscience, Cardiovascular Research Institute, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States
| | - Tishya Indran
- Australia Department of Haematology, Monash Health, Clayton, Victoria, Australia
| | - Meganathan Kannan
- Division of Blood and Vascular Biology, Department of Life Sciences, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, India
| | - Bulent Kantarcioglu
- Department of Hematology, Okmeydani Training and Research Hospital, Istanbul, Turkey
| | - Abdoul Aziz Kasse
- Institut du Cancer UCAD, Centre International de Cancérologie de Dakar, Dakar, Senegal
| | - Kostantinos Konstantinidis
- 5th Surgical Department, Group of Vascular Surgery, Hippokrateio General University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Fabio Leivano
- Department of Pharmacology and Neuroscience, Cardiovascular Research Institute, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States
| | - Joseph Lewis
- Department of Surgery, Stony Brook Southampton Hospital, Southampton, New York, United States
| | - Alexander Makatsariya
- Department of Obstetrics and Gynecology, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | | | - Isabelle Mahé
- Innovative Therapies in Haemostasis, Hôpital Louis Mourier, APHP, Colombes, Université de Paris, INSERM, F-75006 Paris, France
| | | | - Dan-Mircea Olinic
- Medical Clinic No. 1, University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Chryssa Papageorgiou
- Service Anesthésie, Réanimation et Médecine Périopératoire, Hôpital Tenon, Hôpitaux Universitaires de l'Est Parisien, Assistance Publique Hôpitaux de Paris, Faculté de médecine, Sorbonne Université, Paris, France
| | - Zsolt Pecsvarady
- Department of Vascular Medicine, Flor Ferenc Teaching Hospital, Kistarcsa, Hungary
| | - Sergio Pillon
- UOSD Angiology, San Camillo-Forlanini Hospital, National Health Institute ISS, AO San Camillo Forlanini, Rome, Italy
| | - Eduardo Ramacciotti
- Hemostasis & Thrombosis Research Laboratories, Loyola University Medical Center, Maywood, Illinois, United States.,Brazilian Clinical Research Institute, São Paulo, Brazil; Science Valley Research Institute, São Paulo, Brazil
| | - Hikmat Abdel-Razeq
- Department of Internal Medicine, King Hussein Cancer Center, Amman, Jordan
| | - Michele Sabbah
- Sorbonne Université, INSERM, UMR_S 938, Research Group Cancer, Biology and Therapeutics, Centre de recherche Saint-Antoine (CRSA), Institut Universitaire de Cancérologie, Paris, France
| | - Mouna Sassi
- Laboratoire de Biologie, Centre de Maternité et de Néonatologie, Hôpital Fattouma Bourguiba, Monastir, Tunisia
| | - Gerit Schernthaner
- Division of Angiology, Department of Internal Medicine 2, Medical University of Vienna, Vienna, Austria
| | - Fakiha Siddiqui
- Cardiovascular Research Institute, Health Sciences Divisions, Loyola University Chicago, Maywood, Illinois, United States
| | | | - Anny Slama-Schwok
- Sorbonne Université, INSERM, UMR_S 938, Research Group Cancer, Biology and Therapeutics, Centre de recherche Saint-Antoine (CRSA), Institut Universitaire de Cancérologie, Paris, France
| | - Jean Claude Wautrecht
- Service de Pathologie Vasculaire, Hôpital ERASME, Université Libre de Bruxelles, Brussels, Belgium
| | - Alfonso Tafur
- Vascular Medicine, Northshore Cardiovascular Institute, Skokie, Illinois, United States
| | - Ali Taher
- Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Peter Klein-Wegel
- Klinik für Angiologie, Zentrum für Innere Medizin II, Ernst von Bergmann Klinikum, Potsdam, Germany
| | - Zenguo Zhai
- Center of Respiratory Medicine, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Peking University Health Science Center, Capital Medical University, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Tazi Mezalek Zoubida
- Clinical Hematology - Internal Medicine, Ibn Sina hospital, Mohammed V University, -Rabat, Morocco
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Janik E, Niemcewicz M, Podogrocki M, Majsterek I, Bijak M. The Emerging Concern and Interest SARS-CoV-2 Variants. Pathogens 2021; 10:633. [PMID: 34064143 PMCID: PMC8224338 DOI: 10.3390/pathogens10060633] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for coronavirus disease 2019 (COVID-19) was discovered in December 2019 in Wuhan, China. Since that time, the virus has spread around the world, which resulted in an announcement of the World Health Organization (WHO), dated in March 2020, that COVID-19 was a worldwide pandemic, and since then, the world has been struggling with this disease. SARS-CoV-2, similar to other RNA viruses, continually mutates, and new variants are appearing. Among large numbers of detected SARS-CoV-2 variants, only an insignificant amount of them are able to pose a risk to public health, as they are more contagious and cause more severe conditions. The emerged variants were classified by the Centers for Disease Control and Prevention (CDC) in collaboration with SARS-CoV-2 Interagency Group (SIG) according to strictly defined pattern. Variants were classified as variants of concern, variants of interest, and variants of high consequence. In the last few months, three variants of concern (B.1.1.7, B.1.351, and P.1) and four variants of interests (B.1.526, B.1.525, B.1.427/B.1.429, and P.2) were distinguished and are essential for close monitoring. This analysis summarizes the principal information concerning SARS-CoV-2 variants, such as their infectivity, severity, mutations, and immune susceptibility.
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Affiliation(s)
- Edyta Janik
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.); (M.P.)
| | - Marcin Niemcewicz
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.); (M.P.)
| | - Marcin Podogrocki
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.); (M.P.)
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, 90-419 Lodz, Poland;
| | - Michal Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.); (M.P.)
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Staub T, Arendt V, Lasso de la Vega EC, Braquet P, Michaux C, Kohnen M, Tsobo C, Abdelrahman T, Wienecke-Baldacchino A, Francois JH. Case series of four re-infections with a SARS-CoV-2 B.1.351 variant, Luxembourg, February 2021. Euro Surveill 2021; 26:2100423. [PMID: 33960291 PMCID: PMC8103728 DOI: 10.2807/1560-7917.es.2021.26.18.2100423] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 11/20/2022] Open
Abstract
We describe four SARS-CoV-2 re-infections with a B.1.351 variant in 2021, in healthcare workers (HCWs) previously infected in 2020, before detection of this variant in Europe. Cases live in France, near the border with Luxembourg, where variants B.1.351 and B.1.1.7 circulated. All work in the same hospital unit where a cluster of COVID 19 with B1.351 variant occurred, affecting patients and HCWs. Before the cluster onset, HCWs used surgical masks, as per recommendations. After cluster onset, HCWs used FFP2 masks.
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Affiliation(s)
- Thérèse Staub
- Infectious Diseases Department, Hospital Center Luxembourg (CHL), Luxembourg
| | - Vic Arendt
- Infectious Diseases Department, Hospital Center Luxembourg (CHL), Luxembourg
| | | | - Pierre Braquet
- Infectious Diseases Department, Hospital Center Luxembourg (CHL), Luxembourg
| | - Christian Michaux
- Infectious Diseases Department, Hospital Center Luxembourg (CHL), Luxembourg
| | - Michel Kohnen
- Microbiology Department, Department (CHL), Luxembourg
| | - Chantal Tsobo
- Microbiology Department, Department (CHL), Luxembourg
| | - Tamir Abdelrahman
- Microbiology department, National Public Health Laboratory (LNS), Luxembourg
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