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Yazdani Z, Rafiei A, Momenizadeh M, Abediankenari S, Yazdani M, Lagzian M. Designing novel peptides for detecting the Omicron variant, specifying SARS-CoV-2, and simultaneously screening coronavirus infections. J Biomol Struct Dyn 2024; 42:4759-4768. [PMID: 37306566 DOI: 10.1080/07391102.2023.2222821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
In this study in silico a candidate diagnostic peptide-based tool was designed in four stages including diagnosis of coronavirus diseases, simultaneously identifying of COVID-19 and SARS from other members of this family, specific identification of SARS-CoV2, and diagnosis of COVID-19 Omicron. Designed candidate peptides consist of four immunodominant peptides from the proteins of the SARS-CoV-2 spike (S) and membrane (M). The tertiary structure of each peptide was predicted. The stimulation ability of the humoral immunity for each peptide was evaluated. Finally, in silico cloning was performed to develop an expression strategy for each peptide. These four peptides have suitable immunogenicity, appropriate construct, and the ability to be expressed in E.coli. These results must be experimentally validated in vitro and in vivo to ensure the immunogenicity of the kit.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Yazdani
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Rafiei
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Momenizadeh
- Students Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Saeid Abediankenari
- Immunogenetics Research Center, Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Milad Lagzian
- Department of Biology, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
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2
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Tian X, Tang Y, Gan J, Ye J. A novel linear B cell epitope of the canine coronavirus nucleocapsid protein identified by a monoclonal antibody. Vet Microbiol 2024; 293:110098. [PMID: 38677126 DOI: 10.1016/j.vetmic.2024.110098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/24/2024] [Accepted: 04/20/2024] [Indexed: 04/29/2024]
Abstract
The infection of canine coronavirus (CCoV) causes a highly contagious disease in dogs with acute gastroenteritis. The efficient serological diagnostics is critical for controlling the disease caused by CCoV. Nucleocapsid (N) protein of CCoV is an important target for developing serological approaches. However, little is known about the antigenic sites in the N protein of CCoV. In this study, we generated a monoclonal antibody (mAb) against the N protein of CCoV, designated as 13E8, through the fusion of the sp2/0 cells with the spleen cells from a mouse immunized with the purified recombinant GST-N protein. Epitope mapping revealed that mAb 13E8 recognized a novel linear B cell epitope in N protein at 294-314aa (named as EP-13E8) by using a serial of truncated N protein through Western blot and ELISA. Sequence analysis showed that the sequence of EP-13E8 was highly conserved (100 %) among different CCoV strains analyzed, but exhibited a low similarity (31.8-63.6 %) with the responding sequence in other coronaviruses of the same genus such as FCoV, PEDV and HCoV except for TGEV (95.5 % identity). Structural assay suggested that the epitope of EP-13E8 were located in the close proximity on the surface of the N protein. Overall, the mAb 13E8 against N protein generated and its epitope EP-13E8 identified here paid the way for further developing epitope-based serological diagnostics for CCoV.
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Affiliation(s)
- Xiaoyan Tian
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ye Tang
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Junji Gan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Jianqiang Ye
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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3
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Addetia A, Stewart C, Seo AJ, Sprouse KR, Asiri AY, Al-Mozaini M, Memish ZA, Alshukairi A, Veesler D. Mapping immunodominant sites on the MERS-CoV spike glycoprotein targeted by infection-elicited antibodies in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.586409. [PMID: 38617298 PMCID: PMC11014493 DOI: 10.1101/2024.03.31.586409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Middle-East respiratory syndrome coronavirus (MERS-CoV) first emerged in 2012 and causes human infections in endemic regions. Most vaccines and therapeutics in development against MERS-CoV focus on the spike (S) glycoprotein to prevent viral entry into target cells. These efforts, however, are limited by a poor understanding of antibody responses elicited by infection along with their durability, fine specificity and contribution of distinct S antigenic sites to neutralization. To address this knowledge gap, we analyzed S-directed binding and neutralizing antibody titers in plasma collected from individuals infected with MERS-CoV in 2017-2019 (prior to the COVID-19 pandemic). We observed that binding and neutralizing antibodies peak 1 to 6 weeks after symptom onset/hospitalization, persist for at least 6 months, and broadly neutralize human and camel MERS-CoV strains. We show that the MERS-CoV S1 subunit is immunodominant and that antibodies targeting S1, particularly the RBD, account for most plasma neutralizing activity. Antigenic site mapping revealed that polyclonal plasma antibodies frequently target RBD epitopes, particularly a site exposed irrespective of the S trimer conformation, whereas targeting of S2 subunit epitopes is rare, similar to SARS-CoV-2. Our data reveal in unprecedented details the humoral immune responses elicited by MERS-CoV infection, which will guide vaccine and therapeutic design.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ayed Y Asiri
- Al-Hayat National Hospital, Riyadh, Saudi Arabia
| | - Maha Al-Mozaini
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ziad A Memish
- King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Kyung Hee University, Seoul, South Korea
| | - Abeer Alshukairi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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4
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Hattab D, Amer MFA, Al-Alami ZM, Bakhtiar A. SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants. Infection 2024:10.1007/s15010-024-02223-y. [PMID: 38554253 DOI: 10.1007/s15010-024-02223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 04/01/2024]
Abstract
The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies. The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.
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Affiliation(s)
- Dima Hattab
- School of Pharmacy, The University of Jordan, Queen Rania Street, Amman, Jordan
| | - Mumen F A Amer
- Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Zina M Al-Alami
- Department of Basic Medical Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Athirah Bakhtiar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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5
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Guo Y, Song W, Dong Y, Wang X, Nie G, Li F. A Poly Aptamer Encoded DNA Nanocatcher Informs Efficient Virus Trapping. NANO LETTERS 2024; 24:3614-3623. [PMID: 38497742 DOI: 10.1021/acs.nanolett.3c04510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Broad-spectrum antiviral platforms are always desired but still lack the ability to cope with the threats to global public health. Herein, we develop a poly aptamer encoded DNA nanocatcher platform that can trap entire virus particles to inhibit infection with a broad antiviral spectrum. Ultralong single-stranded DNA (ssDNA) containing repeated aptamers was synthesized as the scaffold of a nanocatcher via a biocatalytic process, wherein mineralization of magnesium pyrophosphate on the ssDNA could occur and consequently lead to the formation of nanocatcher with interfacial nanocaves decorated with virus-binding aptamers. Once the viruses were recognized by the apatmers, they would be captured and trapped in the nanocaves via multisite synergistic interactions. Meanwhile, the size of nanocatchers was optimized to prevent their cellular uptake, which further guaranteed inhibition of virus infection. By taking SARS-CoV-2 variants as a model target, we demonstrated the broad virus-trapping capability of a DNA nanocatcher in engulfing the variants and blocking the infection to host cells.
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Affiliation(s)
- Yunhua Guo
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenzhe Song
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuhang Dong
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xuejun Wang
- Bioinformatics Center of AMMS, Taiping Rd, Haidian District, Beijing, 100850, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Feng Li
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
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6
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Lu Y, Lou J, Yu B, Bu Y, Ni F, Lu D. The prevalence and risk of depression in aged COVID-19 survivors: a bibliometric and meta-analysis. Psychogeriatrics 2024; 24:458-472. [PMID: 38115236 DOI: 10.1111/psyg.13057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 12/21/2023]
Abstract
To explore depression prevalence and related risk factors among elderly coronavirus disease 2019 (COVID-19) survivors, while also evaluating research characteristics. We searched Web of Science, PubMed, Embase, Scopus, CNKI and Wanfang Data for studies that reported COVID-19 and depression in older adults. 'Bibliometrix' facilitated bibliometric analysis and information visualisation. Random-effects models merged depression prevalence and relevant risks. Publication bias and its impact were examined using funnel plots, Begg's test, Egger's linear regression, and trim-and-fill method. Meta-regression, bubble plots, and Baujat plots probed heterogeneity. Sensitivity analysis applied the leave-one-out method. The study is registered with PROSPERO, CRD42023417706. The bibliometric analysis comprised 138 studies. Publication frequency peaked in the US, China, and Italy, reflecting significant growth. The meta-analysis comprised 43 studies. Elderly COVID-19 patients exhibit 28.33% depression prevalence (95% CI: 21.24-35.97). Severe cases (43.91%, 95% CI: 32.28-55.88) experienced higher depression prevalence than mild cases (16.45%, 95% CI: 11.92-21.50). Sex had no depression prevalence impact based on bubble plots. Notably, depression risk did not significantly differ between elderly and young COVID-19 patients (odds ratio (OR) = 1.1808, 95% CI: 0.7323-1.9038). However, COVID-19 infection emerged as a substantial elderly depression risk factor (OR = 1.8521, 95% CI: 1.2877-2.6639). Sensitivity analysis confirmed result robustness. Elderly COVID-19 survivors are likely to develop depression symptoms with regional variations. Severe cases are associated with heightened depression prevalence. COVID-19 infection stands out as a key elderly depression risk factor, while sex does not influence prevalence. The field's expansion necessitates sustained collaboration and extensive research endeavours.
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Affiliation(s)
- Yangguang Lu
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jialing Lou
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Bohuai Yu
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Yiran Bu
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Feitian Ni
- The Second Affiliated College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Di Lu
- Tongde Hospital of Zhejiang Province, Hangzhou, China
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7
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Sidorenko VS, Cohen I, Dorjee K, Minetti CA, Remeta DP, Gao J, Potapova I, Wang HZ, Hearing J, Yen WY, Kim HK, Hashimoto K, Moriya M, Dickman KG, Yin X, Garcia-Diaz M, Chennamshetti R, Bonala R, Johnson F, Waldeck AL, Gupta R, Li C, Breslauer KJ, Grollman AP, Rosenquist TA. Mechanisms of antiviral action and toxicities of ipecac alkaloids: Emetine and dehydroemetine exhibit anti-coronaviral activities at non-cardiotoxic concentrations. Virus Res 2024; 341:199322. [PMID: 38228190 PMCID: PMC10831786 DOI: 10.1016/j.virusres.2024.199322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 01/18/2024]
Abstract
The emergence of highly infectious pathogens with their potential for triggering global pandemics necessitate the development of effective treatment strategies, including broad-spectrum antiviral therapies to safeguard human health. This study investigates the antiviral activity of emetine, dehydroemetine (DHE), and congeneric compounds against SARS-CoV-2 and HCoV-OC43, and evaluates their impact on the host cell. Concurrently, we assess the potential cardiotoxicity of these ipecac alkaloids. Significantly, our data reveal that emetine and the (-)-R,S isomer of 2,3-dehydroemetine (designated in this paper as DHE4) reduce viral growth at nanomolar concentrations (i.e., IC50 ∼ 50-100 nM), paralleling those required for inhibition of protein synthesis, while calcium channel blocking activity occurs at elevated concentrations (i.e., IC50 ∼ 40-60 µM). Our findings suggest that the antiviral mechanisms primarily involve disruption of host cell protein synthesis and is demonstrably stereoisomer specific. The prospect of a therapeutic window in which emetine or DHE4 inhibit viral propagation without cardiotoxicity renders these alkaloids viable candidates in strategies worthy of clinical investigation.
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Affiliation(s)
- Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ira Cohen
- Department of Physiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Kunchok Dorjee
- Division of Infectious Diseases, John Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Conceição A Minetti
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - David P Remeta
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Junyuan Gao
- Department of Physiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Irina Potapova
- Department of Physiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Hong Zhan Wang
- Department of Physiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Janet Hearing
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Wan-Yi Yen
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Hwan Keun Kim
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Keiji Hashimoto
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Masaaki Moriya
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kathleen G Dickman
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Xingyu Yin
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Rajesh Chennamshetti
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Radha Bonala
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Francis Johnson
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Amanda L Waldeck
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Pharmacy, Stony Brook University Hospital, Stony Brook, New York 11794, USA
| | - Ramesh Gupta
- ChemMaster International Inc., Happauge, New York 11788, USA
| | - Chaoping Li
- Chemistry Service Unit of Shanghai Haoyuan Chemexpress Co., Ltd., Shanghai, PR China 201203
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Arthur P Grollman
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Thomas A Rosenquist
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
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8
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Doijen J, Heo I, Temmerman K, Vermeulen P, Diels A, Jaensch S, Burcin M, Van den Broeck N, Raeymaekers V, Peremans J, Konings K, Clement M, Peeters D, Van Loock M, Koul A, Buyck C, Van Gool M, Van Damme E. A flexible, image-based, high-throughput platform encompassing in-depth cell profiling to identify broad-spectrum coronavirus antivirals with limited off-target effects. Antiviral Res 2024; 222:105789. [PMID: 38158129 DOI: 10.1016/j.antiviral.2023.105789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) posed a major threat to global health. Although the World Health Organization ended the public health emergency status, antiviral drugs are needed to address new variants of SARS-CoV-2 and future pandemics. To identify novel broad-spectrum coronavirus drugs, we developed a high-content imaging platform compatible with high-throughput screening. The platform is broadly applicable as it can be adapted to include various cell types, viruses, antibodies, and dyes. We demonstrated that the antiviral activity of compounds against SARS-CoV-2 variants (Omicron BA.5 and Omicron XBB.1.5), SARS-CoV, and human coronavirus 229E could easily be assessed. The inclusion of cellular dyes and immunostaining in combination with in-depth image analysis enabled us to identify compounds that induced undesirable phenotypes in host cells, such as changes in cell morphology or in lysosomal activity. With the platform, we screened ∼900K compounds and triaged hits, thereby identifying potential candidate compounds carrying broad-spectrum activity with limited off-target effects. The flexibility and early-stage identification of compounds with limited host cell effects provided by this high-content imaging platform can facilitate coronavirus drug discovery. We anticipate that its rapid deployability and fast turnaround can also be applied to combat future pandemics.
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Affiliation(s)
- Jordi Doijen
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Inha Heo
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Koen Temmerman
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Peter Vermeulen
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Annick Diels
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Steffen Jaensch
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Mark Burcin
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | | | | | - Joren Peremans
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Katrien Konings
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Maxime Clement
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Danielle Peeters
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Marnix Van Loock
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Anil Koul
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Christophe Buyck
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Michiel Van Gool
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Ellen Van Damme
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
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9
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Rahmasari R, Raekiansyah M, Aliyah SH, Yodi P, Baihaqy F, Irhamsyah M, Sari KCDP, Suryadi H, Moi ML, Sauriasari R. Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting. Sci Rep 2024; 14:1817. [PMID: 38245603 PMCID: PMC10799953 DOI: 10.1038/s41598-024-52250-w] [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: 04/27/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
A low-cost SYBR Green-based RT-qPCR method to detect SARS-CoV-2 were developed and validated. Primers targeting a conserved and vital region of the N genes of SARS-CoV-2 were designed. In-silico study was performed to analyse the compatibility of the selected primer pair with Indonesian SARS-CoV-2 genome sequences available from the GISAID database. We determined the linearity of our new assay using serial dilution of SARS-CoV-2 RNA from clinical samples with known virus concentration. The assay was then evaluated using clinically relevant samples in comparison to a commercial TaqMan-based test kit. Finally, we applied the assay in sample pooling strategies for SARS-CoV-2 detection. The SYBR Green-based RT-qPCR method was successfully developed with sufficient sensitivity. There is a very low prevalence of genome variation in the selected N primer binding regions, indicating their high conservation. The validation of the assay using clinical samples demonstrated similar performance to the TaqMan method suggesting the SYBR methods is reliable. The pooling strategy by combining 5 RNA samples for SARS-CoV-2 detection using the SYBR RT-qPCR methods is feasible and provides a high diagnostic yield. However, when dealing with samples having a very low viral load, it may increase the risk of missing positive cases.
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Affiliation(s)
- Ratika Rahmasari
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia.
| | | | - Siti Hana Aliyah
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Priska Yodi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Fathan Baihaqy
- Helix Laboratory & Clinic, Depok, West Java, Indonesia
- Department of Microbiology, School of Life Sciences & Technology, Institut Teknologi Bandung, Bandung, West Java, Indonesia
| | | | | | - Herman Suryadi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Meng Ling Moi
- School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Rani Sauriasari
- Clinical Pharmacy and Social Pharmacy Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
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10
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Mostafa Domiaty D, Ibrahim Al-Hazani TM, Alshehri E, Zamil aldajani H, Fahad Alqassim NA, Mohammed Al-balawi A, Abdullah AlQassim F, Abdullah Alduwish M, Saeed Al-Qahtani W. SARS-CoV-2 impact on ACE2 expression in NSCLC: mRNA and protein insights COVID-19 associated (ACE2) expression in non-small cell lung cancer (NSCLC). Heliyon 2024; 10:e23926. [PMID: 38261909 PMCID: PMC10796980 DOI: 10.1016/j.heliyon.2023.e23926] [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: 07/01/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) is a pervasive and challenging global health concern. This research delves into the intricate relationship between NSCLC and ACE2 expression, exploring the potential impact of COVID-19 history on this interaction. Tissue samples were meticulously gathered from a cohort of 32 NSCLC patients, 18 of whom had a documented history of COVID-19 infection. The methodology included extensive investigations, such as cell dissociation, histopathological analysis, immunohistochemistry, cell culture, adhesion assays, immunocytochemistry, RNA isolation, and RT-PCR analysis. The results of this comprehensive study unearthed intriguing findings regarding ACE2 expression patterns within NSCLC tissues. Notably, variations were observed in ACE2 profiles between individuals with and without a prior record of COVID-19 infection, hinting at a dynamic interplay. These discoveries carry profound implications for both the understanding of NSCLC progression and the response to COVID-19 in patients with pre-existing NSCLC. The interrelationship between ACE2 expression, NSCLC, and COVID-19, as revealed in this study, may significantly influence patient outcomes and, potentially, therapeutic strategies. In summary, this research serves as an essential contribution to the growing body of knowledge on NSCLC, offering unique insights into the intricate connections between ACE2, COVID-19, and NSCLC. This information may open new avenues for tailored treatment approaches and clinical management strategies, ultimately benefiting patients grappling with NSCLC in the background of the current COVID-19 pandemic.
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Affiliation(s)
- Dalia Mostafa Domiaty
- College of Science, Department of Biological Sciences, University of Jeddah, P.O. BOX 13151, Jeddah, 21493, Jeddah, Saudi Arabia
| | - Tahani Mohamed Ibrahim Al-Hazani
- Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, P.O. Box 83, Al-Kharj, 11940, Saudi Arabia
| | - Eman Alshehri
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Haya Zamil aldajani
- King Abdulaziz Medical City, Ministry of National Guard Affairs, Riyadh, Saudi Arabia
| | | | | | | | - Manal Abdullah Alduwish
- Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, P.O. Box 83, Al-Kharj, 11940, Saudi Arabia
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, P.O. Box 6830, 11452, Riyadh, Saudi Arabia
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11
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Al-Kaif LAIK, Al-Ameri H, Alfatlawi WRO, Mahdi AE, Al-Khafaji YAK, Al-Saadi MAK, Al-Charrakh AH, Al-Mammori RT, Akkaif MA. Detection of CTLA-4 level and humeral immune response after the second dose of COVID-19 vaccine in certain Iraqi provinces participants. PLoS One 2024; 19:e0296521. [PMID: 38180994 PMCID: PMC10769031 DOI: 10.1371/journal.pone.0296521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/14/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Evaluating immune responses following COVID-19 vaccination is paramount to understanding vaccine effectiveness and optimizing public health interventions. This study seeks to elucidate individuals' immune status after administering a second dose of diverse COVID-19 vaccines. By analyzing immune responses through serological markers, we aim to contribute valuable insights into the uniformity of vaccine performance. METHODS A total of 80 participants were enrolled in this study, with demographic and COVID-19 infection-related data collected for categorization. Serum samples were acquired within a specified timeframe, and SARS-CoV-2 IgM/IgG rapid tests were conducted. Moreover, CTLA-4 levels were measured through ELISA assays, allowing us to assess the immune responses comprehensively. The participants were divided into eight groups based on various factors, facilitating a multifaceted analysis. RESULTS The outcomes of our investigation demonstrated consistent immune responses across the diverse types of COVID-19 vaccines administered in Iraq. Statistical analysis revealed no significant distinctions among the vaccine categories. In contrast, significant differences were observed in CTLA-4 among the control group (non-infected/non-vaccinated, infected/non-vaccinated) and infected/Pfizer, non-infected/Pfizer, and infected/Sinopharm, non-infected/sinopharm (P = 0.001, < 0.001, 0.023, respectively). This suggests that these vaccines exhibit comparable effectiveness in eliciting an immune response among the study participants. CONCLUSIONS In conclusion, our study's results underscore the lack of discriminatory variations between different COVID-19 vaccine types utilized in Iraq. The uniform immune responses observed signify the equitable efficacy and performance of these vaccines. Despite minor quantitative discrepancies, these variations do not hold statistical significance, reaffirming the notion that the various vaccines serve a similar purpose in conferring protection against COVID-19.
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Affiliation(s)
- Laith A. I. K. Al-Kaif
- Department of Medical Microbiology, Hammurabi College of Medicine, University of Babylon, Hillah, Babylon, Iraq
- Department of Medical Laboratory Techniques, Al-Mustaqbal University, Hillah, Babylon, Iraq
| | - Hussain Al-Ameri
- Department of Medical Laboratory Techniques, Al-Mustaqbal University, Hillah, Babylon, Iraq
| | | | - Ammar Eesa Mahdi
- Basic Science Department, College of Dentistry, University of Babylon, Hillah, Babylon, Iraq
| | | | | | - Alaa H. Al-Charrakh
- Basic Science Department, College of Dentistry, University of Babylon, Hillah, Babylon, Iraq
| | | | - Mohammed Ahmed Akkaif
- Department of Cardiology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
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12
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Chiem K, Nogales A, Almazán F, Ye C, Martínez-Sobrido L. Bacterial Artificial Chromosome Reverse Genetics Approaches for SARS-CoV-2. Methods Mol Biol 2024; 2733:133-153. [PMID: 38064031 DOI: 10.1007/978-1-0716-3533-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new member of the Coronaviridae family responsible for the coronavirus disease 19 (COVID-19) pandemic. To date, SARS-CoV-2 has been accountable for over 624 million infection cases and more than 6.5 million human deaths. The development and implementation of SARS-CoV-2 reverse genetics approaches have allowed researchers to genetically engineer infectious recombinant (r)SARS-CoV-2 to answer important questions in the biology of SARS-CoV-2 infection. Reverse genetics techniques have also facilitated the generation of rSARS-CoV-2 expressing reporter genes to expedite the identification of compounds with antiviral activity in vivo and in vitro. Likewise, reverse genetics has been used to generate attenuated forms of the virus for their potential implementation as live-attenuated vaccines (LAV) for the prevention of SARS-CoV-2 infection. Here we describe the experimental procedures for the generation of rSARS-CoV-2 using a well-established and robust bacterial artificial chromosome (BAC)-based reverse genetics system. The protocol allows to produce wild-type and mutant rSARS-CoV-2 that can be used to understand the contribution of viral proteins and/or amino acid residues in viral replication and transcription, pathogenesis and transmission, and interaction with cellular host factors.
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Affiliation(s)
- Kevin Chiem
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Aitor Nogales
- Centro de Investigación en Sanidad Animal (CISA-INIA/CSIC), Madrid, Spain
| | - Fernando Almazán
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, USA.
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13
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Subramani C, Sharma G, Chaira T, Barman TK. High content screening strategies for large-scale compound libraries with a focus on high-containment viruses. Antiviral Res 2024; 221:105764. [PMID: 38008193 DOI: 10.1016/j.antiviral.2023.105764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
A majority of viral diseases do not have FDA-approved drugs. The recent outbreaks caused by SARS-CoV-2, monkeypox, and Sudan ebolavirus have exposed the critical need for rapid screening and identification of antiviral compounds against emerging/re-emerging viral pathogens. A high-content screening (HCS) platform is becoming an essential part of the drug discovery process, thanks to developments in image acquisition and analysis. While HCS has several advantages, its full potential has not been realized in antiviral drug discovery compared to conventional drug screening approaches, such as fluorescence or luminescence-based microplate assays. Therefore, this review aims to summarize HCS workflow, strategies, and developments in image-based drug screening, focusing on high-containment viruses.
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Affiliation(s)
- Chandru Subramani
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, Galveston, TX, USA
| | - Ghanshyam Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Tridib Chaira
- Department of Pharmacology, SGT University, Gurugram, Haryana, India
| | - Tarani Kanta Barman
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, Galveston, TX, USA.
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14
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Rokni M, Rohani Bastami T, Meshkat Z, Reza Rahimi H, Zibaee S, Meshkat M, Fotouhi F, Serki E, Khoshakhlagh M, Dabirifar Z. Rapid and sensitive detection of SARS-CoV-2 virus in human saliva samples using glycan based nanozyme: a clinical study. Mikrochim Acta 2023; 191:36. [PMID: 38108890 DOI: 10.1007/s00604-023-06120-3] [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: 04/04/2023] [Accepted: 11/25/2023] [Indexed: 12/19/2023]
Abstract
A highly sensitive colorimetric method (glycan-based nano(e)zyme) was developed for sensitive and rapid detection of the SARS-CoV-2 virus based on N-acetyl neuraminic acid (sialic acid)-functionalized gold nanoparticles (SA-Au NZs). A number of techniques were used to characterize the prepared nanomaterials including XRD, FT-IR, UV-vis, DLS, and TEM. DLS analysis indicates an average hydrodynamic size of 34 nm, whereas TEM analysis indicates an average particle size of 15.78 nm. This observation confirms that water interacts with nanoparticle surfaces, resulting in a large hydrodynamic diameter. The peroxidase-like activity of SA-Au NZs was examined with SARS-CoV-2 and influenza viruses (influenza A (H1N1), influenza A (H3N2), and influenza B). UV-visible spectroscopy was used to monitor and record the results, as well as naked eye detection (photographs). SA-Au NZs exhibit a change in color from light red to purple when SARS-CoV-2 is present, and they exhibit a redshift in their spectrum. N-acetyl neuraminic acid interacts with SARS-CoV-2 spike glycoprotein, confirming its ability to bind glycans. As a result, SA-Au NZs can detect COVID-19 with sensitivity and specificity of over 95% and 98%, respectively. This method was approved by testing saliva samples from 533 suspected individuals at Ghaem Hospital of Mashhad, Mashhad, Iran. Sensitivity and specificity were calculated by comparing the results with the definitive results. The positive results were accompanied by a color change from bright red to purple within five minutes. Statistical analysis was performed based on variables such as age, gender, smoking, diabetes, hypertension, and lung involvement. In clinical trials, it was demonstrated that this method can be used to diagnose SARS-CoV-2 in a variety of places, such as medical centers, hospitals, airports, universities, and schools.
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Affiliation(s)
- Mehrdad Rokni
- Department of Chemical Engineering and Energy, Quchan University of Technology, Quchan, 94771-67335, Iran
| | - Tahereh Rohani Bastami
- Department of Chemical Engineering and Energy, Quchan University of Technology, Quchan, 94771-67335, Iran.
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Hamid Reza Rahimi
- Department of Medical Genetics and Molecular Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Zibaee
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Mashhad, Iran
| | - Mojtaba Meshkat
- Department of Community Medicine, Faculty of Medicine, Mashhad Medical Sciences, Islamic Azad University, Mashhad, Iran
| | - Fatemeh Fotouhi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Serki
- Department of Clinical Biochemistry, Mashhad University of Medical Science, Mashhad, Iran Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdieh Khoshakhlagh
- Department of Clinical Biochemistry, Mashhad University of Medical Science, Mashhad, Iran Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zeynab Dabirifar
- Department of Chemical Engineering and Energy, Quchan University of Technology, Quchan, 94771-67335, Iran
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15
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Jiang S, Qian S, Zhu S, Lu J, Hu Y, Zhang C, Geng Y, Chen X, Guo Y, Chen Z, Pu J, Guo Z, Liu S. A Point-of-Care Testing Device Utilizing Graphene-Enhanced Fiber Optic SPR Sensor for Real-Time Detection of Infectious Pathogens. BIOSENSORS 2023; 13:1029. [PMID: 38131789 PMCID: PMC10741924 DOI: 10.3390/bios13121029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Timely detection of highly infectious pathogens is essential for preventing and controlling public health risks. However, most traditional testing instruments require multiple tedious steps and ultimately testing in hospitals and third-party laboratories. The sample transfer process significantly prolongs the time to obtain test results. To tackle this aspect, a portable fiber optic surface plasmon resonance (FO-SPR) device was developed for the real-time detection of infectious pathogens. The portable device innovatively integrated a compact FO-SPR sensing component, a signal acquisition and processing system, and an embedded power supply unit. A gold-plated fiber is used as the FO-SPR sensing probe. Compared with traditional SPR sensing systems, the device is smaller size, lighter weight, and higher convenience. To enhance the detection capacity of pathogens, a monolayer graphene was coated on the sensing region of the FO-SPR sensing probe. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was used to evaluate the performance of the portable device. The device can accurately detect the SARS-CoV-2 spike S1 protein in phosphate-buffered saline (PBS) and artificial saliva within just 20 min, and the device successfully detected cultured SARS-CoV-2 virus. Furthermore, the FO-SPR probe has long-term stability, remaining stable for up to 8 days. It could distinguish between the SARS-CoV-2 spike protein and the MERS-CoV spike protein. Hence, this FO-SPR device provides reliable, rapid, and portable access to test results. It provides a promising point-of-care testing (POCT) tool for on-site screening of infectious pathogens.
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Affiliation(s)
- Shiyu Jiang
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
- School of Electronic Engineering, Heilongjiang University, Harbin 150080, China
| | - Siyu Qian
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Shunning Zhu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Jinxin Lu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Yunxin Hu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
- School of Electronic Engineering, Heilongjiang University, Harbin 150080, China
| | - Cheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Yikai Geng
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Xuefeng Chen
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Ying Guo
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Zhaoliang Chen
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Jie Pu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Zhendong Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Shengchun Liu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
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16
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Xie Y, Chen C, Zhang D, Jiao Z, Chen Y, Wang G, Tan Y, Zhang W, Xiao S, Peng G, Shi Y. Diversity for endoribonuclease nsp15-mediated regulation of alpha-coronavirus propagation and virulence. Microbiol Spectr 2023; 11:e0220923. [PMID: 37938022 PMCID: PMC10715224 DOI: 10.1128/spectrum.02209-23] [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: 05/25/2023] [Accepted: 08/24/2023] [Indexed: 11/09/2023] Open
Abstract
IMPORTANCE Understanding the role of the endoribonuclease non-structural protein 15 (nsp15) (EndoU) in coronavirus (CoV) infection and pathogenesis is essential for vaccine target discovery. Whether the EndoU activity of CoV nsp15, as a virulence-related protein, has a diverse effect on viral virulence needs to be further explored. Here, we found that the transmissible gastroenteritis virus (TGEV) and feline infectious peritonitis virus (FIPV) nsp15 proteins antagonize SeV-induced interferon-β (IFN-β) production in human embryonic kidney 293 cells. Interestingly, compared with wild-type infection, infection with EnUmt-TGEV or EnUmt-FIPV did not change the IFN-β response or reduce viral propagation in immunocompetent cells. The results of animal experiments showed that EnUmt viruses did not reduce the clinical presentation and mortality caused by TGEV and FIPV. Our findings enrich the understanding of nsp15-mediated regulation of alpha-CoV propagation and virulence and reveal that the conserved functions of nonstructural proteins have diverse effects on the pathogenicity of CoVs.
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Affiliation(s)
- Yunfei Xie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Chener Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Ding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Zhe Jiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Yixi Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Gang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Yubei Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Wanpo Zhang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Yuejun Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
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17
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Alotaibi MA, Al-Hazani TMI, Alwaili MA, Jalal AS, Alshaya DS, Safhi FA, Alamoudi MO, Alarifi S, Saeed Al-Qahtani W. SARS-CoV-2 virus associated angiotensin converting enzyme 2 expression modulation in colorectal cancer: Insights from mRNA and protein analysis COVID-19 associated (ACE2) expression in colorectal cancer. Microb Pathog 2023; 185:106389. [PMID: 37839761 DOI: 10.1016/j.micpath.2023.106389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
The SARS-CoV-2 virus gains entry into human cells by exploiting the angiotensin-converting enzyme 2 (ACE2), a key component known as the spike protein (S), as a point of entry. Initially, SARS-CoV-2 suppresses the natural function of ACE2, leading to a gradual decline in cell health. Additionally, individuals with cancer are considered more susceptible to COVID-19. This study investigates the expression patterns of ACE2 in colorectal cancer (CRC) patients with and without a history of COVID-19 infection. RT-PCR was used to analyze samples from both cancerous and adjacent non-affected colorectal tissues of 47 CRC patients, comprising two groups: 24 CRC patients with no history of COVID-19 and 23 CRC patients with a recent history of COVID-19 infection. Epithelial CR cells were isolated from both types of tissues and cultured to evaluate cell adhesion. Immunohistochemistry analyses were conducted to examine ACE2 protein expression using various ACE2 antibodies for both cell types. The study revealed ACE2 mRNA expression in all CRC tissues of patients with and without a history of COVID-19. ACE2 expression was significantly higher in CRC patients without a history of COVID-19. Notably, the non-affected colorectal cancer (NACRC) tissues of patients without a history of COVID-19 also showed ACE2 expression, whereas no ACE2 expression was detected in the biopsies of CRC patients with a positive COVID-19 history. ACE2 antibodies were employed to validate ACE2 protein expression at the mRNA level. COVID-19 appears to downregulate ACE2 expression in both CRC and NACRC tissues of CRC patients with a positive history of COVID-19 infection.
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Affiliation(s)
| | - Tahani Mohamed Ibrahim Al-Hazani
- Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, P.O. Box 83, Al-Kharj, 11940, Saudi Arabia.
| | - Maha Abdulla Alwaili
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Areej Saud Jalal
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Dalal S Alshaya
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Muna O Alamoudi
- Department of Biology, Faculty of Science, University of Hail, Hail, 81411, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, P.O. Box 6830, Riyadh, 11452, Saudi Arabia.
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18
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Emad R, Naga IS. Comparative genotyping of SARS-CoV-2 among Egyptian patients: near-full length genomic sequences versus selected spike and nucleocapsid regions. Med Microbiol Immunol 2023; 212:437-446. [PMID: 37789185 PMCID: PMC10618331 DOI: 10.1007/s00430-023-00783-8] [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: 07/10/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
Several tools have been developed for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genotyping based on either whole genome or spike sequencing. We aimed to highlight the molecular epidemiological landscape of SARS-CoV-2 in Egypt since the start of the pandemic, to describe discrepancies between the 3 typing tools: Global Initiative on Sharing Avian Influenza Data (GISAID), Nextclade, and Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) and to assess the fitness of spike and nucleocapsid regions for lineage assignment compared to the whole genome. A total of 3935 sequences isolated from Egypt (March 2020-2023) were retrieved from the GISAID database. A subset of data (n = 1212) with high coverage whole genome was used for tool discrimination and agreement analyses. Among 1212 sequences, the highest discriminatory power was 0.895 for PANGOLIN, followed by GISAID (0.872) and Nextclade (0.866). There was a statistically significant difference (p = 0.0418) between lineages assigned via spike (30%) and nucleocapsid (46%) compared to their whole genome-assigned lineages. The first 3 pandemic waves were dominated by B.1, followed by C.36 and then C.36.3, while the fourth to sixth waves were dominated by the B.1.617.2, BA, and BA.5.2 lineages, respectively. Current shift in lineage typing to recombinant forms. The 3 typing tools showed comparable discrimination among SARS-CoV-2 lineages. The nucleocapsid region could be used for lineage assignment.
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Affiliation(s)
- Rasha Emad
- Alexandria Main University Hospital, Alexandria, Egypt.
| | - Iman S Naga
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
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Geng Q, Wan Y, Hsueh FC, Shang J, Ye G, Bu F, Herbst M, Wilkens R, Liu B, Li F. Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein. eLife 2023; 12:e74060. [PMID: 37991488 PMCID: PMC10695562 DOI: 10.7554/elife.74060] [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: 09/20/2021] [Accepted: 11/21/2023] [Indexed: 11/23/2023] Open
Abstract
SARS-CoV-2 spike protein plays a key role in mediating viral entry and inducing host immune responses. It can adopt either an open or closed conformation based on the position of its receptor-binding domain (RBD). It is yet unclear what causes these conformational changes or how they influence the spike's functions. Here, we show that Lys417 in the RBD plays dual roles in the spike's structure: it stabilizes the closed conformation of the trimeric spike by mediating inter-spike-subunit interactions; it also directly interacts with ACE2 receptor. Hence, a K417V mutation has opposing effects on the spike's function: it opens up the spike for better ACE2 binding while weakening the RBD's direct binding to ACE2. The net outcomes of this mutation are to allow the spike to bind ACE2 with higher probability and mediate viral entry more efficiently, but become more exposed to neutralizing antibodies. Given that residue 417 has been a viral mutational hotspot, SARS-CoV-2 may have been evolving to strike a balance between infection potency and immune evasion, contributing to its pandemic spread.
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Affiliation(s)
- Qibin Geng
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Yushun Wan
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fu-Chun Hsueh
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Jian Shang
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Gang Ye
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fan Bu
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Morgan Herbst
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Rowan Wilkens
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Bin Liu
- Hormel Institute, University of MinnesotaAustinUnited States
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
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Neves A, Cuesta I, Hjerde E, Klemetsen T, Salgado D, van Helden J, Rahman N, Fatima N, Karathanasis N, Zmora P, Åkerström WN, Grellscheid SN, Waheed Z, Blomberg N. FAIR+E pathogen data for surveillance and research: lessons from COVID-19. Front Public Health 2023; 11:1289945. [PMID: 38074768 PMCID: PMC10703184 DOI: 10.3389/fpubh.2023.1289945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
The COVID-19 pandemic has exemplified the importance of interoperable and equitable data sharing for global surveillance and to support research. While many challenges could be overcome, at least in some countries, many hurdles within the organizational, scientific, technical and cultural realms still remain to be tackled to be prepared for future threats. We propose to (i) continue supporting global efforts that have proven to be efficient and trustworthy toward addressing challenges in pathogen molecular data sharing; (ii) establish a distributed network of Pathogen Data Platforms to (a) ensure high quality data, metadata standardization and data analysis, (b) perform data brokering on behalf of data providers both for research and surveillance, (c) foster capacity building and continuous improvements, also for pandemic preparedness; (iii) establish an International One Health Pathogens Portal, connecting pathogen data isolated from various sources (human, animal, food, environment), in a truly One Health approach and following FAIR principles. To address these challenging endeavors, we have started an ELIXIR Focus Group where we invite all interested experts to join in a concerted, expert-driven effort toward sustaining and ensuring high-quality data for global surveillance and research.
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Affiliation(s)
- Aitana Neves
- SIB Swiss Institute of Bioinformatics, Clinical Bioinformatics, Geneva, Switzerland
| | - Isabel Cuesta
- Bioinformatics Unit, Institute of Health Carlos III, Madrid, Spain
| | - Erik Hjerde
- Institute of Chemistry, The Arctic University of Norway, Tromsø, Norway
| | - Terje Klemetsen
- Institute of Chemistry, The Arctic University of Norway, Tromsø, Norway
| | - David Salgado
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Jacques van Helden
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
- Aix-Marseille Univ, INSERM, Lab. Theory and Approaches of Genome Complexity (TAGC), Marseille, France
| | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nazeefa Fatima
- ELIXIR Norway, Centre for Bioinformatics, University of Oslo, Oslo, Norway
| | - Nestoras Karathanasis
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pawel Zmora
- Department of Molecular Virology, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Wolmar Nyberg Åkerström
- NBIS National Bioinformatics Infrastructure Sweden, SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Niklas Blomberg
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, United Kingdom
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21
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Potamias G, Gkoublia P, Kanterakis A. The two-stage molecular scenery of SARS-CoV-2 infection with implications to disease severity: An in-silico quest. Front Immunol 2023; 14:1251067. [PMID: 38077337 PMCID: PMC10699200 DOI: 10.3389/fimmu.2023.1251067] [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: 06/30/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction The two-stage molecular profile of the progression of SARS-CoV-2 (SCOV2) infection is explored in terms of five key biological/clinical questions: (a) does SCOV2 exhibits a two-stage infection profile? (b) SARS-CoV-1 (SCOV1) vs. SCOV2: do they differ? (c) does and how SCOV2 differs from Influenza/INFL infection? (d) does low viral-load and (e) does COVID-19 early host response relate to the two-stage SCOV2 infection profile? We provide positive answers to the above questions by analyzing the time-series gene-expression profiles of preserved cell-lines infected with SCOV1/2 or, the gene-expression profiles of infected individuals with different viral-loads levels and different host-response phenotypes. Methods Our analytical methodology follows an in-silico quest organized around an elaborate multi-step analysis pipeline including: (a) utilization of fifteen gene-expression datasets from NCBI's gene expression omnibus/GEO repository; (b) thorough designation of SCOV1/2 and INFL progression stages and COVID-19 phenotypes; (c) identification of differentially expressed genes (DEGs) and enriched biological processes and pathways that contrast and differentiate between different infection stages and phenotypes; (d) employment of a graph-based clustering process for the induction of coherent groups of networked genes as the representative core molecular fingerprints that characterize the different SCOV2 progression stages and the different COVID-19 phenotypes. In addition, relying on a sensibly selected set of induced fingerprint genes and following a Machine Learning approach, we devised and assessed the performance of different classifier models for the differentiation of acute respiratory illness/ARI caused by SCOV2 or other infections (diagnostic classifiers), as well as for the prediction of COVID-19 disease severity (prognostic classifiers), with quite encouraging results. Results The central finding of our experiments demonstrates the down-regulation of type-I interferon genes (IFN-1), interferon induced genes (ISGs) and fundamental innate immune and defense biological processes and molecular pathways during the early SCOV2 infection stages, with the inverse to hold during the later ones. It is highlighted that upregulation of these genes and pathways early after infection may prove beneficial in preventing subsequent uncontrolled hyperinflammatory and potentially lethal events. Discussion The basic aim of our study was to utilize in an intuitive, efficient and productive way the most relevant and state-of-the-art bioinformatics methods to reveal the core molecular mechanisms which govern the progression of SCOV2 infection and the different COVID-19 phenotypes.
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Affiliation(s)
- George Potamias
- Computational Biomedicine Laboratory (CBML), Institute of Computer Science, Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Polymnia Gkoublia
- Computational Biomedicine Laboratory (CBML), Institute of Computer Science, Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
- Graduate Bioinformatics Program, School of Medicine, University of Crete, Heraklion, Greece
| | - Alexandros Kanterakis
- Computational Biomedicine Laboratory (CBML), Institute of Computer Science, Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
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Wang R, Han Y, Zhang R, Zhu J, Nan X, Liu Y, Yang Z, Zhou B, Yu J, Lin Z, Li J, Chen P, Wang Y, Li Y, Liu D, Shi X, Wang X, Zhang Q, Yang YR, Li T, Zhang L. Dissecting the intricacies of human antibody responses to SARS-CoV-1 and SARS-CoV-2 infection. Immunity 2023; 56:2635-2649.e6. [PMID: 37924813 DOI: 10.1016/j.immuni.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to SARS-CoV-1 infection remains incomplete. Herein, we studied the antibody responses in 25 SARS-CoV-1 convalescent patients. Plasma neutralization was higher and lasted longer in SARS-CoV-1 patients than in severe SARS-CoV-2 patients. Among 77 monoclonal antibodies (mAbs) isolated, 60 targeted the receptor-binding domain (RBD) and formed 7 groups (RBD-1 to RBD-7) based on their distinct binding and structural profiles. Notably, RBD-7 antibodies bound to a unique RBD region interfaced with the N-terminal domain of the neighboring protomer (NTD proximal) and were more prevalent in SARS-CoV-1 patients. Broadly neutralizing antibodies for SARS-CoV-1, SARS-CoV-2, and bat and pangolin coronaviruses were also identified. These results provide further insights into the antibody response to SARS-CoV-1 and inform the design of more effective strategies against diverse human and animal coronaviruses.
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Affiliation(s)
- Ruoke Wang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Yang Han
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China
| | - Rui Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jiayi Zhu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Xuanyu Nan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yaping Liu
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ziqing Yang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bini Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zichun Lin
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jinqian Li
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peng Chen
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yangjunqi Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China.
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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23
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Saleki K, Alijanizadeh P, Azadmehr A. Is neuropilin-1 the neuroimmune initiator of multi-system hyperinflammation in COVID-19? Biomed Pharmacother 2023; 167:115558. [PMID: 37748412 DOI: 10.1016/j.biopha.2023.115558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023] Open
Abstract
A major immunopathological feature of Coronavirus disease-2019 (COVID-19) is excessive inflammation in the form of "cytokine storm". The storm is characterized by injurious levels of cytokines which form a complicated network damaging different organs, including the lungs and the brain. The main starter of "cytokine network" hyperactivation in COVID-19 has not been discovered yet. Neuropilins (NRPs) are transmembrane proteins that act as neuronal guidance and angiogenesis modulators. The crucial function of NRPs in forming the nervous and vascular systems has been well-studied. NRP1 and NRP2 are the two identified homologs of NRP. NRP1 has been shown as a viral entry pathway for SARS-CoV2, which facilitates neuroinvasion by the virus within the central or peripheral nervous systems. These molecules directly interact with various COVID-19-related molecules, such as specific regions of the spike protein (major immune element of SARS-CoV2), vascular endothelial growth factor (VEGF) receptors, VEGFR1/2, and ANGPTL4 (regulator of vessel permeability and integrity). NRPs mainly play a role in hyperinflammatory injury of the CNS and lungs, and also the liver, kidney, pancreas, and heart in COVID-19 patients. New findings have suggested NRPs good candidates for pharmacotherapy of COVID-19. However, therapeutic targeting of NRP1 in COVID-19 is still in the preclinical phase. This review presents the implications of NRP1 in multi-organ inflammation-induced injury by SARS-CoV2 and provides insights for NRP1-targeting treatments for COVID-19 patients.
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Affiliation(s)
- Kiarash Saleki
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran; Department of e-Learning, Virtual School of Medical Education and Management, Shahid Beheshti University of Medical Sciences(SBMU), Tehran, Iran; USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Parsa Alijanizadeh
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran; USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Abbas Azadmehr
- Immunology Department, Babol University of Medical Sciences, Babol, Iran; Cellular and Molecular Biology Research Center Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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Tambe LAM, Mathobo P, Munzhedzi M, Bessong PO, Mavhandu-Ramarumo LG. Prevalence and Molecular Epidemiology of Human Coronaviruses in Africa Prior to the SARS-CoV-2 Outbreak: A Systematic Review. Viruses 2023; 15:2146. [PMID: 38005824 PMCID: PMC10675249 DOI: 10.3390/v15112146] [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: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Coronaviruses, re-emerging in human populations, cause mild or severe acute respiratory diseases, and occasionally epidemics. This study systematically reviewed human coronavirus (HCoVs) infections in Africa prior to the SARS-CoV-2 outbreak. Forty studies on the prevalence or molecular epidemiology of HCoVs were available from 13/54 African countries (24%). The first published data on HCoV was from South Africa in 2008. Eight studies (20%) reported on HCoV molecular epidemiology. Endemic HCoV prevalence ranged from 0.0% to 18.2%. The prevalence of zoonotic MERS-CoV ranged from 0.0% to 83.5%. Two studies investigated SARS-CoV infection, for which a prevalence of 0.0% was reported. There was heterogeneity in the type of tests used in determining HCoV prevalence. Two studies reported that risk factors for HCoV include exposure to infected animals or humans. The quantity of virologic investigations on HCoV on the African continent was scant, and Africa was not prepared for SARS-CoV-2.
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Affiliation(s)
- Lisa Arrah Mbang Tambe
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Phindulo Mathobo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mukhethwa Munzhedzi
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Pascal Obong Bessong
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Centre for Global Health Equity, School of Medicine, 1400 University Ave, Charlottesville, VA 22903, USA
| | - Lufuno Grace Mavhandu-Ramarumo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
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25
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Roev GV, Borisova NI, Chistyakova NV, Agletdinov MR, Akimkin VG, Khafizov K. Unlocking the Viral Universe: Metagenomic Analysis of Bat Samples Using Next-Generation Sequencing. Microorganisms 2023; 11:2532. [PMID: 37894190 PMCID: PMC10608967 DOI: 10.3390/microorganisms11102532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Next-generation sequencing technologies have revolutionized the field of virology by enabling the reading of complete viral genomes, extensive metagenomic studies, and the identification of novel viral pathogens. Although metagenomic sequencing has the advantage of not requiring specific probes or primers, it faces significant challenges in analyzing data and identifying novel viruses. Traditional bioinformatics tools for sequence identification mainly depend on homology-based strategies, which may not allow the detection of a virus significantly different from known variants due to the extensive genetic diversity and rapid evolution of viruses. In this work, we performed metagenomic analysis of bat feces from different Russian cities and identified a wide range of viral pathogens. We then selected sequences with minimal homology to a known picornavirus and used "Switching Mechanism at the 5' end of RNA Template" technology to obtain a longer genome fragment, allowing for more reliable identification. This study emphasizes the importance of integrating advanced computational methods with experimental strategies for identifying unknown viruses to better understand the viral universe.
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Affiliation(s)
- German V. Roev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Dolgoprudny, Russia
| | | | - Nadezhda V. Chistyakova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Matvey R. Agletdinov
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Dolgoprudny, Russia
| | | | - Kamil Khafizov
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
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26
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Du Q, Liang R, Wu M, Yang M, Xie Y, Liu Q, Tang K, Lin X, Yuan S, Shen J. Alisol B 23-acetate broadly inhibits coronavirus through blocking virus entry and suppresses proinflammatory T cells responses for the treatment of COVID-19. J Adv Res 2023:S2090-1232(23)00294-1. [PMID: 37802148 DOI: 10.1016/j.jare.2023.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/11/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
INTRODUCTION Emerging severe acute respiratory syndrome (SARS) coronavirus (CoV)-2 causes a global health disaster and pandemic. Seeking effective anti-pan-CoVs drugs benefit critical illness patients of coronavirus disease 2019 (COVID-19) but also may play a role in emerging CoVs of the future. OBJECTIVES This study tested the hypothesis that alisol B 23-acetate could be a viral entry inhibitor and would have proinflammatory inhibition for COVID-19 treatment. METHODS SARS-CoV-2 and its variants infected several cell lines were applied to evaluate the anti-CoVs activities of alisol B 23-aceate in vitro. The effects of alisol B 23-acetate on in vivo models were assessed by using SARS-CoV-2 and its variants challenged hamster and human angiotensin-converting enzyme 2 (ACE2) transgenic mice. The target of alisol B 23-acetate to ACE2 was analyzed using hydrogen/deuterium exchange (HDX) mass spectrometry (MS). RESULTS Alisol B 23-acetate had inhibitory effects on different species of coronavirus. By using HDX-MS, we found that alisol B 23-acetate had inhibition potency toward ACE2. In vivo experiments showed that alisol B 23-acetate treatment remarkably decreased viral copy, reduced CD4+ T lymphocytes and CD11b+ macrophages infiltration and ameliorated lung damages in the hamster model. In Omicron variant infected human ACE2 transgenic mice, alisol B 23-acetate effectively alleviated viral load in nasal turbinate and reduced proinflammatory cytokines interleukin 17 (IL17) and interferon γ (IFNγ) in peripheral blood. The prophylactic treatment of alisol B 23-acetate by intranasal administration significantly attenuated Omicron viral load in the hamster lung tissues. Moreover, alisol B 23-acetate treatment remarkably inhibited proinflammatory responses through mitigating the secretions of IFNγ and IL17 in the cultured human and mice lymphocytes in vitro. CONCLUSION Alisol B 23-acetate could be a promising therapeutic agent for COVID-19 treatment and its underlying mechanisms might be attributed to viral entry inhibition and anti-inflammatory activities.
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Affiliation(s)
- Qiaohui Du
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region; State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Ronghui Liang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Meiling Wu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Minxiao Yang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Yubin Xie
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Qing Liu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Kaiming Tang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Xiang Lin
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China.
| | - Jiangang Shen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region; State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong Special Administrative Region.
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Bakkaloglu OK, Onal U, Eskazan T, Kurt EA, Candan S, Karaali R, Borekci S, Urkmez S, Dikmen Y, Tabak F, Tuncer M, Hatemi I. Increase in transaminase levels during COVID-19 infection and its association with poor prognosis. Singapore Med J 2023; 64:640-644. [PMID: 37861645 PMCID: PMC10645006 DOI: 10.4103/singaporemedj.smj-2021-111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/01/2021] [Indexed: 05/13/2023]
Affiliation(s)
- Oguz Kagan Bakkaloglu
- Section of Gastroenterology, Department of Internal Medicine, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ugur Onal
- Section of Gastroenterology, Department of Internal Medicine, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Tugce Eskazan
- Section of Gastroenterology, Department of Internal Medicine, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Enes Ali Kurt
- Section of Gastroenterology, Department of Internal Medicine, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Selcuk Candan
- Section of Gastroenterology, Department of Internal Medicine, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ridvan Karaali
- Department of Infectious Diseases and Clinical Microbiology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Sermin Borekci
- Department of Chest Diseases, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Seval Urkmez
- Department of Anesthesiology and Intensive Care, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Yalim Dikmen
- Department of Anesthesiology and Intensive Care, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Fehmi Tabak
- Department of Infectious Diseases and Clinical Microbiology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Murat Tuncer
- Section of Gastroenterology, Department of Internal Medicine, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ibrahim Hatemi
- Section of Gastroenterology, Department of Internal Medicine, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
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Sharma G, Kumar N, Sharma CS, Mishra SS. In silico guided screening of active components of C. lanceolata as 3-chymotrypsin-like protease inhibitors of novel coronavirus. 3 Biotech 2023; 13:324. [PMID: 37663751 PMCID: PMC10471561 DOI: 10.1007/s13205-023-03745-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/14/2023] [Indexed: 09/05/2023] Open
Abstract
Despite the intense worldwide efforts towards the identification of potential anti-CoV therapeutics, no antiviral drugs have yet been discovered. Numerous vaccines are now approved for use, but they all serve as preventative measures. To effectively treat viral infections, it is crucial to find new antiviral drugs that are derived from natural sources. Various compounds with potential activity against 3 chymotrypsin-like protease (3CLpro) were reported and some are validated by bioassay studies. Therefore, we performed the computational screening of phytoconstituents of Codonopsis lanceolata to search for potential antiviral hit candidates. The curated compounds of the plant C. lanceolata were collected and downloaded from the literature. The binding affinity of the curated datasets was predicted for the target 3CLpro. Stigmasterol exhibits the highest docking score for the 3CLpro target. In addition, molecular dynamics (MD) simulations were conducted for the validation of docking results using root mean square deviation and root mean square fluctuation plots. The MD results indicated that the docked complex was stable and retained hydrogen bonding and non-bonding interactions. Furthermore, the calculation of pharmacokinetic parameters and Lipinski's rule of five suggest that C. lanceolata has the potential for drug-likeness. In order to develop new medicines for this debilitating disease, we will focus on the primary virus-based and host-based targets that can direct medicinal chemists to identify novel treatments to produce new drugs for it. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03745-2.
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Affiliation(s)
- Ganesh Sharma
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ University, Udaipur, 313002 India
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ University, Udaipur, 313002 India
| | - Chandra Shekhar Sharma
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ University, Udaipur, 313002 India
| | - Shashank Shekher Mishra
- Faculty of Pharmacy, School of Pharmaceutical and Populations Health Informatics, DIT University, Dehradun, 248009 India
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Xia CS, Zhan M, Liu Y, Yue ZH, Song Y, Zhang F, Wang H. SARS-CoV-2 antibody response in SARS survivors with and without the COVID-19 vaccine. Int J Antimicrob Agents 2023; 62:106947. [PMID: 37544384 DOI: 10.1016/j.ijantimicag.2023.106947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 07/12/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
OBJECTIVES Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread worldwide. However, it remains unknown whether individuals with prior SARS-CoV-1 infection are protected from SARS-CoV-2 infection. This study assessed protective antibody levels in SARS survivors with and without the COVID-19 vaccine. METHODS We recruited 17 SARS survivors infected with SARS-CoV-1 in 2003, including 8 not vaccinated with the COVID-19 vaccine and 9 vaccinated with two doses of inactivated whole-virion COVID-19 vaccine (Sinopharm). In addition, 105 healthy adult volunteers without SARS-CoV-1 and SARS-CoV-2 infections were used as controls. The relative concentrations of three protective antibodies including anti-SARS-CoV-2 spike IgG (nCoV S-IgG), anti-SARS-CoV-2 spike receptor-binding domain IgG (nCoV RBD-IgG), and anti-SARS-CoV-2 neutralizing antibodies (nCoV NAbs) were measured to evaluate humoral immunity. RESULTS We found that the positive rates of these antibodies in unvaccinated SARS survivors were 37.5%, 37.5%, and 62.5%, respectively. In contrast, the corresponding positive rates were all 0% in controls before vaccination. In controls, the levels of protective antibodies reached a peak ca. 28 days after the second dose of vaccine and then started to decline. Surprisingly, the levels of these antibodies were maintained at very high levels even 166 days after the second dose of vaccine in SARS survivors. CONCLUSION Our study suggests that there are protective antibodies cross-reacting with SARS-CoV-2 in recovered SARS patients and that SARS survivors can generate a much stronger antibody response induced by the COVID-19 vaccine than can controls. These initial findings show the feasibility of developing novel pan-sarbecovirus vaccines.
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Affiliation(s)
- Chang-Sheng Xia
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Minghua Zhan
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yudong Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhi-Hong Yue
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Ying Song
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Feifei Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
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Poirier AC, Riaño Moreno RD, Takaindisa L, Carpenter J, Mehat JW, Haddon A, Rohaim MA, Williams C, Burkhart P, Conlon C, Wilson M, McClumpha M, Stedman A, Cordoni G, Branavan M, Tharmakulasingam M, Chaudhry NS, Locker N, Fernando A, Balachandran W, Bullen M, Collins N, Rimer D, Horton DL, Munir M, La Ragione RM. VIDIIA Hunter diagnostic platform: a low-cost, smartphone connected, artificial intelligence-assisted COVID-19 rapid diagnostics approved for medical use in the UK. Front Mol Biosci 2023; 10:1144001. [PMID: 37842636 PMCID: PMC10572354 DOI: 10.3389/fmolb.2023.1144001] [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: 01/13/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: Accurate and rapid diagnostics paired with effective tracking and tracing systems are key to halting the spread of infectious diseases, limiting the emergence of new variants and to monitor vaccine efficacy. The current gold standard test (RT-qPCR) for COVID-19 is highly accurate and sensitive, but is time-consuming, and requires expensive specialised, lab-based equipment. Methods: Herein, we report on the development of a SARS-CoV-2 (COVID-19) rapid and inexpensive diagnostic platform that relies on a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and a portable smart diagnostic device. Automated image acquisition and an Artificial Intelligence (AI) deep learning model embedded in the Virus Hunter 6 (VH6) device allow to remove any subjectivity in the interpretation of results. The VH6 device is also linked to a smartphone companion application that registers patients for swab collection and manages the entire process, thus ensuring tests are traced and data securely stored. Results: Our designed AI-implemented diagnostic platform recognises the nucleocapsid protein gene of SARS-CoV-2 with high analytical sensitivity and specificity. A total of 752 NHS patient samples, 367 confirmed positives for coronavirus disease (COVID-19) and 385 negatives, were used for the development and validation of the test and the AI-assisted platform. The smart diagnostic platform was then used to test 150 positive clinical samples covering a dynamic range of clinically meaningful viral loads and 250 negative samples. When compared to RT-qPCR, our AI-assisted diagnostics platform was shown to be reliable, highly specific (100%) and sensitive (98-100% depending on viral load) with a limit of detection of 1.4 copies of RNA per µL in 30 min. Using this data, our CE-IVD and MHRA approved test and associated diagnostic platform has been approved for medical use in the United Kingdom under the UK Health Security Agency's Medical Devices (Coronavirus Test Device Approvals, CTDA) Regulations 2022. Laboratory and in-silico data presented here also indicates that the VIDIIA diagnostic platform is able to detect the main variants of concern in the United Kingdom (September 2023). Discussion: This system could provide an efficient, time and cost-effective platform to diagnose SARS-CoV-2 and other infectious diseases in resource-limited settings.
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Affiliation(s)
- Aurore C. Poirier
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | | | - Leona Takaindisa
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Jessie Carpenter
- VIDIIA Ltd., Surrey Technology Centre, Guildford, United Kingdom
| | - Jai W. Mehat
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
| | - Abi Haddon
- Berkshire and Surrey Pathology Services, Molecular Diagnostics, Royal Surrey County Hospital, Guildford, United Kingdom
| | - Mohammed A. Rohaim
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom
| | - Craig Williams
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom
| | - Peter Burkhart
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom
| | - Chris Conlon
- GB Electronics (UK) Ltd, Worthing, United Kingdom
| | | | | | - Anna Stedman
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Guido Cordoni
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Manoharanehru Branavan
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom
| | | | - Nouman S. Chaudhry
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom
| | - Nicolas Locker
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
| | - Anil Fernando
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom
| | - Wamadeva Balachandran
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Mark Bullen
- GB Electronics (UK) Ltd, Worthing, United Kingdom
| | - Nadine Collins
- Berkshire and Surrey Pathology Services, Molecular Diagnostics, Royal Surrey County Hospital, Guildford, United Kingdom
| | - David Rimer
- VIDIIA Ltd., Surrey Technology Centre, Guildford, United Kingdom
| | - Daniel L. Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom
| | - Roberto M. La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
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Cheng J, Zeng H, Chen H, Fan L, Xu C, Huang H, Tang T, Li M. Current knowledge of thrombocytopenia in sepsis and COVID-19. Front Immunol 2023; 14:1213510. [PMID: 37841241 PMCID: PMC10568455 DOI: 10.3389/fimmu.2023.1213510] [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: 04/28/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Thrombocytopenia, characterized by a decrease in platelet count, is commonly observed in sepsis and COVID-19. In sepsis, thrombocytopenia can result from various mechanisms, including impaired platelet production in the bone marrow, accelerated platelet destruction due to increased inflammation, sequestration of platelets in the spleen, immune-mediated platelet destruction, or dysregulated host responses. Similarly, thrombocytopenia has been reported in COVID-19 patients, but the immune-related mechanisms underlying this association remain unclear. Notably, interventions targeting thrombocytopenia have shown potential for improving outcomes in both sepsis and COVID-19 patients. Understanding these mechanisms is crucial for developing effective treatments.
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Affiliation(s)
- Junjie Cheng
- Intensive Care Unit, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China
| | - Hanhai Zeng
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huaijun Chen
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Linfeng Fan
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chaoran Xu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huaping Huang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Tianchi Tang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Min Li
- Intensive Care Unit, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China
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32
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Daniels A, Fletcher S, Kerr HEM, Kratzel A, Pinto RM, Kriplani N, Craig N, Hastie CJ, Davies P, Digard P, Thiel V, Tait-Burkard C. One for all-human kidney Caki-1 cells are highly susceptible to infection with corona- and other respiratory viruses. J Virol 2023; 97:e0055523. [PMID: 37668370 PMCID: PMC10537734 DOI: 10.1128/jvi.00555-23] [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: 04/13/2023] [Accepted: 07/05/2023] [Indexed: 09/06/2023] Open
Abstract
In vitro investigations of host-virus interactions are reliant on suitable cell and tissue culture models. Results are only as good as the model they are generated in. However, choosing cell models for in vitro work often depends on availability and previous use alone. Despite the vast increase in coronavirus research over the past few years, scientists are still heavily reliant on: non-human, highly heterogeneous or not fully differentiated, or naturally unsusceptible cells requiring overexpression of receptors and other accessory factors. Complex primary or stem cell models are highly representative of human tissues but are expensive and time-consuming to develop and maintain with limited suitability for high-throughput experiments.Using tissue-specific expression patterns, we identified human kidney cells as an ideal target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and broader coronavirus infection. We show the use of the well-characterized human kidney cell line Caki-1 for infection with three human coronaviruses (hCoVs): Betacoronaviruses SARS-CoV-2 and Middle Eastern respiratory syndrome coronavirus and Alphacoronavirus hCoV 229E. Caki-1 cells show equal or superior susceptibility to all three coronaviruses when compared to other commonly used cell lines for the cultivation of the respective virus. Antibody staining against SARS-CoV-2 N protein shows comparable replication rates. A panel of 26 custom antibodies shows the location of SARS-CoV-2 proteins during replication using immunocytochemistry. In addition, Caki-1 cells were found to be susceptible to two other human respiratory viruses, influenza A virus and respiratory syncytial virus, making them an ideal model for cross-comparison for a broad range of respiratory viruses. IMPORTANCE Cell lines remain the backbone of virus research, but results are only as good as their originating model. Despite increased research into human coronaviruses following the COVID-19 pandemic, researchers continue to rely on suboptimal cell line models of: non-human origin, incomplete differentiation, or lacking active interferon responses. We identified the human kidney Caki-1 cell line as a potential target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This cell line could be shown to be infectable with a wide range of coronaviruses including common cold virus hCoV-229E, epidemic virus MERS-CoV, and SARS-CoV-2 as well as other important respiratory viruses influenza A virus and respiratory syncytial virus. We could show the localization of 26 SARS-CoV-2 proteins in Caki-1 cells during natural replication and the cells are competent of forming a cellular immune response. Together, this makes Caki-1 cells a unique tool for cross-virus comparison in one cell line.
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Affiliation(s)
- Alison Daniels
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- Infection Medicine, University of Edinburgh, Little France Crescent, United Kingdom
| | - Sarah Fletcher
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Holly E. M. Kerr
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rute Maria Pinto
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nisha Kriplani
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nicky Craig
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - C. James Hastie
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul Davies
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul Digard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christine Tait-Burkard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
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Misra G, Manzoor A, Chopra M, Upadhyay A, Katiyar A, Bhushan B, Anvikar A. Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India. Sci Rep 2023; 13:14847. [PMID: 37684328 PMCID: PMC10491582 DOI: 10.1038/s41598-023-42065-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023] Open
Abstract
The various strains and mutations of SARS-CoV-2 have been tracked using several forms of genomic classification systems. The present study reports high-throughput sequencing and analysis of 99 SARS-CoV-2 specimens from Western Uttar Pradesh using sequences obtained from the GISAID database, followed by phylogeny and clade classification. Phylogenetic analysis revealed that Omicron lineages BA-2-like (55.55%) followed by Delta lineage-B.1.617.2 (45.5%) were predominantly circulating in this area Signature substitution at positions S: N501Y, S: D614G, S: T478K, S: K417N, S: E484A, S: P681H, and S: S477N were commonly detected in the Omicron variant-BA-2-like, however S: D614G, S: L452R, S: P681R and S: D950N were confined to Delta variant-B.1.617.2. We have also identified three escape variants in the S gene at codon position 19 (T19I/R), 484 (E484A/Q), and 681 (P681R/H) during the fourth and fifth waves in India. Based on the phylogenetic diversification studies and similar changes in other lineages, our analysis revealed indications of convergent evolution as the virus adjusts to the shifting immunological profile of its human host. To the best of our knowledge, this study is an approach to comprehensively map the circulating SARS-CoV-2 strains from Western Uttar Pradesh using an integrated approach of whole genome sequencing and phylogenetic analysis. These findings will be extremely valuable in developing a structured approach toward pandemic preparedness and evidence-based intervention plans in the future.
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Affiliation(s)
- Gauri Misra
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India.
| | - Ashrat Manzoor
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Meenu Chopra
- National Dairy Research Institute, Karnal, Haryana, India
| | - Archana Upadhyay
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Amit Katiyar
- Bioinformatics Facility, Centralized Core Research Facility, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Brij Bhushan
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Anup Anvikar
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
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Shenoy RD, Nithin Kuriakose, Vijaykrishnaraj M, Patil P, Jayaswamy PK, Alagundagi DB, Shetty P. Tissue plasminogen activator receptor ANXA2 and its complementary regulator anti-inflammatory ANXA1 as prognostic indicators of inflammatory response in COVID-19 pathogenesis. Immunobiology 2023; 228:152728. [PMID: 37579635 DOI: 10.1016/j.imbio.2023.152728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/27/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023]
Abstract
COVID-19 patients demonstrating hyperactive immunologic response appear to have a severe illness with a poor prognosis. This study hypothesizes that the pro-inflammatory Annexin A2 (ANXA2) has role in COVID-19 pathogenesis. In thisobservational study, serum levels of ANXA2 along with interleukin 1 beta (IL1β), IL6, tumour necrosis factor-alpha (TNFα), and anti-inflammatory ANXA1 were determined by sandwich ELISA in 20 each control, mild, moderate, and severe COVID-19 subjects.The ANXA2 levels (130 ng/mL, p < 0.001) were significantly elevated in severe COVID-19 subjects, compared to mild, moderate and controls. Similarly, all the other pro-inflammatory biomarkers levels were also significantly correlated with disease severity (p < 0.0001). However, ANXA1 showed significantly negative correlation with disease severity (p < 0.0001). Furthermore, the pro-inflammatory ANXA2 showed utility in mortality prediction with 86% sensitivity and specificity, and 57% positive predictive value at a serum threshold of 94 ng/mL. Overall,ANXA2 and ANXA1 along with IL1β, IL6, TNFα, would be beneficial biomarkers in assessing the COVID-19 severity and mortality prediction.
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Affiliation(s)
- Rathika D Shenoy
- Department of Pediatrics, Justice K S Hegde Charitable Hospital, K S Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, Karnataka, India
| | - Nithin Kuriakose
- Division of Proteomics and Cancer Biology, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakatte, Mangaluru, 575018, India
| | - Vijaykrishnaraj M
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, Karnataka, India
| | - Prakash Patil
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, Karnataka, India.
| | - Pavan K Jayaswamy
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, Karnataka, India
| | - Dhananjay B Alagundagi
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, Karnataka, India
| | - Praveenkumar Shetty
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, Karnataka, India; Department of Biochemistry, K S Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, Karnataka, India.
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Keshtgar Z, Chalabianloo G, Esmaeili N. Probable Neuropsychological and Cognitive Complications Due to Cytokine Storm in Patients With COVID-19. Basic Clin Neurosci 2023; 14:549-564. [PMID: 38628831 PMCID: PMC11016882 DOI: 10.32598/bcn.2022.3202.1] [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: 01/23/2021] [Revised: 09/28/2021] [Accepted: 06/28/2023] [Indexed: 04/19/2024] Open
Abstract
Introduction COVID-19 (coronavirus disease 2019) was first identified in China in December 2019 and is rapidly spreading worldwide as a pandemic. Since COVID-19 causes mild to severe acute respiratory syndrome, most studies in this context have focused on pathogenesis primarily in the respiratory system. However, evidence shows that the central nervous system (CNS) may also be affected by COVID-19. Since COVID-19 is spreading, it is necessary to study its possible cognitive effects on COVID-19 patients and their recovery. Methods The articles used in this study were searched by keywords, such as cytokine storm and COVID-19, COVID-19 and executive dysfunction, cognitive disorder, and COVID-19, central nervous system (CNS) and COVID-19, coronavirus, neuroinvasion in Science Direct, Scopus, PubMed, Embase, and Web of Science databases based on preferred reporting items for systematic reviews and meta-analysis (PRISMA) checklist. The study evaluates all observational studies published between December 2019 and April 2021 in peer-reviewed journals, including cross-sectional, cohort, case-control studies, case reports, and case series. The search result was 106 articles, of which 73 articles related to COVID-19, the stages of infection by this virus, its effect on the nervous system and neurological symptoms, the cytokine storm caused by this infection, and the possible cognitive consequences caused by this virus in patients, has been reviewed. Other articles were not checked due to their limited relevance to the topic under discussion. Results Studies showed that neurons may be directly affected by severe acute respiratory syndrome coronavirus (SARS-CoV)-1 and SARS-CoV-2. Furthermore, various studies indicated that systemic inflammation (so-called "cytokine storm") is also responsible for brain damage induced by infection with SARS-CoV-1 and SARS-CoV-2. In such a way that these patients showed elevated levels of interleukin (IL-), 6, 8, and 10 and of tumor necrosis factor-alpha (TNF-α) in their blood. Conclusion Various cognitive defects have been observed following an increased level of cytokines, such as tumor necrosis factor-alpha (TNF-α) and interleukin (IL)-6, 8. Therefore, due to the increased level of these pro-inflammatory factors in the brains of these patients, cognitive deficits can be expected, which need further investigation.
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Affiliation(s)
- Zahra Keshtgar
- Department of Neuroscience, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamreza Chalabianloo
- Department of Neuroscience, School of Educational Sciences and Psychology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Niloofar Esmaeili
- Department of Hematology & Oncology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Aghamohamadi N, Shahba F, Zarezadeh Mehrabadi A, Khorramdelazad H, Karimi M, Falak R, Emameh RZ. Age-dependent immune responses in COVID-19-mediated liver injury: focus on cytokines. Front Endocrinol (Lausanne) 2023; 14:1139692. [PMID: 37654571 PMCID: PMC10465349 DOI: 10.3389/fendo.2023.1139692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 07/21/2023] [Indexed: 09/02/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is potentially pathogenic and causes severe symptoms; in addition to respiratory syndromes, patients might experience other severe conditions such as digestive complications and liver complications injury. The abnormality in the liver is manifested by hepatobiliary dysfunction and enzymatic elevation, which is associated with morbidity and mortality. The direct cytopathic effect, immune dysfunction, cytokine storm, and adverse effects of therapeutic regimens have a crucial role in the severity of liver injury. According to aging and immune system alterations, cytokine patterns may also change in the elderly. Moreover, hyperproduction of cytokines in the inflammatory response to SARS-CoV-2 can lead to multi-organ dysfunction. The mortality rate in elderly patients, particularly those with other comorbidities, is also higher than in adults. Although the pathogenic effect of SARS-CoV-2 on the liver has been widely studied, the impact of age and immune-mediated responses at different ages remain unclear. This review discusses the association between immune system responses in coronavirus disease 2019 (COVID-19) patients of different ages and liver injury, focusing on cytokine alterations.
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Affiliation(s)
- Nazanin Aghamohamadi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Faezeh Shahba
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Zarezadeh Mehrabadi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Khorramdelazad
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Milad Karimi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Falak
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Awoke MA, Adane A, Assefa B, Getawa S, Legese GL, Yimer M. Hematological parameters and their predictive value for assessing disease severity in laboratory-confirmed COVID-19 patients: a retrospective study. AMERICAN JOURNAL OF BLOOD RESEARCH 2023; 13:117-129. [PMID: 37736538 PMCID: PMC10509465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/07/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND The coronavirus disease 19 (COVID-19) infection has spread globally and caused a substantial amount of mortality and morbidity. Early detection of severe infections will improve care and reduce deaths. The use of hematological parameters in predicting COVID-19 disease severity, patient outcomes, and early risk stratification is limited. Therefore, the study was aimed at determining hematological parameters and their predictive value for assessing disease severity in laboratory-confirmed COVID-19 patients in Northwest Ethiopia. METHODS A retrospective cross-sectional study was conducted at the University of Gondar comprehensive specialized hospital and Tibebe Ghion comprehensive specialized referral hospital on 253 patients diagnosed with COVID-19 and admitted between March 2021 and February 2022. Data were extracted, and entered into Epi-data 4.2.0.0, and analyzed using SPSS version 25 software. Hematological parameters were provided as the median and interquartile range (IQR). Categorical variables were represented by their frequency, and the χ2 test was applied to compare observed results with expected results. The receiver-operating curve (ROC) was used to establish the predictive value of hematological parameters for COVID-19 severity. A p-value < 0.05 was considered statistically significant. RESULTS On a total of 253 patients, there were 43.87% severe cases, with a mortality rate of 26.9%. The ROC analysis showed the optimal cutoff values for hematological parameters were ANC (3370), lymphocyte (680), NLR (9.34), PLR (290.77), platelets (332,000), and WBCs (4390.65). The area under the curve (AUC) values for NLR (0.679) and ANC (0.631) were high, with the highest sensitivity and specificity, and could potentially be used to predict COVID-19 severity. CONCLUSION This study proved that high NLR and high ANC have prognostic value for assessing disease severity in COVID-19. Thus, assessing and considering these hematological parameters when triaging COVID-19 patients may prevent complications and improve the patient's outcome.
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Affiliation(s)
- Mezgebu Alemayehu Awoke
- Department of Internal Medicine, School of Medicine, College of Medicine and Health Sciences, University of GondarGondar, Ethiopia
| | - Ayinshet Adane
- Department of Internal Medicine, School of Medicine, College of Medicine and Health Sciences, University of GondarGondar, Ethiopia
| | - Belete Assefa
- Department of Internal Medicine, School of Medicine, College of Medicine and Health Sciences, University of GondarGondar, Ethiopia
| | - Solomon Getawa
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of GondarGondar, Ethiopia
| | - Gebrehiwot Lema Legese
- Department of Internal Medicine, School of Medicine, College of Medicine and Health Sciences, University of GondarGondar, Ethiopia
| | - Mekonen Yimer
- Department of Internal Medicine, School of Medicine, College of Medicine and Health Sciences, University of GondarGondar, Ethiopia
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Iqbal B, Rahman NM, Hallifax RJ. COVID-19-Related Pleural Diseases. Semin Respir Crit Care Med 2023; 44:437-446. [PMID: 37429295 DOI: 10.1055/s-0043-1769616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Coronavirus disease 2019 (COVID-19)-related pleural diseases are now well recognized. Since the beginning of the pandemic, increasing cases of pleural diseases including pneumothorax, pneumomediastinum, and pleural effusion with severe COVID-19 infection have attracted the attention of physicians and are not incidental or due to barotrauma. The complicated course of COVID-19 illness highlights the complex pathophysiological underpinnings of pleural complications. The management of patients with pneumothorax and pneumomediastinum is challenging as the majority require assisted ventilation; physicians therefore appear to have a low threshold to intervene. Conversely, pleural effusion cases, although sharing some similar patient characteristics with pneumothorax and pneumomediastinum, are in general managed more conservatively. The evidence suggests that patients with COVID-19-related pleural diseases, either due to air leak or effusion, have more severe disease with a worse prognosis. This implies that prompt recognition of these complications and targeted management are key to improve outcomes.
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Affiliation(s)
- Beenish Iqbal
- Respiratory Trials Unit, Oxford Centre for Respiratory Disease, Oxford University Hospital, Oxford Centre for Respiratory Medicine, Churchill Hospital, NHS Trust, Oxford, United Kingdom
| | - Najib M Rahman
- Respiratory Trials Unit, Oxford Centre for Respiratory Disease, Oxford University Hospital, Oxford Centre for Respiratory Medicine, Churchill Hospital, NHS Trust, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Rob J Hallifax
- Respiratory Trials Unit, Oxford Centre for Respiratory Disease, Oxford University Hospital, Oxford Centre for Respiratory Medicine, Churchill Hospital, NHS Trust, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
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Williams DM, Hornsby HR, Shehata OM, Brown R, Gallis M, Meardon N, Newman TAH, Plowright M, Zafred D, Shun-Shion ASM, Hodder AJ, Bliss D, Metcalfe A, Edgar JR, Gordon DE, Sayers JR, Nicklin MJ, Carroll M, Collini PJ, Brown S, de Silva TI, Peden AA. Establishing SARS-CoV-2 membrane protein-specific antibodies as a valuable serological target via high-content microscopy. iScience 2023; 26:107056. [PMID: 37346049 PMCID: PMC10246304 DOI: 10.1016/j.isci.2023.107056] [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: 12/15/2022] [Revised: 03/31/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
The prevalence and strength of serological responses mounted toward SARS-CoV-2 proteins other than nucleocapsid (N) and spike (S), which may be of use as additional serological markers, remains underexplored. Using high-content microscopy to assess antibody responses against full-length StrepTagged SARS-CoV-2 proteins, we found that 85% (166/196) of unvaccinated individuals with RT-PCR confirmed SARS-CoV-2 infections and 74% (31/42) of individuals infected after being vaccinated developed detectable IgG against the structural protein M, which is higher than previous estimates. Compared with N antibodies, M IgG displayed a shallower time-dependent decay and greater specificity. Sensitivity for SARS-CoV-2 seroprevalence was enhanced when N and M IgG detection was combined. These findings indicate that screening for M seroconversion may be a good approach for detecting additional vaccine breakthrough infections and highlight the potential to use HCM as a rapidly deployable method to identify the most immunogenic targets of newly emergent pathogens.
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Affiliation(s)
- Daniel M Williams
- School of Bioscience, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Hailey R Hornsby
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Ola M Shehata
- School of Bioscience, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Rebecca Brown
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Marta Gallis
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Naomi Meardon
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
- South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Glossop Road, Sheffield S10 2JF, UK
| | - Thomas A H Newman
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
- South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Glossop Road, Sheffield S10 2JF, UK
| | - Megan Plowright
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
- South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Glossop Road, Sheffield S10 2JF, UK
| | - Domen Zafred
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Amber S M Shun-Shion
- School of Bioscience, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Anthony J Hodder
- School of Bioscience, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Deepa Bliss
- School of Bioscience, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Andrew Metcalfe
- School of Bioscience, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - James R Edgar
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - David E Gordon
- Department of Pathology, Emory University, Whitehead Building, Atlanta, GA, USA
| | - Jon R Sayers
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Martin J Nicklin
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Paul J Collini
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
- South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Glossop Road, Sheffield S10 2JF, UK
| | - Stephen Brown
- School of Bioscience, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
- South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Glossop Road, Sheffield S10 2JF, UK
| | - Andrew A Peden
- School of Bioscience, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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Sanders S, Jensen Y, Reimer R, Bosse JB. From the beginnings to multidimensional light and electron microscopy of virus morphogenesis. Adv Virus Res 2023; 116:45-88. [PMID: 37524482 DOI: 10.1016/bs.aivir.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Individual functional viral morphogenesis events are often dynamic, short, and infrequent and might be obscured by other pathways and dead-end products. Volumetric live cell imaging has become an essential tool for studying viral morphogenesis events. It allows following entire dynamic processes while providing functional evidence that the imaged process is involved in viral production. Moreover, it allows to capture many individual events and allows quantitative analysis. Finally, the correlation of volumetric live-cell data with volumetric electron microscopy (EM) can provide crucial insights into the ultrastructure and mechanisms of viral morphogenesis events. Here, we provide an overview and discussion of suitable imaging methods for volumetric correlative imaging of viral morphogenesis and frame them in a historical summary of their development.
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Affiliation(s)
- Saskia Sanders
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Yannick Jensen
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | | | - Jens B Bosse
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
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Olgun Yıldızeli S, Kocakaya D, Saylan YH, Tastekin G, Yıldız S, Akbal Ş, Özkan S, Arıkan H, Karakurt S. Anxiety, Depression, and Sleep Disorders After COVID-19 Infection. Cureus 2023; 15:e42637. [PMID: 37644934 PMCID: PMC10461218 DOI: 10.7759/cureus.42637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/31/2023] Open
Abstract
Introduction As of December 2019, the COVID-19 infection had spread rapidly across the globe, causing a pandemic. Although the virus primarily affects the respiratory and circulatory systems, neuropsychiatric disorders have been reported in a significant number of infected individuals. The aim of this study is to identify anxiety, depression, and sleep disturbances in the early post-COVID period, as well as potential risk factors. Method Symptomatic cases whose COVID-19 diagnosis was confirmed by polymerase chain reaction (PCR) positivity within the previous three months were evaluated in the COVID-19 follow-up clinic, where they were observed for at least four weeks after the diagnosis. Cases with no suspicious symptoms and no documented PCR positivity were selected as the control group. All participants completed the Hospital Anxiety Depression Scale (HADS) questionnaire and the Pittsburgh sleep quality questionnaire. The laboratory parameters of hospitalized patients with infection were recorded. Results A total of 283 patients were included in the study. While the median age of 144 patients with COVID-19 infection was 44 years, and 104 of them (72.2%) were female, the median age of the controls without COVID-19 infection was 52 years, and 65 of them (46.8%) were female. About 89 (61.8%) of the 144 patients with COVID-19 infections were hospitalized. When the results of the applied HADS questionnaire were analyzed, the median total value of all study participants was 10 points, whereas it was 13 in cases with COVID-19 and nine in those who did not have it (p<0.001). Taking into account the subgroups of the anxiety and depression questionnaires, both results are statistically significantly higher (p<0.001 and p=0.022, respectively) in post-COVID patients. When the hospitalization status of COVID-19 patients was compared, there was no difference in the development of anxiety (p=0.23), but depression(p<0.024) and poor sleep quality(p<0.001) were prevalent in hospitalized patients. The median PSQI score of the entire study population was five points, while it was seven points in cases with COVID-19 infection and four points in cases who did not have it (p<0.001). Sleep latency (p<0.003), sleep disturbances (p<0.001), and daytime dysfunction (p<0.001) were statistically significantly worse in COVID-19-infected patients. Female gender (p<0.01) and the presence of past anxiety-depression symptoms (p<0.013) were found to be as risk factors in patients with infection. The correlation between the total HADS score, the PSQI, and the results of the complete blood count and biochemical analysis at the time of diagnosis in hospitalized patients was also investigated. CRP (CI 0.26-0.58) p<0.001 vs (CI 0.09-0.45) p=0.004 and ferritin (CI 0.05-0.43) p=0.017 vs (CI 0.01-0.40) p=0.047exhibited a positive correlation. Similarly, lymphocyte count (CI -0.65 to -0.37) p<0.001 vs (CI -0.39 to -0.01) p<0.001 and lymphocyte percentage (-0.57 to -0.24) p=0.001 vs (-0.65 to -0.37) p=0.039 were negatively correlated. Conclusion Early post-infection anxiety, depression, and sleep disturbances increased significantly in COVID-19 patients. Female gender and previous symptoms of anxiety and depression are risk factors, and inpatient treatment increases depression and poor sleep quality. High HADS and poor sleep quality scores are positively correlated with inflammatory parameters and should be evaluated in post-infection in particular.
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Affiliation(s)
- Sehnaz Olgun Yıldızeli
- Pulmonary and Critical Care Medicine, Marmara University School of Medicine, Istanbul, TUR
| | - Derya Kocakaya
- Pulmonary and Critical Care Medicine, Marmara University School of Medicine, Istanbul, TUR
| | - Yüsra Hafza Saylan
- Pulmonary and Critical Care Medicine, Marmara University School of Medicine, Istanbul, TUR
| | - Gözde Tastekin
- Pulmonary and Critical Care Medicine, Marmara University School of Medicine, Istanbul, TUR
| | - Sudenur Yıldız
- Pulmonary and Critical Care Medicine, Marmara University School of Medicine, Istanbul, TUR
| | - Şükran Akbal
- Pulmonary and Critical Care Medicine, Marmara University School of Medicine, Istanbul, TUR
| | - Sümeyra Özkan
- Pulmonary and Critical Care Medicine, Marmara University School of Medicine, Istanbul, TUR
| | - Hüseyin Arıkan
- Pulmonary and Critical Care Medicine, Marmara University School of Medicine, Istanbul, TUR
| | - Sait Karakurt
- Pulmonary and Critical Care Medicine, Marmara University School of Medicine, Istanbul, TUR
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Slanina H, Madhugiri R, Wenk K, Reinke T, Schultheiß K, Schultheis J, Karl N, Linne U, Ziebuhr J. Conserved Characteristics of NMPylation Activities of Alpha- and Betacoronavirus NiRAN Domains. J Virol 2023; 97:e0046523. [PMID: 37199624 PMCID: PMC10308930 DOI: 10.1128/jvi.00465-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Coronavirus genome replication and expression are mediated by the viral replication-transcription complex (RTC) which is assembled from multiple nonstructural proteins (nsp). Among these, nsp12 represents the central functional subunit. It harbors the RNA-directed RNA polymerase (RdRp) domain and contains, at its N terminus, an additional domain called NiRAN which is widely conserved in coronaviruses and other nidoviruses. In this study, we produced bacterially expressed coronavirus nsp12s to investigate and compare NiRAN-mediated NMPylation activities from representative alpha- and betacoronaviruses. We found that the four coronavirus NiRAN domains characterized to date have a number of conserved properties, including (i) robust nsp9-specific NMPylation activities that appear to operate largely independently of the C-terminal RdRp domain, (ii) nucleotide substrate preference for UTP followed by ATP and other nucleotides, (iii) dependence on divalent metal ions, with Mn2+ being preferred over Mg2+, and (iv) a key role of N-terminal residues (particularly Asn2) of nsp9 for efficient formation of a covalent phosphoramidate bond between NMP and the N-terminal amino group of nsp9. In this context, a mutational analysis confirmed the conservation and critical role of Asn2 across different subfamilies of the family Coronaviridae, as shown by studies using chimeric coronavirus nsp9 variants in which six N-terminal residues were replaced with those from other corona-, pito- and letovirus nsp9 homologs. The combined data of this and previous studies reveal a remarkable degree of conservation among coronavirus NiRAN-mediated NMPylation activities, supporting a key role of this enzymatic activity in viral RNA synthesis and processing. IMPORTANCE There is strong evidence that coronaviruses and other large nidoviruses evolved a number of unique enzymatic activities, including an additional RdRp-associated NiRAN domain, that are conserved in nidoviruses but not in most other RNA viruses. Previous studies of the NiRAN domain mainly focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and suggested different functions for this domain, such as NMPylation/RNAylation of nsp9, RNA guanylyltransferase activities involved in canonical and/or unconventional RNA capping pathways, and other functions. To help resolve partly conflicting information on substrate specificities and metal ion requirements reported previously for the SARS-CoV-2 NiRAN NMPylation activity, we extended these earlier studies by characterizing representative alpha- and betacoronavirus NiRAN domains. The study revealed that key features of NiRAN-mediated NMPylation activities, such as protein and nucleotide specificity and metal ion requirements, are very well conserved among genetically divergent coronaviruses, suggesting potential avenues for future antiviral drug development targeting this essential viral enzyme.
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Affiliation(s)
- Heiko Slanina
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | | | - Kai Wenk
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Tess Reinke
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Karin Schultheiß
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Julia Schultheis
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Nadja Karl
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility, Department of Chemistry, Philipps University, Marburg, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
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Zhang D, Qiao L, Lei X, Dong X, Tong Y, Wang J, Wang Z, Zhou R. Mutagenesis and structural studies reveal the basis for the specific binding of SARS-CoV-2 SL3 RNA element with human TIA1 protein. Nat Commun 2023; 14:3715. [PMID: 37349329 PMCID: PMC10287707 DOI: 10.1038/s41467-023-39410-8] [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: 10/04/2022] [Accepted: 06/12/2023] [Indexed: 06/24/2023] Open
Abstract
Viral RNA-host protein interactions are indispensable during RNA virus transcription and replication, but their detailed structural and dynamical features remain largely elusive. Here, we characterize the binding interface for the SARS-CoV-2 stem-loop 3 (SL3) cis-acting element to human TIA1 protein with a combined theoretical and experimental approaches. The highly structured SARS-CoV-2 SL3 has a high binding affinity to TIA1 protein, in which the aromatic stacking, hydrogen bonds, and hydrophobic interactions collectively direct this specific binding. Further mutagenesis studies validate our proposed 3D binding model and reveal two SL3 variants have enhanced binding affinities to TIA1. And disruptions of the identified RNA-protein interactions with designed antisense oligonucleotides dramatically reduce SARS-CoV-2 infection in cells. Finally, TIA1 protein could interact with conserved SL3 RNA elements within other betacoronavirus lineages. These findings open an avenue to explore the viral RNA-host protein interactions and provide a pioneering structural basis for RNA-targeting antiviral drug design.
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Affiliation(s)
- Dong Zhang
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lulu Qiao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xiaobo Lei
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Xiaojing Dong
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yunguang Tong
- College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, China
- Department of Pharmacy, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Sozio E, Hannemann J, Fabris M, Cifù A, Ripoli A, Sbrana F, Cescutti D, Vetrugno L, Fapranzi S, Bassi F, Sponza M, Curcio F, Tascini C, Böger R. The role of asymmetric dimethylarginine (ADMA) in COVID-19: association with respiratory failure and predictive role for outcome. Sci Rep 2023; 13:9811. [PMID: 37330534 PMCID: PMC10276836 DOI: 10.1038/s41598-023-36954-z] [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: 10/12/2022] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
We aimed to assess the potential role of Asymmetric dimethylarginine (ADMA) in conditioning respiratory function and pulmonary vasoregulation during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) infection. Within 72 h from admission, samples from 90 COVID-19 patients were assessed for ADMA, SDMA, L-arginine concentrations. In addition to classical statistics, patients were also clustered by a machine learning approach according to similar features. Multivariable analysis showed that C-reactive protein (OR 1.012), serum ADMA (OR 4.652), white blood cells (OR = 1.118) and SOFA (OR = 1.495) were significantly associated with negative outcomes. Machine learning-based clustering showed three distinct clusters: (1) patients with low severity not requiring invasive mechanical ventilation (IMV), (2) patients with moderate severity and respiratory failure whilst not requiring IMV, and (3) patients with highest severity requiring IMV. Serum ADMA concentration was significantly associated with disease severity and need for IMV although less pulmonary vasodilation was observed by CT scan. High serum levels of ADMA are indicative of high disease severity and requirement of mechanical ventilation. Serum ADMA at the time of hospital admission may therefore help to identify COVID-19 patients at high risk of deterioration and negative outcome.
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Affiliation(s)
- Emanuela Sozio
- Infectious Diseases Clinic, Azienda Sanitaria Universitaria del Friuli Centrale (ASUFC), Udine, Italy
| | - Juliane Hannemann
- Institute of Clinical Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute DECIPHER, German-Chilean Institute for Research on Pulmonary Hypoxia and Its Health Sequelae, Hamburg, Germany
| | - Martina Fabris
- Istituto di Patologia Clinica, Azienda Sanitaria Universitaria Friuli Centrale - Udine (ASUFC), Udine, Italy
| | - Adriana Cifù
- Department of Medical Area (DAME), University of Udine, Udine, Italy
| | - Andrea Ripoli
- Bioengineering Department, Fondazione Toscana Gabriele Monasterio, Pisa, Italy
| | - Francesco Sbrana
- Lipoapheresis Unit - Reference Center for Diagnosis and Treatment of Inherited Dyslipidemias, Fondazione Toscana "Gabriele Monasterio", Via Moruzzi 1, 56124, Pisa, Italy
| | - Demetrio Cescutti
- Infectious Diseases Clinic, Azienda Sanitaria Universitaria del Friuli Centrale (ASUFC), Udine, Italy
| | - Luigi Vetrugno
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti-Pescara, Chieti, Italy
| | - Stefano Fapranzi
- Emergency Radiology Department - Azienda Sanitaria, Universitaria del Friuli Centrale (ASUFC), Udine, Italia
| | - Flavio Bassi
- Department of Anesthesia and Intensive Care Medicine, Azienda Sanitaria Universitaria Friuli Centrale - Udine (ASUFC), Udine, Italy
| | - Massimo Sponza
- Emergency Radiology Department - Azienda Sanitaria, Universitaria del Friuli Centrale (ASUFC), Udine, Italia
| | - Francesco Curcio
- Istituto di Patologia Clinica, Azienda Sanitaria Universitaria Friuli Centrale - Udine (ASUFC), Udine, Italy
- Department of Medical Area (DAME), University of Udine, Udine, Italy
| | - Carlo Tascini
- Infectious Diseases Clinic, Azienda Sanitaria Universitaria del Friuli Centrale (ASUFC), Udine, Italy.
- Department of Medical Area (DAME), University of Udine, Udine, Italy.
- U.O. Malattie Infettive, Azienda Sanitaria Universitaria Integrata di Udine, Via Pozzuolo, 330, 33100, Udine, Italy.
| | - Rainer Böger
- Institute of Clinical Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute DECIPHER, German-Chilean Institute for Research on Pulmonary Hypoxia and Its Health Sequelae, Hamburg, Germany
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45
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Mah MG, Linster M, Low DHW, Zhuang Y, Jayakumar J, Samsudin F, Wong FY, Bond PJ, Mendenhall IH, Su YCF, Smith GJD. Spike-Independent Infection of Human Coronavirus 229E in Bat Cells. Microbiol Spectr 2023; 11:e0348322. [PMID: 37199653 PMCID: PMC10269751 DOI: 10.1128/spectrum.03483-22] [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: 09/06/2022] [Accepted: 04/17/2023] [Indexed: 05/19/2023] Open
Abstract
Bats are the reservoir for numerous human pathogens, including coronaviruses. Despite many coronaviruses having descended from bat ancestors, little is known about virus-host interactions and broader evolutionary history involving bats. Studies have largely focused on the zoonotic potential of coronaviruses with few infection experiments conducted in bat cells. To determine genetic changes derived from replication in bat cells and possibly identify potential novel evolutionary pathways for zoonotic virus emergence, we serially passaged six human 229E isolates in a newly established Rhinolophus lepidus (horseshoe bat) kidney cell line. Here, we observed extensive deletions within the spike and open reading frame 4 (ORF4) genes of five 229E viruses after passaging in bat cells. As a result, spike protein expression and infectivity of human cells was lost in 5 of 6 viruses, but the capability to infect bat cells was maintained. Only viruses that expressed the spike protein could be neutralized by 229E spike-specific antibodies in human cells, whereas there was no neutralizing effect on viruses that did not express the spike protein inoculated on bat cells. However, one isolate acquired an early stop codon, abrogating spike expression but maintaining infection in bat cells. After passaging this isolate in human cells, spike expression was restored due to acquisition of nucleotide insertions among virus subpopulations. Spike-independent infection of human coronavirus 229E may provide an alternative mechanism for viral maintenance in bats that does not rely on the compatibility of viral surface proteins and known cellular entry receptors. IMPORTANCE Many viruses, including coronaviruses, originated from bats. Yet, we know little about how these viruses switch between hosts and enter human populations. Coronaviruses have succeeded in establishing in humans at least five times, including endemic coronaviruses and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In an approach to identify requirements for host switches, we established a bat cell line and adapted human coronavirus 229E viruses by serial passage. The resulting viruses lost their spike protein but maintained the ability to infect bat cells, but not human cells. Maintenance of 229E viruses in bat cells appears to be independent of a canonical spike receptor match, which in turn might facilitate cross-species transmission in bats.
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Affiliation(s)
- Marcus G. Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dolyce H. W. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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46
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Wang W, Zhou Z, Ding S, Yang W, Jin W, Chu W, Xu Z. Degradation kinetics and formation of regulated and emerging disinfection by-products during chlorination of two expectorants ambroxol and bromhexine. WATER RESEARCH 2023; 235:119927. [PMID: 37023645 DOI: 10.1016/j.watres.2023.119927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Ambroxol hydrochloride (AMB) and bromhexine hydrochloride (BRO) are classic expectorants and bronchosecretolytic pharmaceuticals. In 2022, both AMB and BRO were recommended by medical emergency department of China to alleviate cough and expectoration for symptoms caused by COVID-19. The reaction characteristics and mechanism of AMB/BRO with chlorine disinfectant in the disinfection process were investigated in this study. The reaction of chlorine with AMB/BRO were well described by a second-order kinetics model, first-order in both AMB/BRO and chlorine. The second order rate reaction constant of AMB and BRO with chlorine at pH 7.0 were 1.15 × 102 M-1s-1 and 2.03 × 102 M-1s-1, respectively. During chlorination, a new class of aromatic nitrogenous disinfection by-products (DBPs) including 2-chloro-4, 6-dibromoaniline and 2, 4, 6-tribromoaniline were identified as the intermediate aromatic DBPs by gas chromatography-mass spectrometry. The effect of chlorine dosage, pH, and contact time on the formation of 2-chloro-4, 6-dibromoaniline and 2, 4, 6-tribromoaniline were evaluated. In addition, it was found that bromine in AMB/BRO were vital bromine source to greatly promote the formation of classic brominated DBPs, with the highest Br-THMs yields of 23.8% and 37.8%, respectively. This study inspired that bromine in brominated organic compounds may be an important bromine source of brominated DBPs.
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Affiliation(s)
- Wuming Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; International Joint Research Center for Sustainable Urban Water System, Tongji University, Shanghai 200092, China
| | - Zichong Zhou
- Changjiang Survey, Planning, Design and Research Co., Ltd., Wuhan 430010, China
| | - Shunke Ding
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; International Joint Research Center for Sustainable Urban Water System, Tongji University, Shanghai 200092, China.
| | - Wenyuan Yang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; International Joint Research Center for Sustainable Urban Water System, Tongji University, Shanghai 200092, China
| | - Wei Jin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; International Joint Research Center for Sustainable Urban Water System, Tongji University, Shanghai 200092, China
| | - Wenhai Chu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; International Joint Research Center for Sustainable Urban Water System, Tongji University, Shanghai 200092, China.
| | - Zuxin Xu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; International Joint Research Center for Sustainable Urban Water System, Tongji University, Shanghai 200092, China
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Ghimire R, Shrestha R, Amaradhi R, Patton T, Whitley C, Chanda D, Liu L, Ganesh T, More S, Channappanavar R. Toll-like receptor 7 (TLR7)-mediated antiviral response protects mice from lethal SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539929. [PMID: 37214943 PMCID: PMC10197544 DOI: 10.1101/2023.05.08.539929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
SARS-CoV-2-induced impaired antiviral and excessive inflammatory responses cause fatal pneumonia. However, the key pattern recognition receptors that elicit effective antiviral and lethal inflammatory responses in-vivo are not well defined. CoVs possess single-stranded RNA (ssRNA) genome that is abundantly produced during infection and stimulates both antiviral interferon (IFN) and inflammatory cytokine/ chemokine responses. Therefore, in this study, using wild-type control and TLR7 deficient BALB/c mice infected with a mouse-adapted SARS-COV-2 (MA-CoV-2), we evaluated the role of TLR7 signaling in MA-CoV-2-induced antiviral and inflammatory responses and disease outcome. We show that TLR7-deficient mice are more susceptible to MA-CoV-2 infection as compared to infected control mice. Further evaluation of MA-CoV-2 infected lungs showed significantly reduced mRNA levels of antiviral type I (IFNα/β) and type III (IFNλ) IFNs, IFN stimulated genes (ISGs, ISG15 and CXCL10), and several pro-inflammatory cytokines/chemokines in TLR7 deficient compared to control mice. Reduced lung IFN/ISG levels and increased morbidity/mortality in TLR7 deficient mice correlated with high lung viral titer. Detailed examination of total cells from MA-CoV-2 infected lungs showed high neutrophil count in TLR7 deficient mice compared to control mice. Additionally, blocking TLR7 activity post-MA-CoV-2 infection using a specific inhibitor also enhanced disease severity. In summary, our results conclusively establish that TLR7 signaling is protective during SARS-CoV-2 infection, and despite robust inflammatory response, TLR7-mediated IFN/ISG responses likely protect the host from lethal disease. Given similar outcomes in control and TLR7 deficient humans and mice, these results show that MA-CoV-2 infected mice serve as excellent model to study COVID-19.
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48
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Tang H, Qin H, He S, Li Q, Xu H, Sun M, Li J, Lu S, Luo S, Mao P, Han P, Song L, Tong Y, Fan H, Jiang X. Anti-Coronaviral Nanocluster Restrain Infections of SARS-CoV-2 and Associated Mutants through Virucidal Inhibition and 3CL Protease Inactivation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207098. [PMID: 36843252 PMCID: PMC10161070 DOI: 10.1002/advs.202207098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Indexed: 05/06/2023]
Abstract
Antivirals that can combat coronaviruses, including SARS-CoV-2 and associated mutants, are urgently needed but lacking. Simultaneously targeting the viral physical structure and replication cycle can endow antivirals with sustainable and broad-spectrum anti-coronavirus efficacy, which is difficult to achieve using a single small-molecule antiviral. Thus, a library of nanomaterials on GX_P2V, a SARS-CoV-2-like coronavirus of pangolin origin, is screened and a surface-functionalized gold nanocluster (TMA-GNC) is identified as the top hit. TMA-GNC inhibits transcription- and replication-competent SARS-CoV-2 virus-like particles and all tested pseudoviruses of SARS-CoV-2 variants. TMA-GNC prevents viral dissemination through destroying membrane integrity physically to enable a virucidal effect, interfering with viral replication by inactivating 3CL protease and priming the innate immune system against coronavirus infection. TMA-GNC exhibits biocompatibility and significantly reduces viral titers, inflammation, and pathological injury in lungs and tracheas of GX_P2V-infected hamsters. TMA-GNC may have a role in controlling the COVID-19 pandemic and inhibiting future emerging coronaviruses or variants.
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Affiliation(s)
- Hao Tang
- Shenzhen Key Laboratory of Smart Healthcare EngineeringGuangdong Provincial Key Laboratory of Advanced BiomaterialsDepartment of Biomedical EngineeringSouthern University of Science and TechnologyShenzhenGuangdong518055P. R. China
| | - Hongbo Qin
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringCollege of Life Science and TechnologyBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Shiting He
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringCollege of Life Science and TechnologyBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Qizhen Li
- Shenzhen Key Laboratory of Smart Healthcare EngineeringGuangdong Provincial Key Laboratory of Advanced BiomaterialsDepartment of Biomedical EngineeringSouthern University of Science and TechnologyShenzhenGuangdong518055P. R. China
| | - Huan Xu
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhenGuangdong518055P. R. China
| | - Mengsi Sun
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhenGuangdong518055P. R. China
| | - Jiaan Li
- Shenzhen Key Laboratory of Smart Healthcare EngineeringGuangdong Provincial Key Laboratory of Advanced BiomaterialsDepartment of Biomedical EngineeringSouthern University of Science and TechnologyShenzhenGuangdong518055P. R. China
| | - Shanshan Lu
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringCollege of Life Science and TechnologyBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Shengdong Luo
- The Fifth Medical CenterChinese People's Liberation Army General HospitalBeijing100039P. R. China
| | - Panyong Mao
- The Fifth Medical CenterChinese People's Liberation Army General HospitalBeijing100039P. R. China
| | - Pengjun Han
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringCollege of Life Science and TechnologyBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Lihua Song
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringCollege of Life Science and TechnologyBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringCollege of Life Science and TechnologyBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Huahao Fan
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringCollege of Life Science and TechnologyBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Xingyu Jiang
- Shenzhen Key Laboratory of Smart Healthcare EngineeringGuangdong Provincial Key Laboratory of Advanced BiomaterialsDepartment of Biomedical EngineeringSouthern University of Science and TechnologyShenzhenGuangdong518055P. R. China
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49
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Kimura Y, Cristancho-Rojas CN, Kimura-Sandoval Y, Tapia-Sosa R, Guerrero-Torres L, Licano-Zubiate M, Chapa-Ibargüengoitia M. Prognostic utility of the chest computed tomography severity score for the requirement of mechanical ventilation and mortality in hospitalized patients with COVID-19. Heliyon 2023; 9:e16020. [PMID: 37153411 PMCID: PMC10151249 DOI: 10.1016/j.heliyon.2023.e16020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 05/09/2023] Open
Abstract
Purpose To correlate the chest computed tomography severity score (CT-SS) with the need for mechanical ventilation and mortality in hospitalized patients with COVID-19. Materials and methods The chest CT images of 224 inpatients with COVID-19, confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR), were retrospectively reviewed from April 1 to 25, 2020, in a tertiary health care center. We calculated the CT-SS (dividing each lung into 20 segments and assigning scores of 0, 1, and 2 due to opacification involving 0%, <50%, and ≥50% of each region for a global range of 0-40 points, including both lungs), and collected clinical data. The receiver operating characteristic curve and Youden Index analysis was performed to calculate the CT-SS threshold and accuracy for classification for risk of mortality or MV requirement. Results 136 men and 88 women were recruited, with an age range of 23-91 years and a mean of 50.17 years; 79 met the MV criteria, and 53 were nonsurvivors. The optimal threshold was >27.5 points for mortality (area under ROC curve >0.96), with a sensitivity of 93% and specificity of 87%, and >25.5 points for the need for MV (area under ROC curve >0.94), with a sensitivity of 90% and specificity of 89%. The Kaplan-Meier curves show a significant difference in mortality by the CT-SS threshold (Log Rank p < 0.001). Conclusions In our cohort of hospitalized patients with COVID-19, the CT-SS accurately discriminates the need for MV and mortality risk. In conjunction with clinical status and laboratory data, the CT-SS may be a useful imaging tool that could be included in establishing a prognosis for this population.
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Affiliation(s)
- Yukiyoshi Kimura
- Department of Radiology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, 14080, Mexico City, Mexico
| | | | - Yumi Kimura-Sandoval
- Department of Radiology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, 14080, Mexico City, Mexico
| | - Ramiro Tapia-Sosa
- Department of Gastroenterology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, 14080, Mexico City, Mexico
| | - Lorena Guerrero-Torres
- Department of Infectious Diseases, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, 14080, Mexico City, Mexico
| | - Mariana Licano-Zubiate
- Department of Radiology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, 14080, Mexico City, Mexico
| | - Monica Chapa-Ibargüengoitia
- Department of Radiology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, 14080, Mexico City, Mexico
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50
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Orf GS, Olivo A, Harris B, Weiss SL, Achari A, Yu G, Federman S, Mbanya D, James L, Mampunza S, Chiu CY, Rodgers MA, Cloherty GA, Berg MG. Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance. Viruses 2023; 15:v15041022. [PMID: 37113001 PMCID: PMC10145552 DOI: 10.3390/v15041022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.
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Affiliation(s)
- Gregory S Orf
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Ana Olivo
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Barbara Harris
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Sonja L Weiss
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Asmeeta Achari
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Guixia Yu
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Scot Federman
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
| | - Linda James
- School of Medicine, Université Protestante au Congo, Kinshasa P.O. Box 4745, Democratic Republic of the Congo
| | - Samuel Mampunza
- School of Medicine, Université Protestante au Congo, Kinshasa P.O. Box 4745, Democratic Republic of the Congo
| | - Charles Y Chiu
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Mary A Rodgers
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Gavin A Cloherty
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Michael G Berg
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
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