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Liu W, Huang Z, Xiao J, Wu Y, Xia N, Yuan Q. Evolution of the SARS-CoV-2 Omicron Variants: Genetic Impact on Viral Fitness. Viruses 2024; 16:184. [PMID: 38399960 PMCID: PMC10893260 DOI: 10.3390/v16020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Over the last three years, the pandemic of COVID-19 has had a significant impact on people's lives and the global economy. The incessant emergence of variant strains has compounded the challenges associated with the management of COVID-19. As the predominant variant from late 2021 to the present, Omicron and its sublineages, through continuous evolution, have demonstrated iterative viral fitness. The comprehensive elucidation of the biological implications that catalyzed this evolution remains incomplete. In accordance with extant research evidence, we provide a comprehensive review of subvariants of Omicron, delineating alterations in immune evasion, cellular infectivity, and the cross-species transmission potential. This review seeks to clarify the underpinnings of biology within the evolution of SARS-CoV-2, thereby providing a foundation for strategic considerations in the post-pandemic era of COVID-19.
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Affiliation(s)
- Wenhao Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Zehong Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Jin Xiao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Yangtao Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Quan Yuan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361000, China; (W.L.); (N.X.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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Boniardi I, Corona A, Basquin J, Basquin C, Milia J, Nagy I, Tramontano E, Zinzula L. Suramin inhibits SARS-CoV-2 nucleocapsid phosphoprotein genome packaging function. Virus Res 2023; 336:199221. [PMID: 37704176 PMCID: PMC10514558 DOI: 10.1016/j.virusres.2023.199221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is fading, however its etiologic agent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues posing - despite the availability of licensed vaccines - a global health threat, due to the potential emergence of vaccine-resistant SARS-CoV-2 variants. This makes the development of new drugs against COVID-19 a persistent urgency and sets as research priority the validation of novel therapeutic targets within the SARS-CoV-2 proteome. Among these, a promising one is the SARS-CoV-2 nucleocapsid (N) phosphoprotein, a major structural component of the virion with indispensable role in packaging the viral genome into a ribonucleoprotein (RNP) complex, which also contributes to SARS-CoV-2 innate immune evasion by inhibiting the host cell type-I interferon (IFN-I) response. By combining miniaturized differential scanning fluorimetry with microscale thermophoresis, we found that the 100-year-old drug Suramin interacts with SARS-CoV-2 N-terminal domain (NTD) and C-terminal domain (CTD), thereby inhibiting their single-stranded RNA (ssRNA) binding function with low-micromolar Kd and IC50 values. Molecular docking suggests that Suramin interacts with basic NTD cleft and CTD dimer interface groove, highlighting three potentially druggable ssRNA binding sites. Electron microscopy shows that Suramin inhibits the formation in vitro of RNP complex-like condensates by SARS-CoV-2 N with a synthetic ssRNA. In a dose-dependent manner, Suramin also reduced SARS-CoV-2-induced cytopathic effect on Vero E6 and Calu-3 cells, partially reverting the SARS-CoV-2 N-inhibited IFN-I production in 293T cells. Our findings indicate that Suramin inhibits SARS-CoV-2 replication by hampering viral genome packaging, thereby representing a starting model for design of new COVID-19 antivirals.
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Affiliation(s)
- Irene Boniardi
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - Jerome Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Jessica Milia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - István Nagy
- Center of Research and Development, Eszterházy Károly Catholic University, Eger 3300, Hungary
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy.
| | - Luca Zinzula
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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Finci I, Rojas Castro MY, Hasibra I, Sulo J, Fico A, Daja R, Vasili A, Kota M, Preza I, Mühlemann B, Drosten C, Pebody R, Lafond KE, Kissling E, Katz MA, Bino S. Primary Series and Booster Coronavirus Disease 2019 Vaccine Effectiveness in a Cohort of Healthcare Workers in Albania During a BA.1 and BA.2 Variant Period, January-May 2022. Open Forum Infect Dis 2023; 10:ofad479. [PMID: 37885795 PMCID: PMC10599317 DOI: 10.1093/ofid/ofad479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
Background Healthcare workers (HCWs) have experienced high rates of coronavirus disease 2019 (COVID-19) morbidity and mortality. We estimated COVID-19 2-dose primary series and monovalent booster vaccine effectiveness (VE) against symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron (BA.1 and BA.2) infection among HCWs in 3 Albanian hospitals during January-May 2022. Methods Study participants completed weekly symptom questionnaires, underwent polymerase chain reaction (PCR) testing when symptomatic, and provided quarterly blood samples for serology. We estimated VE using Cox regression models (1 - hazard ratio), with vaccination status as the time-varying exposure and unvaccinated HCWs as the reference group, adjusting for potential confounders: age, sex, prior SARS-CoV-2 infection (detected by PCR, rapid antigen test, or serology), and household size. Results At the start of the analysis period, 76% of 1462 HCWs had received a primary series, 10% had received a booster dose, and 9% were unvaccinated; 1307 (89%) HCWs had evidence of prior infection. Overall, 86% of primary series and 98% of booster doses received were BNT162b2. The median time interval from the second dose and the booster dose to the start of the analysis period was 289 (interquartile range [IQR], 210-292) days and 30 (IQR, 22-46) days, respectively. VE against symptomatic PCR-confirmed infection was 34% (95% confidence interval [CI], -36% to 68%) for the primary series and 88% (95% CI, 39%-98%) for the booster. Conclusions Among Albanian HCWs, most of whom had been previously infected, COVID-19 booster dose offered improved VE during a period of Omicron BA.1 and BA.2 circulation. Our findings support promoting booster dose uptake among Albanian HCWs, which, as of January 2023, was only 20%. Clinical Trials Registration. NCT04811391.
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Affiliation(s)
- Iris Finci
- Regional Office for Europe, World Health Organization,Copenhagen, Denmark
| | | | - Iris Hasibra
- Department for the Control of Infectious Diseases, Institute of Public Health, Tirana, Albania
| | - Jonilda Sulo
- Southeast European Center for Surveillance and Control of Infectious Diseases,Tirana, Albania
- Mediterranean and Black Sea Programme in Intervention Epidemiology Training, European Centre for Disease Prevention and Control, Solna, Sweden
| | - Albana Fico
- Department for the Control of Infectious Diseases, Institute of Public Health, Tirana, Albania
- Tirana University Hospital Centre, Tirana, Albania
| | - Rovena Daja
- Department for the Control of Infectious Diseases, Institute of Public Health, Tirana, Albania
| | - Adela Vasili
- Department for the Control of Infectious Diseases, Institute of Public Health, Tirana, Albania
| | - Majlinda Kota
- Department for the Control of Infectious Diseases, Institute of Public Health, Tirana, Albania
| | - Iria Preza
- Country Office Albania, World Health Organization, Tirana, Albania
| | - Barbara Mühlemann
- Institute of Virology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health,Berlin, Germany
- German Centre for Infection Research, partner site Charité, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health,Berlin, Germany
- German Centre for Infection Research, partner site Charité, Berlin, Germany
| | - Richard Pebody
- Regional Office for Europe, World Health Organization,Copenhagen, Denmark
| | - Kathryn E Lafond
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Mark A Katz
- Regional Office for Europe, World Health Organization,Copenhagen, Denmark
| | - Silvia Bino
- Department for the Control of Infectious Diseases, Institute of Public Health, Tirana, Albania
- Southeast European Center for Surveillance and Control of Infectious Diseases,Tirana, Albania
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Nimsamer P, Sawaswong V, Klomkliew P, Kaewsapsak P, Puenpa J, Poovorawan Y, Payungporn S. "Nano COVID-19": Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern. Exp Biol Med (Maywood) 2023; 248:1841-1849. [PMID: 37702217 DOI: 10.1177/15353702231190931] [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: 09/14/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide pandemic infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). World Health Organization (WHO) has defined the viral variants of concern (VOC) which cause more severe disease, higher transmissibility, and reduced vaccine efficacy. In this study, the "Nano COVID-19" workflow based on Oxford nanopore sequencing of the full-length spike gene combined with flexible data analysis options was developed to identify SARS-CoV-2 VOCs. The primers were designed to cover the full-length spike gene and can amplify all VOC strains. The results of VOC identification based on phylogenetic analysis of the full-length spike gene were comparable to the whole genome sequencing (WGS). Compared to the standard VOC identification pipeline, the fast analysis based on Read Assignment, Mapping, and Phylogenetic Analysis in Real Time (RAMPART) and the user-friendly method based on EPI2ME yielded 89.3% and 97.3% accuracy, respectively. The EPI2ME pipeline is recommended for researchers without bioinformatic skills, whereas RAMPART is more suitable for bioinformaticians. This workflow provides a cost-effective, simplified pipeline with a rapid turnaround time. Furthermore, it is portable to point-of-care SARS-CoV-2 VOC identification and compatible with large-scale analysis. Therefore, "Nano COVID-19" is an alternative viral epidemic screening and transmission tracking workflow.
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Affiliation(s)
- Pattaraporn Nimsamer
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Vorthon Sawaswong
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavit Klomkliew
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornchai Kaewsapsak
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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Yan D, Yan B. Viral target and metabolism-based rationale for combined use of recently authorized small molecule COVID-19 medicines: Molnupiravir, nirmatrelvir, and remdesivir. Fundam Clin Pharmacol 2023; 37:726-738. [PMID: 36931725 PMCID: PMC10505250 DOI: 10.1111/fcp.12889] [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: 10/26/2022] [Revised: 02/12/2023] [Accepted: 02/27/2023] [Indexed: 03/19/2023]
Abstract
The COVID-19 pandemic remains a major health concern worldwide, and SARS-CoV-2 is continuously evolving. There is an urgent need to identify new antiviral drugs and develop novel therapeutic strategies. Combined use of newly authorized COVID-19 medicines including molnupiravir, nirmatrelvir, and remdesivir has been actively pursued. Mechanistically, nirmatrelvir inhibits SARS-CoV-2 replication by targeting the viral main protease (Mpro ), a critical enzyme in the processing of the immediately translated coronavirus polyproteins for viral replication. Molnupiravir and remdesivir, on the other hand, inhibit SARS-CoV-2 replication by targeting RNA-dependent RNA-polymerase (RdRp), which is directly responsible for genome replication and production of subgenomic RNAs. Molnupiravir targets RdRp and induces severe viral RNA mutations (genome), commonly referred to as error catastrophe. Remdesivir, in contrast, targets RdRp and causes chain termination and arrests RNA synthesis of the viral genome. In addition, all three medicines undergo extensive metabolism with strong therapeutic significance. Molnupiravir is hydrolytically activated by carboxylesterase-2 (CES2), nirmatrelvir is inactivated by cytochrome P450-based oxidation (e.g., CYP3A4), and remdesivir is hydrolytically activated by CES1 but covalently inhibits CES2. Additionally, remdesivir and nirmatrelvir are oxidized by the same CYP enzymes. The distinct mechanisms of action provide strong rationale for their combined use. On the other hand, these drugs undergo extensive metabolism that determines their therapeutic potential. This review discusses how metabolism pathways and enzymes involved should be carefully considered during their combined use for therapeutic synergy.
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Affiliation(s)
- Daisy Yan
- Department of Dermatology, Boston University School of Medicine 609 Albany Street Boston, MA 02118
| | - Bingfang Yan
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH 45229
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Fang L, Xu J, Zhao Y, Fan J, Shen J, Liu W, Cao G. The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2. Front Microbiol 2023; 14:1228128. [PMID: 37560529 PMCID: PMC10409611 DOI: 10.3389/fmicb.2023.1228128] [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: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Over three years' pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.
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Affiliation(s)
- Letian Fang
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jie Xu
- Department of Foreign Languages, International Exchange Center for Military Medicine, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jiaying Shen
- School of Medicine, Tongji University, Shanghai, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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Makulo JR, Wumba R, Mandina MN, Mbala P, Aziza AA, Nlandu YM, Kabwe B, Mangala D, Bepouka BI, Odio JO, Longokolo M, Mukenge E, Kamwiziku G, Kingand EL, Bashengezi C, Kabanda G, Longo-Mbenza B. SARS-CoV2 mutations and impact on mortality: observational study in a sub-saharan Africa hospital. Virol J 2023; 20:56. [PMID: 36998042 PMCID: PMC10062261 DOI: 10.1186/s12985-023-02014-1] [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: 12/04/2022] [Accepted: 03/19/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND One year after the coronavirus disease 2019 (COVID-19) pandemic, the focus of attention has shifted to the emergence and spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs). The aim of the study was to assess the frequency of VOCs in patients followed for COVID-19 at Kinshasa university hospital (KUH) during the 3rd and 4th waves of the pandemic in Kinshasa. Hospital mortality was compared to that of the first two waves. METHOD The present study included all patients in whom the diagnosis of SARS-CoV-2 infection was confirmed by the polymerase chain reaction (PCR). The laboratory team sequenced a subset of all SARS-CoV-2 positive samples with high viral loads define as Ct < 25 to ensure the chances to generate complete genome sequence. RNA extraction was performed using the Viral RNA Mini Kit (Qiagen). Depending on the platform, we used the iVar bioinformatics or artic environments to generate consensus genomes from the raw sequencing output in FASTQ format. RESULTS During the study period, the original strain of the virus was no longer circulating. The Delta VOC was predominant from June (92%) until November 2021 (3rd wave). The Omicron VOC, which appeared in December 2021, became largely predominant one month later (96%) corresponding the 4th wave. In-hospital mortality associated with COVID-19 fell during the 2nd wave (7% vs. 21% 1st wave), had risen during the 3rd (16%) wave before falling again during the 4th wave (7%) (p < 0.001). CONCLUSION The Delta (during the 3rd wave) and Omicron VOCs (during the 4th wave) were very predominant among patients followed for Covid-19 in our hospital. Contrary to data in the general population, hospital mortality associated with severe and critical forms of COVID-19 had increased during the 3rd wave of the pandemic in Kinshasa.
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Affiliation(s)
- Jean-Robert Makulo
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo.
| | - Roger Wumba
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Madone Ndona Mandina
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Placide Mbala
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
- Institut National de Recherche Biomédicale (INRB), République démocratique, Kinshasa, Congo
- Secrétariat technique de la riposte contre la COVID-19, République démocratique du Congo, Kinshasa, Congo
| | - Adrienne Amuri Aziza
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
- Institut National de Recherche Biomédicale (INRB), République démocratique, Kinshasa, Congo
| | - Yannick Mayamba Nlandu
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Benjanmin Kabwe
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
- Centre de Recherche en phytothérapie, pharmacopée africaine et technologie pharmaceutique a (CREPPAT), Kinshasa, Congo
| | - Donatien Mangala
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Ben Izizag Bepouka
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Jerome Ossam Odio
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Murielle Longokolo
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Eric Mukenge
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Guyguy Kamwiziku
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Eddy Lusamaki Kingand
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
| | - Constantin Bashengezi
- Centre de Recherche en phytothérapie, pharmacopée africaine et technologie pharmaceutique a (CREPPAT), Kinshasa, Congo
| | - Gilbert Kabanda
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
- Centre de Recherche en phytothérapie, pharmacopée africaine et technologie pharmaceutique a (CREPPAT), Kinshasa, Congo
| | - Benjamin Longo-Mbenza
- Cliniques Universitaires de Kinshasa, Université de Kinshasa, République démocratique du Congo, Kinshasa, Congo
- Centre de Recherche en phytothérapie, pharmacopée africaine et technologie pharmaceutique a (CREPPAT), Kinshasa, Congo
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Hammett DL, Loiselle C, Palmer KM, Loiselle JM, Attia MW. COVID-19 Screening in the Pediatric Emergency Department. Cureus 2023; 15:e35731. [PMID: 37016637 PMCID: PMC10066930 DOI: 10.7759/cureus.35731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Screening for COVID-19 infection in pediatrics is challenging as its clinical presentation may be asymptomatic or mimic other common childhood infections. We examined the use of a COVID-19 screening protocol (CSP) in the pediatric emergency department (PED) to determine the incidence of positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) tests in patients who are CSP+ and CSP-. METHODS We conducted a retrospective cohort study of pediatric patients with SARS-CoV-2 testing completed in an urban tertiary care PED from November 1 to December 31, 2020. Demographics, CSP designation, test results, and disposition were compared. Statistical significance was determined using chi-square or a comparison of means. Sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) with 95% confidence intervals (CI) were calculated. RESULTS A total of 1,613 patients had SARS-CoV-2 tests completed with 9.1% (N=147) having positive test results. Of 1,014 (62.9%) patients who were CSP+, 12.9% tested positive. Comparatively, 599 (37.1%) patients were CSP- with only 2.7% positive tests, p<0.0001. The sensitivity, specificity, NPV, and PPV of the CSP in all tested patients were 89.1%, 39.8%, 97.3%, and 12.9%, respectively. Of tested patients, 887 (55.0%) were admitted to the hospital and were more likely to be positive if CSP+, p≤0.001. Within the admitted group, 16.8% were admitted to the operating room, of whom 83.9% were CSP- with 4.0% testing positive for SARS-CoV-2. CONCLUSIONS COVID-19 screening in the pediatric population is a useful modality to risk stratify most patients presenting to the PED for the purpose of selective testing and guiding personal protective equipment use. This may be particularly useful in low-resource settings.
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Fatal cases after Omicron BA.1 and BA.2 infection: Results of an autopsy study. Int J Infect Dis 2023; 128:51-57. [PMID: 36584746 DOI: 10.1016/j.ijid.2022.12.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES Omicron lineages BA.1/2 are considered to cause mild clinical courses. Nevertheless, fatal cases after those infections are recognized but little is known about risk factors. METHODS A total of 23 full and three partial autopsies in deceased with known Omicron BA.1/2 infections have been consecutively performed. The investigations included histology, blood analyses, and molecular virus detection. RESULTS COVID-19-associated diffuse alveolar damage was found in only eight cases (31%). This rate is significantly lower compared with previous studies, including non-Omicron variants, where rates between 69% and 92% were observed. Neither vaccination nor known risk factors were significantly associated with a direct cause of death by COVID-19. Only those patients who were admitted to the clinic because of COVID-19 but not for other reasons had a significant association with a direct COVID-19 -caused death (P >0.001). CONCLUSION Diffuse alveolar damage still occurred in the Omicron BA.1/BA.2 era but at a considerably lower frequency than seen with previous variants of concern. None of the known risk factors discriminated the cases with COVID-19-caused death from those that died because of a different disease. Therefore, the host's genomics might play a key role in this regard. Further studies should elucidate the existence of such a genomic risk factor.
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10
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Huang J, Yang X, Ren L, Jiang W, Huang Y, Liu Y, Liu C, Chen X, Li S. A novel, ultrafast, ultrasensitive diagnosis platform for the detection of SARS-COV-2 using restriction endonuclease-mediated reverse transcription multiple cross displacement amplification. J Med Virol 2023; 95:e28444. [PMID: 36579774 PMCID: PMC9880628 DOI: 10.1002/jmv.28444] [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: 08/29/2022] [Revised: 12/07/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). Though many methods have been used for detecting SARS-COV-2, development of an ultrafast and highly sensitive detection strategy to screen and/or diagnose suspected cases in the population, especially early-stage patients with low viral load, is significant for the prevention and treatment of COVID-19. In this study, a novel restriction endonuclease-mediated reverse transcription multiple cross displacement amplification (MCDA) combined with real-time fluorescence analysis (rRT-MCDA) was successfully established and performed to diagnose COVID-19 infection (COVID-19 rRT-MCDA). Two sets of specific SARS-COV-2 rRT-MCDA primers targeting opening reading frame 1a/b (ORF1ab) and nucleoprotein (NP) genes were designed and modified according to the reaction mechanism. The SARS-COV-2 rRT-MCDA test was optimized and evaluated using various pathogens and clinical samples. The optimal reaction condition of SARS-COV-2 rRT-MCDA assay was 65°C for 36 min. The SARS-COV-2 rRT-MCDA limit of detection (LoD) was 6.8 copies per reaction. Meanwhile, the specificity of SARS-COV-2 rRT-MCDA assay was 100%, and there was no cross-reaction with nucleic acids of other pathogens. In addition, the whole detection process of SARS-COV-2 rRT-MCDA, containing the RNA template processing (15 min) and real-time amplification (36 min), can be accomplished within 1 h. The SARS-COV-2 rRT-MCDA test established in the current report is a novel, ultrafast, ultrasensitive, and highly specific detection method, which can be performed as a valuable screening and/or diagnostic tool for COVID-19 in clinical application.
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Affiliation(s)
- Junfei Huang
- Guizhou Provincial Center for Disease Control and PreventionGuiyangGuizhouChina
| | - Xinggui Yang
- Guizhou Provincial Center for Disease Control and PreventionGuiyangGuizhouChina,Public Health SchoolGuizhou Medical UniversityGuiyangGuizhouChina
| | - Lijuan Ren
- Guizhou Provincial Center for Disease Control and PreventionGuiyangGuizhouChina
| | - Weijia Jiang
- Guizhou Provincial Center for Disease Control and PreventionGuiyangGuizhouChina
| | - Yan Huang
- Guizhou Provincial Center for Disease Control and PreventionGuiyangGuizhouChina
| | - Ying Liu
- Guizhou Provincial Center for Disease Control and PreventionGuiyangGuizhouChina
| | - Chunting Liu
- Guizhou Provincial Center for Disease Control and PreventionGuiyangGuizhouChina
| | - Xu Chen
- The Second Affiliated HospitalGuizhou University of Traditional Chinese MedicineGuiyangGuizhouChina
| | - Shijun Li
- Guizhou Provincial Center for Disease Control and PreventionGuiyangGuizhouChina,Public Health SchoolGuizhou Medical UniversityGuiyangGuizhouChina
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11
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Tartof SY, Slezak JM, Puzniak L, Hong V, Frankland TB, Xie F, Ackerson BK, Valluri SR, Jodar L, McLaughlin JM. Effectiveness and durability of BNT162b2 vaccine against hospital and emergency department admissions due to SARS-CoV-2 omicron sub-lineages BA.1 and BA.2 in a large health system in the USA: a test-negative, case-control study. THE LANCET. RESPIRATORY MEDICINE 2023; 11:176-187. [PMID: 36216013 PMCID: PMC9765328 DOI: 10.1016/s2213-2600(22)00354-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND The SARS-CoV-2 omicron (B.1.1.529 BA.1) lineage was first detected in November, 2021, and is associated with reduced vaccine effectiveness. By March, 2022, BA.1 had been replaced by sub-lineage BA.2 in the USA. As new variants evolve, vaccine performance must be continually assessed. We aimed to evaluate the effectiveness and durability of BNT162b2 (Pfizer-BioNTech) against hospital and emergency department admissions for BA.1 and BA.2. METHODS In this test-negative, case-control study, we sourced data from the electronic health records of adult (aged ≥18 years) members of Kaiser Permanente Southern California (KPSC), which is a health-care system in the USA, who were admitted to one of 15 KPSC hospitals or emergency departments (without subsequent hospitalisation) between Dec 27, 2021, and June 4, 2022, with an acute respiratory infection and were tested for SARS-CoV-2 by RT-PCR. Omicron sub-lineage was determined by use of sequencing, spike gene target failure, and the predominance of variants in certain time periods. Our main outcome was the effectiveness of two or three doses of BNT162b2 in preventing emergency department or hospital admission. Variant-specific vaccine effectiveness was evaluated by comparing the odds ratios from logistic regression models of vaccination between test-positive cases and test-negative controls, adjusting for the month of admission, age, sex, race and ethnicity, body-mass index, Charlson Comorbidity Index, previous influenza or pneumococcal vaccines, and previous SARS-CoV-2 infection. We also assessed effectiveness by the time since vaccination. This study is registered at ClinicalTrials.gov, NCT04848584, and is ongoing. FINDINGS Of 65 813 total admissions during the study period, we included 16 994 in our analyses, of which 7435 were due to BA.1, 1056 were due to BA.2, and 8503 were not due to SARS-CoV-2. In adjusted analyses, two-dose vaccine effectiveness was 40% (95% CI 27 to 50) for hospitalisation and 29% (18 to 38) for emergency department admission against BA.1 and 56% (31 to 72) for hospitalisation and 16% (-5 to 33) for emergency department admission against BA.2. Three-dose vaccine effectiveness was 79% (74 to 83) for hospitalisation and 72% (67 to 77) for emergency department admission against BA.1 and 71% (55 to 81) for hospitalisation and 21% (1 to 37) for emergency department admission against BA.2. Less than 3 months after the third dose, vaccine effectiveness was 80% (74 to 84) for hospitalisation and 74% (69 to 78) for emergency department admission against BA.1. Vaccine effectiveness 3 months or more after the third dose was 76% (69 to 82) against BA.1-related hospitalisation and 65% (56 to 73) against BA.1-related emergency department admission. Against BA.2, vaccine effectiveness was 74% (47 to 87) for hospitalisation and 59% (40 to 72) for emergency department admission at less than 3 months after the third dose and 70% (53 to 81) for hospitalisation and 5% (-21 to 25) for emergency department admission at 3 months or more after the third dose. INTERPRETATION Two doses of BNT162b2 provided only partial protection against BA.1-related and BA.2-related hospital and emergency department admission, which underscores the need for booster doses against omicron. Although three doses offered high levels of protection (≥70%) against hospitalisation, variant-adapted vaccines are probably needed to improve protection against less severe endpoints, like emergency department admission, especially for BA.2. FUNDING Pfizer.
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Affiliation(s)
- Sara Y Tartof
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA; Department of Health Systems Science, Kaiser Permanente Bernard J Tyson School of Medicine, Pasadena, CA, USA.
| | - Jeff M Slezak
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | | | - Vennis Hong
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Timothy B Frankland
- Center for Integrated Health Care Research, Kaiser Permanente Hawaii, Honolulu, HI, USA
| | - Fagen Xie
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
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12
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Zhang Z, Hao M, Zhang X, He Y, Chen X, Taylor EW, Zhang J. Potential of green tea EGCG in neutralizing SARS-CoV-2 Omicron variant with greater tropism toward the upper respiratory tract. Trends Food Sci Technol 2023; 132:40-53. [PMID: 36594074 PMCID: PMC9796359 DOI: 10.1016/j.tifs.2022.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/24/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022]
Abstract
Background COVID-19 due to SARS-CoV-2 infection has had an enormous adverse impact on global public health. As the COVID-19 pandemic evolves, the WHO declared several variants of concern (VOCs), including Alpha, Beta, Gamma, Delta, and Omicron. Compared with earlier variants, Omicron, now a dominant lineage, exhibits characteristics of enhanced transmissibility, tropism shift toward the upper respiratory tract, and attenuated disease severity. The robust transmission of Omicron despite attenuated disease severity still poses a great challenge for pandemic control. Under this circumstance, its tropism shift may be utilized for discovering effective preventive approaches. Scope and approach This review aims to estimate the potential of green tea epigallocatechin gallate (EGCG), the most potent antiviral catechin, in neutralizing SARS-CoV-2 Omicron variant, based on current knowledge concerning EGCG distribution in tissues and Omicron tropism. Key findings and conclusions EGCG has a low bioavailability. Plasma EGCG levels are in the range of submicromolar concentrations following green tea drinking, or reach at most low μM concentrations after pharmacological intervention. Nonetheless, its levels in the upper respiratory tract could reach concentrations as high as tens or even hundreds of μM following green tea consumption or pharmacological intervention. An approach for delivering sufficiently high concentrations of EGCG in the pharynx has been developed. Convincing data have demonstrated that EGCG at tens to hundreds of μM can dramatically neutralize SARS-CoV-2 and effectively eliminate SARS-CoV-2-induced cytopathic effects and plaque formation. Thus, EGCG, which exhibits hyperaccumulation in the upper respiratory tract, deserves closer investigation as an antiviral in the current global battle against COVID-19, given Omicron's greater tropism toward the upper respiratory tract.
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Key Words
- ACE2, angiotensin-converting enzyme 2
- COVID-19
- EGCG
- EGCG, epigallocatechin-3-gallate
- GRP78, glucose-regulated protein 78
- HO-1, hemeoxygenase 1
- IFN-β, interferon-β
- Mpro, main protease
- MxA, MxGTPases
- Nrf2, nuclear factor erythroid 2 p45-related factor 2
- Nsp15, nonstructural protein 15
- Omicron variant
- SARS-CoV-2
- TMPRSS2, transmembrane serine protease 2
- The upper respiratory tract
- Tropism
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Affiliation(s)
- Zhichao Zhang
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Meng Hao
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, 230036, China
| | - Xiangchun Zhang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Yufeng He
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, 230036, China
| | - Xiongsheng Chen
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ethan Will Taylor
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA
| | - Jinsong Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, 230036, China
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13
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Characteristics of the Severe Acute Respiratory Syndrome Coronavirus 2 Omicron BA.2 Subvariant in Jilin, China from March to May 2022. J Transl Int Med 2023; 10:349-358. [PMID: 36860638 PMCID: PMC9969560 DOI: 10.2478/jtim-2022-0054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background and Objectives In the midst of the pandemic, new coronavirus mutants continue to emerge; the most relevant variant worldwide is omicron. Here, patients who recovered from the disease living in Jilin Province were analyzed to identify factors affecting the severity of omicron infection and to provide insights into its spread and early indication. Methods In this study, 311 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were divided into two groups. Data on the patients' demographic characteristics and laboratory tests, including platelet count (PLT), neutrophil count (NE), C-reactive protein (CRP), serum creatinine (SCR), and neutrophil-to-lymphocyte ratio (NLR), were collected. The biomarkers for moderate and severe coronavirus disease 2019 (COVID-19) and factors affecting the incubation period and time to subsequent negative nucleic acid amplification test (NAAT) were also investigated. Results Age, gender, vaccination, hypertension, stroke, chronic obstructive pulmonary disease (COPD)/chronic bronchitis/asthma, and some laboratory tests were statistically different between the two groups. In the receiver operating characteristic (ROC) analysis, PLT and CRP had higher area under the ROC curve values. In the multivariate analysis, age, hypertension, COPD/chronic bronchitis/asthma, and CRP were correlated with moderate and severe COVID-19. Moreover, age was correlated with longer incubation. In the Kaplan-Meier curve analysis, gender (male), CRP, and NLR were associated with longer time to subsequent negative NAAT. Conclusions Older patients with hypertension and lung diseases were likely to have moderate or severe COVID-19, and younger patients might have a shorter incubation. A male patient with high CRP and NLR levels might take more time to turn back negative in the NAAT.
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14
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Wang Y, Long Y, Wang F, Li C, Liu W. Characterization of SARS-CoV-2 recombinants and emerging Omicron sublineages. Int J Med Sci 2023; 20:151-162. [PMID: 36619228 PMCID: PMC9812801 DOI: 10.7150/ijms.79116] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/10/2022] [Indexed: 01/06/2023] Open
Abstract
The SARS-CoV-2 Omicron is currently the predominant circulating variant in the COVID-19 pandemic. The dominating Omicron sublineages respond to host immune pressure and develop advantageous mutations or genetic recombination, which result in variants that are more contagious or better at escaping immune responses in response to previous infection or vaccination. Meanwhile, multiple genetic recombination events have been reported in coinfection cases, the majority of which have resulted from the recombination between co-circulating Omicron BA.1 (or BA.1.1) and Delta variant or BA.2. Here, we review the knowledge and characterization of recombination for SARS-CoV-2 at the population level, provide an update on the occurrence of newly circulating Omicron sublineages, and discuss the effectiveness of novel vaccines/therapeutic drugs against the Omicron variant.
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Affiliation(s)
- Yuliang Wang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yiyin Long
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Feng Wang
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Changlin Li
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Wei Liu
- Tianjin Children's Hospital, Children's Hospital, Tianjin University, Tianjin, China
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15
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Aristokleous A, Christodoulou C, Gregoriou I, Ioannides M, Kalakouta O, Karagiannis C, Koumbaris G, Loizides C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Richter J, Schmitt M, Shammas C, Stylianou DC, Themistokleous G, Lemey P, Kostrikis LG. Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern. Viruses 2022; 15:108. [PMID: 36680148 PMCID: PMC9862594 DOI: 10.3390/v15010108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, Larnaca 6301, Cyprus
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | - Christina Christodoulou
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | | | | | - Michail Mendris
- Microbiology Department, Limassol General Hospital, Limassol 4131, Cyprus
| | | | - Philippos C. Patsalis
- NIPD Genetics, Nicosia 2409, Cyprus
- Medical School, University of Nicosia, Nicosia 2417, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, Nicosia 2029, Cyprus
| | - Jan Richter
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Markus Schmitt
- Eurofins Genomics Sequencing Europe, 85560 Ebersberg, Germany
| | - Christos Shammas
- S.C.I.N.A Bioanalysis Sciomedical Centre Ltd., Limassol 4040, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | | | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, Nicosia 1011, Cyprus
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16
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Wu Y, Long Y, Wang F, Liu W, Wang Y. Emergence of SARS-CoV-2 Omicron variant and strategies for tackling the infection. Immun Inflamm Dis 2022; 10:e733. [PMID: 36444634 PMCID: PMC9639460 DOI: 10.1002/iid3.733] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION Nowadays, emerging SARS-CoV-2 Omicron, the novel highly mutated VOC, has quickly spread as the dominant variant in over 190 countries worldwide through the first part of 2022, which is influencing the infectivity, transmissibility, pathogenicity, and severity of COVID-19 pandemic. Additionally, clinical cases and experimental studies have reported that Omicron variant likely leads to weakened immune protection elicited by infection, antibody therapies, and vaccines. The new wave, from late February, 2022, was escalated abruptly by higher levels of transmission of Omicron BA.2 sublineage in China. METHODS AND RESULTS Following a systematic database search, this review summarizes the salient features of Omicron sublineages, and their impact on transmissibility, disease severity as well as the efficacy of the available vaccines and treatment against the Omicron. CONCLUSION We hope this study will provide a scientific reference for alleviating the burden of COVID-19.
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Affiliation(s)
- Yan Wu
- Department of Clinical Laboratory MedicineTianjin TEDA HospitalTianjinChina
| | - Yiyin Long
- Tianjin Institute of UrologyThe Second Hospital of Tianjin Medical UniversityTianjinChina
| | - Feng Wang
- Department of Genetics, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Wei Liu
- Tianjin Children's HospitalChildren's Hospital of Tianjin UniversityTianjinChina
| | - Yuliang Wang
- Tianjin Institute of UrologyThe Second Hospital of Tianjin Medical UniversityTianjinChina
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17
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Darwish DBE. Insight into SARS-CoV-2 Omicron variants in Saudi Arabian genomic isolates. Saudi Med J 2022; 43:1276-1279. [PMID: 36379532 PMCID: PMC10043908 DOI: 10.15537/smj.2022.43.11.20220381] [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: 05/15/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023] Open
Abstract
OBJECTIVES To investigate the emergent mutations involved in the evolutionary stages of the virus for better management of pandemic. METHODS This cross-sectional genomic investigation was performed on February 28, 2022, at the Biology Department, Faculty of Science, Tabuk University. Numerous mutations were searched in genomic isolates of Omicron variant prevalent in the Kingdom of Saudi Arabian. Whole-genome sequences were retrieved from genomic databases and were subjected to the Global Initiative on Sharing Avian Influenza Data (GISAID) CoVsurver for the Omicron variant detection and mutations. RESULTS Approximately 8.755 million SARS-CoV-2 genomes were reported to GISAID on February 28, 2022, of which 1270 have been reported from the Kingdom of Saudi Arabia. Among the 1270 genomes, 30 were Omicron variants. Among the Saudi Arabian genomes, 30 were detected as Omicron variants. Twenty-four unique mutations have been detected in membrane, envelope, spike and non-structural proteins (NSP) 12, NSP3, and NSP2. Ten of these unique mutations have been detected in spike protein. CONCLUSION The current study provides useful information for further experimental investigation of mutation's effects on virus transmission, severity, and vaccine efficacy.
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Affiliation(s)
- Doaa Bahaa E. Darwish
- From the Biology Department, Faculty of Science, University of Tabuk, Tabuk, Kingdom of Saudi Arabia; and from the Botany Department, Faculty of Science, Mansoura University, Mansoura, Egypt.
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18
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Xu Z, Zou Y, Gao X, Niu MM, Li J, Xue L, Jiang S. Dual-targeting cyclic peptides of receptor-binding domain (RBD) and main protease (Mpro) as potential drug leads for the treatment of SARS-CoV-2 infection. Front Pharmacol 2022; 13:1041331. [PMID: 36339564 PMCID: PMC9627161 DOI: 10.3389/fphar.2022.1041331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/10/2022] [Indexed: 12/01/2023] Open
Abstract
The receptor-binding domain (RBD) and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) play a crucial role in the entry and replication of viral particles, and co-targeting both of them could be an attractive approach for the treatment of SARS-CoV-2 infection by setting up a "double lock" in the viral lifecycle. However, few dual RBD/Mpro-targeting agents have been reported. Here, four novel RBD/Mpro dual-targeting peptides, termed as MRs 1-4, were discovered by an integrated virtual screening scheme combining molecular docking-based screening and molecular dynamics simulation. All of them possessed nanomolar binding affinities to both RBD and Mpro ranging from 14.4 to 39.2 nM and 22.5-40.4 nM, respectively. Further pseudovirus infection assay revealed that the four selected peptides showed >50% inhibition against SARS-CoV-2 pseudovirus at a concentration of 5 µM without significant cytotoxicity to host cells. This study leads to the identification of a class of dual RBD/Mpro-targeting agents, which may be developed as potential and effective SARS-CoV-2 therapeutics.
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Affiliation(s)
- Zhen Xu
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yunting Zou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Xi Gao
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Jindong Li
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Lu Xue
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Su Jiang
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
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Alba JMG, Pérez-Martínez Z, Boga JA, Rojo-Alba S, de Oña JG, Alvarez-Argüelles ME, Rodríguez GM, Gonzalez IC, González IH, Coto E, García SM. Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy. Microorganisms 2022; 10:1954. [PMID: 36296230 PMCID: PMC9610377 DOI: 10.3390/microorganisms10101954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/07/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants. METHODS From January to June 2022, 34,591 variants were determined by the SNP method. From them, 445 were characterized by the WGS method and classified following pangolin program and phylogenic analysis. RESULTS The Omicron variant went from being detected in 2438 (78%) samples in the first week of January 2021 to 4074 (98%) in the third week, according to the SNP method. Using the WGS method, 159 BA.1 (35.7%), 256 BA.2 (57.6%), 1 BA.4 (0.2%) and 10 BA.5 (2.2%) Omicron variants were found. Phylogenetic analysis detected that three new sub-clades, BA.2,3.5, BA.2.56 and BF1, were circulating. CONCLUSIONS The increase in the incidence of SARS-CoV2 caused the circulation of new emerging variants. Viral evolution calls for continuous genomic surveillance.
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Affiliation(s)
- José María González Alba
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Zulema Pérez-Martínez
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - José A. Boga
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Susana Rojo-Alba
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Juan Gómez de Oña
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Genetic Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Marta E. Alvarez-Argüelles
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Garbriel Martín Rodríguez
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Isabel Costales Gonzalez
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | | | - Eliecer Coto
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Genetic Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Santiago Melón García
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Li Z, Hu Y, Zeng M, Hu Q, Ye F, Liu R, Cai H, Li Q, Wang X. The role transition of radiotherapy for the treatment of liver cancer in the COVID-19 era. Front Oncol 2022; 12:976143. [PMID: 36185295 PMCID: PMC9516283 DOI: 10.3389/fonc.2022.976143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
The uncontrollable COVID-19 crises in the SARS-CoV-2 high-prevalence areas have greatly disrupted the routine treatment of liver cancer and triggered a role transformation of radiotherapy for liver cancer. The weight of radiotherapy in the treatment algorithm for liver cancer has been enlarged by the COVID-19 pandemic, which is helpful for the optimal risk-benefit profile.
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Affiliation(s)
- Zheng Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Lanzhou Heavy Ion Hospital, Lanzhou, China
| | - Yue Hu
- Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ming Zeng
- Department of Radiation Oncology, MetroHealth Medical Center, Case Western Reserve University, Cleveland, OH, United States
| | - Qinyong Hu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fei Ye
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Ruifeng Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Lanzhou Heavy Ion Hospital, Lanzhou, China
| | - Hongyi Cai
- Department of Radiotherapy, Gansu Provincial Hospital, Lanzhou, China
| | - Qiang Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Lanzhou Heavy Ion Hospital, Lanzhou, China
| | - Xiaohu Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Lanzhou Heavy Ion Hospital, Lanzhou, China
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21
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Liu Y, Chen X, Wang H, Yao C, Gou X, Gao Z, Sun L, Liu D, Tang C, Wei Y, Ding Q, Yang H, Lin J, Chen K, Chen J, Zhao L, Li M, Han L, Wang J, Ren J, Zhang Y. Effectiveness and safety analysis of SanHanHuaShi granules for the treatment of coronavirus disease 2019: Study protocol and statistical analysis plan for a randomized, parallel-controlled, open-label clinical trial. Front Pharmacol 2022; 13:936925. [PMID: 36052134 PMCID: PMC9425051 DOI: 10.3389/fphar.2022.936925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Coronavirus disease 2019 (COVID-19) was declared a global pandemic in March 2020 by the World Health Organization (WHO). As of July 2, 2022, COVID-19 has caused more than 545 million infections and 6.3 million deaths worldwide, posing a significant threat to human health. Currently, there is still a lack of effective prevention and control strategies for the variation and transmission of SARS-CoV-2. Traditional Chinese medicine (TCM), which has a unique theoretical system, has treated various conditions for thousands of years. Importantly, recent studies have revealed that TCM contributed significantly to COVID-19. SanHanHuaShi (SHHS) granules, a Chinese herbal medicine, which has been included in Protocol for the Diagnosis and Treatment of Novel Coronavirus Disease 2019 (6th to 9th editions) issued by the National Health Commission of China and used to prevent and treat COVID-19 disease. A previous retrospective cohort study showed that SHHS could significantly reduce the severity of mild and moderate COVID-19. However, there is an absence of high-quality randomized controlled clinical studies to confirm the clinical effectiveness of SHHS. Therefore, a clinical study protocol and a statistical analysis plan were designed to investigate the efficacy and safety of SHHS for the prevention and treatment of COVID-19. This study will increase the integrity and data transparency of the clinical research process, which is of great significance for improving the practical application of SHHS granules in the future. Methods and analysis: The study was designed as a 7-day, randomized, parallel controlled, open-label, noninferiority clinical trial of positive drugs. A total of 240 patients with mild and moderate COVID-19 will be enrolled and randomly assigned to receive SanHanHuaShi granules or LianHuaQingWen granules treatment in a 1:1 ratio. Disease classification, vital signs, SARS-CoV-2 nucleic acid testing, symptoms, medications, adverse events, and safety evaluations will be recorded at each visit. The primary outcome will be the clinical symptom recovery rate. Secondary outcomes will include the recovery time of clinical symptoms, negative conversion time of SARS-CoV-2 nucleic acid test negative conversion rate, hospitalization time, antipyretic time, rate of conversion to severe patients, and time and rate of single symptom recovery. Adverse incidents and safety assessments will be documented. All data will be analyzed using a predetermined statistical analysis plan, including our method for imputation of missing data, primary and secondary outcome analyses, and safety outcomes. Discussion: The results of this study will provide robust evidence to confirm the effectiveness and safety of SHHS in the treatment of COVID-19. Clinical Trial Registration:http://www.chictr.org.cn. Trial number: ChiCTR2200058080. Registered on 29 March 2022.
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Affiliation(s)
- Yangyang Liu
- Institute of Integrated Traditional Chinese and Western Medicine, Beijing University of Chinese Medicine, Beijing, China
- The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Xi Chen
- The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Hongan Wang
- The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Chensi Yao
- Department of Endocrinology, Guang’anmen Hospital of China, Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaowen Gou
- Department of Endocrinology, Guang’anmen Hospital of China, Academy of Chinese Medical Sciences, Beijing, China
| | - Zezheng Gao
- Department of Endocrinology, Guang’anmen Hospital of China, Academy of Chinese Medical Sciences, Beijing, China
| | - Linlin Sun
- The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Dan Liu
- The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Cheng Tang
- The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Yu Wei
- Graduate College, Beijing University of Traditional Chinese Medicine, Beijing, China
| | - Qiyou Ding
- Graduate College, Beijing University of Traditional Chinese Medicine, Beijing, China
| | - Haoyu Yang
- Graduate College, Beijing University of Traditional Chinese Medicine, Beijing, China
| | - Jiaran Lin
- Graduate College, Beijing University of Traditional Chinese Medicine, Beijing, China
| | - Keyu Chen
- Graduate College, Beijing University of Traditional Chinese Medicine, Beijing, China
| | - Jia Chen
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Linhua Zhao
- Institute of Metabolic Diseases, Guang’anmen Hospital of China, Academy of Chinese Medical Sciences, Beijing, China
| | - Min Li
- Molecular Biology Laboratory, Guang’anmen Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Lin Han
- Institute of Metabolic Diseases, Guang’anmen Hospital of China, Academy of Chinese Medical Sciences, Beijing, China
| | - Jian Wang
- The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
- *Correspondence: Jian Wang, ; Jixiang Ren, ; Ying Zhang,
| | - Jixiang Ren
- The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
- *Correspondence: Jian Wang, ; Jixiang Ren, ; Ying Zhang,
| | - Ying Zhang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Jian Wang, ; Jixiang Ren, ; Ying Zhang,
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