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Dinh Thiem V, Van Anh PT, Van Men C, Hung DT, Pollard AJ, Kamitani A, Tada Y, Fukuyama H, Iwasaki Y, Ariyasu M, Sonoyama T. A SARS-CoV-2 recombinant spike protein vaccine (S-268019-b) for COVID-19 prevention during the Omicron-dominant period: A phase 3, randomised, placebo-controlled clinical trial. Vaccine 2024; 42:3699-3709. [PMID: 38734495 DOI: 10.1016/j.vaccine.2024.04.084] [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: 12/28/2023] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024]
Abstract
Clinical trials of new vaccines based on existing variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are often impacted by the emergence of new virus variants. We evaluated the efficacy, immunogenicity, and safety of S-268019-b, a recombinant spike protein subunit vaccine based on the ancestral strain, for preventing symptomatic coronavirus disease 2019 (COVID-19) during the Omicron (BA.2)-dominant period in Vietnam. In this multicentre, phase 3, randomised (2:1), observer-blind, placebo-controlled crossover study, participants received 2 intramuscular doses (28 days apart) of either 10 µg of S-268019-b (Recombinant S-protein vaccine) or placebo. The primary endpoint was incidence of laboratory-confirmed symptomatic COVID-19 before crossover, with onset within 14 days following the second dose, in participants who were seronegative and reverse transcription polymerase chain reaction (RT-PCR)-negative at baseline. The secondary endpoints included immunogenicity and safety. In total, 8,594 participants were randomised (S-268019-b [n = 5,727]; placebo [n = 2,867]). Vaccine efficacy versus placebo was 39·1 % (95 % confidence interval [CI]:26·6-49·5; one-sided P = 0·0723). The incidence rate (95 % CI) of symptomatic COVID-19 was 776·41/1,000 person-years (682·04-880·19) in the S-268019-b group and 1272·87/1,000 person-years (1101·32-1463·57) in the placebo group. The geometric mean titres (95 % CI) of the SARS-CoV-2 neutralising antibody increased on Day 57 versus baseline with S-268019-b (34·66 [27·04-44·41] versus 2·50 (non-estimable) but not with placebo. There were no safety concerns regarding S-268019-b. S-268019-b did not demonstrate the targeted efficacy threshold against symptomatic COVID-19; however, findings were comparable with other prophylactic vaccines based on ancestor strain during the Omicron-dominant period. S-268019-b demonstrated immunogenicity and was well-tolerated. ClinicalTrials.gov identifier: NCT05212948.
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MESH Headings
- Humans
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/adverse effects
- COVID-19/prevention & control
- COVID-19/immunology
- Male
- Female
- Adult
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- Middle Aged
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/adverse effects
- Vietnam
- Young Adult
- Immunogenicity, Vaccine
- Cross-Over Studies
- Adolescent
- Vaccine Efficacy
- Aged
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Vaccines, Subunit
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Affiliation(s)
- Vu Dinh Thiem
- Centre for Clinical Trials, National Institute of Hygiene and Epidemiology, Ha Noi, Viet Nam
| | | | - Chu Van Men
- Viet Nam Military Medical University, Ha Noi, Viet Nam
| | - Do Thai Hung
- Pasteur Institute in Nha Trang, Khanh Hoa, Viet Nam
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
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Tsukamoto A, Jae Man L, Oyama K, Masuda A, Mon H, Ueda T, Kusakabe T. Effective expression and characterization of the receptor binding domains in SARS-CoV-2 Spike proteins from original strain and variants of concern using Bombyx mori nucleopolyhedrovirus in silkworm. Protein Expr Purif 2024; 218:106450. [PMID: 38395208 DOI: 10.1016/j.pep.2024.106450] [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: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the global pandemic of COVID-19 in 2020. Through structural analysis, it was found that several amino acid residues in the human angiotensin-converting enzyme-2 (hACE2) receptor directly interact with those in the receptor binding domain (RBD) of the spike glycoprotein (S-protein). Various cell lines, including HEK293, HeLa cells, and the baculovirus expression vector system (BEVS) with the insect cell line Sf9, have been utilized to produce the RBD. In this study, we investigated the use of Bombyx mori nucleopolyhedrovirus (BmNPV) and BEVS. For efficient production of a highly pure recombinant RBD protein, we designed it with two tags (His tag and STREP tag) at the C-terminus and a solubilizing tag (SUMO) at the N-terminus. After expressing the protein using BmNPV and silkworm and purifying it with a HisTrap excel column, the eluted protein was digested with SUMO protease and further purified using a Strep-Tactin Superflow column. As a result, we obtained the RBD as a monomer with a yield of 2.6 mg/10 mL serum (equivalent to 30 silkworms). The RBD showed an affinity for the hACE2 receptor. Additionally, the RBDs from the Alpha, Beta, Gamma, Delta, and Omicron variants were expressed and purified using the same protocol. It was found that the RBD from the Alpha, Beta, Gamma, and Delta variants could be obtained with yields of 1.4-2.6 mg/10 mL serum and had an affinity to the hACE2 receptor.
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Affiliation(s)
- Akira Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Lee Jae Man
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kosuke Oyama
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akitsu Masuda
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroaki Mon
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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Shi FS, Xie YH, Yang YL, Xu LD, Li JJ, Wang X, Zhu LY, Wang WW, Shen PL, Huang YW, Li XQ. Fucoidan from Ascophyllum nodosum and Undaria pinnatifida attenuate SARS-CoV-2 infection in vitro and in vivo by suppressing ACE2 and alleviating inflammation. Carbohydr Polym 2024; 332:121884. [PMID: 38431405 DOI: 10.1016/j.carbpol.2024.121884] [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: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024]
Abstract
The global healthcare challenge posed by COVID-19 necessitates the continuous exploration for novel antiviral agents. Fucoidans have demonstrated antiviral activity. However, the underlying structure-activity mechanism responsible for the inhibitory activity of fucoidans from Ascophyllum nodosum (FUCA) and Undaria pinnatifida (FUCU) against SARS-CoV-2 remains unclear. FUCA was characterized as a homopolymer with a backbone structure of repeating (1 → 3) and (1 → 4) linked α-l-fucopyranose residues, whereas FUCU was a heteropolysaccharide composed of Fuc1-3Gal1-6 repeats. Furthermore, FUCA demonstrated significantly higher anti-SARS-CoV-2 activity than FUCU (EC50: 48.66 vs 69.52 μg/mL), suggesting the degree of branching rather than sulfate content affected the antiviral activity. Additionally, FUCA exhibited a dose-dependent inhibitory effect on ACE2, surpassing the inhibitory activity of FUCU. In vitro, both FUCA and FUCU treatments downregulated the expression of pro-inflammatory cytokines (IL-6, IFN-α, IFN-γ, and TNF-α) and anti-inflammatory cytokines (IL-10 and IFN-β) induced by viral infection. In hamsters, FUCA demonstrated greater effectiveness in attenuating lung and gastrointestinal injury and reducing ACE2 expression, compared to FUCU. Analysis of the 16S rRNA gene sequencing revealed that only FUCU partially alleviated the gut microbiota dysbiosis caused by SARS-CoV-2. Consequently, our study provides a scientific basis for considering fucoidans as poteintial prophylactic food components against SARS-CoV-2.
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Affiliation(s)
- Fang-Shu Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Department of Veterinary Medicine, Zhejiang University, Hangzhou 310028, China
| | - Yv-Hao Xie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Yong-Le Yang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310028, China
| | - Ling-Dong Xu
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310028, China
| | - Jin-Jun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Li-Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wei-Wei Wang
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Pei-Li Shen
- State Key Laboratory of Marine Food Processing & Safety Control, Qingdao Bright Moon Seaweed Group Co., Ltd., Qingdao, Shandong, China
| | - Yao-Wei Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Department of Veterinary Medicine, Zhejiang University, Hangzhou 310028, China.
| | - Xiao-Qiong Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Han Y, Yuan Z, Yi Z. Identification of a membrane-associated element (MAE) in the C-terminal region of SARS-CoV-2 nsp6 that is essential for viral replication. J Virol 2024; 98:e0034924. [PMID: 38639488 PMCID: PMC11092323 DOI: 10.1128/jvi.00349-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/29/2024] [Indexed: 04/20/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the novel coronavirus severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has rapidly spread worldwide since its emergence in late 2019. Its ongoing evolution poses challenges for antiviral drug development. Coronavirus nsp6, a multiple-spanning transmembrane protein, participates in the biogenesis of the viral replication complex, which accommodates the viral replication-transcription complex. The roles of its structural domains in viral replication are not well studied. Herein, we predicted the structure of the SARS-CoV-2 nsp6 protein using AlphaFold2 and identified a highly folded C-terminal region (nsp6C) downstream of the transmembrane helices. The enhanced green fluorescent protein (EGFP)-fused nsp6C was found to cluster in the cytoplasm and associate with membranes. Functional mapping identified a minimal membrane-associated element (MAE) as the region from amino acids 237 to 276 (LGV-KLL), which is mainly composed of the α-helix H1 and the α-helix H2; the latter exhibits characteristics of an amphipathic helix (AH). Mutagenesis studies and membrane flotation experiments demonstrate that AH-like H2 is required for MAE-mediated membrane association. This MAE was functionally conserved across MERS-CoV, HCoV-OC43, HCoV-229E, HCoV-HKU1, and HCoV-NL63, all capable of mediating membrane association. In a SARS-CoV-2 replicon system, mutagenesis studies of H2 and replacements of H1 and H2 with their homologous counterparts demonstrated requirements of residues on both sides of the H2 and properly paired H1-H2 for MAE-mediated membrane association and viral replication. Notably, mutations I266A and K274A significantly attenuated viral replication without dramatically affecting membrane association, suggesting a dual role of the MAE in viral replication: mediating membrane association as well as participating in protein-protein interactions.IMPORTANCESevere acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) assembles a double-membrane vesicle (DMV) by the viral non-structural proteins for viral replication. Understanding the mechanisms of the DMV assembly is of paramount importance for antiviral development. Nsp6, a multiple-spanning transmembrane protein, plays an important role in the DMV biogenesis. Herein, we predicted the nsp6 structure of SARS-CoV-2 and other human coronaviruses using AlphaFold2 and identified a putative membrane-associated element (MAE) in the highly conserved C-terminal regions of nsp6. Experimentally, we verified a functionally conserved minimal MAE composed of two α-helices, the H1, and the amphipathic helix-like H2. Mutagenesis studies confirmed the requirement of H2 for MAE-mediated membrane association and viral replication and demonstrated a dual role of the MAE in viral replication, by mediating membrane association and participating in residue-specific interactions. This functionally conserved MAE may serve as a novel anti-viral target.
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Affiliation(s)
- Yuying Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Zhigang Yi
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Sohrab SS, Alsaqaf F, Hassan AM, Tolah AM, Bajrai LH, Azhar EI. Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses. BIOLOGY 2024; 13:282. [PMID: 38666894 PMCID: PMC11048170 DOI: 10.3390/biology13040282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002-2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent.
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Affiliation(s)
- Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | - Fatima Alsaqaf
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
| | - Ahmed Mohamed Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
| | - Ahmed Majdi Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Science, King Abdulaziz University, P.O. Box 21911, Rabigh 344, Saudi Arabia
| | - Leena Hussein Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
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Mahroum N, Habra M, Alrifaai MA, Shoenfeld Y. Antiphospholipid syndrome in the era of COVID-19 - Two sides of a coin. Autoimmun Rev 2024:103543. [PMID: 38604461 DOI: 10.1016/j.autrev.2024.103543] [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: 01/31/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
In addition to the respiratory symptoms associated with COVID-19, the disease has consistently been linked to many autoimmune diseases such as systemic lupus erythematous and antiphospholipid syndrome (APS). APS in particular was of paramount significance due to its devastating clinical sequela. In fact, the hypercoagulable state seen in patients with acute COVID-19 and the critical role of anticoagulant treatment in affected individuals shed light on the possible relatedness between APS and COVID-19. Moreover, the role of autoimmunity in the assumed association is not less important especially with the accumulated data available regarding the autoimmunity-triggering effect of SARS-CoV-2 infection. This is furtherly strengthened at the time patients with COVID-19 manifested antiphospholipid antibodies of different types following infection. Additionally, the severe form of the APS spectrum, catastrophic APS (CAPS), was shown to have overlapping characteristics with severe COVID-19 such as cytokine storm and multi-organ failure. Interestingly, COVID vaccine-induced autoimmune phenomena described in the medical literature have pointed to an association with APS. Whether the antiphospholipid antibodies were present or de novo, COVID vaccine-induced vascular thrombosis in certain individuals necessitates further investigations regarding the possible mechanisms involved. In our current paper, we aimed to focus on the associations mentioned, their implications, importance, and consequences.
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Affiliation(s)
- Naim Mahroum
- International School of Medicine, Istanbul Medipol University, Istanbul, Turkey.
| | - Mona Habra
- International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | | | - Yehuda Shoenfeld
- Zabludowicz Center for autoimmune diseases, Sheba Medical Center, Ramat-Gan, Israel; Reichman University, Herzliya, Israel
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Buenestado-Serrano S, Herranz M, Otero-Sobrino Á, Molero-Salinas A, Rodríguez-Grande C, Sanz-Pérez A, Durán Galván MJ, Catalán P, Alonso R, Muñoz P, Pérez-Lago L, García de Viedma D. Accelerating SARS-CoV-2 genomic surveillance in a routine clinical setting with nanopore sequencing. Int J Med Microbiol 2024; 314:151599. [PMID: 38290400 DOI: 10.1016/j.ijmm.2024.151599] [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: 07/17/2023] [Revised: 10/27/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND SARS-CoV-2 genomic analysis has been key to the provision of valuable data to meet both epidemiological and clinical demands. High-throughput sequencing, generally Illumina-based, has been necessary to ensure the widest coverage in global variant tracking. However, a speedier response is needed for nosocomial outbreak analyses and rapid identification of patients infected by emerging VOCs. An alternative based on nanopore sequencing may be better suited to delivering a faster response when required; however, although there are several studies offering side-by-side comparisons of Illumina and nanopore sequencing, evaluations of the usefulness in the hospital routine of the faster availability of data provided by nanopore are still lacking. RESULTS We performed a prospective 10-week nanopore-based sequencing in MinION in a routine laboratory setting, including 83 specimens where a faster response time was necessary. The specimens analyzed corresponded to i) international travellers in which lineages were assigned to determine the proper management/special isolation of the patients; ii) nosocomial infections and health-care-worker infections, where SNP-based comparisons were required to rule in/out epidemiological relationships and tailor specific interventions iii) sentinel cases and breakthrough infections to timely report to the Public Health authorities. MinION-based sequencing was compared with the standard procedures, supported on Illumina sequencing; MinION accelerated the delivery of results (anticipating results 1-12 days) and reduced costs per sample by 28€ compared to Illumina, without reducing accuracy in SNP calling. CONCLUSIONS Parallel integration of Illumina and nanopore sequencing strategies is a suitable solution to ensure both high-throughput and rapid response to cope with accelerating the surveillance demands of SARS-CoV-2 while also maintaining accuracy.
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Affiliation(s)
- Sergio Buenestado-Serrano
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Escuela de doctorado, Universidad de Alcalá, Pl. de San Diego, s/n, Alcalá de Henares, 28801 Madrid, Spain
| | - Marta Herranz
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain
| | - Álvaro Otero-Sobrino
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain
| | - Andrea Molero-Salinas
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain
| | - Cristina Rodríguez-Grande
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain
| | - Amadeo Sanz-Pérez
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain
| | - María José Durán Galván
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain
| | - Pilar Catalán
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain
| | - Roberto Alonso
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Department of medicine, Universidad Complutense, Pl. de Ramón y Cajal, s/n, 28040 Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain; Department of medicine, Universidad Complutense, Pl. de Ramón y Cajal, s/n, 28040 Madrid, Spain
| | - Laura Pérez-Lago
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain.
| | - Darío García de Viedma
- Clinical Microbiology and Infectious Diseases service, Hospital General Universitario Gregorio Marañón, C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C. Dr. Esquerdo, 46, 28007 Madrid, Spain; Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain.
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Freedman MB, Kim YJ, Kaur R, Jain BV, Adegunsoye AO, Chung YC, DeLisa JA, Gardner JM, Gordon HS, Greenberg JA, Kaul M, Khouzam N, Labedz SL, Mokhlesi B, Rintz J, Rubinstein I, Taylor A, Vines DL, Ziauddin L, Gerald LB, Krishnan JA. Home Oxygen After Hospitalization for COVID-19: Results From the Multi-Center OXFORD Study. Respir Care 2024; 69:281-289. [PMID: 38176902 PMCID: PMC10984596 DOI: 10.4187/respcare.11436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/16/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND In the first months of the pandemic, prior to the introduction of proven-effective treatments, 15-37% of patients hospitalized with COVID-19 were discharged on home oxygen. After proven-effective treatments for acute COVID-19 were established by evidence-based guidelines, little remains known about home oxygen requirements following hospitalization for COVID-19. METHODS This was a retrospective, multi-center cohort study of subjects hospitalized for COVID-19 between October 2020-September 2021 at 3 academic health centers. Information was abstracted from electronic health records at the index hospitalization and for 60 d after discharge. The World Health Organization COVID-19 Clinical Progression Scale score was used to identify patients with severe COVID-19. RESULTS Of 517 subjects (mean age 58 y, 47% female, 42% Black, 36% Hispanic, 22% with severe COVID-19), 81% were treated with systemic corticosteroids, 61% with remdesivir, and 2.5% with tocilizumab. About one quarter of subjects were discharged on home oxygen (26% [95% CI 22-29]). Older age (adjusted odds ratio [aOR] 1.02 per 5 y [95% CI 1.02-1.02]), higher body mass index (aOR 1.02 per kg/m2 [1.00-1.04]), diabetes (yes vs no, aOR 1.73 [1.46-2.02]), severe COVID-19 (vs moderate, aOR 3.19 [2.19-4.64]), and treatment with systemic corticosteroids (yes vs no, aOR 30.63 [4.51-208.17]) were associated with an increased odds of discharge on home oxygen. Comorbid hypertension (yes vs no, aOR 0.71 [0.66-0.77) was associated with a decreased odds of home oxygen. Within 60 d of hospital discharge, 50% had documentation of pulse oximetry; in this group, home oxygen was discontinued in 46%. CONCLUSIONS About one in 4 subjects were prescribed home oxygen after hospitalization for COVID-19, even after guidelines established proven-effective treatments for acute illness. Evidence-based strategies to reduce the requirement for home oxygen in patients hospitalized for COVID-19 are needed.
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Affiliation(s)
- Michael B Freedman
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois.
| | - Yoo Jin Kim
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Ramandeep Kaur
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Bijal V Jain
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Ayodeji O Adegunsoye
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Yu-Che Chung
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Julie A DeLisa
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Jessica M Gardner
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Howard S Gordon
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Jared A Greenberg
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Malvika Kaul
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Nader Khouzam
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Stephanie L Labedz
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Babak Mokhlesi
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Jacob Rintz
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Israel Rubinstein
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Analisa Taylor
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - David L Vines
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Lubna Ziauddin
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Lynn B Gerald
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
| | - Jerry A Krishnan
- Drs Freedman and Kaul are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Kim, Labedz, and Taylor and Ms Ziauddin are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Kaur and Vines and Mr Rintz are affiliated with Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University, Chicago, Illinois. Dr Jain is affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Division of Hospital Medicine, Department of Medicine, Northwestern University, Chicago, Illinois. Dr Adegunsoye is affiliated with Section of Pulmonary Critical and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois. Dr Chung and Ms DeLisa are affiliated with Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois. Ms Gardner is affiliated with Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gordon and Khouzam are affiliated with Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Academic Internal Medicine and Geriatrics, Department of Medicine, University of Illinois Chicago, Chicago, Illinois. Drs Greenberg and Mokhlesi are affiliated with Division Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Rush University, Chicago, Illinois. Dr Rubinstein is affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois; and Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois. Drs Gerald and Krishnan are affiliated with Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois Chicago, Chicago, Illinois; and Office of Population Health Sciences, University of Illinois Hospital and Health Sciences System, Chicago, Illinois
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9
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Kang H, Lee J, Jung J, Oh EJ. Humoral Response Kinetics and Cross-Immunity in Hospitalized Patients with SARS-CoV-2 WT, Delta, or Omicron Infections: A Comparison between Vaccinated and Unvaccinated Cohorts. Vaccines (Basel) 2023; 11:1803. [PMID: 38140207 PMCID: PMC10747008 DOI: 10.3390/vaccines11121803] [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: 11/06/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
With the ongoing evolution of severe acute respiratory virus-2 (SARS-CoV-2), the number of confirmed COVID-19 cases continues to rise. This study aims to investigate the impact of vaccination status, SARS-CoV-2 variants, and disease severity on the humoral immune response, including cross-neutralizing activity, in hospitalized COVID-19 patients. This retrospective cohort study involved 122 symptomatic COVID-19 patients hospitalized in a single center. Patients were categorized based on the causative specific SARS-CoV-2 variants (33 wild-type (WT), 54 Delta and 35 Omicron) and their vaccination history. Sequential samples were collected to assess binding antibody responses (anti-S/RBD and anti-N) and surrogate virus neutralization tests (sVNTs) against WT, Omicron BA.1, and BA.4/5. The vaccinated breakthrough infection group (V) exhibited higher levels of anti-S/RBD compared to the variant-matched unvaccinated groups (UVs). The Delta infection resulted in a more rapid production of anti-S/RBD levels compared to infections with WT or Omicron variants. Unvaccinated severe WT or Delta infections had higher anti-S/RBD levels compared to mild cases, but this was not the case with Omicron infection. In vaccinated patients, there was no difference in antibody levels between mild and severe infections. Both Delta (V) and Omicron (V) groups showed strong cross-neutralizing activity against WT and Omicron (BA.1 and BA.4/5), ranging from 79.3% to 97.0%. WT (UV) and Delta (UV) infections had reduced neutralizing activity against BA.1 (0.8% to 12.0%) and BA.4/5 (32.8% to 41.0%). Interestingly, patients who received vaccines based on the ancestral spike exhibited positive neutralizing activity against BA.4/5, even though none of the study participants had been exposed to BA.4/5 and it is antigenically more advanced. Our findings suggest that a previous vaccination enhanced the humoral immune response and broadened cross-neutralizing activity to SARS-CoV-2 variants in hospitalized COVID-19 patients.
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Affiliation(s)
- Hyunhye Kang
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (H.K.); (J.J.)
- Research and Development Institute for In Vitro Diagnostic Medical Devices, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jihyun Lee
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea;
| | - Jin Jung
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (H.K.); (J.J.)
- Research and Development Institute for In Vitro Diagnostic Medical Devices, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Eun-Jee Oh
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (H.K.); (J.J.)
- Research and Development Institute for In Vitro Diagnostic Medical Devices, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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10
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Fricke C, Pfaff F, Ulrich L, Halwe NJ, Schön J, Timm L, Hoffmann W, Rauch S, Petsch B, Hoffmann D, Beer M, Corleis B, Dorhoi A. SARS-CoV-2 variants of concern elicit divergent early immune responses in hACE2 transgenic mice. Eur J Immunol 2023; 53:e2250332. [PMID: 37609807 DOI: 10.1002/eji.202250332] [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: 12/13/2022] [Revised: 07/20/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
Knowledge about early immunity to SARS-CoV-2 variants of concern mainly comes from the analysis of human blood. Such data provide limited information about host responses at the site of infection and largely miss the initial events. To gain insights into compartmentalization and the early dynamics of host responses to different SARS-CoV-2 variants, we utilized human angiotensin converting enzyme 2 (hACE2) transgenic mice and tracked immune changes during the first days after infection by RNAseq, multiplex assays, and flow cytometry. Viral challenge infection led to divergent viral loads in the lungs, distinct inflammatory patterns, and innate immune cell accumulation in response to ancestral SARS-CoV-2, Beta (B.1.351) and Delta (B.1.617.2) variant of concern (VOC). Compared to other SARS-CoV-2 variants, infection with Beta (B.1.351) VOC spread promptly to the lungs, leading to increased inflammatory responses. SARS-CoV-2-specific antibodies and T cells developed within the first 7 days postinfection and were required to reduce viral spread and replication. Our studies show that VOCs differentially trigger transcriptional profiles and inflammation. This information contributes to the basic understanding of immune responses immediately postexposure to SARS-CoV-2 and is relevant for developing pan-VOC interventions including prophylactic vaccines.
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Affiliation(s)
- Charlie Fricke
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Lorenz Ulrich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Nico Joel Halwe
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jacob Schön
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Laura Timm
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Weda Hoffmann
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | | | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Björn Corleis
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Anca Dorhoi
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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11
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Torabi SH, Riahi SM, Ebrahimzadeh A, Salmani F. Changes in symptoms and characteristics of COVID-19 patients across different variants: two years study using neural network analysis. BMC Infect Dis 2023; 23:838. [PMID: 38017395 PMCID: PMC10683353 DOI: 10.1186/s12879-023-08813-9] [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] [Received: 05/23/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Considering the fact that COVID-19 has undergone various changes over time, its symptoms have also varied. The aim of this study is to describe and compare the changes in personal characteristics, symptoms, and underlying conditions of individuals infected with different strains of COVID-19. METHODS This descriptive-analytical study was conducted on 46,747 patients who underwent PCR testing during a two-year period from February 22, 2020 to February 23, 2022, in South Khorasan province, Iran. Patient characteristics and symptoms were extracted based on self-report and the information system. The data were analyzed using logistic regression and artificial neural network approaches. The R software was used for analysis and a significance level of 0.05 was considered for the tests. RESULTS Among the 46,747 cases analyzed, 23,239 (49.7%) were male, and the mean age was 51.48 ± 21.41 years. There was a significant difference in symptoms among different variants of the disease (p < 0.001). The factors with a significant positive association were myalgia (OR: 2.04; 95% CI, 1.76 - 2.36), cough (OR: 1.93; 95% CI, 1.68-2.22), and taste or smell disorder (OR: 2.62; 95% CI, 2.1 - 3.28). Additionally, aging was found to increase the likelihood of testing positive across the six periods. CONCLUSION We found that older age, myalgia, cough and taste/smell disorder are better factors compared to dyspnea or high body temperature, for identifying a COVID-19 patient. As the disease evolved, chills and diarrhea, demonstrated prognostic strength as in Omicron.
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Affiliation(s)
- Seyed Hossein Torabi
- School of Medicine, Birjand University of Medical Sciences, Birjand, South Khorasan Province, Iran
| | - Seyed Mohammad Riahi
- Epidemiology Department of Family and Community Medicine, School of Medicine Cardiovascular Diseases Research Center, Birjand University of Medical Sciences, Birjand, South Khorasan Province, Iran
| | - Azadeh Ebrahimzadeh
- Department of Infectious Diseases, School of Medicine Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, South Khorasan Province, Iran
| | - Fatemeh Salmani
- Department of Epidemiology and Biostatistics, School of Health Social Determinants of Health Research Center, Birjand University of Medical Sciences, Birjand, South Khorasan Province, Iran.
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12
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Lu Y, Ye Z, Liu X, Zhou L, Ding X, Hou Y. Role of SARS‑CoV‑2 nucleocapsid protein in affecting immune cells and insights on its molecular mechanisms. Exp Ther Med 2023; 26:504. [PMID: 37822585 PMCID: PMC10562965 DOI: 10.3892/etm.2023.12203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/07/2023] [Indexed: 10/13/2023] Open
Abstract
The present study aimed to explore the immune regulatory function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and related mechanisms. In a series of protein activity experiments, SARS-CoV-2 N protein promoted proliferation of three immune cell lines: mouse Raw264.7, human Jurkat and human Raji in a dose-dependent manner. A total of 10 µg/ml N protein could significantly change cell cycle progression of the aforementioned three immune cell lines and could promote quick entry of Raw264.7 cells into G2/M phase from S phase to achieve rapid growth. Additionally, the N protein could also stimulate Raw264.7 cells to secrete a number of proinflammatory factors such as TNF-α, IL-6 and IL-10. RNA sequencing analysis indicated that the N protein changed the expression of certain genes involved in immune-related functions and four important signaling pathways, including JAK-STAT, TNF, NF-κB and MAPK signaling pathways, which suggested that the N protein may not only regulate the expression of genes involved in the process of resisting viral infection in macrophages of the immune system, but also change cellular signal processing.
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Affiliation(s)
- Yan Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Ziyu Ye
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Xinlan Liu
- Key Laboratory of Nanchong City of Ecological Environment Protection and Pollution Prevention in Jialing River Basin, College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Liqian Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Xiang Ding
- Key Laboratory of Nanchong City of Ecological Environment Protection and Pollution Prevention in Jialing River Basin, College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan 637009, P.R. China
| | - Yiling Hou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, Sichuan 637009, P.R. China
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13
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Longsompurana P, Rungrotmongkol T, Plongthongkum N, Wangkanont K, Wolschann P, Poo-arporn RP. Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2. PLoS One 2023; 18:e0293263. [PMID: 37874836 PMCID: PMC10597523 DOI: 10.1371/journal.pone.0293263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
The COVID-19 pandemic has created an urgent need for effective therapeutic and diagnostic strategies to manage the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the emergence of numerous variants of concern (VOCs) has made it challenging to develop targeted therapies that are broadly specific in neutralizing the virus. In this study, we aimed to develop neutralizing nanobodies (Nbs) using computational techniques that can effectively neutralize the receptor-binding domain (RBD) of SARS-CoV-2 VOCs. We evaluated the performance of different protein-protein docking programs and identified HDOCK as the most suitable program for Nb/RBD docking with high accuracy. Using this approach, we designed 14 novel Nbs with high binding affinity to the VOC RBDs. The Nbs were engineered with mutated amino acids that interacted with key amino acids of the RBDs, resulting in higher binding affinity than human angiotensin-converting enzyme 2 (ACE2) and other viral RBDs or haemagglutinins (HAs). The successful development of these Nbs demonstrates the potential of molecular modeling as a low-cost and time-efficient method for engineering effective Nbs against SARS-CoV-2. The engineered Nbs have the potential to be employed in RBD-neutralizing assays, facilitating the identification of novel treatment, prevention, and diagnostic strategies against SARS-CoV-2.
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Affiliation(s)
- Phoomintara Longsompurana
- Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Nongluk Plongthongkum
- Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Peter Wolschann
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Rungtiva P. Poo-arporn
- Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
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14
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Du T, Gao C, Lu S, Liu Q, Yang Y, Yu W, Li W, Qiao Sun Y, Tang C, Wang J, Gao J, Zhang Y, Luo F, Yang Y, Yang YG, Peng X. Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1014-1029. [PMID: 37451436 PMCID: PMC10928377 DOI: 10.1016/j.gpb.2023.06.002] [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: 01/25/2023] [Revised: 04/27/2023] [Accepted: 06/04/2023] [Indexed: 07/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the persistent coronavirus disease 2019 (COVID-19) pandemic, which has resulted in millions of deaths worldwide and brought an enormous public health and global economic burden. The recurring global wave of infections has been exacerbated by growing variants of SARS-CoV-2. In this study, the virological characteristics of the original SARS-CoV-2 strain and its variants of concern (VOCs; including Alpha, Beta, and Delta) in vitro, as well as differential transcriptomic landscapes in multiple organs (lung, right ventricle, blood, cerebral cortex, and cerebellum) from the infected rhesus macaques, were elucidated. The original strain of SARS-CoV-2 caused a stronger innate immune response in host cells, and its VOCs markedly increased the levels of subgenomic RNAs, such as N, Orf9b, Orf6, and Orf7ab, which are known as the innate immune antagonists and the inhibitors of antiviral factors. Intriguingly, the original SARS-CoV-2 strain and Alpha variant induced larger alteration of RNA abundance in tissues of rhesus monkeys than Beta and Delta variants did. Moreover, a hyperinflammatory state and active immune response were shown in the right ventricles of rhesus monkeys by the up-regulation of inflammation- and immune-related RNAs. Furthermore, peripheral blood may mediate signaling transmission among tissues to coordinate the molecular changes in the infected individuals. Collectively, these data provide insights into the pathogenesis of COVID-19 at the early stage of infection by the original SARS-CoV-2 strain and its VOCs.
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Affiliation(s)
- Tingfu Du
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China; State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Chunchun Gao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuaiyao Lu
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Qianlan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Yang
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Wenhai Yu
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Wenjie Li
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yong Qiao Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Cong Tang
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Junbin Wang
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Jiahong Gao
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Yong Zhang
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Fangyu Luo
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiaozhong Peng
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China; State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China; Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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15
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Peissert F, Pedotti M, Corbellari R, Simonelli L, De Gasparo R, Tamagnini E, Plüss L, Elsayed A, Matasci M, De Luca R, Cassaniti I, Sammartino JC, Piralla A, Baldanti F, Neri D, Varani L. Adapting Neutralizing Antibodies to Viral Variants by Structure-Guided Affinity Maturation Using Phage Display Technology. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2300088. [PMID: 37829677 PMCID: PMC10566804 DOI: 10.1002/gch2.202300088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Indexed: 10/14/2023]
Abstract
Neutralizing monoclonal antibodies have achieved great efficacy and safety for the treatment of numerous infectious diseases. However, their neutralization potency is often rapidly lost when the target antigen mutates. Instead of isolating new antibodies each time a pathogen variant arises, it can be attractive to adapt existing antibodies, making them active against the new variant. Potential benefits of this approach include reduced development time, cost, and regulatory burden. Here a methodology is described to rapidly evolve neutralizing antibodies of proven activity, improving their function against new pathogen variants without losing efficacy against previous ones. The reported procedure is based on structure-guided affinity maturation using combinatorial mutagenesis and phage display technology. Its use against the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is demonstrated, but it is suitable for any other pathogen. As proof of concept, the method is applied to CoV-X2, a human bispecific antibody that binds with high affinity to the early SARS-CoV-2 variants but lost neutralization potency against Delta. Antibodies emerging from the affinity maturation selection exhibit significantly improved neutralization potency against Delta and no loss of efficacy against the other viral sequences tested. These results illustrate the potential application of structure-guided affinity maturation in facilitating the rapid adaptation of neutralizing antibodies to pathogen variants.
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Affiliation(s)
| | - Mattia Pedotti
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | | | - Luca Simonelli
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Raoul De Gasparo
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Elia Tamagnini
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Louis Plüss
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
| | | | | | | | - Irene Cassaniti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Jose’ Camilla Sammartino
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Antonio Piralla
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Fausto Baldanti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
- Department of Clinical Surgical Diagnostic and Pediatric SciencesUniversità degli Studi di PaviaPavia27100Italy
| | - Dario Neri
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
- Philogen SpALocalità Bellaria 35Sovicille (SI)53018Italy
| | - Luca Varani
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
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16
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De Vito A, Colpani A, Poliseno M, Diella L, Ieva FRP, Belati A, Papale R, Babudieri S, De Santis L, Saracino A, Lo Caputo S, Madeddu G. What Is the Efficacy of Sotrovimab in Reducing Disease Progression and Death in People with COVID-19 during the Omicron Era? Answers from a Real-Life Study. Viruses 2023; 15:1757. [PMID: 37632099 PMCID: PMC10458484 DOI: 10.3390/v15081757] [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: 07/19/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
(1) Introduction: Since May 2021, sotrovimab has been available in Italy for early treatment of SARS-CoV-2 infection and to prevent disease progression. However, some in vitro studies have questioned its efficacy on Omicron variants. Therefore, we aim to further investigate the efficacy of sotrovimab in real-life settings. (2) Methods: We conducted a retrospective study collecting medical records of people with SARS-CoV-2 infection evaluated in the infectious diseases units of Sassari, Foggia, and Bari, Italy. We included people with SARS-CoV-2 infection treated with sotrovimab and people who did not receive any treatment in 2022. The primary study outcome was to evaluate the efficacy of sotrovimab in reducing disease progression (defined as the necessity of starting oxygen supplementation) and COVID-19-related death. The secondary outcome was to evaluate the safety of sotrovimab. (3) Results: We included 689 people; of them, 341 were treated with sotrovimab, while 348 did not receive any treatment. Overall, we registered 161 (23.4%) disease progressions and 65 (9.4%) deaths, with a significant difference between treated and not-treated people (p < 0.001). In the multivariate logistic regression, increasing age [OR for ten years increasing age 1.23 (95%CI 1.04-1.45)] was associated with a higher risk of disease progression. In addition, cardiovascular disease [OR 1.69 (1.01-2.80), fever [OR 3.88 (95%CI 2.35-6.38)], and dyspnea [OR 7.24 (95%CI 4.17-12.58)] were associated with an increased risk of disease progression. In contrast, vaccination [OR 0.21 (95%CI 0.12-0.37)] and sotrovimab administration [OR 0.05 (95%CI 0.02-0.11)] were associated with a lower risk of developing severe COVID-19. Regarding mortality, people with older age [OR for ten years increasing age 1.36 (95%CI 1.09-1.69)] had a higher risk of death. In addition, in the multivariate analysis, cardiovascular disease lost statistical significance, while people on chemotherapy for haematological cancer [OR 4.07 (95%CI 1.45-11.4)] and those with dyspnea at diagnosis [OR 3.63 (95%CI 2.02-6.50)] had an increased risk of death. In contrast, vaccination [OR 0.37 (95%CI 0.20-0.68)] and sotrovimab treatment [OR 0.16 (95%CI 0.06-0.42)] were associated with lower risk. Only two adverse events were reported; one person complained of diarrhoea a few hours after sotrovimab administration, and one had an allergic reaction with cutaneous rash and itching. (4) Conclusions: Our study showed that sotrovimab treatment was associated with a reduction of the risk of disease progression and death in SARS-CoV-2-infected people, 70% of whom were over 65 years and a with high vaccination rate, with excellent safety. Therefore, our results reinforce the evidence about the efficacy and safety of sotrovimab during the Omicron era in a real-world setting.
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Affiliation(s)
- Andrea De Vito
- Unit of Infectious Diseases, Department of Medicine, Surgery, and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (G.M.)
| | - Agnese Colpani
- Unit of Infectious Diseases, Department of Medicine, Surgery, and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (G.M.)
| | - Mariacristina Poliseno
- S.C. Malattie Infettive, Dipartimento di Medicina Clinica e Sperimentale, University of Foggia, 71100 Foggia, Italy; (M.P.); (S.L.C.)
| | - Lucia Diella
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area—(DiMePRe-J), University of Bari “Aldo Moro”, Piazza Giulio Cesare n. 11, 70100 Bari, Italy (A.B.); (L.D.S.); (A.S.)
| | - Francesco Rosario Paolo Ieva
- S.C. Malattie Infettive, Dipartimento di Medicina Clinica e Sperimentale, University of Foggia, 71100 Foggia, Italy; (M.P.); (S.L.C.)
| | - Alessandra Belati
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area—(DiMePRe-J), University of Bari “Aldo Moro”, Piazza Giulio Cesare n. 11, 70100 Bari, Italy (A.B.); (L.D.S.); (A.S.)
| | - Roberto Papale
- S.C. Malattie Infettive, Dipartimento di Medicina Clinica e Sperimentale, University of Foggia, 71100 Foggia, Italy; (M.P.); (S.L.C.)
| | - Sergio Babudieri
- Unit of Infectious Diseases, Department of Medicine, Surgery, and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (G.M.)
| | - Laura De Santis
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area—(DiMePRe-J), University of Bari “Aldo Moro”, Piazza Giulio Cesare n. 11, 70100 Bari, Italy (A.B.); (L.D.S.); (A.S.)
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area—(DiMePRe-J), University of Bari “Aldo Moro”, Piazza Giulio Cesare n. 11, 70100 Bari, Italy (A.B.); (L.D.S.); (A.S.)
| | - Sergio Lo Caputo
- S.C. Malattie Infettive, Dipartimento di Medicina Clinica e Sperimentale, University of Foggia, 71100 Foggia, Italy; (M.P.); (S.L.C.)
| | - Giordano Madeddu
- Unit of Infectious Diseases, Department of Medicine, Surgery, and Pharmacy, University of Sassari, 07100 Sassari, Italy; (A.C.); (G.M.)
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17
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Liang T, Xiao S, Wu Z, Lv X, Liu S, Hu M, Li G, Li P, Ma X. Phenothiazines Inhibit SARS-CoV-2 Entry through Targeting Spike Protein. Viruses 2023; 15:1666. [PMID: 37632009 PMCID: PMC10458444 DOI: 10.3390/v15081666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Novel coronavirus disease 2019 (COVID-19), a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has brought an unprecedented public health crisis and continues to threaten humanity due to the persistent emergence of new variants. Therefore, developing more effective and broad-spectrum therapeutic and prophylactic drugs against infection by SARS-CoV-2 and its variants, as well as future emerging CoVs, is urgently needed. In this study, we screened several US FDA-approved drugs and identified phenothiazine derivatives with the ability to potently inhibit the infection of pseudotyped SARS-CoV-2 and distinct variants of concern (VOCs), including B.1.617.2 (Delta) and currently circulating Omicron sublineages XBB and BQ.1.1, as well as pseudotyped SARS-CoV and MERS-CoV. Mechanistic studies suggested that phenothiazines predominantly inhibited SARS-CoV-2 pseudovirus (PsV) infection at the early stage and potentially bound to the spike (S) protein of SARS-CoV-2, which may prevent the proteolytic cleavage of the S protein, thereby exhibiting inhibitory activity against SARS-CoV-2 infection. In summary, our findings suggest that phenothiazines can serve as a potential broad-spectrum therapeutic drug for the treatment of SARS-CoV-2 infection as well as the infection of future emerging human coronaviruses (HCoVs).
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Affiliation(s)
- Taizhen Liang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (T.L.); (S.X.); (S.L.); (M.H.); (G.L.); (P.L.)
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
| | - Shiqi Xiao
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (T.L.); (S.X.); (S.L.); (M.H.); (G.L.); (P.L.)
| | - Ziyao Wu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China;
| | - Xi Lv
- School of Medicine, South China University of Technology, Guangzhou 510006, China;
| | - Sen Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (T.L.); (S.X.); (S.L.); (M.H.); (G.L.); (P.L.)
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Meilin Hu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (T.L.); (S.X.); (S.L.); (M.H.); (G.L.); (P.L.)
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
| | - Guojie Li
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (T.L.); (S.X.); (S.L.); (M.H.); (G.L.); (P.L.)
| | - Peiwen Li
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (T.L.); (S.X.); (S.L.); (M.H.); (G.L.); (P.L.)
| | - Xiancai Ma
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (T.L.); (S.X.); (S.L.); (M.H.); (G.L.); (P.L.)
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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18
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Lista F, Peragallo MS, Biselli R, De Santis R, Mariotti S, Nisini R, D'Amelio R. Have Diagnostics, Therapies, and Vaccines Made the Difference in the Pandemic Evolution of COVID-19 in Comparison with "Spanish Flu"? Pathogens 2023; 12:868. [PMID: 37513715 PMCID: PMC10384375 DOI: 10.3390/pathogens12070868] [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: 04/26/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
In 1918 many countries, but not Spain, were fighting World War I. Spanish press could report about the diffusion and severity of a new infection without censorship for the first-time, so that this pandemic is commonly defined as "Spanish flu", even though Spain was not its place of origin. "Spanish flu" was one of the deadliest pandemics in history and has been frequently compared with the coronavirus disease (COVID)-19 pandemic. These pandemics share similarities, being both caused by highly variable and transmissible respiratory RNA viruses, and diversity, represented by diagnostics, therapies, and especially vaccines, which were made rapidly available for COVID-19, but not for "Spanish flu". Most comparison studies have been carried out in the first period of COVID-19, when these resources were either not yet available or their use had not long started. Conversely, we wanted to analyze the role that the advanced diagnostics, anti-viral agents, including monoclonal antibodies, and innovative COVID-19 vaccines, may have had in the pandemic containment. Early diagnosis, therapies, and anti-COVID-19 vaccines have markedly reduced the pandemic severity and mortality, thus preventing the collapse of the public health services. However, their influence on the reduction of infections and re-infections, thus on the transition from pandemic to endemic condition, appears to be of minor relevance. The high viral variability of influenza and coronavirus may probably be contained by the development of universal vaccines, which are not easy to be obtained. The only effective weapon still remains the disease prevention, to be achieved with the reduction of promiscuity between the animal reservoirs of these zoonotic diseases and humans.
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Affiliation(s)
- Florigio Lista
- Istituto di Scienze Biomediche della Difesa, Ispettorato Generale della Sanità Militare, Stato Maggiore della Difesa, 00184 Roma, Italy
| | - Mario Stefano Peragallo
- Centro Studi e Ricerche di Sanità e Veterinaria, Comando Logistico dell'Esercito, 00184 Roma, Italy
| | - Roberto Biselli
- Ispettorato Generale della Sanità Militare, Stato Maggiore della Difesa, 00184 Roma, Italy
| | - Riccardo De Santis
- Istituto di Scienze Biomediche della Difesa, Ispettorato Generale della Sanità Militare, Stato Maggiore della Difesa, 00184 Roma, Italy
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza, Università di Roma, 00161 Roma, Italy
| | - Sabrina Mariotti
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Roberto Nisini
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Raffaele D'Amelio
- Dipartimento di Medicina Clinica e Molecolare, Sapienza, Università di Roma, 00198 Roma, Italy
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19
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Russo E, Corrao S, Di Gaudio F, Alberti G, Caprnda M, Kubatka P, Kruzliak P, Miceli V, Conaldi PG, Borlongan CV, La Rocca G. Facing the Challenges in the COVID-19 Pandemic Era: From Standard Treatments to the Umbilical Cord-Derived Mesenchymal Stromal Cells as a New Therapeutic Strategy. Cells 2023; 12:1664. [PMID: 37371134 DOI: 10.3390/cells12121664] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which counts more than 650 million cases and more than 6.6 million of deaths worldwide, affects the respiratory system with typical symptoms such as fever, cough, sore throat, acute respiratory distress syndrome (ARDS), and fatigue. Other nonpulmonary manifestations are related with abnormal inflammatory response, the "cytokine storm", that could lead to a multiorgan disease and to death. Evolution of effective vaccines against SARS-CoV-2 provided multiple options to prevent the infection, but the treatment of the severe forms remains difficult to manage. The cytokine storm is usually counteracted with standard medical care and anti-inflammatory drugs, but researchers moved forward their studies on new strategies based on cell therapy approaches. The perinatal tissues, such as placental membranes, amniotic fluid, and umbilical cord derivatives, are enriched in mesenchymal stromal cells (MSCs) that exert a well-known anti-inflammatory role, immune response modulation, and tissue repair. In this review, we focused on umbilical-cord-derived MSCs (UC-MSCs) used in in vitro and in vivo studies in order to evaluate the weakening of the severe symptoms, and on recent clinical trials from different databases, supporting the favorable potential of UC-MSCs as therapeutic strategy.
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Affiliation(s)
- Eleonora Russo
- Section of Histology and Embryology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
| | - Simona Corrao
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per per i Trapianti e Terapie Ad Alta Specializzazione), 90127 Palermo, Italy
| | | | - Giusi Alberti
- Section of Histology and Embryology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
| | - Martin Caprnda
- 1st Department of Internal Medicine, Faculty of Medicine, Comenius University, University Hospital Bratislava, 81499 Bratislava, Slovakia
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03649 Martin, Slovakia
| | - Peter Kruzliak
- Research and Development Services, Pradlacka 18, 61300 Brno, Czech Republic
| | - Vitale Miceli
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per per i Trapianti e Terapie Ad Alta Specializzazione), 90127 Palermo, Italy
| | - Pier Giulio Conaldi
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per per i Trapianti e Terapie Ad Alta Specializzazione), 90127 Palermo, Italy
| | - Cesario Venturina Borlongan
- Department of Neurosurgery and Brain Repair, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Giampiero La Rocca
- Section of Histology and Embryology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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20
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Diarimalala RO, Wei Y, Hu D, Hu K. Inflammasomes during SARS-CoV-2 infection and development of their corresponding inhibitors. Front Cell Infect Microbiol 2023; 13:1218039. [PMID: 37360532 PMCID: PMC10288989 DOI: 10.3389/fcimb.2023.1218039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Corona Virus Disease 2019 (COVID-19) continues to be a burden for human health since its outbreak in Wuhan, China in December 2019. Recently, the emergence of new variants of concerns (VOCs) is challenging for vaccines and drugs efficiency. In severe cases, SARS-CoV-2 provokes inappropriate hyperinflammatory immune responses leading to acute respiratory distress syndrome (ARDS) and even death. This process is regulated by inflammasomes which are activated after binding of the viral spike (S) protein to cellular angiotensin-converting enzyme 2 (ACE2) receptor and triggers innate immune responses. Therefore, the formation of "cytokines storm" leads to tissue damage and organ failure. NOD-like receptor family pyrin domain containing 3 (NLRP3) is the best studied inflammasome known to be activated during SARS-CoV-2 infection. However, some studies suggest that SARS-CoV-2 infection is associated with other inflammasomes as well; such as NLRP1, absent in melanoma-2 (AIM-2), caspase-4 and -8 which were mostly found during dsRNA virus or bacteria infection. Multiple inflammasome inhibitors that exist for other non-infectious diseases have the potential to be used to treat severe SARS-CoV-2 complications. Some of them have showed quite encouraging results during pre- and clinical trials. Nevertheless, further studies are in need for the understanding and targeting of SARS-Cov-2-induced inflammasomes; mostly an update of its role during the new VOCs infection is necessary. Hence, this review highlights all reported inflammasomes involved in SARS-CoV-2 infection and their potential inhibitors including NLRP3- and Gasdermin D (GSDMD)-inhibitors. Further strategies such as immunomodulators and siRNA are also discussed. As highly related to COVID-19 severe cases, developing inflammasome inhibitors holds a promise to treat severe COVID-19 syndrome effectively and reduce mortality.
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21
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Woods H, Schiano DL, Aguirre JI, Ledwitch KV, McDonald EF, Voehler M, Meiler J, Schoeder CT. Computational modeling and prediction of deletion mutants. Structure 2023; 31:713-723.e3. [PMID: 37119820 PMCID: PMC10247520 DOI: 10.1016/j.str.2023.04.005] [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: 11/16/2022] [Revised: 03/02/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
In-frame deletion mutations can result in disease. The impact of these mutations on protein structure and subsequent functional changes remain understudied, partially due to the lack of comprehensive datasets including a structural readout. In addition, the recent breakthrough in structure prediction through deep learning demands an update of computational deletion mutation prediction. In this study, we deleted individually every residue of a small α-helical sterile alpha motif domain and investigated the structural and thermodynamic changes using 2D NMR spectroscopy and differential scanning fluorimetry. Then, we tested computational protocols to model and classify observed deletion mutants. We show a method using AlphaFold2 followed by RosettaRelax performs the best overall. In addition, a metric containing pLDDT values and Rosetta ΔΔG is most reliable in classifying tolerated deletion mutations. We further test this method on other datasets and show they hold for proteins known to harbor disease-causing deletion mutations.
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Affiliation(s)
- Hope Woods
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA
| | - Dominic L Schiano
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan I Aguirre
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Kaitlyn V Ledwitch
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Eli F McDonald
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Markus Voehler
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jens Meiler
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Institute for Drug Discovery, Leipzig University Medical School, 04103 Leipzig, Germany.
| | - Clara T Schoeder
- Center of Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Institute for Drug Discovery, Leipzig University Medical School, 04103 Leipzig, Germany.
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22
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Meletis G, Tychala A, Ntritsos G, Verrou E, Savvidou F, Dermitzakis I, Chatzidimitriou A, Gkeka I, Fyntanidou B, Gkarmiri S, Tzallas AT, Protonotariou E, Makedou K, Tsalikakis DG, Skoura L. Variant-Related Differences in Laboratory Biomarkers among Patients Affected with Alpha, Delta and Omicron: A Retrospective Whole Viral Genome Sequencing and Hospital-Setting Cohort Study. Biomedicines 2023; 11:biomedicines11041143. [PMID: 37189760 DOI: 10.3390/biomedicines11041143] [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: 03/09/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
During the COVID-19 pandemic, different SARS-CoV-2 variants of concern (VOC) with specific characteristics have emerged and spread worldwide. At the same time, clinicians routinely evaluate the results of certain blood tests upon patient admission as well as during hospitalization to assess disease severity and the overall patient status. In the present study, we searched for significant cell blood count and biomarker differences among patients affected with the Alpha, Delta and Omicron VOCs at admission. Data from 330 patients were retrieved regarding age, gender, VOC, cell blood count results (WBC, Neut%, Lymph%, Ig%, PLT), common biomarkers (D-dimers, urea, creatinine, SGOT, SGPT, CRP, IL-6, suPAR), ICU admission and death. Statistical analyses were performed using ANOVA, the Kruskal-Wallis test, two-way ANOVA, Chi-square, T-test, the Mann-Whitney test and logistic regression was performed where appropriate using SPSS v.28 and STATA 14. Age and VOC were significantly associated with hospitalization, whereas significant differences among VOC groups were found for WBC, PLT, Neut%, IL-6, creatinine, CRP, D-dimers and suPAR. Our analyses showed that throughout the current pandemic, not only the SARS-CoV-2 VOCs but also the laboratory parameters that are used to evaluate the patient's status at admission are subject to changes.
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Affiliation(s)
- Georgios Meletis
- Department of Microbiology, AHEPA University Hospital, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Areti Tychala
- Department of Microbiology, AHEPA University Hospital, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Georgios Ntritsos
- Department of Informatics and Telecommunications, School of Informatics and Telecommunications, University of Ioannina, 47100 Arta, Greece
- Department of Hygiene and Epidemiology, School of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Eleni Verrou
- School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Filio Savvidou
- School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Iasonas Dermitzakis
- School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Bioscience, Centre for Research and Technology Hellas, 6th km Charilaou-Thermi Rd., Thermi, 57001 Thessaloniki, Greece
| | - Ioanna Gkeka
- Department of Microbiology, AHEPA University Hospital, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Barbara Fyntanidou
- Department of Emergency Medicine, AHEPA University Hospital, 54636 Thessaloniki, Greece
| | - Sofia Gkarmiri
- Department of Emergency Medicine, AHEPA University Hospital, 54636 Thessaloniki, Greece
| | - Alexandros T Tzallas
- Department of Informatics and Telecommunications, School of Informatics and Telecommunications, University of Ioannina, 47100 Arta, Greece
| | - Efthymia Protonotariou
- Department of Microbiology, AHEPA University Hospital, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Kali Makedou
- Laboratory of Biochemistry, AHEPA University Hospital, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dimitrios G Tsalikakis
- Department of Electrical and Computer Engineering, University of Western Macedonia, 50131 Kozani, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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23
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Gao L, Li Y, He P, Chen Z, Yang H, Li F, Zhang S, Wang D, Wang G, Yang S, Gong L, Ding F, Ling M, Wang X, Ci L, Dai L, Gao GF, Huang T, Hu Z, Ying Z, Sun J, Zuo X. Safety and immunogenicity of a protein subunit COVID-19 vaccine (ZF2001) in healthy children and adolescents aged 3-17 years in China: a randomised, double-blind, placebo-controlled, phase 1 trial and an open-label, non-randomised, non-inferiority, phase 2 trial. THE LANCET. CHILD & ADOLESCENT HEALTH 2023; 7:269-279. [PMID: 36803632 PMCID: PMC9937662 DOI: 10.1016/s2352-4642(22)00376-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 02/19/2023]
Abstract
BACKGROUND ZF2001 is a recombinant protein subunit vaccine against SARS-CoV-2 that has been approved for use in China, Colombia, Indonesia, and Uzbekistan in adults aged 18 years or older, but not yet in children and adolescents younger than 18 years. We aimed to evaluate the safety and immunogenicity of ZF2001 in children and adolescents aged 3-17 years in China. METHODS The randomised, double-blind, placebo-controlled, phase 1 trial and the open-label, non-randomised, non-inferiority, phase 2 trial were done at the Xiangtan Center for Disease Control and Prevention (Hunan Province, China). Healthy children and adolescents aged 3-17 years, without a history of SARS-CoV-2 vaccination, without a history of COVID-19, without COVID-19 at the time of the study, and without contact with patients with confirmed or suspected COVID-19 were included in the phase 1 and phase 2 trials. In the phase 1 trial, participants were divided into three groups according to age (3-5 years, 6-11 years, and 12-17 years). Each group was randomly assigned (4:1), using block randomisation with five blocks, each with a block size of five, to receive three 25 μg doses of the vaccine, ZF2001, or placebo intramuscularly in the arm 30 days apart. The participants and investigators were masked to treatment allocation. In the phase 2 trial, participants received three 25 μg doses of ZF2001 30 days apart and remained stratified by age group. For phase 1, the primary endpoint was safety and the secondary endpoint was immunogenicity (humoral immune response on day 30 after the third vaccine dose: geometric mean titre [GMT] of prototype SARS-CoV-2 neutralising antibodies and seroconversion rate, and geometric mean concentration [GMC] of prototype SARS-CoV-2 receptor-binding domain [RBD]-binding IgG antibodies and seroconversion rate). For phase 2, the primary endpoint was the GMT of SARS-CoV-2 neutralising antibodies with seroconversion rate on day 14 after the third vaccine dose, and the secondary endpoints included the GMT of RBD-binding antibodies and seroconversion rate on day 14 after the third vaccine dose, the GMT of neutralising antibodies against the omicron BA.2 subvariant and seroconversion rate on day 14 after the third vaccine dose, and safety. Safety was analysed in participants who received at least one dose of the vaccine or placebo. Immunogenicity was analysed in the full-analysis set (ie, participants who received at least one dose and had antibody results) by intention to treat and in the per-protocol set (ie, participants who completed the whole vaccination course and had antibody results). Non-inferiority in the phase 2 trial (neutralising antibody titre of participants from this trial aged 3-17 years vs that of participants aged 18-59 years from a separate phase 3 trial) for clinical outcome assessment was based on the geometric mean ratio (GMR) and was considered met if the lower bound of the 95% CI for the GMR was 0·67 or greater. These trials are registered with ClinicalTrials.gov, NCT04961359 (phase 1) and NCT05109598 (phase 2). FINDINGS Between July 10 and Sept 4, 2021, 75 children and adolescents were randomly assigned to receive ZF2001 (n=60) or placebo (n=15) in the phase 1 trial and were included in safety and immunogenicity analyses. Between Nov 5, 2021, and Feb 14, 2022, 400 participants (130 aged 3-7 years, 210 aged 6-11 years, and 60 aged 12-17 years) were included in the phase 2 trial and were included in the safety analysis; six participants were excluded from the immunogenicity analyses. 25 (42%) of 60 participants in the ZF2001 group and seven (47%) of 15 participants in the placebo group in phase 1, and 179 (45%) of 400 participants in phase 2, had adverse events within 30 days after the third vaccination, without a significant difference between groups in phase 1. Most adverse events were grade 1 or 2 (73 [97%] of 75 in the phase 1 trial, and 391 [98%] of 400 in the phase 2 trial). One participant in the phase 1 trial and three in the phase 2 trial who received ZF2001 had serious adverse events. One serious adverse event (acute allergic dermatitis) in the phase 2 trial was possibly related to the vaccine. In the phase 1 trial, on day 30 after the third dose, in the ZF2001 group, seroconversion of neutralising antibodies against SARS-CoV-2 was observed in 56 (93%; 95% CI 84-98) of 60 participants, with a GMT of 176·5 (95% CI 118·6-262·8), and seroconversion of RBD-binding antibodies was observed in all 60 (100%; 95% CI 94-100) participants, with a GMC of 47·7 IU/mL (95% CI 40·1-56·6). In the phase 2 trial, on day 14 after the third dose, seroconversion of neutralising antibodies against SARS-CoV-2 was seen in 392 (99%; 95% CI 98-100) participants, with a GMT of 245·4 (95% CI 220·0-273·7), and seroconversion of RBD-binding antibodies was observed in all 394 (100%; 99-100) participants, with a GMT of 8021 (7366-8734). On day 14 after the third dose, seroconversion of neutralising antibodies against the omicron subvariant BA.2 was observed in 375 (95%; 95% CI 93-97) of 394 participants, with a GMT of 42·9 (95% CI 37·9-48·5). For the non-inferiority comparison of participants aged 3-17 years with those aged 18-59 years for SARS-CoV-2 neutralising antibodies, the adjusted GMR was 8·6 (95% CI 7·0-10·4), with the lower bound of the GMR greater than 0·67. INTERPRETATION ZF2001 is safe, well tolerated, and immunogenic in children and adolescents aged 3-17 years. Vaccine-elicited sera can neutralise the omicron BA.2 subvariant, but with reduced activity. The results support further studies of ZF2001 in children and adolescents. FUNDING Anhui Zhifei Longcom Biopharmaceutical and the Excellent Young Scientist Program from National Natural Science Foundation of China. TRANSLATION For the Chinese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Lidong Gao
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Yan Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Peng He
- National Institute for Food and Drug Control, Beijing, China
| | - Zhen Chen
- National Institute for Food and Drug Control, Beijing, China
| | - Huaiyu Yang
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Fangjun Li
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Siyuan Zhang
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Danni Wang
- Xiangtan Center for Disease Control and Prevention, Xiangtan, China
| | - Guangyan Wang
- Xiangtan Center for Disease Control and Prevention, Xiangtan, China
| | - Shilong Yang
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Lihui Gong
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Fan Ding
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Mengyu Ling
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Xilu Wang
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Leilei Ci
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Tao Huang
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Zhongyu Hu
- National Institute for Food and Drug Control, Beijing, China
| | - Zhifang Ying
- National Institute for Food and Drug Control, Beijing, China
| | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangzhou, China
| | - Xiaohu Zuo
- Anhui Zhifei Longcom Biopharmaceutical, Hefei, China.
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24
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Molnupiravir: A Versatile Prodrug against SARS-CoV-2 Variants. Metabolites 2023; 13:metabo13020309. [PMID: 36837928 PMCID: PMC9962121 DOI: 10.3390/metabo13020309] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The nucleoside analog β-D-N4-hydroxycytidine is the active metabolite of the prodrug molnupiravir and is accepted as an efficient drug against COVID-19. Molnupiravir targets the RNA-dependent RNA polymerase (RdRp) enzyme, which is responsible for replicating the viral genome during the replication process of certain types of viruses. It works by disrupting the normal function of the RdRp enzyme, causing it to make mistakes during the replication of the viral genome. These mistakes can prevent the viral RNA from being transcribed, converted into a complementary DNA template, translated, or converted into a functional protein. By disrupting these crucial steps in the viral replication process, molnupiravir can effectively inhibit the replication of the virus and reduce its ability to cause disease. This review article sheds light on the impact of molnupiravir and its metabolite on SARS-CoV-2 variants of concern, such as delta, omicron, and hybrid/recombinant variants. The detailed mechanism and molecular interactions using molecular docking and dynamics have also been covered. The safety and tolerability of molnupiravir in patients with comorbidities have also been emphasized.
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25
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O’Shea KM, Schuler CF, Chen J, Troost JP, Wong PT, Chen K, O’Shea DR, Peng W, Gherasim C, Manthei DM, Valdez R, Baldwin JL, Baker JR. Wild-type SARS-CoV-2 neutralizing immunity decreases across variants and over time but correlates well with diagnostic testing. Front Immunol 2023; 14:1055429. [PMID: 36845123 PMCID: PMC9945103 DOI: 10.3389/fimmu.2023.1055429] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Importance The degree of immune protection against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants provided by infection versus vaccination with wild-type virus remains unresolved, which could influence future vaccine strategies. The gold-standard for assessing immune protection is viral neutralization; however, few studies involve a large-scale analysis of viral neutralization against the Omicron variant by sera from individuals infected with wild-type virus. Objectives 1) To define the degree to which infection versus vaccination with wild-type SARS-CoV-2 induced neutralizing antibodies against Delta and Omicron variants.2) To determine whether clinically available data, such as infection/vaccination timing or antibody status, can predict variant neutralization. Methods We examined a longitudinal cohort of 653 subjects with sera collected three times at 3-to-6-month intervals from April 2020 to June 2021. Individuals were categorized according to SARS-CoV-2 infection and vaccination status. Spike and nucleocapsid antibodies were detected via ADVIA Centaur® (Siemens) and Elecsys® (Roche) assays, respectively. The Healgen Scientific® lateral flow assay was used to detect IgG and IgM spike antibody responses. Pseudoviral neutralization assays were performed on all samples using human ACE2 receptor-expressing HEK-293T cells infected with SARS-CoV-2 spike protein pseudotyped lentiviral particles for wild-type (WT), B.1.617.2 (Delta), and B.1.1.529 (Omicron) variants. Results Vaccination after infection led to the highest neutralization titers at all timepoints for all variants. Neutralization was also more durable in the setting of prior infection versus vaccination alone. Spike antibody clinical testing effectively predicted neutralization for wild-type and Delta. However, nucleocapsid antibody presence was the best independent predictor of Omicron neutralization. Neutralization of Omicron was lower than neutralization of either wild-type or Delta virus across all groups and timepoints, with significant activity only present in patients that were first infected and later immunized. Conclusions Participants having both infection and vaccination with wild-type virus had the highest neutralizing antibody levels against all variants and had persistence of activity. Neutralization of WT and Delta virus correlated with spike antibody levels against wild-type and Delta variants, but Omicron neutralization was better correlated with evidence of prior infection. These data help explain why 'breakthrough' Omicron infections occurred in previously vaccinated individuals and suggest better protection is observed in those with both vaccination and previous infection. This study also supports the concept of future SARS-CoV-2 Omicron-specific vaccine boosters.
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Affiliation(s)
- Kelly M. O’Shea
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
| | - Charles F. Schuler
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
| | - Jesse Chen
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States,Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Jonathan P. Troost
- Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor, MI, United States
| | - Pamela T. Wong
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States,Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Kelsea Chen
- Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
| | - Daniel R. O’Shea
- Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
| | - Westley Peng
- Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
| | - Carmen Gherasim
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - David M. Manthei
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Riccardo Valdez
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - James L. Baldwin
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
| | - James R. Baker
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States,Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI, United States,*Correspondence: James R. Baker Jr.,
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26
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Wang X, Chen Y, Cheng X, Wang SQ, Hu Y, Feng Y, Jin R, Zhou K, Liu T, Wang J, Pan K, Liu B, Xiang J, Wang Y, Zhou Q, Zhang Y, Pan W, Li W. CDetection.v2: One-pot assay for the detection of SARS-CoV-2. Front Microbiol 2023; 14:1158163. [PMID: 37032875 PMCID: PMC10076661 DOI: 10.3389/fmicb.2023.1158163] [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: 02/06/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The ongoing 2019 coronavirus disease pandemic (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its variants, is a global public health threat. Early diagnosis and identification of SARS-CoV-2 and its variants plays a critical role in COVID-19 prevention and control. Currently, the most widely used technique to detect SARS-CoV-2 is quantitative reverse transcription real-time quantitative PCR (RT-qPCR), which takes nearly 1 hour and should be performed by experienced personnel to ensure the accuracy of results. Therefore, the development of a nucleic acid detection kit with higher sensitivity, faster detection and greater accuracy is important. Methods Here, we optimized the system components and reaction conditions of our previous detection approach by using RT-RAA and Cas12b. Results We developed a Cas12b-assisted one-pot detection platform (CDetection.v2) that allows rapid detection of SARS-CoV-2 in 30 minutes. This platform was able to detect up to 5,000 copies/ml of SARS-CoV-2 without cross-reactivity with other viruses. Moreover, the sensitivity of this CRISPR system was comparable to that of RT-qPCR when tested on 120 clinical samples. Discussion The CDetection.v2 provides a novel one-pot detection approach based on the integration of RT-RAA and CRISPR/Cas12b for detecting SARS-CoV-2 and screening of large-scale clinical samples, offering a more efficient strategy for detecting various types of viruses.
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Affiliation(s)
- Xinge Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Institute of Zoology, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Chinese Academy of Sciences, Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Institute of Zoology, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Chinese Academy of Sciences, Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xuejia Cheng
- Beijing SynsorBio Technology Co., Ltd., Beijing, China
| | - Si-Qi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Institute of Zoology, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Chinese Academy of Sciences, Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yanping Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Institute of Zoology, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Chinese Academy of Sciences, Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yingmei Feng
- Department of Science and Technology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Kangping Zhou
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Ti Liu
- Shandong Center for Disease Control and Prevention, Jinan, China
| | - Jianxing Wang
- Shandong Center for Disease Control and Prevention, Jinan, China
| | - Kai Pan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Bing Liu
- Tonghua Central Hospital, Tonghua, Jilin, China
| | - Jie Xiang
- Tongji Medical College of Huazhang, Wuhan Jinyintan Hospital, University of Science and Technology, Wuhan, China
| | - Yanping Wang
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Institute of Zoology, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Chinese Academy of Sciences, Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Institute of Zoology, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Chinese Academy of Sciences, Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Weiye Pan
- Beijing SynsorBio Technology Co., Ltd., Beijing, China
- Weiye Pan,
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Institute of Zoology, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Chinese Academy of Sciences, Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Wei Li,
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27
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Kostaki EG, Mossialos E, Tseti I, Sfikakis PP, Paraskevis D. Mapping the Early Dispersal Patterns of SARS-CoV-2 Omicron BA.4 and BA.5 Subvariants in the Absence of Travel Restrictions and Testing at the Borders in Europe. Viruses 2022; 15:133. [PMID: 36680171 PMCID: PMC9865345 DOI: 10.3390/v15010133] [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: 11/16/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
The circulation of SARS-CoV-2 omicron BA.4 and BA.5 subvariants with enhanced transmissibility and capacity for immune evasion resulted in a recent pandemic wave that began in April-May of 2022. We performed a statistical phylogeographic study that aimed to define the cross-border transmission patterns of BA.4 and BA.5 at the earliest stages of virus dispersal. Our sample included all BA.4 and BA.5 sequences that were publicly available in the GISAID database through mid-May 2022. Viral dispersal patterns were inferred using maximum likelihood phylogenetic trees with bootstrap support. We identified South Africa as the major source of both BA.4 and BA.5 that migrated to other continents. By contrast, we detected no significant export of these subvariants from Europe. Belgium was identified as a major hub for BA.4 transmission within Europe, while Portugal and Israel were identified as major sources of BA.5. Western and Northern European countries exhibited the highest rates of cross-border transmission, as did several popular tourist destinations in Southern and Central/Western Europe. Our study provides a detailed map of the early dispersal patterns of two highly transmissible SARS-CoV-2 omicron subvariants at a time when there was an overall relaxation of public health measures in Europe.
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Affiliation(s)
- Evangelia Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Elias Mossialos
- Department of Health Policy, London School of Economics and Political Science, London WC2A 2AE, UK
- Institute of Global Health Innovation, Imperial College London, London SW7 2AZ, UK
| | | | - Petros P. Sfikakis
- 1st Department of Propaedeutic Internal Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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28
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Liotti FM, De Maio F, Ippoliti C, Santarelli G, Monzo FR, Sali M, Santangelo R, Ceccherini-Silberstein F, Sanguinetti M, Posteraro B. Two-Period Study Results from a Large Italian Hospital Laboratory Attesting SARS-CoV-2 Variant PCR Assay Evolution. Microbiol Spectr 2022; 10:e0292222. [PMID: 36409091 PMCID: PMC9769628 DOI: 10.1128/spectrum.02922-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/24/2022] [Indexed: 11/23/2022] Open
Abstract
In keeping with the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 causative agent, PCR assays have been developed to rapidly detect SARS-CoV-2 variants, which have emerged since the first (Alpha) variant was identified. Based on specific assortment of SARS-CoV-2 spike-protein mutations (ΔH69/V70, E484K, N501Y, W152C, L452R, K417N, and K417T) among the major variants known to date, Seegene Allplex SARS-CoV-2 Variants I and Variants II assays have been available since a few months before the last (Omicron) variant became predominant. Using S gene next-generation sequencing (NGS) as the SARS-CoV-2 variant identification reference method, we assessed the results of SARS-CoV-2-positive nasopharyngeal swab samples from two testing periods, before (n = 288, using only Variants I) and after (n = 77, using both Variants I and Variants II) the appearance of Omicron. The Variants I assay allowed correct identification for Alpha (37/37), Beta/Gamma (28/30), or Delta (220/221) variant-positive samples. The combination of the Variants I and Variants II assays allowed correct identification for 61/77 Omicron variant-positive samples. While 16 samples had the K417N mutation undetected with the Variants II assay, 74/77 samples had both ΔH69/V70 and N501Y mutations detected with the Variants I assay. If considering only the results by the Variants I assay, 6 (2 Beta variant positive, 1 Delta variant positive, and 3 Omicron variant positive) of 365 samples tested in total provided incorrect identification. We showed that the Variants I assay alone might be more suitable than both the Variants I and Variants II assays to identify currently circulating SARS-CoV-2 variants. Inclusion of additional variant-specific mutations should be expected in the development of future assays. IMPORTANCE Omicron variants of SARS-CoV-2 pose more important public health concerns than the previously circulating Alpha or Delta variants, particularly regarding the efficacy of anti-SARS-CoV-2 vaccines and therapeutics. Precise identification of these variants highly requires performant PCR-based assays that allow us to reduce the reliance on NGS-based assays, which remain the reference method in this topic. While the current epidemiological SARS-CoV-2 pandemic context suggests that PCR assays such as the Seegene Variants II may be dispensable, we took advantage of NGS data obtained in this study to show that the array of SARS-CoV-2 spike protein mutations in the Seegene Variants II assay may be suboptimal. This reinforces the concept that initially developed PCR assays for SARS-CoV-2 variant detection could be no longer helpful if the SARS-CoV-2 pandemic evolves to newly emerging variants.
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Affiliation(s)
- Flora Marzia Liotti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Chiara Ippoliti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulia Santarelli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesca Romana Monzo
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Michela Sali
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rosaria Santangelo
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Lancemaside A from Codonopsis lanceolata: Studies on Antiviral Activity and Mechanism of Action against SARS-CoV-2 and Its Variants of Concern. Antimicrob Agents Chemother 2022; 66:e0120122. [PMID: 36374087 PMCID: PMC9765103 DOI: 10.1128/aac.01201-22] [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] [Indexed: 11/16/2022] Open
Abstract
Several plant-derived natural products with anti-SARS-CoV-2 activity have been evaluated for the potential to serve as chemotherapeutic agents for the treatment of COVID-19. Codonopsis lanceolata (CL) has long been used as a medicinal herb in East Asian countries to treat inflammatory diseases of the respiratory system but its antiviral activity has not been investigated so far. Here, we showed that CL extract and its active compound lancemaside A (LA) displayed potent inhibitory activity against SARS-CoV-2 infection using a pseudotyped SARS-CoV-2 entry assay system. We demonstrated that this inhibitory effect of LA was due to the alteration of membrane cholesterol and blockade of the membrane fusion between SARS-CoV-2 and host cells by filipin staining and cell-based membrane fusion assays. Our findings also showed that LA, as a membrane fusion blocker, could impede the endosomal entry pathway of SARS-CoV-2 and its variants of concern (VOCs), including Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529), in Vero cells with similar of IC50 values ranging from 2.23 to 3.37 μM as well as the TMPRSS2-mediated viral entry pathway in A549 cells overexpressing ACE2 and TMPRSS2 with IC50 value of 3.92 μM. We further demonstrated that LA could prevent the formation of multinucleated syncytia arising from SARS-CoV-2 spike protein-mediated membrane fusion. Altogether, the findings reported here suggested that LA could be a broad-spectrum anti-SARS-CoV-2 therapeutic agent by targeting the fusion of viral envelope with the host cell membrane.
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Kopsidas I, Karagiannidou S, Kostaki EG, Kousi D, Douka E, Sfikakis PP, Moustakidis S, Kokkotis C, Tsaopoulos D, Tseti I, Zaoutis T, Paraskevis D. Global Distribution, Dispersal Patterns, and Trend of Several Omicron Subvariants of SARS-CoV-2 across the Globe. Trop Med Infect Dis 2022; 7:373. [PMID: 36422924 PMCID: PMC9698960 DOI: 10.3390/tropicalmed7110373] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 08/27/2023] Open
Abstract
Our study aims to describe the global distribution and dispersal patterns of the SARS-CoV-2 Omicron subvariants. Genomic surveillance data were extracted from the CoV-Spectrum platform, searching for BA.1*, BA.2*, BA.3*, BA.4*, and BA.5* variants by geographic region. BA.1* increased in November 2021 in South Africa, with a similar increase across all continents in early December 2021. BA.1* did not reach 100% dominance in all continents. The spread of BA.2*, first described in South Africa, differed greatly by geographic region, in contrast to BA.1*, which followed a similar global expansion, firstly occurring in Asia and subsequently in Africa, Europe, Oceania, and North and South America. BA.4* and BA.5* followed a different pattern, where BA.4* reached high proportions (maximum 60%) only in Africa. BA.5* is currently, by Mid-August 2022, the dominant strain, reaching almost 100% across Europe, which is the first continent aside from Africa to show increasing proportions, and Asia, the Americas, and Oceania are following. The emergence of new variants depends mostly on their selective advantage, translated as enhanced transmissibility and ability to invade people with existing immunity. Describing these patterns is useful for a better understanding of the epidemiology of the VOCs' transmission and for generating hypotheses about the future of emerging variants.
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Affiliation(s)
- Ioannis Kopsidas
- Center for Clinical Epidemiology and Outcomes Research (CLEO), 15451 Athens, Greece
| | | | - Evangelia Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitra Kousi
- Center for Clinical Epidemiology and Outcomes Research (CLEO), 15451 Athens, Greece
| | - Eirini Douka
- National Public Health Organisation (NPHO), 15123 Athens, Greece
| | - Petros P. Sfikakis
- First Department of Propaedeutic and Internal Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | - Christos Kokkotis
- Department of Physical Education and Sport Science, Democritus University of Thrace, 69100 Komotini, Greece
| | - Dimitrios Tsaopoulos
- Center for Research and Technology Hellas, Institute for Bio-Economy & Agri-Technology, 38333 Volos, Greece
| | | | - Theoklis Zaoutis
- National Public Health Organisation (NPHO), 15123 Athens, Greece
| | - Dimitrios Paraskevis
- National Public Health Organisation (NPHO), 15123 Athens, Greece
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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31
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Khamis F, Al Awaidy S, Ba’Omar M, Osman W, Chhetri S, Ambusaid Z, Al Fahdi Z, Al Lawati J, Al Sulaimi K, Al Bulushi SA, Al Bahrani M, Al-Zakwani I. The Impact of Demographic, Clinical Characteristics and the Various COVID-19 Variant Types on All-Cause Mortality: A Case-Series Retrospective Study. Diseases 2022; 10:100. [PMID: 36412594 PMCID: PMC9680441 DOI: 10.3390/diseases10040100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
(1) Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved into a pandemic affecting virtually every country in the world. We evaluated the demographic, clinical, laboratory, and all-cause mortality of moderate and severe COVID-19 patients admitted to a tertiary care hospital in Oman during the different COVID-19 waves and variant types. (2) Methods: A case-series retrospective study was carried out between 12 March 2020 and 30 June 2022. All adults over the age of 18 with laboratory-confirmed COVID-19 were enrolled. Analyses were performed using univariate and multivariate statistics. (3) Results: A total of 1462 confirmed cases enrolled with the mean age of the cohort was 55 ± 17 years with significant differences among the groups (p = 0.006). A total of 63% and 80% of the patients were males and citizens of Oman, respectively. Patients infected with the Alpha COVID-19 variant type were more likely to have acute respiratory distress syndrome (ARDS) (p < 0.001), stay longer in the hospital (p < 0.001), and get admitted to the intensive care unit (ICU) (p < 0.001). At the same time, those who had the Omicron COVID-19 type were more likely to have renal impairment (p < 0.001) and less likely to be associated with non-invasive ventilation (NIV) (p = 0.001) compared with other COVID-19 variant types. The Delta (adjusted odds ratio (aOR), 1.8; 95% confidence interval (CI): 1.22−2.66; p = 0.003) and Omicron (aOR, 1.88; 95% CI: 1.09−3.22; p = 0.022) COVID-19 variant types were associated with higher all-cause mortality when compared to the initial COVID-19 variant. Old age (aOR, 1.05; 95% CI: 1.04−1.06; p < 0.001), the presence of respiratory disease (aOR, 1.58; 95% CI: 1.02−2.44; p = 0.04), ICU admission (aOR, 3.41; 95% CI: 2.16−5.39; p < 0.001), lower eGFR (aOR, 1.61; 95% CI: 1.17−2.23; p = 0.004), and ARDS (aOR, 5.75; 95% CI: 3.69−8.98; p < 0.001) were also associated with higher mortality while NIV requirements were associated with lower odds of dying (aOR, 0.65; 95% CI: 0.46−0.91; p = 0.012). (4) Conclusions: Alpha and Delta variants were associated with a longer hospital stay, need for intensive care, mechanical ventilation, and increased mortality. Old age, cardiac renal dysfunction were commonly associated with Omicron variants. Large-scale national studies to further assess the risk factors for mortality related to COVID-19 waves are warranted.
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Affiliation(s)
- Faryal Khamis
- Department of Infectious Disease, The Royal Hospital, Muscat, PC 111, Oman
| | | | - Muna Ba’Omar
- Department of Infectious Disease, The Royal Hospital, Muscat, PC 111, Oman
| | - Wessam Osman
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Shabnam Chhetri
- Department of Infectious Disease, The Royal Hospital, Muscat, PC 111, Oman
| | - Zaiyana Ambusaid
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Zakariya Al Fahdi
- Department of Medicine, Nizwa Hospital, Ministry of Health, Nizwa, PC 611, Oman
| | - Jaber Al Lawati
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Khalsa Al Sulaimi
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | | | - Maher Al Bahrani
- Department of Anaesthesia, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Ibrahim Al-Zakwani
- Department of Pharmacology & Clinical Pharmacy, College of Medicine & Health Sciences, Sultan Qaboos University, Al Khoudh, PC 123, Oman
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