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Mahrokhian SH, Tostanoski LH, Vidal SJ, Barouch DH. COVID-19 vaccines: Immune correlates and clinical outcomes. Hum Vaccin Immunother 2024; 20:2324549. [PMID: 38517241 PMCID: PMC10962618 DOI: 10.1080/21645515.2024.2324549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/24/2024] [Indexed: 03/23/2024] Open
Abstract
Severe disease due to COVID-19 has declined dramatically as a result of widespread vaccination and natural immunity in the population. With the emergence of SARS-CoV-2 variants that largely escape vaccine-elicited neutralizing antibody responses, the efficacy of the original vaccines has waned and has required vaccine updating and boosting. Nevertheless, hospitalizations and deaths due to COVID-19 have remained low. In this review, we summarize current knowledge of immune responses that contribute to population immunity and the mechanisms how vaccines attenuate COVID-19 disease severity.
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Affiliation(s)
- Shant H. Mahrokhian
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Lisa H. Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Samuel J. Vidal
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
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2
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Ackerson BK, Bruxvoort KJ, Qian L, Sy LS, Qiu S, Tubert JE, Lee GS, Ku JH, Florea A, Luo Y, Bathala R, Stern J, Choi SK, Takhar HS, Aragones M, Marks MA, Anderson EJ, Zhou CK, Sun T, Talarico CA, Tseng HF. Effectiveness and durability of mRNA-1273 BA.4/BA.5 bivalent vaccine (mRNA-1273.222) against SARS-CoV-2 BA.4/BA.5 and XBB sublineages. Hum Vaccin Immunother 2024; 20:2335052. [PMID: 38575149 PMCID: PMC10996830 DOI: 10.1080/21645515.2024.2335052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
Emerging SARS-CoV-2 sublineages continue to cause serious COVID-19 disease, but most individuals have not received any COVID-19 vaccine for >1 year. Assessment of long-term effectiveness of bivalent COVID-19 vaccines against circulating sublineages is important to inform the potential need for vaccination with updated vaccines. In this test-negative study at Kaiser Permanente Southern California, sequencing-confirmed BA.4/BA.5- or XBB-related SARS-CoV-2-positive cases (September 1, 2022 to June 30, 2023), were matched 1:3 to SARS-CoV-2-negative controls. We assessed mRNA-1273 bivalent relative (rVE) and absolute vaccine effectiveness (VE) compared to ≥2 or 0 doses of original monovalent vaccine, respectively. The rVE analysis included 20,966 cases and 62,898 controls. rVE (95%CI) against BA.4/BA.5 at 14-60 days and 121-180 days was 52.7% (46.9-57.8%) and 35.5% (-2.8-59.5%) for infection, and 59.3% (49.7-67.0%) and 33.2% (-28.2-68.0%) for Emergency Department/Urgent Care (ED/UC) encounters. For BA.4/BA.5-related hospitalizations, rVE was 71.3% (44.9-85.1%) and 52.0% (-1.2-77.3%) at 14-60 days and 61-120 days, respectively. rVE against XBB at 14-60 days and 121-180 days was 48.8% (33.4-60.7%) and -3.9% (-18.1-11.3%) for infection, 70.7% (52.4-82.0%) and 15.7% (-6.0-33.2%) for ED/UC encounters, and 87.9% (43.8-97.4%) and 57.1% (17.0-77.8%) for hospitalization. VE and subgroup analyses (age, immunocompromised status, previous SARS-CoV-2 infection) results were similar to rVE analyses. rVE of mRNA-1273 bivalent vaccine against BA.4/BA.5 and XBB infections, ED/UC encounters, and hospitalizations waned over time. Periodic revaccination with vaccines targeting emerging variants may be important in reducing COVID-19 morbidity and mortality.
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Affiliation(s)
- Bradley K. Ackerson
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Katia J. Bruxvoort
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lei Qian
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Lina S. Sy
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Sijia Qiu
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Julia E. Tubert
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Gina S. Lee
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Jennifer H. Ku
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Ana Florea
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Yi Luo
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Radha Bathala
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Julie Stern
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Soon K. Choi
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Harpreet S. Takhar
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Michael Aragones
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Morgan A. Marks
- Infectious Disease, Epidemiology, Moderna Inc, Cambridge, MA, USA
| | - Evan J. Anderson
- Infectious Disease, Epidemiology, Moderna Inc, Cambridge, MA, USA
| | - Cindy Ke Zhou
- Infectious Disease, Epidemiology, Moderna Inc, Cambridge, MA, USA
| | - Tianyu Sun
- Infectious Disease, Epidemiology, Moderna Inc, Cambridge, MA, USA
| | - Carla A. Talarico
- Infectious Disease, Epidemiology, Moderna Inc, Cambridge, MA, USA
- Epidemiology, AstraZeneca, Gaithersburg, MD, USA
| | - Hung Fu Tseng
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA
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3
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Kirk NM, Liang Y, Ly H. Pathogenesis and virulence of coronavirus disease: Comparative pathology of animal models for COVID-19. Virulence 2024; 15:2316438. [PMID: 38362881 PMCID: PMC10878030 DOI: 10.1080/21505594.2024.2316438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/04/2024] [Indexed: 02/17/2024] Open
Abstract
Animal models that can replicate clinical and pathologic features of severe human coronavirus infections have been instrumental in the development of novel vaccines and therapeutics. The goal of this review is to summarize our current understanding of the pathogenesis of coronavirus disease 2019 (COVID-19) and the pathologic features that can be observed in several currently available animal models. Knowledge gained from studying these animal models of SARS-CoV-2 infection can help inform appropriate model selection for disease modelling as well as for vaccine and therapeutic developments.
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Affiliation(s)
- Natalie M. Kirk
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Yuying Liang
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
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4
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Li J, Cheng R, Bian Z, Niu J, Xia J, Mao G, Liu H, Wu C, Hao C. Development of multiplex allele-specific RT-qPCR assays for differentiation of SARS-CoV-2 Omicron subvariants. Appl Microbiol Biotechnol 2024; 108:35. [PMID: 38183475 DOI: 10.1007/s00253-023-12941-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 01/08/2024]
Abstract
Quick differentiation of current circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmissions. However, the widely applied gene sequencing method is time-consuming and costly especially when facing recombinant variants, because a large part or whole genome sequencing is required. Allele-specific reverse transcriptase real time RT-PCR (RT-qPCR) represents a quick and cost-effective method for SNP (single nucleotide polymorphism) genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 5 multiplex allele-specific RT-qPCR assays targeting 20 key mutations for quick differentiation of the Omicron subvariants (BA.1 to BA.5 and their descendants) and the recombinant variants (XBB.1 and XBB.1.5). Two parallel multiplex RT-qPCR reactions were designed to separately target the prototype allele and the mutated allele of each mutation in the allele-specific RT-qPCR assay. Optimal annealing temperatures, primer and probe dosage, and time for annealing/extension for each reaction were determined by multi-factor and multi-level orthogonal test. The variation of Cp (crossing point) values (ΔCp) between the two multiplex RT-qPCR reactions was applied to determine if a mutation occurs or not. SARS-CoV-2 subvariants and related recombinant variants were differentiated by their unique mutation patterns. The developed multiplex allele-specific RT-qPCR assays exhibited excellent analytical sensitivities (with limits of detection (LoDs) of 1.47-18.52 copies per reaction), wide linear detection ranges (109-100 copies per reaction), good amplification efficiencies (88.25 to 110.68%), excellent reproducibility (coefficient of variations (CVs) < 5% in both intra-assay and inter-assay tests), and good clinical performances (99.5-100% consistencies with Sanger sequencing). The developed multiplex allele-specific RT-qPCR assays in the present study provide an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants. KEY POINTS: • A panel of five multiplex allele-specific RT-qPCR assays for quick differentiation of 11 SARS-CoV-2 Omicron subvariants (BA.1, BA.2, BA.4, BA.5, and their descendants) and 2 recombinant variants (XBB.1 and XBB.1.5). • The developed assays exhibited good analytical sensitivities and reproducibility, wide linear detection ranges, and good clinical performances, providing an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants.
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Affiliation(s)
- Jianguo Li
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China.
| | - Ruiling Cheng
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Zixin Bian
- College of Life Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Jiahui Niu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Juan Xia
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Guoli Mao
- Shanxi Guoxin Caregeno Biotechnology Co., Ltd., Taiyuan, 030032, People's Republic of China
| | - Hulong Liu
- Shanxi Guoxin Caregeno Biotechnology Co., Ltd., Taiyuan, 030032, People's Republic of China
| | - Changxin Wu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, People's Republic of China
| | - Chunyan Hao
- School of Environment and Resources, Taiyuan University of Science and Technology, Taiyuan, 030024, People's Republic of China.
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5
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Murai A, Kubo T, Ohkuri T, Yanagawa J, Yajima Y, Kosaka A, Li D, Nagato T, Murata K, Kanaseki T, Tsukahara T, Nagasaki T, Hirohashi Y, Kobayashi H, Torigoe T. NF9 peptide specific cytotoxic T lymphocyte clone cross react to Y453F mutation of SARS-CoV-2 virus spike protein. Immunol Med 2024; 47:93-99. [PMID: 38236134 DOI: 10.1080/25785826.2024.2304363] [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: 10/03/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
The recognition by cytotoxic T cells (CTLs) is essential for the clearance of SARS-CoV-2 virus-infected cells. Several viral proteins have been described to be recognized by CTLs. Among them, the spike (S) protein is one of the immunogenic proteins. The S protein acts as a ligand for its receptors, and several mutants with different affinities for its cognate receptors have been reported, and certain mutations in the S protein, such as L452R and Y453F, have been found to inhibit the HLA-A24-restricted CTL response. In this study, we conducted a screening of candidate peptides derived from the S protein, specifically targeting those carrying the HLA-A24 binding motif. Among these peptides, we discovered that NF9 (NYNYLYRLF) represents an immunogenic epitope. CTL clones specific to the NF9 peptide were successfully established. These CTL clones exhibited the ability to recognize endogenously expressed NF9 peptide. Interestingly, the CTL clone demonstrated cross-reactivity with the Y453F peptide (NYNYLFRLF) but not with the L452R peptide (NYNYRYRLF). The CTL clone was able to identify the endogenously expressed Y453F mutant peptide. These findings imply that the NF9-specific CTL clone possesses the capability to recognize and respond to the Y453F mutant peptide.
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Affiliation(s)
- Aiko Murai
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Terufumi Kubo
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takayuki Ohkuri
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Junko Yanagawa
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yuki Yajima
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
- Department of Oral and Maxillofacial Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Akemi Kosaka
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Dongliang Li
- Tsukuba Laboratory, Medical & Biological Laboratories Co., Ltd, Ina, Japan
| | - Toshihiro Nagato
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Kenji Murata
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takayuki Kanaseki
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | | | - Takeshi Nagasaki
- Tsukuba Laboratory, Medical & Biological Laboratories Co., Ltd, Ina, Japan
| | - Yoshihiko Hirohashi
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroya Kobayashi
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Toshihiko Torigoe
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
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6
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Baek K, Kim D, Kim J, Kang BM, Park H, Park S, Shin HE, Lee MH, Maharjan S, Kim M, Kim S, Park MS, Lee Y, Kwon HJ. Analysis of SARS-CoV-2 omicron mutations that emerged during long-term replication in a lung cancer xenograft mouse model. Virus Genes 2024; 60:251-262. [PMID: 38587722 DOI: 10.1007/s11262-024-02067-6] [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: 11/22/2023] [Accepted: 03/12/2024] [Indexed: 04/09/2024]
Abstract
SARS-CoV-2 Omicron has the largest number of mutations among all the known SARS-CoV-2 variants. The presence of these mutations might explain why Omicron is more infectious and vaccines have lower efficacy to Omicron than other variants, despite lower virulence of Omicron. We recently established a long-term in vivo replication model by infecting Calu-3 xenograft tumors in immunodeficient mice with parental SARS-CoV-2 and found that various mutations occurred majorly in the spike protein during extended replication. To investigate whether there are differences in the spectrum and frequency of mutations between parental SARS-CoV-2 and Omicron, we here applied this model to Omicron. At 30 days after infection, we found that the virus was present at high titers in the tumor tissues and had developed several rare sporadic mutations, mainly in ORF1ab with additional minor spike protein mutations. Many of the mutant isolates had higher replicative activity in Calu-3 cells compared with the original SARS-CoV-2 Omicron virus, suggesting that the novel mutations contributed to increased viral replication. Serial propagation of SARS-CoV-2 Omicron in cultured Calu-3 cells resulted in several rare sporadic mutations in various viral proteins with no mutations in the spike protein. Therefore, the genome of SARS-CoV-2 Omicron seems largely stable compared with that of the parental SARS-CoV-2 during extended replication in Calu-3 cells and xenograft model. The sporadic mutations and modified growth properties observed in Omicron might explain the emergence of Omicron sublineages. However, we cannot exclude the possibility of some differences in natural infection.
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Affiliation(s)
- Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Ha-Eun Shin
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Myeong-Heon Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hyung-Joo Kwon
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea.
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea.
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Kapar A, Xie S, Guo Z, Nan Y, Du Y, Yin X, Gong T, Gu X, Zhou Y, Lu W, Yang A, Luo Z, Dai J, Wang K, Zhao S, Wang K. Effectiveness of azvudine against severe outcomes among hospitalized COVID-19 patients in Xinjiang, China: a single-center, retrospective, matched cohort study. Expert Rev Anti Infect Ther 2024. [PMID: 38822541 DOI: 10.1080/14787210.2024.2362900] [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: 04/07/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Since the end of 2022, Azvudine was widely used to treat hospitalized novel coronavirus disease 2019 (COVID-19) patients in China. However, data on the clinical effectiveness of Azvudine against severe outcomes and post-COVID-19-conditions (PCC) among patients infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants was limited. This study evaluates the effectiveness of Azvudine in hospitalized COVID-19 patients during a SARS-CoV-2 Omicron BA.5 dominance period. METHODS From 1 November 2022 to 1 July 2023, we conducted a single-center retrospective cohort study based on hospitalized COVID-19 patients from a tertiary hospital in Shihezi, China, recruiting laboratory-confirmed hospitalized patients with SARS-CoV-2 infection. Patients treated with Azvudine and usual care were propensity-score matched (PSM) at a 1:1 ratio to a control group in which patients undergone usual care only, with matching based on covariates such as sex, age, ethnicity, number of preexisting conditions, antibiotic use upon admission, and complete blood cell count. The primary outcomes were all-cause death and PCC at short-term (60 days) post discharge. The secondary outcomes included the initiation of invasive mechanical ventilation and PCC at long-term post discharge (120 days). Cox proportional hazards (PH) regression models were employed to estimate the hazard ratios (HR) for both all-cause death and invasive mechanical ventilation, and logistic regression models were used to estimate the odds ratios (OR) for short-term and long-term PCC. Subgroup analyses were performed based on the matched covariates. RESULTS A total of 2,639 hospitalized patients diagnosed with COVID-19 were initially identified, and 2,069 patients were screened following the exclusion criteria. After matching, 297 Azvudine recipients and 297 matched controls were eligible for analyses. The incidence rate of all-cause death was lower in the Azvudine group than in the control group (0.007 per person, 95% confidence interval [CI]: 0.001, 0.024 vs 0.128, 95% CI: 0.092, 0.171), and the use of Azvudine was associated with a significant lower risk of death and the use of Azvudine was associated with a reduced risk of death (HR: 0.049, 95% CI: 0.012, 0.205). Subgroup analyses indicated a significant effectiveness of Azvudine against the risk of all-cause death among men, age over 65, patients without the preexisting conditions, and patients with antibiotics dispensed at admission. Statistical difference were not observed between Azvudine group and control group in the invasive mechanical ventilation and short-term and long-term PCC. CONCLUSIONS The present findings indicate that receipt of Azvudine was associated with lower risk of all-cause death among hospitalized patients with Omicron BA.5 infection a in real-world setting. Further research is urgently needed to validate the effectiveness of Azvudine on the PCC.
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Affiliation(s)
- Abiden Kapar
- School of Public Health, Xinjiang Medical University, Urumqi, China
| | - Songsong Xie
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital of Shihezi University, Shihezi, China
| | - Zihao Guo
- CUHK Shenzhen Research Institute, Shenzhen, China
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | - Yan Nan
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital of Shihezi University, Shihezi, China
| | - Yaling Du
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital of Shihezi University, Shihezi, China
| | - Xi Yin
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital of Shihezi University, Shihezi, China
| | - Tao Gong
- Shihezi People's Hospital, Shihezi, China
| | - Xiu Gu
- School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Yang Zhou
- School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Wenli Lu
- School of Public Health, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin, China
- The Sixth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Aimin Yang
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong, China
| | - Zhaohui Luo
- Key Laboratory of Prevention and Control of Major Diseases in the Population (MoE), Tianjin Medical University, Tianjin, China
| | - Jianghong Dai
- School of Public Health, Xinjiang Medical University, Urumqi, China
| | - Kailu Wang
- CUHK Shenzhen Research Institute, Shenzhen, China
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | - Shi Zhao
- School of Public Health, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin, China
- Key Laboratory of Prevention and Control of Major Diseases in the Population (MoE), Tianjin Medical University, Tianjin, China
| | - Kai Wang
- School of Public Health, Xinjiang Medical University, Urumqi, China
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8
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Yang Y, Li F, Du L. Therapeutic nanobodies against SARS-CoV-2 and other pathogenic human coronaviruses. J Nanobiotechnology 2024; 22:304. [PMID: 38822339 PMCID: PMC11140877 DOI: 10.1186/s12951-024-02573-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024] Open
Abstract
Nanobodies, single-domain antibodies derived from variable domain of camelid or shark heavy-chain antibodies, have unique properties with small size, strong binding affinity, easy construction in versatile formats, high neutralizing activity, protective efficacy, and manufactural capacity on a large-scale. Nanobodies have been arisen as an effective research tool for development of nanobiotechnologies with a variety of applications. Three highly pathogenic coronaviruses (CoVs), SARS-CoV-2, SARS-CoV, and MERS-CoV, have caused serious outbreaks or a global pandemic, and continue to post a threat to public health worldwide. The viral spike (S) protein and its cognate receptor-binding domain (RBD), which initiate viral entry and play a critical role in virus pathogenesis, are important therapeutic targets. This review describes pathogenic human CoVs, including viral structures and proteins, and S protein-mediated viral entry process. It also summarizes recent advances in development of nanobodies targeting these CoVs, focusing on those targeting the S protein and RBD. Finally, we discuss potential strategies to improve the efficacy of nanobodies against emerging SARS-CoV-2 variants and other CoVs with pandemic potential. It will provide important information for rational design and evaluation of therapeutic agents against emerging and reemerging pathogens.
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MESH Headings
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/pharmacology
- Single-Domain Antibodies/therapeutic use
- Single-Domain Antibodies/chemistry
- Humans
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/metabolism
- Animals
- COVID-19/virology
- COVID-19/immunology
- COVID-19/therapy
- Coronavirus Infections/drug therapy
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Middle East Respiratory Syndrome Coronavirus/immunology
- Virus Internalization/drug effects
- Pandemics
- Betacoronavirus/immunology
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/virology
- Pneumonia, Viral/immunology
- Severe acute respiratory syndrome-related coronavirus/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
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Affiliation(s)
- Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, USA.
- Center for Coronavirus Research, University of Minnesota, Minneapolis, MN, USA.
| | - Lanying Du
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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9
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Lytton SD, Ghosh AK, Bulbul RH, Nasifa T, Mamunur R, Meier C, Landt O, Kaiser M. The severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) omicron sub-variants in Bangladesh cause mild COVID-19 and associate with similar antibody responses irrespective of natural infection or vaccination history. Heliyon 2024; 10:e31011. [PMID: 38770337 PMCID: PMC11103536 DOI: 10.1016/j.heliyon.2024.e31011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/22/2024] Open
Abstract
Objective Genomic surveillance and seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) in Bangladesh is paramount for COVID-19 pandemic preparedness yet lagging the high-income countries due to limited resources. Methods SARS-CoV-2 variants, COVID-19 symptoms, and serology were prospectively evaluated in a cross-sectional study of Bangladeshi adults testing RT-PCR positive in 2021 and 2022. Results SARS CoV-2 Omicron variants of asymptomatic or mild COVID-19 in 2022 replaced Delta variant infections requiring hospitalization and oxygen support. The omicron XBB became predominant in July 2022 and associated with cough, headache or body ache and loss of smell; 47 of 68 (69 %), 30 of 68 (44 %) and 27 of 68 (40 %) respectively at higher frequency than BA.1/BA.2; 16 of 88 (18 %), 13 of 88 (15 %) and 0 of 88 (0 %) p < 0.01, p < 0.01 and p < 0.0001. Linear regression analysis reveals no associations between the number of previous infections and the number of symptoms, r = -0.084, p = 0.68. The anti-nucleoprotein (N)-protein IgG post COVID-19 and anti-Spike (S) protein IgG post-COVID-19 vaccination were similar between BA.2, BA.4/BA.5 and XBB and significantly lower than the levels in delta variant infections (p < 0.001). Conclusions Omicron XBB subvariants emerged in Bangladesh two months prior to previous reports and include unique patterns of S-protein mutations not assigned in PANGO lineage. The SARS CoV-2 omicron break-through infections persist in the presence of sustained antibody responses and vaccinations, underscoring the importance of molecular surveillance in low-income countries.
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Affiliation(s)
| | - Asish Kumar Ghosh
- Department of Virology, Dhaka Medical College Hospital, Dhaka, 1000, Bangladesh
| | | | - Tasnim Nasifa
- National Institute of Laboratory Medicine and Referral Center, Sher E-Bangla Nagar, Dhaka, 1207, Bangladesh
| | - Rashid Mamunur
- Bangladesh Institute Tropical Infectious Disease (BITID), Fouzderhat, Chittagong, 4317, Bangladesh
| | - Christian Meier
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103, Berlin, Germany
| | - Olfert Landt
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103, Berlin, Germany
| | - Marco Kaiser
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103, Berlin, Germany
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10
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Pasev M, Trifonova A, Velichkov A, Terzieva V. Duration of antibody response to the receptor binding domain of SARS-CoV-2 in infected or vaccinated individuals - A one year retrospective cohort study. Int Immunopharmacol 2024; 133:112084. [PMID: 38621337 DOI: 10.1016/j.intimp.2024.112084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
The 2019 coronavirus (COVID-19) pandemic raised many scientific and medical questions. Of interest are the duration and effectiveness of the humoral immune response, especially since part of the pandemic occurred in the presence of anti-SARS-CoV-2 vaccines. We retrospectively studied 564 serum samples from 393 post-infected and vaccinated individuals to investigate the longevity and magnitude of the anti-spike IgG response. Our results showed that SARS-CoV-2 anti-spike IgG antibodies are retained for nine-twelve months, in both groups. In the vaccinated group we found higher IgG levels, but with a steeper decrease in titer over the study period. The recovered group's antibody levels correlated well with the national infection trendline for 2021. Both groups showed different, but distinct neutralizing capabilities towards RBD. The anti-Spike IgG response was sustained and efficient, independently of the triggering event, infection or vaccination, with the adaptive capacity against new viral variants being more valuable after infection.
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Affiliation(s)
- Martin Pasev
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia University "Sv. Kliment Ohridski", Sofia, Bulgaria
| | - Angelina Trifonova
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia University "Sv. Kliment Ohridski", Sofia, Bulgaria
| | - Andrey Velichkov
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction "Acad. Kiril Bratanov", Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Velislava Terzieva
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia University "Sv. Kliment Ohridski", Sofia, Bulgaria; Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction "Acad. Kiril Bratanov", Bulgarian Academy of Sciences, Sofia, Bulgaria.
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11
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Abousamra E, Figgins MD, Bedford T. Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.30.23299240. [PMID: 38076866 PMCID: PMC10705624 DOI: 10.1101/2023.11.30.23299240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Genomic surveillance of pathogen evolution is essential for public health response, treatment strategies, and vaccine development. In the context of SARS-COV-2, multi- ple models have been developed including Multinomial Logistic Regression (MLR) de- scribing variant frequency growth as well as Fixed Growth Advantage (FGA), Growth Advantage Random Walk (GARW) and Piantham parameterizations describing vari- ant Rt. These models provide estimates of variant fitness and can be used to forecast changes in variant frequency. We introduce a framework for evaluating real-time fore- casts of variant frequencies, and apply this framework to the evolution of SARS-CoV-2 during 2022 in which multiple new viral variants emerged and rapidly spread through the population. We compare models across representative countries with different intensities of genomic surveillance. Retrospective assessment of model accuracy high- lights that most models of variant frequency perform well and are able to produce reasonable forecasts. We find that the simple MLR model provides ∼0.6% median ab- solute error and ∼6% mean absolute error when forecasting 30 days out for countries with robust genomic surveillance. We investigate impacts of sequence quantity and quality across countries on forecast accuracy and conduct systematic downsampling to identify that 1000 sequences per week is fully sufficient for accurate short-term fore- casts. We conclude that fitness models represent a useful prognostic tool for short-term evolutionary forecasting.
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12
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Hamar Á, Mohammed D, Váradi A, Herczeg R, Balázsfalvi N, Fülesdi B, László I, Gömöri L, Gergely PA, Kovacs GL, Jáksó K, Gombos K. COVID-19 mortality prediction in Hungarian ICU settings implementing random forest algorithm. Sci Rep 2024; 14:11941. [PMID: 38789490 PMCID: PMC11126653 DOI: 10.1038/s41598-024-62791-9] [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: 03/13/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024] Open
Abstract
The emergence of newer SARS-CoV-2 variants of concern (VOCs) profoundly changed the ICU demography; this shift in the virus's genotype and its correlation to lethality in the ICUs is still not fully investigated. We aimed to survey ICU patients' clinical and laboratory parameters in correlation with SARS-CoV-2 variant genotypes to lethality. 503 COVID-19 ICU patients were included in our study beginning in January 2021 through November 2022 in Hungary. Furthermore, we implemented random forest (RF) as a potential predictor regarding SARS-CoV-2 lethality among 649 ICU patients in two ICU centers. Survival analysis and comparison of hypertension (HT), diabetes mellitus (DM), and vaccination effects were conducted. Logistic regression identified DM as a significant mortality risk factor (OR: 1.55, 95% CI 1.06-2.29, p = 0.025), while HT showed marginal significance. Additionally, vaccination demonstrated protection against mortality (p = 0.028). RF detected lethality with 81.42% accuracy (95% CI 73.01-88.11%, [AUC]: 91.6%), key predictors being PaO2/FiO2 ratio, lymphocyte count, and chest Computed Tomography Severity Score (CTSS). Although a smaller number of patients require ICU treatment among Omicron cases, the likelihood of survival has not proportionately increased for those who are admitted to the ICU. In conclusion, our RF model supports more effective clinical decision-making among ICU COVID-19 patients.
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Affiliation(s)
- Ágoston Hamar
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
- Molecular Medicine Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Daryan Mohammed
- Molecular Medicine Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Alex Váradi
- Molecular Medicine Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - Róbert Herczeg
- Molecular Medicine Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Norbert Balázsfalvi
- Department of Anaesthesiology and Intensive Care, University of Debrecen, Debrecen, Hungary
| | - Béla Fülesdi
- Department of Anaesthesiology and Intensive Care, University of Debrecen, Debrecen, Hungary
| | - István László
- Department of Anaesthesiology and Intensive Care, University of Debrecen, Debrecen, Hungary
| | - Lídia Gömöri
- Doctoral School of Neuroscience, University of Debrecen, Debrecen, Hungary
| | | | - Gabor Laszlo Kovacs
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
- Molecular Medicine Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Krisztián Jáksó
- Department of Anaesthesiology and Intensive Care, Clinical Centre, University of Pécs, Pécs, Hungary
| | - Katalin Gombos
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary.
- Molecular Medicine Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
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13
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Chang YH, Hsu MF, Chen WN, Wu MH, Kong WL, Lu MYJ, Huang CH, Chang FJ, Chang LY, Tsai HY, Tung CP, Yu JH, Kuo Y, Chou YC, Bai LY, Chang YC, Chen AY, Chen CC, Chen YH, Liao CC, Chang CS, Liang JJ, Lin YL, Angata T, Hsu STD, Lin KI. Functional and structural investigation of a broadly neutralizing SARS-CoV-2 antibody. JCI Insight 2024; 9:e179726. [PMID: 38775156 PMCID: PMC11141937 DOI: 10.1172/jci.insight.179726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/12/2024] [Indexed: 06/02/2024] Open
Abstract
Since its emergence, SARS-CoV-2 has been continuously evolving, hampering the effectiveness of current vaccines against COVID-19. mAbs can be used to treat patients at risk of severe COVID-19. Thus, the development of broadly protective mAbs and an understanding of the underlying protective mechanisms are of great importance. Here, we isolated mAbs from donors with breakthrough infection with Omicron subvariants using a single-B cell screening platform. We identified a mAb, O5C2, which possesses broad-spectrum neutralization and antibody-dependent cell-mediated cytotoxic activities against SARS-CoV-2 variants, including EG.5.1. Single-particle analysis by cryo-electron microscopy revealed that O5C2 targeted an unusually large epitope within the receptor-binding domain of spike protein that overlapped with the angiotensin-converting enzyme 2 binding interface. Furthermore, O5C2 effectively protected against BA.5 Omicron infection in vivo by mediating changes in transcriptomes enriched in genes involved in apoptosis and interferon responses. Our findings provide insights into the development of pan-protective mAbs against SARS-CoV-2.
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Affiliation(s)
- Yi-Hsuan Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | | | - Wei-Nan Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Wye-Lup Kong
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Heng Huang
- Institute of Preventive Medicine
- Graduate Institute of Medical Sciences, and
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Fang-Ju Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Ho-Yang Tsai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jou-Hui Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yali Kuo
- Biomedical Translation Research Center (BioTReC)
| | - Yu-Chi Chou
- Biomedical Translation Research Center (BioTReC)
| | - Li-Yang Bai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yuan-Chih Chang
- Institute of Biological Chemistry and
- Academia Sinica Cryo-EM Center, and
| | - An-Yu Chen
- Institute of Preventive Medicine
- Graduate Institute of Medical Sciences, and
| | - Cheng-Cheung Chen
- Institute of Preventive Medicine
- Graduate Institute of Medical Sciences, and
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lin
- Biomedical Translation Research Center (BioTReC)
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Takashi Angata
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry and
| | - Shang-Te Danny Hsu
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry and
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKC M2, ) Hiroshima University, Hiroshima, Japan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center (BioTReC)
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14
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Tamura T, Ito H, Torii S, Wang L, Suzuki R, Tsujino S, Kamiyama A, Oda Y, Tsuda M, Morioka Y, Suzuki S, Shirakawa K, Sato K, Yoshimatsu K, Matsuura Y, Iwano S, Tanaka S, Fukuhara T. Akaluc bioluminescence offers superior sensitivity to track in vivo dynamics of SARS-CoV-2 infection. iScience 2024; 27:109647. [PMID: 38638572 PMCID: PMC11025001 DOI: 10.1016/j.isci.2024.109647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/25/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Monitoring in vivo viral dynamics can improve our understanding of pathogenicity and tissue tropism. Because the gene size of RNA viruses is typically small, NanoLuc is the primary choice for accommodation within viral genome. However, NanoLuc/Furimazine and also the conventional firefly luciferase/D-luciferin are known to exhibit relatively low tissue permeability and thus less sensitivity for visualization of deep tissue including lungs. Here, we demonstrated in vivo sufficient visualization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection using the pair of a codon-optimized Akaluc and AkaLumine. We engineered the codon-optimized Akaluc gene possessing the similar GC ratio of SARS-CoV-2. Using the SARS-CoV-2 recombinants carrying the codon-optimized Akaluc, we visualized in vivo infection of respiratory organs, including the tissue-specific differences associated with particular variants. Additionally, we could evaluate the efficacy of antivirals by monitoring changes in Akaluc signals. Overall, we offer an effective technology for monitoring viral dynamics in live animals.
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Affiliation(s)
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
| | - Shiho Torii
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
| | - Akifumi Kamiyama
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Yuhei Morioka
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Tokyo 113-0033, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Tokyo 108-8639, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Kumamoto 860-0811, Japan
| | - Kumiko Yoshimatsu
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Satoshi Iwano
- Institute for Tenure Track Promotion, University of Miyazaki, Miyazaki, Miyazaki 889-2192, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Tokyo 100-0004, Japan
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15
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Jacob-Dolan C, Lifton M, Powers OC, Miller J, Hachmann NP, Vu M, Surve N, Mazurek CR, Fisher JL, Rodrigues S, Patio RC, Anand T, Le Gars M, Sadoff J, Schmidt AG, Barouch DH. B cell somatic hypermutation following COVID-19 vaccination with Ad26.COV2.S. iScience 2024; 27:109716. [PMID: 38655202 PMCID: PMC11035370 DOI: 10.1016/j.isci.2024.109716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/02/2024] [Accepted: 04/07/2024] [Indexed: 04/26/2024] Open
Abstract
The viral vector-based COVID-19 vaccine Ad26.COV2.S has been recommended by the WHO since 2021 and has been administered to over 200 million people. Prior studies have shown that Ad26.COV2.S induces durable neutralizing antibodies (NAbs) that increase in coverage of variants over time, even in the absence of boosting or infection. Here, we studied humoral responses following Ad26.COV2.S vaccination in individuals enrolled in the initial Phase 1/2a trial of Ad26.COV2.S in 2020. Through 8 months post vaccination, serum NAb responses increased to variants, including B.1.351 (Beta) and B.1.617.2 (Delta), without additional boosting or infection. The level of somatic hypermutation, measured by nucleotide changes in the VDJ region of the heavy and light antibody chains, increased in Spike-specific B cells. Highly mutated mAbs from these sequences neutralized more SARS-CoV-2 variants than less mutated comparators. These findings suggest that the increase in NAb breadth over time following Ad26.COV2.S vaccination is mediated by affinity maturation.
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Affiliation(s)
- Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Microbiology, Boston, MA, USA
- Harvard Medical School, Department of Immunology, Boston, MA, USA
| | - Michelle Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Olivia C. Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nicole P. Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mya Vu
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Nehalee Surve
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Camille R. Mazurek
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jana L. Fisher
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Stefanie Rodrigues
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert C. Patio
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Trisha Anand
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mathieu Le Gars
- Janssen Vaccines and Prevention B.V., Leiden, the Netherlands
| | - Jerald Sadoff
- Janssen Vaccines and Prevention B.V., Leiden, the Netherlands
| | - Aaron G. Schmidt
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Microbiology, Boston, MA, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Immunology, Boston, MA, USA
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16
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De Greve H, Fioravanti A. Single domain antibodies from camelids in the treatment of microbial infections. Front Immunol 2024; 15:1334829. [PMID: 38827746 PMCID: PMC11140111 DOI: 10.3389/fimmu.2024.1334829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/29/2024] [Indexed: 06/04/2024] Open
Abstract
Infectious diseases continue to pose significant global health challenges. In addition to the enduring burdens of ailments like malaria and HIV, the emergence of nosocomial outbreaks driven by antibiotic-resistant pathogens underscores the ongoing threats. Furthermore, recent infectious disease crises, exemplified by the Ebola and SARS-CoV-2 outbreaks, have intensified the pursuit of more effective and efficient diagnostic and therapeutic solutions. Among the promising options, antibodies have garnered significant attention due to their favorable structural characteristics and versatile applications. Notably, nanobodies (Nbs), the smallest functional single-domain antibodies of heavy-chain only antibodies produced by camelids, exhibit remarkable capabilities in stable antigen binding. They offer unique advantages such as ease of expression and modification and enhanced stability, as well as improved hydrophilicity compared to conventional antibody fragments (antigen-binding fragments (Fab) or single-chain variable fragments (scFv)) that can aggregate due to their low solubility. Nanobodies directly target antigen epitopes or can be engineered into multivalent Nbs and Nb-fusion proteins, expanding their therapeutic potential. This review is dedicated to charting the progress in Nb research, particularly those derived from camelids, and highlighting their diverse applications in treating infectious diseases, spanning both human and animal contexts.
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Affiliation(s)
- Henri De Greve
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Antonella Fioravanti
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Fondazione ParSeC – Parco delle Scienze e della Cultura, Prato, Italy
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17
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Futatsusako H, Hashimoto R, Yamamoto M, Ito J, Matsumura Y, Yoshifuji H, Shirakawa K, Takaori-Kondo A, Sato K, Nagao M, Takayama K. Longitudinal analysis of genomic mutations in SARS-CoV-2 isolates from persistent COVID-19 patient. iScience 2024; 27:109597. [PMID: 38638575 PMCID: PMC11024907 DOI: 10.1016/j.isci.2024.109597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
A primary reason for the ongoing spread of coronavirus disease 2019 (COVID-19) is the continuous acquisition of mutations by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the mechanism of acquiring mutations is not fully understood. In this study, we isolated SARS-CoV-2 from an immunocompromized patient persistently infected with Omicron strain BF.5 for approximately 4 months to analyze its genome and evaluate drug resistance. Although the patient was administered the antiviral drug remdesivir (RDV), there were no acquired mutations in RDV binding site, and all isolates exhibited susceptibility to RDV. Notably, upon analyzing the S protein sequence of the day 119 isolate, we identified mutations acquired by mutant strains emerging from the BF.5 variant, suggesting that viral genome analysis in persistent COVID-19 patients may be useful in predicting viral evolution. These results suggest mutations in SARS-CoV-2 are acquired during long-term viral replication rather than in response to antiviral drugs.
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Affiliation(s)
- Hiroki Futatsusako
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 6068507, Japan
| | - Rina Hashimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 6068507, Japan
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 1138654, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Kotaro Shirakawa
- Department of Hematology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - The Genotype to Phenotype Japan (G2P-Japan) Consortium
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 6068507, Japan
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 1138654, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
- Department of Hematology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2770882, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo 1000004, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 1138654, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2770882, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 6068507, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo 1000004, Japan
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18
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Shim K, Hwang EH, Kim G, Woo YM, An YJ, Baek SH, Oh T, Kim Y, Jang K, Hong JJ, Koo BS. Molecular evolutionary characteristics of severe acute respiratory syndrome coronavirus 2 and the relatedness of epidemiological and socio-environmental factors. Heliyon 2024; 10:e30222. [PMID: 38737246 PMCID: PMC11088249 DOI: 10.1016/j.heliyon.2024.e30222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
After the first outbreak, SARS-CoV-2 infection continues to occur due to the emergence of new variants. There is limited information available on the comparative evaluation of evolutionary characteristics of SARS-CoV-2 among different countries over time, and its relatedness to epidemiological and socio-environmental factors within those countries. We assessed comparative Bayesian evolutionary characteristics for SARS-CoV-2 in eight countries from 2020 to 2022 using BEAST version 2.6.7. Additionally, the relatedness between virus evolution factors and both epidemiological and socio-environmental factors was analyzed using Pearson's correlation coefficient. The estimated substitution rates in the gene encoding S protein of SARS-CoV-2 exhibited a continuous increase from 2020 to 2022 and were divided into two distinct groups in 2022 (p value < 0.05). Effective population size (Ne) generally showed decreased patterns by time. Notably, the change rates of the substitution rates were negatively correlated with the cumulative vaccination rates in 2021. A strict and rapid vaccination policy in the United Arab Emirates dramatically reduced the evolution of the virus, compared to other countries. Also, the average yearly temperature in countries were negatively correlated with the substitution rates. The changes of six epitopes in SARS-CoV-2 were related to various socio-environmental factors. We figured out comparative virus evolutionary traits and the association of epidemiological and socio-environmental factors especially cumulative vaccination rates and average temperature.
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Affiliation(s)
- Kyuyoung Shim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Eun-Ha Hwang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Green Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Young Min Woo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - You Jung An
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Seung Ho Baek
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Taehwan Oh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Yujin Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Kiwon Jang
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Bon-Sang Koo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
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19
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Han T, Song L, Niu X, Qiu M, Wang Y, Wang J, Sun X, Ma J, Hu S, Feng Z. Synergistic peptide combinations designed to suppress SARS-CoV-2. Heliyon 2024; 10:e30489. [PMID: 38726116 PMCID: PMC11079089 DOI: 10.1016/j.heliyon.2024.e30489] [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: 10/18/2023] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024] Open
Abstract
The SARS-CoV-2, responsible for the COVID-19 pandemic, poses a significant threat to global healthcare. Peptide and peptide-based inhibitors, known for their safety, efficacy, and selectivity, have recently emerged as promising candidates for treating late-developing viral infections. In this study, three peptides were selected to target different stages of viral invasion, specifically ACE2 and S protein binding, as well as membrane fusion. The objective was to assess their ability to impede the entry of the SARS-CoV-2 Spike pseudotyped virus. Our findings revealed that a combination of these three peptides demonstrated enhanced antiviral effects. This outcome substantiates the feasibility of developing effective peptide combinations to combat diseases related to SARS-CoV-2. Moreover, the three-peptide combinations, designed to target multiple aspects of SARS-CoV-2 viral entry, exhibited heightened viral inhibition and broad-spectrum antiviral properties.
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Affiliation(s)
- Tao Han
- Department of Neonatology, Senior Department of Pediatrics, the Seventh Medical Center of Chinese PLA General Hospital, China
| | - Linhong Song
- Department of Pediatric Cardiac Surgery, Senior Department of Pediatrics, the Seventh Medical Center of Chinese PLA General Hospital, China
| | - Xinxin Niu
- Department of Organ Transplantation, the Third Medical Center of Chinese PLA General Hospital, China
| | - Meng Qiu
- Senior Department of Pediatrics, the Seventh Medical Center of Chinese PLA General Hospital, China
| | - Yi Wang
- Institute of Pediatrics, Senior Department of Pediatrics, the Seventh Medical Center of Chinese PLA General Hospital, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, the Seventh Medical Center of Chinese PLA General Hospital, China
| | - Xiuyan Sun
- Department of Obstetrics and Gynecology, the Seventh Medical Center of Chinese PLA General Hospital, China
| | - Jiali Ma
- Department of Clinical Laboratory, the Seventh Medical Center of Chinese PLA General Hospital, China
| | - Siqi Hu
- Institute of Pediatrics, Senior Department of Pediatrics, the Seventh Medical Center of Chinese PLA General Hospital, China
| | - Zhichun Feng
- Senior Department of Pediatrics, the Seventh Medical Center of Chinese PLA General Hospital, China
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20
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Kemper S, de Vries M, de Weger E, Bongers M, Kupper F, Timen A. The public's considerations about implementing non-pharmaceutical interventions to manage a novel COVID-19 epidemic. Heliyon 2024; 10:e30390. [PMID: 38737250 PMCID: PMC11088335 DOI: 10.1016/j.heliyon.2024.e30390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
In the future, new variants of the SARS-CoV-2 virus might emerge and cause outbreaks. If this occurs, the implementation of non-pharmaceutical interventions (NPIs) can be reconsidered. Consideration of the potential benefits and harms of implementing NPIs, and ultimately deciding about implementing NPIs, is currently mainly executed by experts and governments. However, general literature on public engagement suggests that integrating public perspectives into decision-making can enhance the quality of decisions and foster greater public understanding of them. In this study, a deliberative mini-public was conducted to integrate this public perspective. The aim was to elicit public considerations regarding non-pharmaceutical interventions by asking a diverse group of citizens to participate as decision-makers and convene, learn and deliberate about implementing non-pharmaceutical interventions during a hypothetical outbreak of a new SARS-CoV-2 variant. Participants emphasized the importance of early implementation during the outbreak, to prevent exceeding healthcare capacity, long-term mental health issues, educational deficits, and bankruptcies. Additionally, participants stressed taking public support into account, and shared ideas on maintaining support. Furthermore, participants wanted to give citizens personal responsibility and freedom in making their own assessment regarding adherence to interventions and how much risk of infection they would be willing to accept. Participants also expressed the need for the government to adopt a learning attitude towards improvements in pandemic response, and to generate more focus on long-term strategies. The deliberative mini-public, revealed public considerations that reflected public values and needs. These considerations might be helpful in better aligning epidemic management policies with public perspectives. Regarding the deliberative mini-public, uncertainties remain about the design and impact on a bigger scale.
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Affiliation(s)
- Sophie Kemper
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Athena Institute, Faculty of Science, VU Amsterdam, Amsterdam, the Netherlands
| | - Marion de Vries
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Esther de Weger
- Athena Institute, Faculty of Science, VU Amsterdam, Amsterdam, the Netherlands
| | - Marloes Bongers
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Frank Kupper
- Athena Institute, Faculty of Science, VU Amsterdam, Amsterdam, the Netherlands
| | - Aura Timen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Athena Institute, Faculty of Science, VU Amsterdam, Amsterdam, the Netherlands
- Department of Primary and Community Care, Radboud University Medical Center, Nijmegen, the Netherlands
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21
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Takada K, Orba Y, Kida Y, Wu J, Ono C, Matsuura Y, Nakagawa S, Sawa H, Watanabe T. Genes involved in the limited spread of SARS-CoV-2 in the lower respiratory airways of hamsters may be associated with adaptive evolution. J Virol 2024; 98:e0178423. [PMID: 38624229 PMCID: PMC11092350 DOI: 10.1128/jvi.01784-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
Novel respiratory viruses can cause a pandemic and then evolve to coexist with humans. The Omicron strain of severe acute respiratory syndrome coronavirus 2 has spread worldwide since its emergence in late 2021, and its sub-lineages are now established in human society. Compared to previous strains, Omicron is markedly less invasive in the lungs and causes less severe disease. One reason for this is that humans are acquiring immunity through previous infection and vaccination, but the nature of the virus itself is also changing. Using our newly established low-volume inoculation system, which reflects natural human infection, we show that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain. Furthermore, by characterizing chimeric viruses with the Omicron gene in the Wuhan strain genetic background and vice versa, we found that viral genes downstream of ORF3a, but not the S gene, were responsible for the limited spread of the Omicron strain in the lower airways of the virus-infected hamsters. Moreover, molecular evolutionary analysis of SARS-CoV-2 revealed a positive selection of genes downstream of ORF3a (M and E genes). Our findings provide insight into the adaptive evolution of the virus in humans during the pandemic convergence phase.IMPORTANCEThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread worldwide since its emergence in late 2021, and its sub-lineages are established in human society. Compared to previous strains, the Omicron strain is less invasive in the lower respiratory tract, including the lungs, and causes less severe disease; however, the mechanistic basis for its restricted replication in the lower airways is poorly understood. In this study, using a newly established low-volume inoculation system that reflects natural human infection, we demonstrated that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain and found that viral genes downstream of ORF3a are responsible for replication restriction in the lower respiratory tract of Omicron-infected hamsters. Furthermore, we detected a positive selection of genes downstream of ORF3a (especially the M and E genes) in SARS-CoV-2, suggesting that these genes may undergo adaptive changes in humans.
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Grants
- 16H06429, 16K21723, 16H06434, JP22H02521 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H02736 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP16K21723, JP16H06432 MEXT | Japan Society for the Promotion of Science (JSPS)
- 22K15469, 21J01036 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20fk0108281, JP19fk0108113, JP20pc0101047 Japan Agency for Medical Research and Development (AMED)
- JP20fk0108401, JP21fk0108493 Japan Agency for Medical Research and Development (AMED)
- JP23wm0125008, JP223fa627005 Japan Agency for Medical Research and Development (AMED)
- JP19fk018113, JP223fa627002h, 22gm1610010h0001 Japan Agency for Medical Research and Development (AMED)
- JPMJMS2025 MEXT | Japan Science and Technology Agency (JST)
- JPMJCR20H6 MEXT | Japan Science and Technology Agency (JST)
- Takeda Science Foundation (TSF)
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Affiliation(s)
- Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yurie Kida
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hirofumi Sawa
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Virus Network, Baltimore, Maryland, USA
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
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22
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Mao D, Liu S, Phan AT, Renner S, Sun Y, Wang TT, Zhu Y. The TRAF3-DYRK1A-RAD54L2 complex maintains ACE2 expression to promote SARS-CoV-2 infection. J Virol 2024; 98:e0034724. [PMID: 38651897 PMCID: PMC11092330 DOI: 10.1128/jvi.00347-24] [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: 02/21/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Angiotensin converting enzyme 2 (ACE2), the host receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, is differentially expressed in a wide variety of tissues and cell types. The expression of ACE2 is under tight regulation, but the mechanisms regulating ACE2 expression have not yet been well defined. Through a genome-wide CRISPR knockout screen, we discovered that host factors TRAF3, DYRK1A, and RAD54L2 (TDR) form a complex to regulate the expression of ACE2. Knockout of TRAF3, DYRK1A, or RAD54L2 reduces the mRNA levels of ACE2 and inhibits the cellular entry of SARS-CoV-2. On the other hand, SARS-CoV-2 continuously evolves by genetic mutations for the adaption to the host. We have identified mutations in spike (S) (P1079T) and nucleocapsid (N) (S194L) that enhance the replication of SARS-CoV-2 in cells that express ACE2 at a low level. Our results have revealed the mechanisms for the transcriptional regulation of ACE2 and the adaption of SARS-CoV-2. IMPORTANCE The expression of ACE2 is essential for the entry of SARS-CoV-2 into host cells. We identify a new complex-the TDR complex-that acts to maintain the abundance of ACE2 in host cells. The identification and characterization of the TDR complex provide new targets for the development of therapeutics against SARS-CoV-2 infection. By analysis of SARS-CoV-2 virus replicating in cells expressing low levels of ACE2, we identified mutations in spike (P1079T) and nucleocapsid (S194L) that overcome the restriction of limited ACE2. Functional analysis of these key amino acids in S and N extends our knowledge of the impact of SARS-CoV-2 variants on virus infection and transmission.
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Affiliation(s)
- Dexin Mao
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Shufeng Liu
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - An Thanh Phan
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Stephanie Renner
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Yan Sun
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Tony T. Wang
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yiping Zhu
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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23
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Chen W, Jiang X, Liang W, Bai H, Xu M, Liu Z, Yi L, Liu Y, Huang Y, Zhang Y, Xu L, Xie B, Zhang N, Yu J, Lu J, Xiao H, Li X. SARS-CoV-2 Omicron Variants Show Attenuated Neurovirulence Compared with the Wild-Type Strain in Elderly Human Brain Spheroids. RESEARCH (WASHINGTON, D.C.) 2024; 7:0376. [PMID: 38741604 PMCID: PMC11089278 DOI: 10.34133/research.0376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/13/2024] [Indexed: 05/16/2024]
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 Omicron variants still causes neurological complications in elderly individuals. However, whether and how aging brains are affected by Omicron variants in terms of neuroinvasiveness and neurovirulence are unknown. Here, we utilize resected paracarcinoma brain tissue from elderly individuals to generate primary brain spheroids (BSs) for investigating the replication capability of live wild-type (WT) strain and Omicron (BA.1/BA.2), as well as the mechanisms underlying their neurobiological effects. We find that both WT and Omicron BA.1/BA.2 are able to enter BSs but weakly replicate. There is no difference between Omicron BA.1/BA.2 and WT strains in neurotropism in aging BSs. However, Omicron BA.1/BA.2 exhibits ameliorating neurological damage. Transcriptional profiling indicates that Omicron BA.1/BA.2 induces a lower neuroinflammatory response than WT strain in elderly BSs, suggesting a mechanistic explanation for their attenuated neuropathogenicity. Moreover, we find that both Omicron BA.1/BA.2 and WT strain infections disrupt neural network activity associated with neurodegenerative disorders by causing neuron degeneration and amyloid-β deposition in elderly BSs. These results uncover Omicron-specific mechanisms and cellular immune responses associated with severe acute respiratory syndrome coronavirus 2-induced neurological complications.
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Affiliation(s)
- Weikang Chen
- Department of Neurosurgery,
The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Xiaobing Jiang
- Department of Neurosurgery/Neuro-Oncology, State Key Laboratory of Oncology in South China,
Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou 510000, China
| | - Wei Liang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Haojie Bai
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Mingze Xu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Zhe Liu
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 510000, China
| | - Lina Yi
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 510000, China
| | - Yanming Liu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Yanxia Huang
- Department of Neurosurgery,
The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Yongxin Zhang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Lixia Xu
- Department of Oncology,
The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Baoshu Xie
- Department of Neurosurgery,
The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Nu Zhang
- Department of Neurosurgery,
The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Jun Yu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
- Department of Medicine and Therapeutics and Institute of Digestive Disease, State Key Laboratory of Digestive Disease,
The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Jing Lu
- Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 510000, China
| | - Haipeng Xiao
- Department of Endocrinology,
The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Xiaoxing Li
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
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24
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Yao F, Xu M, Dong L, Shen X, Shen Y, Jiang Y, Zhu T, Zhang C, Yu G. Sinomenine attenuates pulmonary fibrosis by downregulating TGF-β1/Smad3, PI3K/Akt and NF-κB signaling pathways. BMC Pulm Med 2024; 24:229. [PMID: 38730387 PMCID: PMC11088103 DOI: 10.1186/s12890-024-03050-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/07/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Since COVID-19 became a global epidemic disease in 2019, pulmonary fibrosis (PF) has become more prevalent among persons with severe infections, with IPF being the most prevalent form. In traditional Chinese medicine, various disorders are treated using Sinomenine (SIN). The SIN's strategy for PF defense is unclear. METHODS Bleomycin (BLM) was used to induce PF, after which inflammatory factors, lung histological alterations, and the TGF-/Smad signaling pathway were assessed. By administering various dosages of SIN and the TGF- receptor inhibitor SB-431,542 to human embryonic lung fibroblasts (HFL-1) and A549 cells, we were able to examine proliferation and migration as well as the signaling molecules implicated in Epithelial-Mesenchymal Transition (EMT) and Extra-Cellular Matrix (ECM). RESULTS In vivo, SIN reduced the pathological changes in the lung tissue induced by BLM, reduced the abnormal expression of inflammatory cytokines, and improved the weight and survival rate of mice. In vitro, SIN inhibited the migration and proliferation by inhibiting TGF-β1/Smad3, PI3K/Akt, and NF-κB pathways, prevented the myofibroblasts (FMT) of HFL-1, reversed the EMT of A549 cells, restored the balance of matrix metalloenzymes, and reduced the expression of ECM proteins. CONCLUSION SIN attenuated PF by down-regulating TGF-β/Smad3, PI3K/Akt, and NF-κB signaling pathways, being a potential effective drug in the treatment of PF.
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Affiliation(s)
- Fuqiang Yao
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, Zhejiang, China
| | - Minghao Xu
- School of Medicine, ShaoXing University, Shaoxing, Zhejiang, China
| | - Lingjun Dong
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, Zhejiang, China
| | - Xiao Shen
- School of Medicine, ShaoXing University, Shaoxing, Zhejiang, China
| | - Yujie Shen
- School of Medicine, ShaoXing University, Shaoxing, Zhejiang, China
| | - Yisheng Jiang
- School of Medicine, ShaoXing University, Shaoxing, Zhejiang, China
| | - Ting Zhu
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, Zhejiang, China
| | - Chu Zhang
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, Zhejiang, China
| | - Guangmao Yu
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, Zhejiang, China.
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25
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Ose NJ, Campitelli P, Modi T, Kazan IC, Kumar S, Ozkan SB. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 2024; 12:RP92063. [PMID: 38713502 PMCID: PMC11076047 DOI: 10.7554/elife.92063] [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] [Indexed: 05/08/2024] Open
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
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Affiliation(s)
- Nicholas James Ose
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - I Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple UniversityPhiladelphiaUnited States
- Department of Biology, Temple UniversityPhiladelphiaUnited States
- Center for Genomic Medicine Research, King Abdulaziz UniversityJeddahSaudi Arabia
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
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Er AG, Ding DY, Er B, Uzun M, Cakmak M, Sadee C, Durhan G, Ozmen MN, Tanriover MD, Topeli A, Aydin Son Y, Tibshirani R, Unal S, Gevaert O. Multimodal data fusion using sparse canonical correlation analysis and cooperative learning: a COVID-19 cohort study. NPJ Digit Med 2024; 7:117. [PMID: 38714751 PMCID: PMC11076490 DOI: 10.1038/s41746-024-01128-2] [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] [Accepted: 04/25/2024] [Indexed: 05/10/2024] Open
Abstract
Through technological innovations, patient cohorts can be examined from multiple views with high-dimensional, multiscale biomedical data to classify clinical phenotypes and predict outcomes. Here, we aim to present our approach for analyzing multimodal data using unsupervised and supervised sparse linear methods in a COVID-19 patient cohort. This prospective cohort study of 149 adult patients was conducted in a tertiary care academic center. First, we used sparse canonical correlation analysis (CCA) to identify and quantify relationships across different data modalities, including viral genome sequencing, imaging, clinical data, and laboratory results. Then, we used cooperative learning to predict the clinical outcome of COVID-19 patients: Intensive care unit admission. We show that serum biomarkers representing severe disease and acute phase response correlate with original and wavelet radiomics features in the LLL frequency channel (cor(Xu1, Zv1) = 0.596, p value < 0.001). Among radiomics features, histogram-based first-order features reporting the skewness, kurtosis, and uniformity have the lowest negative, whereas entropy-related features have the highest positive coefficients. Moreover, unsupervised analysis of clinical data and laboratory results gives insights into distinct clinical phenotypes. Leveraging the availability of global viral genome databases, we demonstrate that the Word2Vec natural language processing model can be used for viral genome encoding. It not only separates major SARS-CoV-2 variants but also allows the preservation of phylogenetic relationships among them. Our quadruple model using Word2Vec encoding achieves better prediction results in the supervised task. The model yields area under the curve (AUC) and accuracy values of 0.87 and 0.77, respectively. Our study illustrates that sparse CCA analysis and cooperative learning are powerful techniques for handling high-dimensional, multimodal data to investigate multivariate associations in unsupervised and supervised tasks.
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Affiliation(s)
- Ahmet Gorkem Er
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey.
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey.
| | - Daisy Yi Ding
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Berrin Er
- Department of Internal Medicine, Division of Intensive Care Medicine, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Mertcan Uzun
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Mehmet Cakmak
- Department of Internal Medicine, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Christoph Sadee
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Gamze Durhan
- Department of Radiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Mustafa Nasuh Ozmen
- Department of Radiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Mine Durusu Tanriover
- Department of Internal Medicine, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Arzu Topeli
- Department of Internal Medicine, Division of Intensive Care Medicine, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Yesim Aydin Son
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Robert Tibshirani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Serhat Unal
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, 06230, Ankara, Turkey
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
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27
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Razonable RR. Protecting the vulnerable: addressing the COVID-19 care needs of people with compromised immunity. Front Immunol 2024; 15:1397040. [PMID: 38756784 PMCID: PMC11096526 DOI: 10.3389/fimmu.2024.1397040] [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: 03/06/2024] [Accepted: 04/08/2024] [Indexed: 05/18/2024] Open
Abstract
While the general population regained a certain level of normalcy with the end of the global health emergency, the risk of contracting COVID-19 with a severe outcome is still a major concern for people with compromised immunity. This paper reviews the impact of COVID-19 on people with immunocompromised status, identifies the gaps in the current management landscape, and proposes actions to address this unmet need. Observational studies have demonstrated that people with immune dysfunction have a higher risk of COVID-19-related hospitalization and death, despite vaccination, than the general population. More research is needed to define the optimal prevention and treatment strategies that are specific to people with immunocompromised status, including novel vaccination strategies, monoclonal antibodies that provide passive immunity and complement suboptimal vaccination responses, and improved and safer antiviral treatment for COVID-19. Preventive measures beyond vaccination alone are urgently needed to protect this vulnerable population.
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Affiliation(s)
- Raymund R. Razonable
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, United States
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN, United States
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28
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Hyun H, Nham E, Seong H, Yoon JG, Noh JY, Cheong HJ, Kim WJ, Yoon SK, Park SJ, Gwak W, Lee JW, Kim B, Song JY. Long-term humoral and cellular immunity against vaccine strains and Omicron subvariants (BQ.1.1, BN.1, XBB.1, and EG.5) after bivalent COVID-19 vaccination. Front Immunol 2024; 15:1385135. [PMID: 38756783 PMCID: PMC11096540 DOI: 10.3389/fimmu.2024.1385135] [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: 02/12/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Background The assessment of long-term humoral and cellular immunity post-vaccination is crucial for establishing an optimal vaccination strategy. Methods This prospective cohort study evaluated adults (≥18 years) who received a BA.4/5 bivalent vaccine. We measured the anti-receptor binding domain immunoglobulin G antibody and neutralizing antibodies (NAb) against wild-type and Omicron subvariants (BA.5, BQ.1.1, BN.1, XBB.1 and EG.5) up to 9 months post-vaccination. T-cell immune responses were measured before and 4 weeks after vaccination. Results A total of 108 (28 SARS-CoV-2-naïve and 80 previously infected) participants were enrolled. Anti-receptor binding domain immunoglobulin G (U/mL) levels were higher at 9 months post-vaccination than baseline in SAR-CoV-2-naïve individuals (8,339 vs. 1,834, p<0.001). NAb titers against BQ.1.1, BN.1, and XBB.1 were significantly higher at 9 months post-vaccination than baseline in both groups, whereas NAb against EG.5 was negligible at all time points. The T-cell immune response (median spot forming unit/106 cells) was highly cross-reactive at both baseline (wild-type/BA.5/XBB.1.5, 38.3/52.5/45.0 in SARS-CoV-2-naïve individuals; 51.6/54.9/54.9 in SARS-CoV-2-infected individuals) and 4 weeks post-vaccination, with insignificant boosting post-vaccination. Conclusion Remarkable cross-reactive neutralization was observed against BQ.1.1, BN.1, and XBB.1 up to 9 months after BA.4/5 bivalent vaccination, but not against EG.5. The T-cell immune response was highly cross-reactive.
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Affiliation(s)
- Hakjun Hyun
- Department of Infectious Diseases, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Eliel Nham
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hye Seong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Gu Yoon
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Yun Noh
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee Jin Cheong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woo Joo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sun Kyung Yoon
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Se-Jin Park
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - WonSeok Gwak
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - June-Woo Lee
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Byoungguk Kim
- Division of Vaccine Clinical Research, Center for Vaccine Research National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Joon Young Song
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Research and Development, Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea
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29
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Zanoni I. Aged nasal epithelium is more prone to severe COVID-19. Nat Immunol 2024; 25:722-724. [PMID: 38641720 DOI: 10.1038/s41590-024-01824-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Affiliation(s)
- Ivan Zanoni
- Harvard Medical School, and Boston Children's Hospital, Division of Immunology, Division of Gastroenterology, Boston, MA, USA.
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30
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Apostolopoulos V, Feehan J, Chavda VP. How do we change our approach to COVID with the changing face of disease? Expert Rev Anti Infect Ther 2024; 22:279-287. [PMID: 38642067 DOI: 10.1080/14787210.2024.2345881] [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: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
INTRODUCTION The emergence of SARS-CoV-2 triggered a global health emergency, causing > 7 million deaths thus far. Limited early knowledge spurred swift research, treatment, and vaccine developments. Implementation of public health measures such as, lockdowns and social distancing, disrupted economies and strained healthcare. Viral mutations highlighted the need for flexible strategies and strong public health infrastructure, with global collaboration crucial for pandemic control. AREAS COVERED (i) Revisiting diagnostic strategies, (ii) adapting to the evolving challenge of the virus, (iii) vaccines against new variants, (iv) vaccine hesitancy in the light of the evolving disease, (v) treatment strategies, (vi) hospital preparedness for changing clinical needs, (vii) global cooperation and data sharing, (viii) economic implications, and (ix) education and awareness- keeping communities informed. EXPERT OPINION The COVID-19 crisis forced unprecedented adaptation, emphasizing public health readiness, global unity, and scientific advancement. Key lessons highlight the importance of adaptability and resilience against uncertainties. As the pandemic evolves into a 'new normal,' ongoing vigilance, improved understanding, and available vaccines and treatments equip us for future challenges. Priorities now include proactive pandemic strategies, early warnings, supported healthcare, public education, and addressing societal disparities for better health resilience and sustainability.
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Affiliation(s)
- Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Immunology Program, St Albans, Australia
| | - Jack Feehan
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Immunology Program, St Albans, Australia
| | - Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L.M. College of Pharmacy, Ahmedabad, Gujarat, India
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31
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Tan CCS, van Dorp L, Balloux F. The evolutionary drivers and correlates of viral host jumps. Nat Ecol Evol 2024; 8:960-971. [PMID: 38528191 DOI: 10.1038/s41559-024-02353-4] [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: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epidemics and pandemics. While zoonotic host jumps have been extensively studied from an ecological perspective, little attention has gone into characterizing the evolutionary drivers and correlates underlying these events. To address this gap, we harnessed the entirety of publicly available viral genomic data, employing a comprehensive suite of network and phylogenetic analyses to investigate the evolutionary mechanisms underpinning recent viral host jumps. Surprisingly, we find that humans are as much a source as a sink for viral spillover events, insofar as we infer more viral host jumps from humans to other animals than from animals to humans. Moreover, we demonstrate heightened evolution in viral lineages that involve putative host jumps. We further observe that the extent of adaptation associated with a host jump is lower for viruses with broader host ranges. Finally, we show that the genomic targets of natural selection associated with host jumps vary across different viral families, with either structural or auxiliary genes being the prime targets of selection. Collectively, our results illuminate some of the evolutionary drivers underlying viral host jumps that may contribute to mitigating viral threats across species boundaries.
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Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, London, UK.
- The Francis Crick Institute, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
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32
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Zhong Y, Kang AYH, Tay CJX, Li HE, Elyana N, Tan CW, Yap WC, Lim JME, Le Bert N, Chan KR, Ong EZ, Low JG, Shek LP, Tham EH, Ooi EE. Correlates of protection against symptomatic SARS-CoV-2 in vaccinated children. Nat Med 2024; 30:1373-1383. [PMID: 38689059 DOI: 10.1038/s41591-024-02962-3] [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: 09/22/2023] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
The paucity of information on longevity of vaccine-induced immune responses and uncertainty of the correlates of protection hinder the development of evidence-based COVID-19 vaccination policies for new birth cohorts. Here, to address these knowledge gaps, we conducted a cohort study of healthy 5-12-year-olds vaccinated with BNT162b2. We serially measured binding and neutralizing antibody titers (nAbs), spike-specific memory B cell (MBC) and spike-reactive T cell responses over 1 year. We found that children mounted antibody, MBC and T cell responses after two doses of BNT162b2, with higher antibody and T cell responses than adults 6 months after vaccination. A booster (third) dose only improved antibody titers without impacting MBC and T cell responses. Among children with hybrid immunity, nAbs and T cell responses were highest in those infected after two vaccine doses. Binding IgG titers, MBC and T cell responses were predictive, with T cells being the most important predictor of protection against symptomatic infection before hybrid immunity; nAbs only correlated with protection after hybrid immunity. The stable MBC and T cell responses over time suggest sustained protection against symptomatic SARS-CoV-2 infection, even when nAbs wane. Booster vaccinations do not confer additional immunological protection to healthy children.
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Affiliation(s)
- Youjia Zhong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System (NUHS), Singapore, Singapore.
| | - Alicia Y H Kang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Carina J X Tay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Hui' En Li
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Nurul Elyana
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Chee Wah Tan
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee Chee Yap
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joey M E Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Nina Le Bert
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Kuan Rong Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Eugenia Z Ong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Jenny G Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Lynette P Shek
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System (NUHS), Singapore, Singapore
| | - Elizabeth Huiwen Tham
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System (NUHS), Singapore, Singapore
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
- Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore.
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33
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Li K, Xia Y, Ye H, Sun X, Shi B, Wu J. Effectiveness and safety of immune response to SARS‑CoV‑2 vaccine in patients with chronic kidney disease and dialysis: A systematic review and meta‑analysis. Biomed Rep 2024; 20:78. [PMID: 38590946 PMCID: PMC10999903 DOI: 10.3892/br.2024.1766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/02/2024] [Indexed: 04/10/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) vaccination is the most effective way to prevent COVID-19. However, for chronic kidney disease patients on long-term dialysis, there is a lack of evidence regarding the efficacy and safety of the immune response to the vaccine. The present meta-analysis explores the efficacy and safety of COVID-19 vaccine in the immune response of patients with chronic kidney disease (CKD) undergoing dialysis. PubMed, Web of Science, Science Direct, and Cochrane Library databases were systematically searched from January 1, 2020, to December 31, 2022. Data analysis was performed using REVMAN 5.1s and Stata14 software. Baseline data and endpoint events were extracted, mainly including age, sex, dialysis vintage, body mass index (BMI), vaccine type and dose, history of COVID-19 infection, seropositivity rate, antibody titer, pain at injection site, headache and other safety events. The meta-analysis included 33 trials involving 81,348 patients. The immune efficacy of patients with CKD and dialysis was 80% (95 CI, 73-87%). The seropositivity rate of individuals without COVID-19 infection was 76.48% (3,824/5,000), while the seropositivity rate of individuals with COVID-19 infection was 80.82% (1,858/2,299). The standard mean difference of antibody titers in CKD and dialysis patients with or without COVID-19 infection was 27.73 (95% CI, -19.58-75.04). A total of nine studies reported the most common adverse events: Pain at the injection site, accounting for 18% (95 CI, 6-29%), followed by fatigue and headache, accounting for 8 (95 CI, 4-13%) and 6% (95 CI, 2-9%), respectively. COVID-19 vaccine benefitted patients with CKD undergoing dialysis with seropositivity rate ≥80%. Adverse events such as fatigue, headache, and pain at the injection site may occur after COVID-19 vaccination but the incidence is low.
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Affiliation(s)
- Kejia Li
- Department of Nephrology, The First People's Hospital of Jiashan, Jiaxing, Zhejiang 314100, P.R. China
| | - Yang Xia
- Department of Nephrology, The First People's Hospital of Jiashan, Jiaxing, Zhejiang 314100, P.R. China
| | - Hua Ye
- Department of Nephrology, The First People's Hospital of Jiashan, Jiaxing, Zhejiang 314100, P.R. China
| | - Xian Sun
- Department of Nephrology, The First People's Hospital of Jiashan, Jiaxing, Zhejiang 314100, P.R. China
| | - Bairu Shi
- Department of Nephrology, The First People's Hospital of Jiashan, Jiaxing, Zhejiang 314100, P.R. China
| | - Jiajun Wu
- Department of Nephrology, The First People's Hospital of Jiashan, Jiaxing, Zhejiang 314100, P.R. China
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Balasco N, Damaggio G, Esposito L, Colonna V, Vitagliano L. A comprehensive analysis of SARS-CoV-2 missense mutations indicates that all possible amino acid replacements in the viral proteins occurred within the first two-and-a-half years of the pandemic. Int J Biol Macromol 2024; 266:131054. [PMID: 38522702 DOI: 10.1016/j.ijbiomac.2024.131054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
The surveillance of COVID-19 pandemic has led to the determination of millions of genome sequences of the SARS-CoV-2 virus, with the accumulation of a wealth of information never collected before for an infectious disease. Exploring the information retrieved from the GISAID database reporting at that time >13 million genome sequences, we classified the 141,639 unique missense mutations detected in the first two-and-a-half years (up to October 2022) of the pandemic. Notably, our analysis indicates that 98.2 % of all possible conservative amino acid replacements occurred. Even non-conservative mutations were highly represented (73.9 %). For a significant number of residues (3 %), all possible replacements with the other nineteen amino acids have been observed. These observations strongly indicate that, in this time interval, the virus explored all possible alternatives in terms of missense mutations for all sites of its polypeptide chain and that those that are not observed severely affect SARS-CoV-2 integrity. The implications of the present findings go well beyond the structural biology of SARS-CoV-2 as the huge amount of information here collected and classified may be valuable for the elucidation of the sequence-structure-function relationships in proteins.
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Affiliation(s)
- Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Dep. Chemistry, Sapienza University of Rome, Rome, Italy.
| | - Gianluca Damaggio
- Institute of Genetics and Biophysics, CNR, Naples, Italy; Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases, Department of Biosciences, University of Milan, Milan, Italy; University of Naples Federico II, Naples, Italy
| | | | - Vincenza Colonna
- Institute of Genetics and Biophysics, CNR, Naples, Italy; Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
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Suwanchaikasem P, Rattanapisit K, Strasser R, Phoolcharoen W. Quality control in SARS-CoV-2 RBD-Fc vaccine production using LC-MS to confirm strain selection and detect contaminations from other strains. Sci Rep 2024; 14:9629. [PMID: 38671013 PMCID: PMC11053075 DOI: 10.1038/s41598-024-59860-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Coronavirus disease of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing outbreak, disrupting human life worldwide. Vaccine development was prioritized to obtain a biological substance for combating the viral pathogen and lessening disease severity. In vaccine production, biological origin and relevant materials must be carefully examined for potential contaminants in conformity with good manufacturing practice. Due to fast mutation, several SARS-CoV-2 variants and sublineages have been identified. Currently, most of COVID-19 vaccines are developed based on the protein sequence of the Wuhan wild type strain. New vaccines specific for emerging SARS-CoV-2 strains are continuously needed to tackle the incessant evolution of the virus. Therefore, in vaccine development and production, a reliable method to identify the nature of subunit vaccines is required to avoid cross-contamination. In this study, liquid chromatography-mass spectrometry using quadrupole-time of flight along with tryptic digestion was developed for distinguishing protein materials derived from different SARS-CoV-2 strains. After analyzing the recombinantly produced receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, nine characteristic peptides were identified with acceptable limits of detection. They can be used together to distinguish 14 SARS-CoV-2 strains, except Kappa and Epsilon. Plant-produced RBD-Fc protein derived from Omicron strains can be easily distinguished from the others with 4-5 unique peptides. Eventually, a peptide key was developed based on the nine peptides, offering a prompt and precise flowchart to facilitate SARS-CoV-2 strain identification in COVID-19 vaccine manufacturing.
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Affiliation(s)
| | | | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, 1180, Vienna, Austria
| | - Waranyoo Phoolcharoen
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, 10330, Thailand.
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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Santos JD, Sobral D, Pinheiro M, Isidro J, Bogaardt C, Pinto M, Eusébio R, Santos A, Mamede R, Horton DL, Gomes JP, Borges V. INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance. Genome Med 2024; 16:61. [PMID: 38659008 PMCID: PMC11044337 DOI: 10.1186/s13073-024-01334-3] [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: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification. RESULTS The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis. CONCLUSIONS The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).
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Affiliation(s)
- João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine-iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Carlijn Bogaardt
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rodrigo Eusébio
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - André Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rafael Mamede
- Faculdade de Medicina, Instituto de Microbiologia, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel L Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
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Ambrożek-Latecka M, Kozlowski P, Hoser G, Bandyszewska M, Hanusek K, Nowis D, Gołąb J, Grzanka M, Piekiełko-Witkowska A, Schulz L, Hornung F, Deinhardt-Emmer S, Kozlowska E, Skirecki T. SARS-CoV-2 and its ORF3a, E and M viroporins activate inflammasome in human macrophages and induce of IL-1α in pulmonary epithelial and endothelial cells. Cell Death Discov 2024; 10:191. [PMID: 38664396 PMCID: PMC11045860 DOI: 10.1038/s41420-024-01966-9] [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: 02/23/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Inflammasome assembly is a potent mechanism responsible for the host protection against pathogens, including viruses. When compromised, it can allow viral replication, while when disrupted, it can perpetuate pathological responses by IL-1 signaling and pyroptotic cell death. SARS-CoV-2 infection was shown to activate inflammasome in the lungs of COVID-19 patients, however, potential mechanisms responsible for this response are not fully elucidated. In this study, we investigated the effects of ORF3a, E and M SARS-CoV-2 viroporins in the inflammasome activation in major populations of alveolar sentinel cells: macrophages, epithelial and endothelial cells. We demonstrated that each viroporin is capable of activation of the inflammasome in macrophages to trigger pyroptosis-like cell death and IL-1α release from epithelial and endothelial cells. Small molecule NLRP3 inflammasome inhibitors reduced IL-1 release but weakly affected the pyroptosis. Importantly, we discovered that while SARS-CoV-2 could not infect the pulmonary microvascular endothelial cells it induced IL-1α and IL-33 release. Together, these findings highlight the essential role of macrophages as the major inflammasome-activating cell population in the lungs and point to endothelial cell expressed IL-1α as a potential novel component driving the pulmonary immunothromobosis in COVID-19.
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Affiliation(s)
- Magdalena Ambrożek-Latecka
- Department of Translational Immunology and Experimental Intensive Care, Centre of Translational Research, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Piotr Kozlowski
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Grażyna Hoser
- Department of Translational Immunology and Experimental Intensive Care, Centre of Translational Research, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Magdalena Bandyszewska
- Department of Translational Immunology and Experimental Intensive Care, Centre of Translational Research, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Karolina Hanusek
- Department of Biochemistry and Molecular Biology, Centre of Translational Research, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Dominika Nowis
- Laboratory of Experimental Medicine, Faculty of Medicine, Medial University of Warsaw, Warsaw, Poland
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Grzanka
- Department of Biochemistry and Molecular Biology, Centre of Translational Research, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Translational Research, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Luise Schulz
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Franziska Hornung
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | | | - Ewa Kozlowska
- Department of Immunology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Tomasz Skirecki
- Department of Translational Immunology and Experimental Intensive Care, Centre of Translational Research, Centre of Postgraduate Medical Education, Warsaw, Poland.
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Behera LM, Gupta PK, Ghosh M, Shadangi S, Rana S. A Rationally Designed Synthetic Antiviral Peptide Binder Targeting the Receptor-Binding Domain of SARS-CoV-2. J Phys Chem B 2024. [PMID: 38657271 DOI: 10.1021/acs.jpcb.4c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel coronavirus, is the causative agent responsible for the spread of the COVID19 pandemic across the globe. The global impact of the COVID19 pandemic, the successful approval of vaccines for controlling the pandemic, and the further resurgence of COVID19 necessitate the exploration and validation of alternative therapeutic avenues targeting SARS-CoV-2. The initial entry and further invasion by SARS-CoV-2 require strong protein-protein interactions (PPIs) between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptors expressed on the cell surfaces of various tissues. In principle, disruption of the PPIs between the RBD of SARS-CoV-2 and the ACE2 receptor by designer peptides with optimized pharmacology appears to be an ideal choice for potentially preventing viral entry with minimal immunogenicity. In this context, the current study describes a short, synthetic designer peptide (codenamed SR16, ≤18 aa, molecular weight ≤2.5 kDa), which has a few noncoded amino acids, demonstrates a helical conformation in solution, and also engages the RBD of SARS-CoV-2 through a high-affinity interaction, as judged from a battery of biophysical studies. Further, the designer peptide demonstrates resistance to trypsin degradation, appears to be nontoxic to mammalian cells, and also does not induce hemolysis in freshly isolated human erythrocytes. In summary, SR16 appears to be an ideal peptide binder targeting the RBD of SARS-CoV-2, which has the potential for further optimization and development as an antiviral agent targeting SARS-CoV-2.
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Affiliation(s)
- Lalita Mohan Behera
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
| | - Pulkit Kr Gupta
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
| | - Manaswini Ghosh
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
| | - Sucharita Shadangi
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar 752050, Odisha, India
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Yarahmadi A, Zare M, Aghayari M, Afkhami H, Jafari GA. Therapeutic bacteria and viruses to combat cancer: double-edged sword in cancer therapy: new insights for future. Cell Commun Signal 2024; 22:239. [PMID: 38654309 PMCID: PMC11040964 DOI: 10.1186/s12964-024-01622-w] [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: 12/04/2023] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
Cancer, ranked as the second leading cause of mortality worldwide, leads to the death of approximately seven million people annually, establishing itself as one of the most significant health challenges globally. The discovery and identification of new anti-cancer drugs that kill or inactivate cancer cells without harming normal and healthy cells and reduce adverse effects on the immune system is a potential challenge in medicine and a fundamental goal in Many studies. Therapeutic bacteria and viruses have become a dual-faceted instrument in cancer therapy. They provide a promising avenue for cancer treatment, but at the same time, they also create significant obstacles and complications that contribute to cancer growth and development. This review article explores the role of bacteria and viruses in cancer treatment, examining their potential benefits and drawbacks. By amalgamating established knowledge and perspectives, this review offers an in-depth examination of the present research landscape within this domain and identifies avenues for future investigation.
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Affiliation(s)
- Aref Yarahmadi
- Department of Biology, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Mitra Zare
- Department of Microbiology, Faculty of Sciences, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Masoomeh Aghayari
- Department of Microbiology, Faculty of Sciences, Urmia Branch, Islamic Azad University, Urmia, Iran
| | - Hamed Afkhami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran.
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran.
| | - Gholam Ali Jafari
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
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Kawasuji H, Morinaga Y, Nagaoka K, Tani H, Yoshida Y, Yamada H, Takegoshi Y, Kaneda M, Murai Y, Kimoto K, Niimi H, Yamamoto Y. High interleukin-6 levels induced by COVID-19 pneumonia correlate with increased circulating follicular helper T cell frequency and strong neutralization antibody response in the acute phase of Omicron breakthrough infection. Front Immunol 2024; 15:1377014. [PMID: 38694512 PMCID: PMC11061453 DOI: 10.3389/fimmu.2024.1377014] [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: 01/26/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
Background Acute immune responses to coronavirus disease 2019 (COVID-19) are influenced by variants, vaccination, and clinical severity. Thus, the outcome of these responses may differ between vaccinated and unvaccinated patients and those with and without COVID-19-related pneumonia. In this study, these differences during infection with the Omicron variant were investigated. Methods A total of 67 patients (including 47 vaccinated and 20 unvaccinated patients) who were hospitalized within 5 days after COVID-19 symptom onset were enrolled in this prospective observational study. Serum neutralizing activity was evaluated using a pseudotyped virus assay and serum cytokines and chemokines were measured. Circulating follicular helper T cell (cTfh) frequencies were evaluated using flow cytometry. Results Twenty-five patients developed COVID-19 pneumonia on hospitalization. Although the neutralizing activities against wild-type and Delta variants were higher in the vaccinated group, those against the Omicron variant as well as the frequency of developing pneumonia were comparable between the vaccinated and unvaccinated groups. IL-6 and CXCL10 levels were higher in patients with pneumonia than in those without it, regardless of their vaccination status. Neutralizing activity against the Omicron variant were higher in vaccinated patients with pneumonia than in those without it. Moreover, a distinctive correlation between neutralizing activity against Omicron, IL-6 levels, and cTfh proportions was observed only in vaccinated patients. Conclusions The present study demonstrates the existence of a characteristic relationship between neutralizing activity against Omicron, IL-6 levels, and cTfh proportions in Omicron breakthrough infection.
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Affiliation(s)
- Hitoshi Kawasuji
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Yoshitomo Morinaga
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Kentaro Nagaoka
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Hideki Tani
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Yoshihiro Yoshida
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Hiroshi Yamada
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Yusuke Takegoshi
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Makito Kaneda
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Yushi Murai
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Kou Kimoto
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Yoshihiro Yamamoto
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
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Beitari S, Yi S, Sharma S, Yung R, Conway B. Exploring COVID-19 vaccine uptake and hesitancy among vulnerable populations in inner city Vancouver, Canada: Insights into characteristics and clinical outcomes. Vaccine 2024:S0264-410X(24)00477-8. [PMID: 38637213 DOI: 10.1016/j.vaccine.2024.04.050] [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: 02/09/2024] [Revised: 04/03/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
The COVID-19 pandemic is having a profound impact on the health, social and economic well-being of people in Canada and around the world. To address vaccine disparity among vulnerable populations facing social-structural challenges, it is crucial to provide evidence-based information on the importance of completion of the recommended vaccination schedule. In this study, we investigated vaccination rates and variables as facilitators or barriers to COVID-19 vaccination among vulnerable populations living in Vancouver's inner-city residents. On a weekly basis, a team (including health care providers [HCPs] and support staff) conducts a Community Pop-up Clinic (CPC) event at single room occupancy dwellings in Vancouver's inner city to provide COVID-19 vaccine and/or related information. Participants also completed a survey about their COVID-19 vaccination status and COVID knowledge, including knowledge about COVID vaccination. We collected data from 892 CPC participants between January 2021-August 2023. The median age at baseline was 45 (IQR 36-55) years, with 317 (35.5 %) female and 285 (31.9 %) self-identified as Indigenous. Within the population, 512 (57.4 %) reported unstable housing and 441 (49.5 %) were active injection drug users. Regarding COVID-19 vaccinations, 235 (26.3 %) were unvaccinated, 119 (13.3 %) had received one dose of the COVID-19 vaccine, 432 (48.4 %) had received 2 doses, and 106 (11.8 %) had received at least 3 doses. Variables such as age (AOR 2.28, 95 % CI 1.37-3.80, p < 0.001) and HCV seropositivity (AOR 1.91, 95 % CI 1.20-3.04, p = 0.005) were significantly associated with higher odds of vaccination uptake. Conversely, unstable housing was significantly associated with a lower odds of vaccination uptake (AOR 0.53, 95 % CI 0.35-0.79, p = 0.002). Results from this study suggest that targeted community focused initiatives are crucial to address vaccine disparity among vulnerable populations living in Vancouver's inner city facing unstable housing and drug use injection.
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Affiliation(s)
- Saina Beitari
- Vancouver Infectious Diseases Centre, Vancouver, British Columbia, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Shana Yi
- Vancouver Infectious Diseases Centre, Vancouver, British Columbia, Canada
| | - Shawn Sharma
- Vancouver Infectious Diseases Centre, Vancouver, British Columbia, Canada
| | - Rossitta Yung
- Vancouver Infectious Diseases Centre, Vancouver, British Columbia, Canada
| | - Brian Conway
- Vancouver Infectious Diseases Centre, Vancouver, British Columbia, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
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Yin Q, Liu W, Jiang Y, Feng Q, Wang X, Dou H, Liu Z, He F, Fan Y, Jiao B, Jiao B. Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022. BMC Genomics 2024; 25:378. [PMID: 38632523 PMCID: PMC11022347 DOI: 10.1186/s12864-024-10246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. METHODS Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites. RESULTS All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites. CONCLUSION SARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.
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Affiliation(s)
- Qiang Yin
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Wei Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Yajuan Jiang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Qiang Feng
- Department of Laboratory, Rencheng Center for Disease Control and Prevention, Jining, China
| | - Xiaoyu Wang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Huixin Dou
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Zanzan Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Feifei He
- Computer Information Technology, Northern Arizona University, Arizona, USA
| | - Yingying Fan
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
| | - Baihai Jiao
- Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA.
| | - Boyan Jiao
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
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Nelson CW, Poon LLM, Gu H. Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data. Nat Commun 2024; 15:3239. [PMID: 38627383 PMCID: PMC11021549 DOI: 10.1038/s41467-024-46262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024] Open
Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China.
- HKU- Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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Li H, Wang X, Wang S, Feng X, Wang L, Li Y. Acceptance, safety, and immunogenicity of a booster dose of inactivated SARS-CoV-2 vaccine in patients with primary biliary cholangitis. Heliyon 2024; 10:e28405. [PMID: 38560178 PMCID: PMC10981126 DOI: 10.1016/j.heliyon.2024.e28405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Inactivated coronavirus disease 2019 (COVID-19) vaccines showed impaired immunogenicity in some autoimmune diseases, but it remains unclear in primary biliary cholangitis (PBC). This study aimed to explore the antibody response to the inactivated COVID-19 vaccine in individuals with PBC, as well as to evaluate coverage, safety, and attitudes toward the COVID-19 vaccine among them. Two cohorts of patients with PBC were enrolled in this study. One cohort was arranged to evaluate the immunogenicity of the inactivated COVID-19 vaccine, another cohort participated in an online survey. The titers of the anti-receptor-binding domain (RBD)-specific immunoglobulin G (IgG), neutralizing antibody (NAb) toward severe acute respiratory syndrome coronavirus 2 wild-type, and NAb toward Omicron BA.4/5 subvariants were detected to assess antibody response from the vaccine. After booster vaccination for more than six months, patients with PBC had significantly lowered levels of anti-RBD-specific IgG compared to HCs, and the inhibition rates of NAb toward wild-type also declined in individuals with PBC. The detected levels of NAb toward Omicron BA.4/5 were below the positive threshold in patients with PBC and HCs. Laboratory parameters did not significantly correlate with any of the three antibodies. The online survey revealed that 24% of patients with PBC received three COVID-19 vaccines, while 63% were unimmunized. Adverse effect rates after the first, second, and third vaccine doses were 6.1%, 10.3%, and 9.5%, respectively. Unvaccinated patients with PBC were more worried about the safety of the vaccine than those who were vaccinated (P = 0.004). As a result, this study fills the immunological assessment gap in patients with PBC who received inactivated COVID-19 vaccines.
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Affiliation(s)
- Haolong Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xu Wang
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Siyu Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xinxin Feng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li Wang
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Tang S, Man Q, Zhu D, Yu X, Chen R, Wang S, Lu Y, Shi Q, Suo C, Xiong L. Risk factors for progression to severe infection and prolonged viral clearance time in hospitalized elderly patients infected with the Omicron variant of SARS-CoV-2: a retrospective study at Shanghai Fourth People's Hospital, School of Medicine, Tongji University. Front Microbiol 2024; 15:1361197. [PMID: 38686116 PMCID: PMC11056568 DOI: 10.3389/fmicb.2024.1361197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction In elderly patients infected with the Omicron variant, disease progression to severe infection can result in poor outcomes. This study aimed to identify risk and protective factors associated with disease progression to severe infection and viral clearance time in elderly Omicron-infected patients. Methods Shanghai Fourth People's Hospital, School of Medicine, Tongji University, was officially designated to provide treatment to patients with COVID-19. This study was conducted on confirmed Omicron cases admitted to the hospital between 10 April 2022 and 21 June 2022. In total, 1,568 patients aged 65 years or older were included. We conducted a retrospective, observational study using logistic regression to analyze risk and protective factors for the development of severe disease and Cox proportional hazards regression models to analyze factors influencing viral clearance time. Results Aged over 80 years, having 2 or more comorbidities, combined cerebrovascular disease, chronic neurological disease, and mental disorders were associated with the development of severe disease, and full vaccination was a protective factor. Furthermore, aged over 80 years, combined chronic respiratory disease, chronic renal disease, cerebrovascular disease, mental disorders, and high viral load were associated with prolonged viral clearance time, and full vaccination was a protective factor. Discussion This study analyzed risk factors for progression to severe infection and prolonged viral clearance time in hospitalized elderly Omicron-infected patients. Aged patients with comorbidities had a higher risk of developing severe infection and had longer viral clearance, while vaccination protected them against the Omicron infection.
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Affiliation(s)
- Siqi Tang
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Department of Epidemiology, Ministry of Education, Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Qiuhong Man
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Dongliang Zhu
- Department of Epidemiology, Ministry of Education, Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Xueying Yu
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ruilin Chen
- Department of Epidemiology, Ministry of Education, Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Shuo Wang
- Department of Epidemiology, Ministry of Education, Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Yihan Lu
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Department of Epidemiology, Ministry of Education, Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Qiqing Shi
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chen Suo
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Department of Epidemiology, Ministry of Education, Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Lize Xiong
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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Shi Y, Ma Y, Zheng Z, Qin Y, Du Z, Liu J. Development and validation of a predicting nomogram for in-hospital mortality of COVID-19 Omicron variant: A cohort study of 1324 cases in Beijing Anzhen Hospital. Heliyon 2024; 10:e28627. [PMID: 38590893 PMCID: PMC11000003 DOI: 10.1016/j.heliyon.2024.e28627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) is continuously posing high global public health concerns due to its high morbidity and mortality. This study aimed to construct a convenient risk model for predicting in-hospital mortality of COVID-19 Omicron variant. A total of 1324 hospitalized patients with Omicron variant were enrolled from Beijing Anzhen Hospital. During hospitalization, the Omicron variant mortality rate was found to be 24.4%. Using the datasets of clinical demographics and laboratory tests, three machine learning algorithms, including best subset selection, stepwise selection, and least absolute shrinkage and selection operator regression analyses were employed to identify the potential predictors of in-hospital mortality. The results found that a panel of twenty-four clinical variables (including age, hyperlipemia, stroke, tumor, and several cardiovascular markers) identified by stepwise selection model exhibited significant performances in predicting the in-hospital mortality of COVID-19. The resultant nomogram showed good discrimination, highlighted by the areas under the curve values of 0.88 for 10 days, 0.81 for 20 days, and 0.82 for 30 days, respectively. Furthermore, decision curve analysis showed a significant reliability and precision for the established stepwise selection model. Collectively, this study developed an accurate and convenience risk model for predicting the in-hospital mortality of COVID-19 Omicron.
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Affiliation(s)
- Yuchen Shi
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Ying Ma
- The State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ze Zheng
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Yanwen Qin
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Zhiyong Du
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Jinghua Liu
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
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Drysdale M, Berktas M, Gibbons DC, Rolland C, Lavoie L, Lloyd EJ. Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 and BA.5 subvariant predominance: a systematic literature review. Infection 2024:10.1007/s15010-024-02245-6. [PMID: 38602623 DOI: 10.1007/s15010-024-02245-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/19/2024] [Indexed: 04/12/2024]
Abstract
PURPOSE To evaluate clinical outcomes associated with sotrovimab use during Omicron BA.2 and BA.5 predominance. METHODS Electronic databases were searched for observational studies published in peer-reviewed journals, preprint articles and conference abstracts from January 1, 2022 to February 27, 2023. RESULTS The 14 studies identified were heterogeneous in terms of study design, population, endpoints and definitions. They included > 1.7 million high-risk patients with COVID-19, of whom approximately 41,000 received sotrovimab (range n = 20-5979 during BA.2 and n = 76-1383 during BA.5 predominance). Four studies compared the effectiveness of sotrovimab with untreated or no monoclonal antibody treatment controls, two compared sotrovimab with other treatments, and three single-arm studies compared outcomes during BA.2 and/or BA.5 versus BA.1. Five studies descriptively reported rates of clinical outcomes in patients treated with sotrovimab. Rates of COVID-19-related hospitalization or mortality (0.95-4.0% during BA.2; 0.5-2.0% during BA.5) and all-cause mortality (1.7-2.0% during BA.2; 3.4% during combined BA.2 and BA.5 periods) among sotrovimab-treated patients were consistently low. During BA.2, a lower risk of all-cause hospitalization or mortality was reported across studies with sotrovimab versus untreated cohorts. Compared with other treatments, sotrovimab was associated with a lower (molnupiravir) or similar (nirmatrelvir/ritonavir) risk of COVID-19-related hospitalization or mortality during BA.2 and BA.5. There was no significant difference in outcomes between the BA.1, BA.2 and BA.5 periods. CONCLUSIONS This systematic literature review suggests continued effectiveness of sotrovimab in preventing severe clinical outcomes during BA.2 and BA.5 predominance, both against active/untreated comparators and compared with BA.1 predominance.
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Affiliation(s)
- Myriam Drysdale
- Value Evidence and Outcomes, GSK, 980 Great West Road, Brentford, Middlesex, TW8 9GS, UK.
| | - Mehmet Berktas
- Value Evidence and Outcomes, GSK, 980 Great West Road, Brentford, Middlesex, TW8 9GS, UK
| | - Daniel C Gibbons
- Value Evidence and Outcomes, GSK, 980 Great West Road, Brentford, Middlesex, TW8 9GS, UK
| | - Catherine Rolland
- Evidence Synthesis, Modelling and Communications, PPD Evidera, London, UK
| | - Louis Lavoie
- Evidence Synthesis, Modelling and Communications, PPD Evidera, Montreal, Canada
| | - Emily J Lloyd
- Value Evidence and Outcomes, GSK, 980 Great West Road, Brentford, Middlesex, TW8 9GS, UK
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Tanneti NS, Patel AK, Tan LH, Marques AD, Perera RAPM, Sherrill-Mix S, Kelly BJ, Renner DM, Collman RG, Rodino K, Lee C, Bushman FD, Cohen NA, Weiss SR. Comparison of SARS-CoV-2 variants of concern in primary human nasal cultures demonstrates Delta as most cytopathic and Omicron as fastest replicating. mBio 2024; 15:e0312923. [PMID: 38477472 PMCID: PMC11005367 DOI: 10.1128/mbio.03129-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
The SARS-CoV-2 pandemic was marked with emerging viral variants, some of which were designated as variants of concern (VOCs) due to selection and rapid circulation in the human population. Here, we elucidate functional features of each VOC linked to variations in replication rate. Patient-derived primary nasal cultures grown at air-liquid interface were used to model upper respiratory infection and compared to cell lines derived from human lung epithelia. All VOCs replicated to higher titers than the ancestral virus, suggesting a selection for replication efficiency. In primary nasal cultures, Omicron replicated to the highest titers at early time points, followed by Delta, paralleling comparative studies of population sampling. All SARS-CoV-2 viruses entered the cell primarily via a transmembrane serine protease 2 (TMPRSS2)-dependent pathway, and Omicron was more likely to use an endosomal route of entry. All VOCs activated and overcame dsRNA-induced cellular responses, including interferon (IFN) signaling, oligoadenylate ribonuclease L degradation, and protein kinase R activation. Among the VOCs, Omicron infection induced expression of the most IFN and IFN-stimulated genes. Infections in nasal cultures resulted in cellular damage, including a compromise of cell barrier integrity and loss of nasal cilia and ciliary beating function, especially during Delta infection. Overall, Omicron was optimized for replication in the upper respiratory tract and least favorable in the lower respiratory cell line, and Delta was the most cytopathic for both upper and lower respiratory cells. Our findings highlight the functional differences among VOCs at the cellular level and imply distinct mechanisms of pathogenesis in infected individuals. IMPORTANCE Comparative analysis of infections by SARS-CoV-2 ancestral virus and variants of concern, including Alpha, Beta, Delta, and Omicron, indicated that variants were selected for efficiency in replication. In infections of patient-derived primary nasal cultures grown at air-liquid interface to model upper respiratory infection, Omicron reached the highest titers at early time points, a finding that was confirmed by parallel population sampling studies. While all infections overcame dsRNA-mediated host responses, infections with Omicron induced the strongest interferon and interferon-stimulated gene response. In both primary nasal cultures and lower respiratory cell line, infections by Delta were most damaging to the cells as indicated by syncytia formation, loss of cell barrier integrity, and nasal ciliary function.
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Affiliation(s)
- Nikhila S. Tanneti
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Anant K. Patel
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Li Hui Tan
- Department of Otorhinolaryngology- Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew D. Marques
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ranawaka A. P. M. Perera
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David M. Renner
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle Rodino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carole Lee
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Noam A. Cohen
- Department of Otorhinolaryngology- Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Corporal Michael J. Crescenz VA Medical Center, Surgical Services, Philadelphia, Pennsylvania, USA
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, USA
| | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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50
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Zhu C, Pang S, Liu J, Duan Q. Current Progress, Challenges and Prospects in the Development of COVID-19 Vaccines. Drugs 2024; 84:403-423. [PMID: 38652356 DOI: 10.1007/s40265-024-02013-8] [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] [Accepted: 02/25/2024] [Indexed: 04/25/2024]
Abstract
The COVID-19 pandemic has resulted in over 772 million confirmed cases, including nearly 7 million deaths, according to the World Health Organization (WHO). Leveraging rapid development, accelerated vaccine approval processes, and large-scale production of various COVID-19 vaccines using different technical platforms, the WHO declared an end to the global health emergency of COVID-19 on May 5, 2023. Current COVID-19 vaccines encompass inactivated, live attenuated, viral vector, protein subunit, nucleic acid (DNA and RNA), and virus-like particle (VLP) vaccines. However, the efficacy of these vaccines is diminishing due to the constant mutation of SARS-CoV-2 and the heightened immune evasion abilities of emerging variants. This review examines the impact of the COVID-19 pandemic, the biological characteristics of the virus, and its diverse variants. Moreover, the review underscores the effectiveness, advantages, and disadvantages of authorized COVID-19 vaccines. Additionally, it analyzes the challenges, strategies, and future prospects of developing a safe, broad-spectrum vaccine that confers sufficient and sustainable immune protection against new variants of SARS-CoV-2. These discussions not only offer insight for the development of next-generation COVID-19 vaccines but also summarize experiences for combating future emerging viruses.
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Affiliation(s)
- Congrui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510000, China
| | - Shengmei Pang
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Jiaqi Liu
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Qiangde Duan
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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