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Bankers L, O'Brien SC, Tapay DM, Ho E, Armistead I, Burakoff A, Dominguez SR, Matzinger SR. SARS-CoV-2 Disease Severity and Cycle Threshold Values in Children Infected during Pre-Delta, Delta, and Omicron Periods, Colorado, USA, 2021-2022. Emerg Infect Dis 2024; 30:1182-1192. [PMID: 38781929 PMCID: PMC11139003 DOI: 10.3201/eid3006.231427] [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: 05/25/2024] Open
Abstract
In adults, viral load and disease severity can differ by SARS-CoV-2 variant, patterns less understood in children. We evaluated symptomatology, cycle threshold (Ct) values, and SARS-CoV-2 variants among 2,299 pediatric SARS-CoV-2 patients (0-21 years of age) in Colorado, USA, to determine whether children infected with Delta or Omicron had different symptom severity or Ct values than during earlier variants. Children infected during the Delta and Omicron periods had lower Ct values than those infected during pre-Delta, and children <1 year of age had lower Ct values than older children. Hospitalized symptomatic children had lower Ct values than asymptomatic patients. Compared with pre-Delta, more children infected during Delta and Omicron were symptomatic (75.4% pre-Delta, 95.3% Delta, 99.5% Omicron), admitted to intensive care (18.8% pre-Delta, 39.5% Delta, 22.9% Omicron), or received oxygen support (42.0% pre-Delta, 66.3% Delta, 62.3% Omicron). Our data reinforce the need to include children, especially younger children, in pathogen surveillance efforts.
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Le HT, Tran LH, Phung HTT. SARS-CoV-2 omicron RBD forms a weaker binding affinity to hACE2 compared to Delta RBD in in-silico studies. J Biomol Struct Dyn 2024; 42:4087-4096. [PMID: 37345564 DOI: 10.1080/07391102.2023.2222827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/21/2023] [Indexed: 06/23/2023]
Abstract
The COVID-19 pandemic sparked an unprecedented race in biotechnology in a search for effective therapies and a preventive vaccine. The continued appearance of SARS-CoV-2 variants of concern (VoCs) further swept the world. The entry of SARS-CoV-2 into cells is mediated by binding the receptor-binding domain (RBD) of the S protein to the cell-surface receptor, human angiotensin-converting enzyme 2 (hACE2). In this study, using a coarse-grained force field to parameterize the system, we employed steered-molecular dynamics (SMD) simulations to reveal the binding of SARS-CoV-2 Delta/Omicron RBD to hACE2. Our benchmarked results demonstrate a good correlation between computed rupture force and experimental binding free energy for known protein-protein systems. Moreover, our findings show that the Omicron RBD has a weaker binding affinity to hACE2, consistent with the respective experimental results. This indicates that our method can effectively be applied to other emerging SARS-CoV-2 strains.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hoa Thanh Le
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Linh Hoang Tran
- Faculty of Civil Engineering, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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Castonguay FM, Barnes A, Jeon S, Fornoff J, Adhikari BB, Fischer LS, Greening B, Hassan AO, Kahn EB, Kang GJ, Kauerauf J, Patrick S, Vohra S, Meltzer MI. Estimated public health impact of concurrent mask mandate and vaccinate-or-test requirement in Illinois, October to December 2021. BMC Public Health 2024; 24:1013. [PMID: 38609903 PMCID: PMC11010411 DOI: 10.1186/s12889-024-18203-8] [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: 11/14/2023] [Accepted: 02/24/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Facing a surge of COVID-19 cases in late August 2021, the U.S. state of Illinois re-enacted its COVID-19 mask mandate for the general public and issued a requirement for workers in certain professions to be vaccinated against COVID-19 or undergo weekly testing. The mask mandate required any individual, regardless of their vaccination status, to wear a well-fitting mask in an indoor setting. METHODS We used Illinois Department of Public Health's COVID-19 confirmed case and vaccination data and investigated scenarios where masking and vaccination would have been reduced to mimic what would have happened had the mask mandate or vaccine requirement not been put in place. The study examined a range of potential reductions in masking and vaccination mimicking potential scenarios had the mask mandate or vaccine requirement not been enacted. We estimated COVID-19 cases and hospitalizations averted by changes in masking and vaccination during the period covering October 20 to December 20, 2021. RESULTS We find that the announcement and implementation of a mask mandate are likely to correlate with a strong protective effect at reducing COVID-19 burden and the announcement of a vaccinate-or-test requirement among frontline professionals is likely to correlate with a more modest protective effect at reducing COVID-19 burden. In our most conservative scenario, we estimated that from the period of October 20 to December 20, 2021, the mask mandate likely prevented approximately 58,000 cases and 1,175 hospitalizations, while the vaccinate-or-test requirement may have prevented at most approximately 24,000 cases and 475 hospitalizations. CONCLUSION Our results indicate that mask mandates and vaccine-or-test requirements are vital in mitigating the burden of COVID-19 during surges of the virus.
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Affiliation(s)
- François M Castonguay
- National Center for Emerging and Zoonotic Infectious Diseases, Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Health Economics and Modeling Unit, U.S. Department of Health and Human Services, 7101 Avenue du Parc, Local 3180, QC H3N 1X9, Atlanta, Georgia.
- Contact Tracing and Innovation Section (CTIS), State Tribal Local and Territorial (STLT) Task Force, CDC COVID-19 Response; Centers for Disease Control and Prevention, Modeling Support Team, U.S. Department of Health and Human Services, Atlanta, Georgia.
- Department of Health Management, Evaluation and Policy, University of Montreal School of Public Health, and Centre for Public Health Research - CReSP, 7101 Av du Parc, 3E Étage, Montréal, QC, H3N 1X9, Canada.
| | - Arti Barnes
- Illinois Department of Public Health, Springfield, IL, USA
| | - Seonghye Jeon
- National Center for Emerging and Zoonotic Infectious Diseases, Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Health Economics and Modeling Unit, U.S. Department of Health and Human Services, 7101 Avenue du Parc, Local 3180, QC H3N 1X9, Atlanta, Georgia
- Contact Tracing and Innovation Section (CTIS), State Tribal Local and Territorial (STLT) Task Force, CDC COVID-19 Response; Centers for Disease Control and Prevention, Modeling Support Team, U.S. Department of Health and Human Services, Atlanta, Georgia
| | - Jane Fornoff
- Illinois Department of Public Health, Springfield, IL, USA
| | - Bishwa B Adhikari
- National Center for Emerging and Zoonotic Infectious Diseases, Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Health Economics and Modeling Unit, U.S. Department of Health and Human Services, 7101 Avenue du Parc, Local 3180, QC H3N 1X9, Atlanta, Georgia
- Contact Tracing and Innovation Section (CTIS), State Tribal Local and Territorial (STLT) Task Force, CDC COVID-19 Response; Centers for Disease Control and Prevention, Modeling Support Team, U.S. Department of Health and Human Services, Atlanta, Georgia
| | - Leah S Fischer
- National Center for Emerging and Zoonotic Infectious Diseases, Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Health Economics and Modeling Unit, U.S. Department of Health and Human Services, 7101 Avenue du Parc, Local 3180, QC H3N 1X9, Atlanta, Georgia
- Contact Tracing and Innovation Section (CTIS), State Tribal Local and Territorial (STLT) Task Force, CDC COVID-19 Response; Centers for Disease Control and Prevention, Modeling Support Team, U.S. Department of Health and Human Services, Atlanta, Georgia
| | - Bradford Greening
- National Center for Emerging and Zoonotic Infectious Diseases, Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Health Economics and Modeling Unit, U.S. Department of Health and Human Services, 7101 Avenue du Parc, Local 3180, QC H3N 1X9, Atlanta, Georgia
- Contact Tracing and Innovation Section (CTIS), State Tribal Local and Territorial (STLT) Task Force, CDC COVID-19 Response; Centers for Disease Control and Prevention, Modeling Support Team, U.S. Department of Health and Human Services, Atlanta, Georgia
| | | | - Emily B Kahn
- National Center for Emerging and Zoonotic Infectious Diseases, Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Health Economics and Modeling Unit, U.S. Department of Health and Human Services, 7101 Avenue du Parc, Local 3180, QC H3N 1X9, Atlanta, Georgia
- Contact Tracing and Innovation Section (CTIS), State Tribal Local and Territorial (STLT) Task Force, CDC COVID-19 Response; Centers for Disease Control and Prevention, Modeling Support Team, U.S. Department of Health and Human Services, Atlanta, Georgia
| | - Gloria J Kang
- National Center for Emerging and Zoonotic Infectious Diseases, Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Health Economics and Modeling Unit, U.S. Department of Health and Human Services, 7101 Avenue du Parc, Local 3180, QC H3N 1X9, Atlanta, Georgia
- Contact Tracing and Innovation Section (CTIS), State Tribal Local and Territorial (STLT) Task Force, CDC COVID-19 Response; Centers for Disease Control and Prevention, Modeling Support Team, U.S. Department of Health and Human Services, Atlanta, Georgia
| | - Judy Kauerauf
- Illinois Department of Public Health, Springfield, IL, USA
| | - Sarah Patrick
- Illinois Department of Public Health, Springfield, IL, USA
| | - Sameer Vohra
- Illinois Department of Public Health, Springfield, IL, USA
| | - Martin I Meltzer
- National Center for Emerging and Zoonotic Infectious Diseases, Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Health Economics and Modeling Unit, U.S. Department of Health and Human Services, 7101 Avenue du Parc, Local 3180, QC H3N 1X9, Atlanta, Georgia
- Contact Tracing and Innovation Section (CTIS), State Tribal Local and Territorial (STLT) Task Force, CDC COVID-19 Response; Centers for Disease Control and Prevention, Modeling Support Team, U.S. Department of Health and Human Services, Atlanta, Georgia
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Zhang H, Zhao Y, Li W, Chai Y, Gu X. Difference in mortality risk predicted by leukocyte and lymphocyte levels in COVID-19 patients infected with the Wild-type, Delta, and Omicron strains. Medicine (Baltimore) 2024; 103:e37516. [PMID: 38457534 PMCID: PMC10919463 DOI: 10.1097/md.0000000000037516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/01/2024] [Accepted: 02/15/2024] [Indexed: 03/10/2024] Open
Abstract
This study aimed to investigate the changing trends, level differences, and prognostic performance of the leukocyte and lymphocyte levels of patients infected with the Wild strains, Delta strains and Omicron strains to provide a reference for prognostic assessment. In the current study, we conducted a retrospective cross-sectional study to evaluate the changing trends, level differences, and prognostic performance of leukocyte and lymphocyte of different strains at admission and discharge may already exist in patients with coronavirus disease-2019 (COVID-19) infected with the Wild type, Delta, and Omicron strains. A retrospective cross-sectional study was conducted. We recruited and screened the 243 cases infected with the Wild-type strains in Wuhan, the 629 cases infected with the Delta and 116 cases infected strains with the Omicron strains in Xi'an. The leukocyte and lymphocyte levels were compared the cohort of Wild-type infection with the cohort of Delta and the Omicron. The changes in the levels of leukocytes and lymphocytes exhibit a completely opposite trend in patients with COVID-19 infected with the different strains. The lymphocyte level at admission and discharge in patients with COVID-19 infected with Omicron strains (area under curve [AUC] receiver operating characteristic curve [ROC] 72.8-90.2%, 82.8-97.2%) presented better performance compared patients with COVID-19 infected with Wild type strains (AUC ROC 60.9-80.7%, 82.3-97.2%) and Delta strains (AUC ROC 56.1-84.7%, 40.3-93.3%). Kaplan-Meier curves showed that the leukocyte levels above newly established cutoff values and the lymphocyte levels below newly established cutoff values had a significantly higher risk of in-hospital mortality in COVID-19 patients with Wild-type and Omicron strains (P < .01). The levels of leukocyte and lymphocyte at admission and discharge in patients with COVID-19 infected with the Wild type, Delta, and Omicron strains may be differences among strains, which indicates different death risks. Our research may help clinicians identify patients with a poor prognosis for severe acute respiratory syndrome coronavirus 2 infection.
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Affiliation(s)
- Hongjun Zhang
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
- Infectious Disease Department, Wuhan Huoshenshan Hospital, Wuhan, Hubei, PR China
| | - Yanjun Zhao
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
| | - Wenjie Li
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
| | - Yaqin Chai
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
| | - Xing Gu
- Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Xi’an, Shaanxi, PR China
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Zhang RG, Liu XJ, Guo YL, Chen CL. SARS-CoV-2 spike protein receptor binding domain promotes IL-6 and IL-8 release via ATP/P2Y 2 and ERK1/2 signaling pathways in human bronchial epithelia. Mol Immunol 2024; 167:53-61. [PMID: 38359646 DOI: 10.1016/j.molimm.2024.02.005] [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: 10/24/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
The spike protein of SARS-CoV-2 as well as its receptor binding domain (RBD) has been demonstrated to be capable of activating the release of pro-inflammatory mediators in endothelial cells and immune cells such as monocytes. However, the effects of spike protein or its RBD on airway epithelial cells and mechanisms underlying these effects have not been adequately characterized. Here, we show that the RBD of spike protein alone can induce bronchial epithelial inflammation in a manner of ATP/P2Y2 dependence. Incubation of human bronchial epithelia with RBD induced IL-6 and IL-8 release, which could be inhibited by antibody. The incubation of RBD also up-regulated the expression of inflammatory indicators such as ho-1 and mkp-1. Furthermore, ATP secretion was observed after RBD treatment, P2Y2 receptor knock down by siRNA significantly suppressed the IL-6 and IL-8 release evoked by RBD. Additionally, S-RBD elevated the phosphorylation level of ERK1/2, and the effect that PD98059 can inhibit the pro-inflammatory cytokine release suggested the participation of ERK1/2. These novel findings provide new evidence of SARS-CoV-2 on airway inflammation and introduce purinergic signaling as promising treatment target.
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Affiliation(s)
- Rui-Gang Zhang
- Department of Physiology, Basic Medical School, Guangdong Medical University, Zhanjiang, China.
| | - Xing-Jian Liu
- Department of Physiology, Basic Medical School, Guangdong Medical University, Zhanjiang, China
| | - Yu-Ling Guo
- First Clinical School, Guangdong Medical University, Zhanjiang, China
| | - Chun-Ling Chen
- Department of Physiology, Basic Medical School, Guangdong Medical University, Zhanjiang, China
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6
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Pung R, Russell TW, Kucharski AJ. Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response. PLoS Comput Biol 2024; 20:e1011967. [PMID: 38517931 PMCID: PMC10990235 DOI: 10.1371/journal.pcbi.1011967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 04/03/2024] [Accepted: 03/04/2024] [Indexed: 03/24/2024] Open
Abstract
The epidemiological characteristics of SARS-CoV-2 transmission have changed over the pandemic due to emergence of new variants. A decrease in the generation or serial intervals would imply a shortened transmission timescale and, hence, outbreak response measures would need to expand at a faster rate. However, there are challenges in measuring these intervals. Alongside epidemiological changes, factors like varying delays in outbreak response, social contact patterns, dependence on the growth phase of an outbreak, and effects of exposure to multiple infectors can also influence measured generation or serial intervals. To guide real-time interpretation of variant data, we simulated concurrent changes in the aforementioned factors and estimated the statistical power to detect a change in the generation and serial interval. We compared our findings to the reported decrease or lack thereof in the generation and serial intervals of different SARS-CoV-2 variants. Our study helps to clarify contradictory outbreak observations and informs the required sample sizes under certain outbreak conditions to ensure that future studies of generation and serial intervals are adequately powered.
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Affiliation(s)
- Rachael Pung
- Ministry of Health, Singapore, Singapore
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Timothy W. Russell
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Adam J. Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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7
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Li L, Zhang J, Sun R, Liu H, Cheng G, Fan F, Wang C, Li A, Liang H, Yu Z, Wang G, Ren Z. Immune Dysregulation in SARS-CoV-2 patients coinfected with Mycobacterium tuberculosis (Mtb) or HIV in China. BMC Public Health 2024; 24:556. [PMID: 38388348 PMCID: PMC10882883 DOI: 10.1186/s12889-024-17905-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND SARS-CoV-2 infections usually cause immune dysregulation in the human body. Studies of immunological changes resulting from coinfections with Mycobacterium tuberculosis (Mtb) or HIV are limited. METHODS We conducted a retrospective study focusing on patients with COVID-19. A total of 550 patients infected with SARS-CoV-2 were enrolled in our study and categorized into four groups based on the presence of coinfections; 166 Delta-infected patients, among whom 103 patients had no coinfections, 52 who were coinfected with Mtb, 11 who were coinfected with HIV, and 384 Omicron-infected patients. By collecting data on epidemiologic information, laboratory findings, treatments, and clinical outcomes, we analyzed and compared clinical and immunological characteristics. RESULTS Compared with those in the Delta group, the median white blood cell, CD4 + T-cell and B-cell counts were lower in the Mtb group and the HIV group. Except for those in the Omicron group, more than half of the patients in the three groups had abnormal chest CT findings. Among the three groups, there were no significant differences in any of the cytokines. Compared with those in the Delta group, the disease duration and LOS were longer in the Mtb group and the HIV group. For unvaccinated Delta-infected patients, in the Mtb and HIV groups, the number of B cells and CD4 + T cells was lower than that in the Delta group, with no significant difference in the LOS or disease duration. In the Mtb group, three (6%) patients presented with a disease duration greater than four months and had decreased lymphocyte and IL17A counts, possibly due to double infections in the lungs caused by SARS-CoV-2 and M. tuberculosis. CONCLUSIONS We found that SARS-CoV-2 patients coinfected with Mtb or HIV exhibited a longer disease duration and longer LOS, with a decrease in B cells and CD4 + T cells, suggesting that these cells are related to immune function. Changes in cytokine levels suggest that coinfection with Mtb or HIV does not result in dysregulation of the immune response. Importantly, we discovered a chronic course of coinfection involving more than four months of Mtb and SARS-CoV-2 infection.
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Affiliation(s)
- Lei Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Jianxiang Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Ranran Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Hong Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Genyang Cheng
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Feifei Fan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Chong Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Ang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Hongxia Liang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Zujiang Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China.
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Guiqiang Wang
- Department of Infectious Diseases and the Center for Liver Diseases, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, 100034, Beijing, China.
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, #1 Jianshe East Road, 450052, Zhengzhou, China.
- State Key Laboratory of Antiviral Drugs, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
- Precision Medicine Center, Gene Hospital of Henan Province, the First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
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Li L, Xie Z, Li Y, Luo M, Zhang L, Feng C, Tang G, Huang H, Hou R, Xu Y, Jia S, Shi J, Fan Q, Gan Q, Yu N, Hu F, Li Y, Lan Y, Tang X, Li F, Deng X. Immune response and severity of Omicron BA.5 reinfection among individuals previously infected with different SARS-CoV-2 variants. Front Cell Infect Microbiol 2023; 13:1277880. [PMID: 38188634 PMCID: PMC10766752 DOI: 10.3389/fcimb.2023.1277880] [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: 08/15/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction COVID-19 continues to spread worldwide, with an increasing number of individuals experiencing reinfection after recovering from their primary infection. However, the nature and progression of this infection remain poorly understood. We aimed to investigate the immune response, severity and outcomes of Omicron BA.5 reinfection among individuals previously infected with different SARS-CoV-2 variants. Methods We enrolled 432 COVID-19 cases who had experienced prior infection with the ancestral SARS-CoV-2 virus, Delta variant or Omicron BA.2 variant between January 2020 and May 2022 in Guangzhou, China. All cases underwent follow-up from March to April, 2023 through telephone questionnaires and clinical visits. Nasal lavage fluid and peripheral blood were collected to assess anti-RBD IgA, anti-RBD IgG and virus-specific IFN-γ secreting T cells. Results Our study shows that 73.1%, 56.7% and 12.5% of individuals with a prior infection of the ancestral virus, Delta or Omicron BA.2 variant experienced reinfection with the BA.5 variant, respectively. Fever, cough and sore throat were the most common symptoms of BA.5 reinfection, with most improving within one week and none progressing to a critical condition. Compared with individuals without reinfection, reinfected patients with a prior Delta infection exhibited elevated levels of nasal anti-RBD IgA, serum anti-RBD IgG and IFN-γ secreting T cells, whereas there was no noticeable change in reinfected individuals with a prior BA.2 infection. Conclusion These results suggest that BA.5 reinfection is common but severe outcomes are relatively rare. Reinfection with a novel SARS-CoV-2 variant different from the prior infection may induce a more robust immune protection, which should be taken into account during vaccine development.
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Affiliation(s)
- Lu Li
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zhiwei Xie
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Youxia Li
- Department of Critical Care Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Minhan Luo
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lieguang Zhang
- Department of Radiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chengqian Feng
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Guofang Tang
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Huang Huang
- Department of Critical Care Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ruitian Hou
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yujuan Xu
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shijie Jia
- Department of Traditional Chinese Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jingrong Shi
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qinghong Fan
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qingxin Gan
- Department of Radiology, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Na Yu
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Fengyu Hu
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Yueping Li
- Department of Infectious Critical Care Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yun Lan
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoping Tang
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Feng Li
- Institute of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Xilong Deng
- Department of Critical Care Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
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Wei D, Xie Y, Liu X, Chen R, Zhou M, Zhang X, Qu J. Pathogen evolution, prevention/control strategy and clinical features of COVID-19: experiences from China. Front Med 2023; 17:1030-1046. [PMID: 38157194 DOI: 10.1007/s11684-023-1043-5] [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: 06/13/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported at the end of 2019 as a worldwide health concern causing a pandemic of unusual viral pneumonia and many other organ damages, which was defined by the World Health Organization as coronavirus disease 2019 (COVID-19). The pandemic is considered a significant threat to global public health till now. In this review, we have summarized the lessons learnt during the emergence and spread of SARS-CoV-2, including its prototype and variants. The overall clinical features of variants of concern (VOC), heterogeneity in the clinical manifestations, radiology and pathology of COVID-19 patients are also discussed, along with advances in therapeutic agents.
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Affiliation(s)
- Dong Wei
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yusang Xie
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Xuefei Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Rong Chen
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Xinxin Zhang
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China.
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Alisoltani A, Simons LM, Agnes MFR, Heald-Sargent TA, Muller WJ, Kociolek LK, Hultquist JF, Lorenzo-Redondo R, Ozer EA. Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient. Virol J 2023; 20:246. [PMID: 37891657 PMCID: PMC10604949 DOI: 10.1186/s12985-023-02186-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: 06/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Persistent SARS-CoV-2 infection in immunocompromised hosts is thought to contribute to viral evolution by facilitating long-term natural selection and viral recombination in cases of viral co-infection or superinfection. However, there are limited data on the longitudinal intra-host population dynamics of SARS-CoV-2 co-infection/superinfection, especially in pediatric populations. Here, we report a case of Delta-Omicron superinfection in a hospitalized, immunocompromised pediatric patient. METHODS We conducted Illumina whole genome sequencing (WGS) for longitudinal specimens to investigate intra-host dynamics of SARS-CoV-2 strains. Topoisomerase PCR cloning of Spike open-reading frame and Sanger sequencing of samples was performed for four specimens to validate the findings. Analysis of publicly available SARS-CoV-2 sequence data was performed to investigate the co-circulation and persistence of SARS-CoV-2 variants. RESULTS Results of WGS indicate the patient was initially infected with the SARS-CoV-2 Delta variant before developing a SARS-CoV-2 Omicron variant superinfection, which became predominant. Shortly thereafter, viral loads decreased below the level of detection before resurgence of the original Delta variant with no residual trace of Omicron. After 54 days of persistent infection, the patient tested negative for SARS-CoV-2 but ultimately succumbed to a COVID-19-related death. Despite protracted treatment with remdesivir, no antiviral resistance mutations emerged. These results indicate a unique case of persistent SARS-CoV-2 infection with the Delta variant interposed by a transient superinfection with the Omicron variant. Analysis of publicly available sequence data suggests the persistence and ongoing evolution of Delta subvariants despite the global predominance of Omicron, potentially indicative of continued transmission in an unknown population or niche. CONCLUSION A better understanding of SARS-CoV-2 intra-host population dynamics, persistence, and evolution during co-infections and/or superinfections will be required to continue optimizing patient care and to better predict the emergence of new variants of concern.
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Affiliation(s)
- Arghavan Alisoltani
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Maria Francesca Reyes Agnes
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | | | - William J Muller
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Larry K Kociolek
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
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11
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Ge J, Zhang C, Peng Z, Chu M, Chen W, Li Z, Liu S, Yang Y, Chu M. Environmental Contamination of SARS-CoV-2 Delta VOC by COVID-19 Patients Staying in the Hospital for More Than Two Weeks. Risk Manag Healthc Policy 2023; 16:2163-2170. [PMID: 37868023 PMCID: PMC10590072 DOI: 10.2147/rmhp.s413639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
Background Patients infected with SARS-CoV-2 Delta VOC have a longer course of disease. We detected the air, surfaces, and patient's personal items in the wards of the second hospital of Nanjing during the outbreak of the COVID-19 Delta Variant to identify the environmental contamination, which provides a theoretical basis for the prevention and control of COVID-19 variation beads in the future. Methods In the cross-sectional study, we collected and analyzed clinical features, demographic and epidemiological data, laboratory and swab test results, and surface and air samples of 144 COVID-19 cases. Results The time from symptom onset to surface sampling was 25 days (IQR, 21 to 33 days). Positive throat swabs were detected in 52(36.1%) patients, of which only 8(5.6%) patients had N or ORF1a/b genes Ct value <35 on the surface sampling day. Among the 692 environmental surface and air specimens collected from 144 COVID-19 cases, 3 specimens (3/692, 0.4%) related to 5 cases (3.5%, 5/144) were detected positive on RT-PCR. Overall, bedside tables (2/144, 1.4%) were most likely to be contaminated, followed by toilet seats (1/81, 1.2%). Conclusion The environmental contamination by SARS-CoV-2 Delta VOC-infected cases with disease duration of more than two weeks is limited.
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Affiliation(s)
- Jingwu Ge
- Department of Infection Management, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, People’s Republic of China
| | - Chuanmeng Zhang
- The Center for Translational Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, 225300, People’s Republic of China
| | - Zhihang Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, People’s Republic of China
| | - Minjuan Chu
- Department of Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, People’s Republic of China
| | - Wensen Chen
- Department of Infection Management, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, People’s Republic of China
| | - Zhanjie Li
- Department of Infection Management, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, People’s Republic of China
| | - Shuangyuan Liu
- Department of Infection Management, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, People’s Republic of China
| | - Yongfeng Yang
- Center of Infectious Diseases, Affiliated Nanjing Hospital of Nanjing University of Chinese Medicine (The No. 2 Hospital of Nanjing), Nanjing, 211113, People’s Republic of China
| | - Ming Chu
- Department of Infection Management, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, 225300, People’s Republic of China
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Guruprasad L, Naresh GKRS, Boggarapu G. Taking stock of the mutations in human SARS-CoV-2 spike proteins: From early days to nearly the end of COVID-19 pandemic. Curr Res Struct Biol 2023; 6:100107. [PMID: 37841365 PMCID: PMC10569959 DOI: 10.1016/j.crstbi.2023.100107] [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: 09/10/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causative agent of the coronavirus disease-2019 (COVID-19) has resulted in several deaths and severe economic losses throughout the world. The spike protein in the virus binds to the human ACE-2 receptor in order to mediate virus-host interactions required for the viral transmission. Since first report of the SARS-CoV-2 sequence during December 2019 from patient infected with the virus in Wuhan, China, the virus has undergone rapid changes leading to mutations comprising substitutions, deletions and insertions in the sequence resulting in several variants of the virus that were more virulent and transmissible or less virulent but highly transmissible. The timely intervention with COVID-19 vaccines proved to be effective in controlling the number of infections. However, rapid mutations in the virus led to the lowering of vaccine efficacies being administered to people. In May 2023, the World Health Organization declared COVID-19 was not a public health emergency of international concern anymore. In order to take stock of mutations in the virus from early days to nearly end of COVID-19 pandemic, sequence analyses of the SARS-CoV-2 spike proteins available in the NCBI Virus database was carried out. The mutations and invariant residues in the SARS-CoV-2 spike protein sequences relative to the reference sequence were analysed. The location of the invariant residues and residues at interface of the protein chains in the spike protein trimer complex structure were examined. A total of 111,298 non-redundant SARS-CoV-2 spike protein sequences representing 2,345,585 spike proteins in the NCBI Virus database showed mutations at 1252 of the 1273 positions in the amino acid sequence. The mutations represented 6129 different mutation types in the sequences analysed. Besides, some sequences also contained insertion mutations. The SARS-CoV-2 spike protein sequences represented 1435 lineages. In addition, several spike protein sequences with mutations whose lineages were either 'not classified' or were 'unclassifiable' indicated the virus could still be evolving.
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13
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Xu X, Wu Y, Kummer AG, Zhao Y, Hu Z, Wang Y, Liu H, Ajelli M, Yu H. Assessing changes in incubation period, serial interval, and generation time of SARS-CoV-2 variants of concern: a systematic review and meta-analysis. BMC Med 2023; 21:374. [PMID: 37775772 PMCID: PMC10541713 DOI: 10.1186/s12916-023-03070-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND After the first COVID-19 wave caused by the ancestral lineage, the pandemic has been fueled from the continuous emergence of new SARS-CoV-2 variants. Understanding key time-to-event periods for each emerging variant of concern is critical as it can provide insights into the future trajectory of the virus and help inform outbreak preparedness and response planning. Here, we aim to examine how the incubation period, serial interval, and generation time have changed from the ancestral SARS-CoV-2 lineage to different variants of concern. METHODS We conducted a systematic review and meta-analysis that synthesized the estimates of incubation period, serial interval, and generation time (both realized and intrinsic) for the ancestral lineage, Alpha, Beta, and Omicron variants of SARS-CoV-2. RESULTS Our study included 280 records obtained from 147 household studies, contact tracing studies, or studies where epidemiological links were known. With each emerging variant, we found a progressive shortening of each of the analyzed key time-to-event periods, although we did not find statistically significant differences between the Omicron subvariants. We found that Omicron BA.1 had the shortest pooled estimates for the incubation period (3.49 days, 95% CI: 3.13-4.86 days), Omicron BA.5 for the serial interval (2.37 days, 95% CI: 1.71-3.04 days), and Omicron BA.1 for the realized generation time (2.99 days, 95% CI: 2.48-3.49 days). Only one estimate for the intrinsic generation time was available for Omicron subvariants: 6.84 days (95% CrI: 5.72-8.60 days) for Omicron BA.1. The ancestral lineage had the highest pooled estimates for each investigated key time-to-event period. We also observed shorter pooled estimates for the serial interval compared to the incubation period across the virus lineages. When pooling the estimates across different virus lineages, we found considerable heterogeneities (I2 > 80%; I2 refers to the percentage of total variation across studies that is due to heterogeneity rather than chance), possibly resulting from heterogeneities between the different study populations (e.g., deployed interventions, social behavior, demographic characteristics). CONCLUSIONS Our study supports the importance of conducting contact tracing and epidemiological investigations to monitor changes in SARS-CoV-2 transmission patterns. Our findings highlight a progressive shortening of the incubation period, serial interval, and generation time, which can lead to epidemics that spread faster, with larger peak incidence, and harder to control. We also consistently found a shorter serial interval than incubation period, suggesting that a key feature of SARS-CoV-2 is the potential for pre-symptomatic transmission. These observations are instrumental to plan for future COVID-19 waves.
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Affiliation(s)
- Xiangyanyu Xu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yanpeng Wu
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Allisandra G Kummer
- Laboratory of Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Yuchen Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Zexin Hu
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Yan Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hengcong Liu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Marco Ajelli
- Laboratory of Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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14
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Ali KM, Rashid PMA, Ali AM, Tofiq AM, Salih GF, Dana OI, Rostam HM. Clinical outcomes and phylogenetic analysis in reflection with three predominant clades of SARS-CoV-2 variants. Eur J Clin Invest 2023; 53:e14004. [PMID: 37036255 DOI: 10.1111/eci.14004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/11/2023]
Abstract
BACKGROUND The pandemic of coronavirus disease 2019 (COVID-19) has a broad spectrum of clinical manifestations. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) undergoes continuous evolution, resulting in the emergence of several variants. Each variant has a different severity and mortality rate. MATERIALS AND METHODS In this study, 1174 COVID-19 patients were studied for mortality and severity over three SARS-CoV-2 predominating variant periods in 2021 and 2022 in Sulaimani Province, Iraq. In each period, a representative, variant virus was subjected to phylogenetic and molecular and clinical analysis. RESULTS Phylogenetic analysis revealed three SARS-CoV-2 variants, belonging to: Delta B.1.617.2, Omicron BA.1.17.2, and Omicron BA.5.6. The Delta variants showed more severe symptoms and a lower PCR-Ct value than Omicron variants regardless of gender, and only 4.3% of the cases were asymptomatic. The mortality rate was lower with Omicron (.5% for BA.5.2 and 1.3% for BA.1.17.2) compared with Delta variants (2.5%). The higher mortality rate with Delta variants was in males (2.84%), while that with Omicron BA1.17.2 and BA.5.2 was in females, 1.05% and .0%, respectively. Age group (≥70) years had the highest mortality rate; however, it was (.0%) in the age group (30-49) years with Omicron variants, compared with (.96%) in Delta variants. CONCLUSIONS There has been a surge in COVID-19 infection in the city due to the predominant lineages of SARS-CoV-2, B.1.617, Omicron BA.1.17.2 and Omicron BA.5.6, respectively. A higher PCR-Ct value and severity of the Delta variant over Omicron BA.1.17.2 and/or BA.5.2 variants were significantly correlated with a higher death rate in the same order.
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Affiliation(s)
- Kameran M Ali
- Medical Laboratory Technology Department, Kalar Technical College, Sulaimani Polytechnic University, Kalar, Iraq
| | - Peshnyar M A Rashid
- Medical Laboratory Science Department, Komar University of Science and Technology, Sulaimania, Iraq
| | - Ayad M Ali
- Department of Chemistry, University of Garmian, Kalar, Iraq
| | - Ahmed M Tofiq
- Department of Biology, College of Education, University of Garmian, Head of International Academic Relations (IRO), Kalar, Iraq
| | - Gaza F Salih
- Biology Department, College of Science, University of Sulaimani, Sulaimania, Iraq
| | - Omer I Dana
- College of Veterinary Medicine, University of Sulaimani, Sulaimani, Iraq
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15
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Hou M, Shi J, Gong Z, Wen H, Lan Y, Deng X, Fan Q, Li J, Jiang M, Tang X, Wu CI, Li F, Ruan Y. Intra- vs. Interhost Evolution of SARS-CoV-2 Driven by Uncorrelated Selection-The Evolution Thwarted. Mol Biol Evol 2023; 40:msad204. [PMID: 37707487 PMCID: PMC10521905 DOI: 10.1093/molbev/msad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
In viral evolution, a new mutation has to proliferate within the host (Stage I) in order to be transmitted and then compete in the host population (Stage II). We now analyze the intrahost single nucleotide variants (iSNVs) in a set of 79 SARS-CoV-2 infected patients with most transmissions tracked. Here, every mutation has two measures: 1) iSNV frequency within each individual host in Stage I; 2) occurrence among individuals ranging from 1 (private), 2-78 (public), to 79 (global) occurrences in Stage II. In Stage I, a small fraction of nonsynonymous iSNVs are sufficiently advantageous to rise to a high frequency, often 100%. However, such iSNVs usually fail to become public mutations. Thus, the selective forces in the two stages of evolution are uncorrelated and, possibly, antagonistic. For that reason, successful mutants, including many variants of concern, have to avoid being eliminated in Stage I when they first emerge. As a result, they may not have the transmission advantage to outcompete the dominant strains and, hence, are rare in the host population. Few of them could manage to slowly accumulate advantageous mutations to compete in Stage II. When they do, they would appear suddenly as in each of the six successive waves of SARS-CoV-2 strains. In conclusion, Stage I evolution, the gate-keeper, may contravene the long-term viral evolution and should be heeded in viral studies.
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Affiliation(s)
- Mei Hou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jingrong Shi
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zanke Gong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yun Lan
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xizi Deng
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qinghong Fan
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiaojiao Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Mengling Jiang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoping Tang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Feng Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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16
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He Y, Martinez L, Ge Y, Feng Y, Chen Y, Tan J, Westbrook A, Li C, Cheng W, Ling F, Cheng H, Wu S, Zhong W, Handel A, Huang H, Sun J, Shen Y. Social Mixing and Network Characteristics of COVID-19 Patients Before and After Widespread Interventions: A Population-based Study. Epidemiol Infect 2023; 151:1-38. [PMID: 37577939 PMCID: PMC10540215 DOI: 10.1017/s0950268823001292] [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: 02/20/2023] [Revised: 06/28/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023] Open
Abstract
SARS-CoV-2 rapidly spreads among humans via social networks, with social mixing and network characteristics potentially facilitating transmission. However, limited data on topological structural features has hindered in-depth studies. Existing research is based on snapshot analyses, preventing temporal investigations of network changes. Comparing network characteristics over time offers additional insights into transmission dynamics. We examined confirmed COVID-19 patients from an eastern Chinese province, analyzing social mixing and network characteristics using transmission network topology before and after widespread interventions. Between the two time periods, the percentage of singleton networks increased from 38.9 to 62.8 ; the average shortest path length decreased from 1.53 to 1.14 ; the average betweenness reduced from 0.65 to 0.11 ; the average cluster size dropped from 4.05 to 2.72 ; and the out-degree had a slight but nonsignificant decline from 0.75 to 0.63 Results show that nonpharmaceutical interventions effectively disrupted transmission networks, preventing further disease spread. Additionally, we found that the networks’ dynamic structure provided more information than solely examining infection curves after applying descriptive and agent-based modeling approaches. In summary, we investigated social mixing and network characteristics of COVID-19 patients during different pandemic stages, revealing transmission network heterogeneities.
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Affiliation(s)
- Yuncong He
- School of Mathematics, Sun Yat-sen University, Guangzhou, China
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, USA
| | - Yang Ge
- School of Health Professions, University of Southern Mississippi, Hattiesburg, USA
| | - Yan Feng
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yewen Chen
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, USA
| | - Jianbin Tan
- School of Mathematics, Sun Yat-sen University, Guangzhou, China
| | - Adrianna Westbrook
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, USA
| | - Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, USA
| | - Wei Cheng
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Feng Ling
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Huimin Cheng
- Department of Statistics, University of Georgia, Athens, USA
| | - Shushan Wu
- Department of Statistics, University of Georgia, Athens, USA
| | - Wenxuan Zhong
- Department of Statistics, University of Georgia, Athens, USA
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, USA
| | - Hui Huang
- Center for Applied Statistics and School of Statistics, Renmin University of China, Beijing, China
| | - Jimin Sun
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Ye Shen
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, USA
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17
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Corchis-Scott R, Geng Q, Al Riahi AM, Labak A, Podadera A, Ng KKS, Porter LA, Tong Y, Dixon JC, Menard SL, Seth R, McKay RM. Actionable wastewater surveillance: application to a university residence hall during the transition between Delta and Omicron resurgences of COVID-19. Front Public Health 2023; 11:1139423. [PMID: 37265515 PMCID: PMC10230041 DOI: 10.3389/fpubh.2023.1139423] [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: 01/07/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Wastewater surveillance has gained traction during the COVID-19 pandemic as an effective and non-biased means to track community infection. While most surveillance relies on samples collected at municipal wastewater treatment plants, surveillance is more actionable when samples are collected "upstream" where mitigation of transmission is tractable. This report describes the results of wastewater surveillance for SARS-CoV-2 at residence halls on a university campus aimed at preventing outbreak escalation by mitigating community spread. Another goal was to estimate fecal shedding rates of SARS-CoV-2 in a non-clinical setting. Passive sampling devices were deployed in sewer laterals originating from residence halls at a frequency of twice weekly during fall 2021 as the Delta variant of concern continued to circulate across North America. A positive detection as part of routine sampling in late November 2021 triggered daily monitoring and further isolated the signal to a single wing of one residence hall. Detection of SARS-CoV-2 within the wastewater over a period of 3 consecutive days led to a coordinated rapid antigen testing campaign targeting the residence hall occupants and the identification and isolation of infected individuals. With knowledge of the number of individuals testing positive for COVID-19, fecal shedding rates were estimated to range from 3.70 log10 gc ‧ g feces-1 to 5.94 log10 gc ‧ g feces-1. These results reinforce the efficacy of wastewater surveillance as an early indicator of infection in congregate living settings. Detections can trigger public health measures ranging from enhanced communications to targeted coordinated testing and quarantine.
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Affiliation(s)
- Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Abdul Monem Al Riahi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Amr Labak
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ana Podadera
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Lisa A. Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Jess C. Dixon
- Department of Kinesiology, University of Windsor, Windsor, ON, Canada
| | | | - Rajesh Seth
- Civil and Environmental Engineering, University of Windsor, Windsor, ON, Canada
| | - R. Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
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18
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Ma Z, Sun Z, Lv X, Chen H, Geng Y, Geng Z. Sensitivity-enhanced nanoplasmonic biosensor using direct immobilization of two engineered nanobodies for SARS-CoV-2 spike receptor-binding domain detection. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 383:133575. [PMID: 36873859 PMCID: PMC9957344 DOI: 10.1016/j.snb.2023.133575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Sensitive, rapid, and easy-to-implement biosensors are critical in responding to highly contagious and fast-spreading severe acute respiratory syndrome coronavirus (SARS-CoV-2) mutations, enabling early infection screening for appropriate isolation and treatment measures to prevent the spread of the virus. Based on the sensing principle of localized surface plasmon resonance (LSPR) and nanobody immunological techniques, an enhanced sensitivity nanoplasmonic biosensor was developed to quantify the SARS-CoV-2 spike receptor-binding domain (RBD) in serum within 30 min. The lowest concentration in the linear range can be detected down to 0.01 ng/mL by direct immobilization of two engineered nanobodies. Both the sensor fabrication process and immune strategy are facile and inexpensive, with the potential for large-scale application. The designed nanoplasmonic biosensor achieved excellent specificity and sensitivity for SARS-CoV-2 spike RBD, providing a potential option for accurate early screening of the novel coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Zhengtai Ma
- State Key Laboratory for Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Zengchao Sun
- The Chinese Academy of Sciences Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoqing Lv
- State Key Laboratory for Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, China
| | - Hongda Chen
- State Key Laboratory for Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, China
| | - Yong Geng
- The Chinese Academy of Sciences Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhaoxin Geng
- School of Information Engineering, Minzu University of China, Beijing, China
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19
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Boeder S, Kobayashi E, Ramesh G, Serences B, Kulasa K, Majithia AR. Accuracy and Glycemic Efficacy of Continuous Glucose Monitors in Critically Ill COVID-19 Patients: A Retrospective Study. J Diabetes Sci Technol 2023; 17:642-648. [PMID: 35876258 PMCID: PMC10159791 DOI: 10.1177/19322968221113865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Continuous glucose monitoring (CGM) is approved for insulin dosing decisions in the ambulatory setting, but not currently for inpatients. CGM has the capacity to reduce patient-provider contact in inpatients with coronavirus disease 2019 (COVID-19), thus potentially reducing in hospital virus transmission. However, there are sparse data on the accuracy and efficacy of CGM to titrate insulin doses in inpatients. METHODS Under an emergency use protocol, CGM (Dexcom G6) was used alongside standard point-of-care (POC) glucose measurements in patients critically ill from complications of COVID-19 requiring intravenous (IV) insulin. Glycemic control during IV insulin therapy was retrospectively assessed comparing periods with and without adjunctive CGM use. Accuracy metrics were computed and Clarke Error Grid analysis performed comparing CGM glucose values with POC measurements. RESULTS Twenty-four critically ill patients who met criteria for emergency use of CGM resulted in 47 333 CGM and 5677 POC glucose values. During IV insulin therapy, individuals' glycemic control improved when CGM was used (mean difference -30.7 mg/dL). Among 2194 matched CGM: POC glucose pairs, a high degree of concordance was observed with a mean absolute relative difference of 14.8% and 99.5% of CGM: POC pairs falling in Zones A and B of the Clarke Error Grid. CONCLUSIONS Continuous glucose monitoring use in critically ill COVID-19 patients improved glycemic control during IV insulin therapy. Continuous glucose monitoring glucose data were highly concordant with POC glucose during IV insulin therapy in critically ill patients suggesting that CGM could substitute for POC measurements in inpatients thus reducing patient-provider contact and mitigating infection transmission.
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Affiliation(s)
- Schafer Boeder
- Division of Endocrinology and
Metabolism, Department of Medicine, University of California, San Diego, La Jolla,
CA, USA
| | - Emily Kobayashi
- Bioinformatics and Systems Biology
Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Gautam Ramesh
- School of Medicine, University of
California, San Diego, La Jolla, CA, USA
| | - Brittany Serences
- Department of Nursing Education,
Development and Research, University of California, San Diego, La Jolla, CA,
USA
| | - Kristen Kulasa
- Division of Endocrinology and
Metabolism, Department of Medicine, University of California, San Diego, La Jolla,
CA, USA
| | - Amit R. Majithia
- Division of Endocrinology and
Metabolism, Department of Medicine, University of California, San Diego, La Jolla,
CA, USA
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20
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Lee J, Mendoza R, Mendoza VMP, Lee J, Seo Y, Jung E. Modelling the effects of social distancing, antiviral therapy, and booster shots on mitigating Omicron spread. Sci Rep 2023; 13:6914. [PMID: 37106066 PMCID: PMC10139668 DOI: 10.1038/s41598-023-34121-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/25/2023] [Indexed: 04/29/2023] Open
Abstract
As the COVID-19 situation changes because of emerging variants and updated vaccines, an elaborate mathematical model is essential in crafting proactive and effective control strategies. We propose a COVID-19 mathematical model considering variants, booster shots, waning, and antiviral drugs. We quantify the effects of social distancing in the Republic of Korea by estimating the reduction in transmission induced by government policies from February 26, 2021 to February 3, 2022. Simulations show that the next epidemic peak can be estimated by investigating the effects of waning immunity. This research emphasizes that booster vaccination should be administered right before the next epidemic wave, which follows the increasing waned population. Policymakers are recommended to monitor the waning population immunity using mathematical models or other predictive methods. Moreover, our simulations considering a new variant's transmissibility, severity, and vaccine evasion suggest intervention measures that can reduce the severity of COVID-19.
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Affiliation(s)
- Jongmin Lee
- Department of Mathematics, Konkuk University, Seoul, 05029, South Korea
| | - Renier Mendoza
- Institute of Mathematics, University of the Philippines Diliman, Quezon City, 1101, Philippines
| | - Victoria May P Mendoza
- Institute of Mathematics, University of the Philippines Diliman, Quezon City, 1101, Philippines
| | - Jacob Lee
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, 07441, South Korea
| | - Yubin Seo
- Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, 07441, South Korea
| | - Eunok Jung
- Department of Mathematics, Konkuk University, Seoul, 05029, South Korea.
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21
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Galmiche S, Cortier T, Charmet T, Schaeffer L, Chény O, von Platen C, Lévy A, Martin S, Omar F, David C, Mailles A, Carrat F, Cauchemez S, Fontanet A. SARS-CoV-2 incubation period across variants of concern, individual factors, and circumstances of infection in France: a case series analysis from the ComCor study. THE LANCET. MICROBE 2023:S2666-5247(23)00005-8. [PMID: 37084751 PMCID: PMC10112864 DOI: 10.1016/s2666-5247(23)00005-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/08/2022] [Accepted: 12/23/2022] [Indexed: 04/23/2023]
Abstract
BACKGROUND The incubation period of SARS-CoV-2 has been estimated for the known variants of concern. However, differences in study designs and settings make comparing variants difficult. We aimed to estimate the incubation period for each variant of concern compared with the historical strain within a unique and large study to identify individual factors and circumstances associated with its duration. METHODS In this case series analysis, we included participants (aged ≥18 years) of the ComCor case-control study in France who had a SARS-CoV-2 diagnosis between Oct 27, 2020, and Feb 4, 2022. Eligible participants were those who had the historical strain or a variant of concern during a single encounter with a known index case who was symptomatic and for whom the incubation period could be established, those who reported doing a reverse-transcription-PCR (RT-PCR) test, and those who were symptomatic by study completion. Sociodemographic and clinical characteristics, exposure information, circumstances of infection, and COVID-19 vaccination details were obtained via an online questionnaire, and variants were established through variant typing after RT-PCR testing or by matching the time that a positive test was reported with the predominance of a specific variant. We used multivariable linear regression to identify factors associated with the duration of the incubation period (defined as the number of days from contact with the index case to symptom onset). FINDINGS 20 413 participants were eligible for inclusion in this study. Mean incubation period varied across variants: 4·96 days (95% CI 4·90-5·02) for alpha (B.1.1.7), 5·18 days (4·93-5·43) for beta (B.1.351) and gamma (P.1), 4·43 days (4·36-4·49) for delta (B.1.617.2), and 3·61 days (3·55-3·68) for omicron (B.1.1.529) compared with 4·61 days (4·56-4·66) for the historical strain. Participants with omicron had a shorter incubation period than participants with the historical strain (-0·9 days, 95% CI -1·0 to -0·7). The incubation period increased with age (participants aged ≥70 years had an incubation period 0·4 days [0·2 to 0·6] longer than participants aged 18-29 years), in female participants (by 0·1 days, 0·0 to 0·2), and in those who wore a mask during contact with the index case (by 0·2 days, 0·1 to 0·4), and was reduced in those for whom the index case was symptomatic (-0·1 days, -0·2 to -0·1). These data were robust to sensitivity analyses correcting for an over-reporting of incubation periods of 7 days. INTERPRETATION SARS-CoV-2 incubation period is notably reduced in omicron cases compared with all other variants of concern, in young people, after transmission from a symptomatic index case, after transmission to a maskless secondary case, and (to a lesser extent) in men. These findings can inform future COVID-19 contact-tracing strategies and modelling. FUNDING Institut Pasteur, the French National Agency for AIDS Research-Emerging Infectious Diseases, Fondation de France, the INCEPTION project, and the Integrative Biology of Emerging Infectious Diseases project.
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Affiliation(s)
- Simon Galmiche
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France; Ecole Doctorale Pierre Louis de Santé Publique, Sorbonne Université, Paris, France
| | - Thomas Cortier
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, Paris, France; Ecole Doctorale Pierre Louis de Santé Publique, Sorbonne Université, Paris, France
| | - Tiffany Charmet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Laura Schaeffer
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Olivia Chény
- Centre for Translational Research, Institut Pasteur, Université Paris Cité, Paris, France
| | - Cassandre von Platen
- Centre for Translational Research, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anne Lévy
- Caisse Nationale de l'Assurance Maladie, Paris, France
| | - Sophie Martin
- Caisse Nationale de l'Assurance Maladie, Paris, France
| | | | | | | | - Fabrice Carrat
- The National Institute of Health and Medical Research, Sorbonne Université, Paris, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France; Conservatoire National des Arts et Métiers, Unité Pasteur-Cnam Risques Infectieux et Émergents, Paris, France.
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22
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Rao R, Musante CJ, Allen R. A quantitative systems pharmacology model of the pathophysiology and treatment of COVID-19 predicts optimal timing of pharmacological interventions. NPJ Syst Biol Appl 2023; 9:13. [PMID: 37059734 PMCID: PMC10102696 DOI: 10.1038/s41540-023-00269-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/09/2023] [Indexed: 04/16/2023] Open
Abstract
A quantitative systems pharmacology (QSP) model of the pathogenesis and treatment of SARS-CoV-2 infection can streamline and accelerate the development of novel medicines to treat COVID-19. Simulation of clinical trials allows in silico exploration of the uncertainties of clinical trial design and can rapidly inform their protocols. We previously published a preliminary model of the immune response to SARS-CoV-2 infection. To further our understanding of COVID-19 and treatment, we significantly updated the model by matching a curated dataset spanning viral load and immune responses in plasma and lung. We identified a population of parameter sets to generate heterogeneity in pathophysiology and treatment and tested this model against published reports from interventional SARS-CoV-2 targeting mAb and antiviral trials. Upon generation and selection of a virtual population, we match both the placebo and treated responses in viral load in these trials. We extended the model to predict the rate of hospitalization or death within a population. Via comparison of the in silico predictions with clinical data, we hypothesize that the immune response to virus is log-linear over a wide range of viral load. To validate this approach, we show the model matches a published subgroup analysis, sorted by baseline viral load, of patients treated with neutralizing Abs. By simulating intervention at different time points post infection, the model predicts efficacy is not sensitive to interventions within five days of symptom onset, but efficacy is dramatically reduced if more than five days pass post symptom onset prior to treatment.
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Affiliation(s)
- Rohit Rao
- Early Clinical Development, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA.
| | - Cynthia J Musante
- Early Clinical Development, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Richard Allen
- Early Clinical Development, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
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23
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Hu F, Jia Y, Zhao D, Fu X, Zhang W, Tang W, Hu S, Wu H, Ge M, Du W, Shen W, Zhu B, Chen H. Clinical outcomes of the SARS-cov-2 omicron and delta variant: systematic review and meta-analysis of 33 studies covering 6,037,144 COVID-19 positive patients. Clin Microbiol Infect 2023:S1198-743X(23)00133-7. [PMID: 36934872 PMCID: PMC10023211 DOI: 10.1016/j.cmi.2023.03.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/06/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023]
Abstract
BACKGROUND Although the SARS-CoV-2 Omicron variant is considered to induce less severe disease, there have been no consistent results on the extent of the decrease in severity. OBJECTIVES To compare the clinical outcomes of COVID-19 positive patients with Omicron and Delta variant infection. DATA SOURCES Searches were implemented up to 8 November 2022 in PubMed, Web of Science, BioRvix, and MedRvix. STUDY ELIGIBILITY CRITERIA Eligible studies were cohort studies reporting the clinical outcomes of COVID-19 positive patients with omicron and delta variant infection, including hospitalization, ICU admission, receiving invasive mechanical ventilation (IMV), and death. PARTICIPANTS COVID-19 positive patients with Omicron and Delta variant infection. Assessment of risk of bias: Risk of bias was assessed employing the Newcastle-Ottawa Scale (NOS). Methods of data synthesis: Random-effect models were employed to pool the Odds ratios (ORs) and 95% confidence intervals (CIs) to compare the risk of clinical outcome. I2 was employed to evaluate heterogeneity between studies. RESULTS A total of 33 studies with 6,037,144 COVID-19 positive patients were included in this meta-analysis. In the general population of COVID-19 positive, compared to Delta, Omicron variant infection resulted in a decreased risk of hospitalization (10.24% Vs 4.14%, OR=2.91, 95%CI=2.35-3.60), ICU admission (3.67% Vs 0.48%, OR=3.64, 95%CI=2.63-5.04), receiving IMV (3.93% Vs 0.34%, OR=3.11, 95%CI=1.76-5.50), and death (2.40% Vs 0.46%, OR=2.97, 95%CI=2.17-4.08). In the hospitalized patients with COVID-19 positive, compared to Delta, Omicron variant infection resulted in a decreased risk of ICU admission (20.70% Vs 12.90%, OR=1.63, 95%CI=1.32-2.02), receiving IMV (10.90% Vs 5.80%, OR=1.65, 95%CI=1.28-2.14), and death (10.72% Vs 7.10%, OR=1.44, 95%CI=1.22-1.71). DISCUSSION Compared to Delta, the severity of Omicron variant infection decreased.
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Affiliation(s)
- Feihong Hu
- Medical School of Nantong University, Nantong, China
| | - Yijie Jia
- Medical School of Nantong University, Nantong, China
| | - Danyan Zhao
- Medical School of Nantong University, Nantong, China
| | - Xuelei Fu
- Medical School of Nantong University, Nantong, China
| | - Wanqing Zhang
- Medical School of Nantong University, Nantong, China
| | - Wen Tang
- Medical School of Nantong University, Nantong, China
| | - Shiqi Hu
- Medical School of Nantong University, Nantong, China
| | - Hua Wu
- Medical School of Nantong University, Nantong, China
| | - Mengwei Ge
- Medical School of Nantong University, Nantong, China
| | - Wei Du
- Medical School of Nantong University, Nantong, China
| | - Wangqin Shen
- Medical School of Nantong University, Nantong, China
| | - Bin Zhu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Nantong University, And Nantong First People's Hospital, Nantong, China.
| | - Honglin Chen
- School of Public Health, Nantong University, Nantong, China.
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24
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Wang B, Li X, Xiao W, Zhang J, Ding H. Comprehensive analysis of clinical indications and viral strain variants among patients infected with SARS-CoV-2 in Inner Mongolia, China. Virus Genes 2023; 59:391-398. [PMID: 36905534 PMCID: PMC10006559 DOI: 10.1007/s11262-023-01986-0] [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: 12/02/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023]
Abstract
Since the first appearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, the virus is still evolving and mutating until now. In this study, we collected 6 throat swabs from patients who diagnosed with COVID-19 in Inner Mongolia, China, to understand the entry of multiple SARS-CoV-2 variants into Inner Mongolia and analyze the relationships between variants and clinical features observed in infected patients. In addition, we performed a combined analysis of clinical parameters associated with SARS-CoV-2 variants of interest, pedigree analysis, and detection of single-nucleotide polymorphisms. Our results showed that the clinical symptoms were generally mild although some patients demonstrated some degree of liver function abnormalities, and the SARS-CoV-2 strain was related to the Delta variant (B.1.617.2), AY.122 lineage. The epidemiological investigations and clinical manifestations confirmed that the variant exhibits strong transmission, a high viral load, and moderate clinical symptoms. SARS-CoV-2 has undergone extensive mutations in various hosts and countries. Timely monitoring of virus mutation can help to monitor the spread of infection and characterize the diversity of genomic variants, thus limiting future waves of SARS-CoV-2 infection.
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Affiliation(s)
- Bo Wang
- Department of Laboratory Medicine, Inner Mongolia People's Hospital, Hohhot, 010000, China
| | - Xiaocong Li
- Department of Laboratory Medicine, Inner Mongolia People's Hospital, Hohhot, 010000, China
| | - Weili Xiao
- Department of Laboratory Medicine, Inner Mongolia People's Hospital, Hohhot, 010000, China
| | - Jiangying Zhang
- Department of ICU, Inner Mongolia People's Hospital, Hohhot, 010000, China
| | - Haitao Ding
- Department of Laboratory Medicine, Inner Mongolia People's Hospital, Hohhot, 010000, China.
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25
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McClymont H, Si X, Hu W. Using weather factors and google data to predict COVID-19 transmission in Melbourne, Australia: A time-series predictive model. Heliyon 2023; 9:e13782. [PMID: 36845036 PMCID: PMC9941072 DOI: 10.1016/j.heliyon.2023.e13782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/23/2023] Open
Abstract
Background Forecast models have been essential in understanding COVID-19 transmission and guiding public health responses throughout the pandemic. This study aims to assess the effect of weather variability and Google data on COVID-19 transmission and develop multivariable time series AutoRegressive Integrated Moving Average (ARIMA) models for improving traditional predictive modelling for informing public health policy. Methods COVID-19 case notifications, meteorological factors and Google data were collected over the B.1.617.2 (Delta) outbreak in Melbourne, Australia from August to November 2021. Timeseries cross-correlation (TSCC) was used to evaluate the temporal correlation between weather factors, Google search trends, Google Mobility data and COVID-19 transmission. Multivariable time series ARIMA models were fitted to forecast COVID-19 incidence and Effective Reproductive Number (R eff ) in the Greater Melbourne region. Five models were fitted to compare and validate predictive models using moving three-day ahead forecasts to test the predictive accuracy for both COVID-19 incidence and R eff over the Melbourne Delta outbreak. Results Case-only ARIMA model resulted in an R squared (R2) value of 0.942, Root Mean Square Error (RMSE) of 141.59, and Mean Absolute Percentage Error (MAPE) of 23.19. The model including transit station mobility (TSM) and maximum temperature (Tmax) had greater predictive accuracy with R2 0.948, RMSE 137.57, and MAPE 21.26. Conclusion Multivariable ARIMA modelling for COVID-19 cases and R eff was useful for predicting epidemic growth, with higher predictive accuracy for models including TSM and Tmax. These results suggest that TSM and Tmax would be useful for further exploration for developing weather-informed early warning models for future COVID-19 outbreaks with potential application for the inclusion of weather and Google data with disease surveillance in developing effective early warning systems for informing public health policy and epidemic response.
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26
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Dash NR, Barqawi HJ, Obaideen AA, Al Chame HQ, Samara KA, Qadri R, Eldesouki S. COVID-19 Breakthrough Infection Among Vaccinated Population in the United Arab Emirates. J Epidemiol Glob Health 2023; 13:67-90. [PMID: 36795274 PMCID: PMC9933808 DOI: 10.1007/s44197-023-00090-8] [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: 06/07/2022] [Accepted: 01/12/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Despite significant efforts to contain the Coronavirus Disease 2019 (COVID-19) pandemic through mass vaccination, numerous nations throughout the world have recorded breakout infections. The incidence and severity of COVID-19 breakthrough infections in the United Arab Emirates (UAE) remain unknown despite extensive COVID-19 vaccine coverage. The goal of this research is to establish the characteristics of COVID-19 breakthrough infections in the UAE's vaccinated population. METHODS Between February and March 2022, we conducted a descriptive cross-sectional study in the UAE with 1533 participants to examine the characteristics of COVID-19 breakthrough infection among the vaccinated population. RESULTS The vaccination coverage was 97.97%, and the COVID-19 breakthrough infection rate was 32.1%, requiring hospitalization in 7.7% of cases. The bulk of the 492 COVID-19 breakthrough infections reported was among young adults (67%), with the majority experiencing mild to moderate symptoms (70.7%) or remaining asymptomatic (21.5%). CONCLUSIONS COVID-19 breakthrough infection were reported in younger age, male sex, non-healthcare professions, vaccination with inactivated whole virus vaccine (Sinopharm), and not receiving a booster dose. Information on breakthrough infection in the UAE might influence public health decisions and motivate measures such as providing additional booster doses of the vaccines to the people.
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Affiliation(s)
- Nihar Ranjan Dash
- Clinical Sciences Department, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates.
| | - Hiba Jawdat Barqawi
- Clinical Sciences Department, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Anas A Obaideen
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Kamel A Samara
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rama Qadri
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Salma Eldesouki
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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27
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Abstract
SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed.
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Affiliation(s)
- Olha Puhach
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
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28
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He J, Wei Z, Leng T, Bao J, Gao X, Chen F. Vaccination options for pregnant women during the Omicron period. J Reprod Immunol 2023; 156:103798. [PMID: 36640675 PMCID: PMC9817340 DOI: 10.1016/j.jri.2023.103798] [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: 09/17/2022] [Revised: 12/02/2022] [Accepted: 01/05/2023] [Indexed: 01/08/2023]
Abstract
Omicron exhibits reduced pathogenicity in general population than the previous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. However, the severity of disease and pregnancy outcomes of Omicron infection among pregnant women have not yet been definitively established. Meanwhile, substantial proportions of this population have doubts about the necessity of vaccination given the reports of declining efficacy of coronavirus disease 2019 (COVID-19) vaccines. Herein, we comprehensively discuss the clinical outcomes of infected pregnant women during the Omicron period and summarize the available data on the safety and efficacy profile of COVID-19 vaccination. The results found that the incidence of moderate and severe disease, maternal mortality, pregnancy loss, preterm delivery, stillbirth, preeclampsia/eclampsia, and gestational hypertension during the Omicron period are similar to those during the Pre-Delta period. In view of the effects of mass vaccination and previous natural infection on disease severity, the virulence of Omicron in pregnant women may be comparable to or even higher than that of the Pre-Delta variant. Moreover, the currently approved COVID-19 vaccines are safe and effective for pregnant women. Particularly, those who received a second or third dose had significantly less severe disease with little progression to critical illness or death compared with those who were unvaccinated or received only one dose. Therefore, in the case of the rapid spread of Omicron, pregnant women should still strictly follow preventive measures to avoid infection and receive the COVID-19 vaccine in a timely manner.
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Affiliation(s)
- Jiarui He
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Zichun Wei
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Taiyang Leng
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Jiaqi Bao
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Xinyao Gao
- Jining Medical University, 133 Hehua Rd, Jining 272067, China
| | - Fei Chen
- Jining Medical University, 133 Hehua Rd, Jining 272067, China.
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W. Lambisia A, H. Mudhune G, M. Morobe J, Said Mohammed K, O. Makori T, Ndwiga L, W. Mburu M, O. Moraa E, Musyoki J, Murunga N, N. Waliaula I, K. Mumelo A, Bejon P, Isabella Ochola-Oyier L, Githinji G, Nokes J, Agoti C. Temporal distribution and clinical characteristics of the Alpha, Delta and Omicron SARS-CoV-2 variants of concern in Laikipia, Kenya: institutional and community-based genomic surveillance. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18306.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Background: Understanding the molecular epidemiology and clinical presentation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) in rural-urban populations in Kenya is important for informing future public health responses and clinical care. Methods: We undertook a retrospective analysis of the clinical presentation and phylogenetic relatedness of specimens from 97 SARS-CoV-2 cases collected between 24th April and 31st December 2021 in Laikipia county, Kenya. VOC were related to observed symptoms. Phylogenetic analyses included contemporaneous sequences from across Kenya and the globe, to contextualise local transmission dynamics. Results: These sequences fell into three VOC; Alpha (n=8), Delta (n=52) and Omicron (n=37). We estimated 75 independent SARS-CoV-2 introductions into the county. The Alpha and Delta VOC were commonly detected in persons aged 31 to 45 years, 50.0% and 30.8%, respectively. The Omicron VOC was mostly detected in 16 to 30-year-olds (51.4%). Whereas relative to the other VOCs, Omicron was associated with mild upper-respiratory tract symptoms (cough, OR 3.78; 95% CI 1.1 – 16.74, p= 0.026) and sore throat, OR 22.42; 95% CI 7.11 – 81.40, p<0.001), Delta was associated with moderate to severe lower-respiratory tract symptoms (shortness of breath, OR 26.8; 95% CI 3.89 – 1158.14, p<0.001) and fever (OR 6.11; 95% CI 1.57 – 35.35, p= 0.004). Post-acute phase neurological complications were suspected in four Delta infected cases (neuralgia, neuritis, peripheral neuropathy, numbness of hand and tinnitus). Conclusion: We highlight the distinctive clinical characteristics of SARS-CoV-2 VOCs, as observed in Laikipia, Kenya, to support evidence-based clinical decisions. Multiple introductions of the VOCs were recorded despite the public health measures that were in place questioning their effectiveness during the study period.
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30
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Effectiveness of Inactivated Vaccine against SARS-CoV-2 Delta Variant Infection in Xiamen, China—A Test-Negative Case-Control Study. Vaccines (Basel) 2023; 11:vaccines11030532. [PMID: 36992116 DOI: 10.3390/vaccines11030532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Objective: Vaccine effectiveness can measure herd immunity, but the effectiveness of inactivated vaccines in Xiamen remains unclear. Our study was designed to understand the herd immunity of the COVID-19 inactivated vaccine against the SARA-CoV-2 Delta variant in the real world of Xiamen. Methods: We carried out a test-negative case-control study to explore the vaccine’s effectiveness. Participants aged over 12 years were recruited. A logistic regression was used to estimate the odds ratio (OR) of the vaccine among cases and controls. Results: This outbreak began with factory transmission clusters, and spread to families and communities during the incubation period. Sixty percent of cases were confirmed in a quarantine site. A huge mass of confirmed cases (94.49%) was identified within three days, and nearly half of them had a low Ct value. Following an adjustment for age and sex, a single dose of inactivated SARS-CoV-2 vaccine yielded the vaccine effectiveness (VE) of the overall case, of 57.01% (95% CI: −91.44~86.39%), the fully VE was 65.72% (95% CI: −48.69~88.63%) against COVID-19, 59.45% against moderate COVID-19 and 38.48% against severe COVID-19, respectively. The VE of fully vaccinated individuals was significantly higher in females than in males (73.99% vs. 46.26%). The VE among participants aged 19~40 and 41~61 years was 78.75% and 66.33%, respectively, which exceeds the WHO’s minimal threshold. Nevertheless, the VE in people under 18 and over 60 years was not observed because of the small sample size. Conclusions: The single-dose vaccine had limited effectiveness in preventing infection of the Delta variant. The two doses of inactivated vaccine could effectively prevent infection, and clinical mild, moderate, and severe illness caused by the SARS-CoV-2 Delta variant in people aged 18–60 years in the real world.
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31
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Azizogli AR, Pai V, Coppola F, Jafari R, Dodd-o JB, Harish R, Balasubramanian B, Kashyap J, Acevedo-Jake AM, Král P, Kumar VA. Scalable Inhibitors of the Nsp3-Nsp4 Coupling in SARS-CoV-2. ACS OMEGA 2023; 8:5349-5360. [PMID: 36798146 PMCID: PMC9923439 DOI: 10.1021/acsomega.2c06384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/29/2022] [Indexed: 06/18/2023]
Abstract
The human Betacoronavirus SARS-CoV-2 is a novel pathogen claiming millions of lives and causing a global pandemic that has disrupted international healthcare systems, economies, and communities. The virus is fast mutating and presenting more infectious but less lethal versions. Currently, some small-molecule therapeutics have received FDA emergency use authorization for the treatment of COVID-19, including Lagevrio (molnupiravir) and Paxlovid (nirmaltrevir/ritonavir), which target the RNA-dependent RNA polymerase and the 3CLpro main protease, respectively. Proteins downstream in the viral replication process, specifically the nonstructural proteins (Nsps1-16), are potential drug targets due to their crucial functions. Of these Nsps, Nsp4 is a particularly promising drug target due to its involvement in the SARS-CoV viral replication and double-membrane vesicle formation (mediated via interaction with Nsp3). Given the degree of sequence conservation of these two Nsps across the Betacoronavirus clade, their protein-protein interactions and functions are likely to be conserved as well in SARS-CoV-2. Through AlphaFold2 and its recent advancements, protein structures were generated of Nsp3 and 4 lumenal loops of interest. Then, using a combination of molecular docking suites and an existing library of lead-like compounds, we virtually screened 7 million ligands to identify five putative ligand inhibitors of Nsp4, which could present an alternative pharmaceutical approach against SARS-CoV-2. These ligands exhibit promising lead-like properties (ideal molecular weight and log P profiles), maintain fixed-Nsp4-ligand complexes in molecular dynamics (MD) simulations, and tightly associate with Nsp4 via hydrophobic interactions. Additionally, alternative peptide inhibitors based on Nsp3 were designed and shown in MD simulations to provide a highly stable binding to the Nsp4 protein. Finally, these therapeutics were attached to dendrimer structures to promote their multivalent binding with Nsp4, especially its large flexible luminal loop (Nsp4LLL). The therapeutics tested in this study represent many different approaches for targeting large flexible protein structures, especially those localized to the ER. This study is the first work targeting the membrane rearrangement system of viruses and will serve as a potential avenue for treating viruses with similar replicative function.
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Affiliation(s)
- Abdul-Rahman Azizogli
- Department
of Biological Sciences, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Varun Pai
- Department
of Biological Sciences, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Francesco Coppola
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
| | - Roya Jafari
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
| | - Joseph B. Dodd-o
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Rohan Harish
- Department
of Electrical and Computer Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Bhavani Balasubramanian
- Department
of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Jatin Kashyap
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Amanda M. Acevedo-Jake
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Petr Král
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
- Departments
of Physics, Pharmaceutical Sciences, and Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Vivek A. Kumar
- Department
of Biological Sciences, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Chemical and Materials Engineering, New
Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department
of Endodontics, Rutgers School of Dental
Medicine, Newark, New Jersey 07103, United States
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32
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Han T, Luo Z, Ji L, Wu P, Li G, Liu X, Lai Y. Identification of natural compounds as SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation. Front Microbiol 2023; 13:1095068. [PMID: 36817101 PMCID: PMC9930647 DOI: 10.3389/fmicb.2022.1095068] [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: 11/10/2022] [Accepted: 12/29/2022] [Indexed: 02/05/2023] Open
Abstract
Background Base mutations increase the contagiousness and transmissibility of the Delta and Lambda strains and lead to the severity of the COVID-19 pandemic. Molecular docking and molecular dynamics (MD) simulations are frequently used for drug discovery and relocation. Small molecular compounds from Chinese herbs have an inhibitory effect on the virus. Therefore, this study used computational simulations to investigate the effects of small molecular compounds on the spike (S) protein and the binding between them and angiotensin-converting enzyme 2 (ACE2) receptors. Methods In this study, molecular docking, MD simulation, and protein-protein analysis were used to explore the medicinal target inhibition of Chinese herbal medicinal plant chemicals on SARS-CoV-2. 12,978 phytochemicals were screened against S proteins of SARS-CoV-2 Lambda and Delta mutants. Results Molecular docking showed that 65.61% and 65.28% of the compounds had the relatively stable binding ability to the S protein of Lambda and Delta mutants (docking score ≤ -6). The top five compounds with binding energy with Lambda and Delta mutants were clematichinenoside AR2 (-9.7), atratoglaucoside,b (-9.5), physalin b (-9.5), atratoglaucoside, a (-9.4), Ochnaflavone (-9.3) and neo-przewaquinone a (-10), Wikstrosin (-9.7), xilingsaponin A (-9.6), ardisianoside G (-9.6), and 23-epi-26-deoxyactein (-9.6), respectively. Four compounds (Casuarictin, Heterophylliin D, Protohypericin, and Glansrin B) could interact with S protein mutation sites of Lambda and Delta mutants, respectively, and MD simulation results showed that four plant chemicals and spike protein have good energy stable complex formation ability. In addition, protein-protein docking was carried out to evaluate the changes in ACE2 binding ability caused by the formation of four plant chemicals and S protein complexes. The analysis showed that the binding of four plant chemicals to the S protein could reduce the stability of the binding to ACE2, thereby reducing the replication ability of the virus. Conclusion To sum up, the study concluded that four phytochemicals (Casuarictin, Heterophylliin D, Protohypericin, and Glansrin B) had significant effects on the binding sites of the SARS-CoV-2 S protein. This study needs further in vitro and in vivo experimental validation of these major phytochemicals to assess their potential anti-SARS-CoV-2. Graphical abstract.
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Affiliation(s)
- Tiantian Han
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ziqing Luo
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lichun Ji
- The Third Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peng Wu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Geng Li
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Geng Li, ✉
| | - Xiaohong Liu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China,Xiaohong Liu, ✉
| | - Yanni Lai
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China,Yanni Lai, ✉
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33
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He Y, Dang S, Ma W, Chen L, Zhang R, Mei S, Wei X, Lv Q, Peng B, Sun Y, Kong D, Chen J, Li S, Tang X, Lu Q, Zhu C, Chen Z, Wan J, Zou X, Li M, Feng T, Ren L, Wang J. Temporal dynamics of SARS-CoV-2 genome mutations that occurred in vivo on an aircraft. BIOSAFETY AND HEALTH 2023; 5:62-67. [PMID: 36320662 PMCID: PMC9613807 DOI: 10.1016/j.bsheal.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
We analyzed variations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during a flight-related cluster outbreak of coronavirus disease 2019 (COVID-19) in Shenzhen, China, to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations (iSNVs) in a confined space. Thirty-three patients with COVID-19 were sampled, and 14 were resampled 3-31 days later. All 47 nasopharyngeal swabs were deep-sequenced. iSNVs and similarities in the consensus genome sequence were analyzed. Three SARS-CoV-2 variants of concern, Delta (n = 31), Beta (n = 1), and C.1.2 (n = 1), were detected among the 33 patients. The viral genome sequences from 30 Delta-positive patients had similar SNVs; 14 of these patients provided two successive samples. Overall, the 47 sequenced genomes contained 164 iSNVs. Of the 14 paired (successive) samples, the second samples (T2) contained more iSNVs (median: 3; 95% confidence interval [95% CI]: 2.77-10.22) than did the first samples (T1; median: 2; 95% CI: 1.63-3.74; Wilcoxon test, P = 0.021). 38 iSNVs were detected in T1 samples, and only seven were also detectable in T2 samples. Notably, T2 samples from two of the 14 paired samples had additional mutations than the T1 samples. The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event. Intra-host diversity increased gradually with time, and new site mutations occurred in vivo without a population transmission bottleneck. Therefore, we could not determine the generational relationship from the mutation site changes alone.
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Affiliation(s)
- Yaqing He
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Shengyuan Dang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Wentai Ma
- University of Chinese Academy of Sciences, Beijing 100190, China
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Long Chen
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Renli Zhang
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Shujiang Mei
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xinyi Wei
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Qiuying Lv
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Bo Peng
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Ying Sun
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Dongfeng Kong
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Jiancheng Chen
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Shimin Li
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xiujuan Tang
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Qingju Lu
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Can Zhu
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Zhigao Chen
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Jia Wan
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xuan Zou
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Tiejiang Feng
- Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen 518055, China
- Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Lili Ren
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Bhattacharya M, Chatterjee S, Sharma AR, Lee SS, Chakraborty C. Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape. Folia Microbiol (Praha) 2023; 68:17-28. [PMID: 35962276 PMCID: PMC9374302 DOI: 10.1007/s12223-022-01001-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/07/2022] [Indexed: 12/01/2022]
Abstract
The Delta variant is one of the alarming variants of the SARS-CoV-2 virus that have been immensely detrimental and a significant cause of the prolonged pandemic (B.1.617.2). During the SARS-CoV-2 pandemic from December 2020 to October 2021, the Delta variant showed global dominance, and afterwards, the Omicron variant showed global dominance. Delta shows high infectivity rate which accounted for nearly 70% of the cases after December 2020. This review discusses the additional attributes that make the Delta variant so infectious and transmissible. The study also focuses on the significant mutations, namely the L452R and T478K present on the receptor-binding domain of spike (S)-glycoprotein, which confers specific alterations to the Delta variant. Considerably, we have also highlighted other notable factors such as the immune escape, infectivity and re-infectivity, vaccine escape, Ro number, S-glycoprotein stability, cleavage pattern, and its binding affinity with the host cell receptor protein. We have also emphasized clinical manifestations, symptomatology, morbidity, and mortality for the Delta variant compared with other significant SARS-CoV-2 variants. This review will help the researchers to get an elucidative view of the Delta variant to adopt some practical strategies to minimize the escalating spread of the SARS-CoV-2 Delta variant.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore-756020, Odisha, India
| | - Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
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Zhang HP, Sun YL, Wang YF, Yazici D, Azkur D, Ogulur I, Azkur AK, Yang ZW, Chen XX, Zhang AZ, Hu JQ, Liu GH, Akdis M, Akdis CA, Gao YD. Recent developments in the immunopathology of COVID-19. Allergy 2023; 78:369-388. [PMID: 36420736 PMCID: PMC10108124 DOI: 10.1111/all.15593] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
There has been an important change in the clinical characteristics and immune profile of Coronavirus disease 2019 (COVID-19) patients during the pandemic thanks to the extensive vaccination programs. Here, we highlight recent studies on COVID-19, from the clinical and immunological characteristics to the protective and risk factors for severity and mortality of COVID-19. The efficacy of the COVID-19 vaccines and potential allergic reactions after administration are also discussed. The occurrence of new variants of concerns such as Omicron BA.2, BA.4, and BA.5 and the global administration of COVID-19 vaccines have changed the clinical scenario of COVID-19. Multisystem inflammatory syndrome in children (MIS-C) may cause severe and heterogeneous disease but with a lower mortality rate. Perturbations in immunity of T cells, B cells, and mast cells, as well as autoantibodies and metabolic reprogramming may contribute to the long-term symptoms of COVID-19. There is conflicting evidence about whether atopic diseases, such as allergic asthma and rhinitis, are associated with a lower susceptibility and better outcomes of COVID-19. At the beginning of pandemic, the European Academy of Allergy and Clinical Immunology (EAACI) developed guidelines that provided timely information for the management of allergic diseases and preventive measures to reduce transmission in the allergic clinics. The global distribution of COVID-19 vaccines and emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with reduced pathogenic potential dramatically decreased the morbidity, severity, and mortality of COVID-19. Nevertheless, breakthrough infection remains a challenge for disease control. Hypersensitivity reactions (HSR) to COVID-19 vaccines are low compared to other vaccines, and these were addressed in EAACI statements that provided indications for the management of allergic reactions, including anaphylaxis to COVID-19 vaccines. We have gained a depth knowledge and experience in the over 2 years since the start of the pandemic, and yet a full eradication of SARS-CoV-2 is not on the horizon. Novel strategies are warranted to prevent severe disease in high-risk groups, the development of MIS-C and long COVID-19.
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Affiliation(s)
- Huan-Ping Zhang
- Department of Allergology, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuan-Li Sun
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan-Fen Wang
- Department of Pediatrics, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Duygu Yazici
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Dilek Azkur
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, University of Kirikkale, Kirikkale, Turkey
| | - Ismail Ogulur
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Ahmet Kursat Azkur
- Department of Virology, Faculty of Veterinary Medicine, University of Kirikkale, Kirikkale, Turkey
| | - Zhao-Wei Yang
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Xue Chen
- Department of Allergology, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Ai-Zhi Zhang
- Intensive Care Unit, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jia-Qian Hu
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guang-Hui Liu
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Ya-Dong Gao
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
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Dhakal S, Charoen P, Pan-ngum W, Luvira V, Sivakorn C, Hanboonkunupakarn B, Chirapongsathorn S, Poovorawan K. Severity of COVID-19 in Patients with Diarrhoea: A Systematic Review and Meta-Analysis. Trop Med Infect Dis 2023; 8:tropicalmed8020084. [PMID: 36828500 PMCID: PMC9966065 DOI: 10.3390/tropicalmed8020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
COVID-19 patients occasionally present with diarrhoea. Our objective was to estimate the risk of developing the severe disease in COVID-19 patients with and without diarrhoea and to provide a more precise estimate of the prevalence of COVID-19-associated digestive symptoms. A total of 88 studies (n = 67,794) on patients with a COVID-19 infection published between 1 January 2020 and 20 October 2022 were included in this meta-analysis. The overall prevalence of digestive symptoms was 27% (95% confidence interval (CI): 21-34%; I2 = 99%). According to our data, the pooled prevalence of diarrhoea symptoms in the 88 studies analysed was 17% (95% CI: 14-20%; I2 = 98%). The pooled estimate of nausea or vomiting in a total of 60 studies was 12% (95% CI: 8-15%; I2 = 98%). We also analysed 23 studies with eligible individuals (n = 3800) to assess the association between the disease severity and diarrhoea. Individuals who had diarrhoea were more likely to have experienced severe COVID-19 (odds ratio: 1.71; 95% CI: 1.31-2.24; p < 0.0001; I2 = 10%). Gastrointestinal symptoms and diarrhoea are frequently presenting COVID-19 manifestations that physicians should be aware of.
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Affiliation(s)
- Sunita Dhakal
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Pimphen Charoen
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Wirichada Pan-ngum
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Viravarn Luvira
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Chaisith Sivakorn
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Borimas Hanboonkunupakarn
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Sakkarin Chirapongsathorn
- Department of Gastroenterology and Hepatology, Phramongkutklao Hospital, College of Medicine, Bangkok 10400, Thailand
| | - Kittiyod Poovorawan
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Correspondence: ; Tel.: +662-354-9100; Fax: +662-354-9168
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37
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Ma R, Zhang Y, Zhang Y, Li X, Ji Z. The Relationship between the Transmission of Different SARS-CoV-2 Strains and Air Quality: A Case Study in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20031943. [PMID: 36767307 PMCID: PMC9916065 DOI: 10.3390/ijerph20031943] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 06/11/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) has been a global public health concern for almost three years, and the transmission characteristics vary among different virus variants. Previous studies have investigated the relationship between air pollutants and COVID-19 infection caused by the original strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, it is unclear whether individuals might be more susceptible to COVID-19 due to exposure to air pollutants, with the SARS-CoV-2 mutating faster and faster. This study aimed to explore the relationship between air pollutants and COVID-19 infection caused by three major SARS-CoV-2 strains (the original strain, Delta variant, and Omicron variant) in China. A generalized additive model was applied to investigate the associations of COVID-19 infection with six air pollutants (PM2.5, PM10, SO2, CO, NO2, and O3). A positive correlation might be indicated between air pollutants (PM2.5, PM10, and NO2) and confirmed cases of COVID-19 caused by different SARS-CoV-2 strains. It also suggested that the mutant variants appear to be more closely associated with air pollutants than the original strain. This study could provide valuable insight into control strategies that limit the concentration of air pollutants at lower levels and would better control the spread of COVID-19 even as the virus continues to mutate.
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Affiliation(s)
- Ruiqing Ma
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
| | - Yeyue Zhang
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
| | - Yini Zhang
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
| | - Xi Li
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
| | - Zheng Ji
- School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
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38
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Characterization of healthcare-associated infections with the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) omicron variant at a tertiary healthcare center. Infect Control Hosp Epidemiol 2023; 44:133-135. [PMID: 35615952 PMCID: PMC9171059 DOI: 10.1017/ice.2022.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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39
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Elfessi Z, Doyle R, Young L, Knaub M, Yamanaka T. Antibody dependent enhancement-induced hypoxic respiratory failure: A case report. VISUAL JOURNAL OF EMERGENCY MEDICINE 2023; 30:101602. [PMID: 36718416 PMCID: PMC9876737 DOI: 10.1016/j.visj.2023.101602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/27/2023]
Affiliation(s)
- Zane Elfessi
- Department of Emergency Medicine, Jesse Brown Veterans Affairs Medical Center, 820 S Damen Avenue, Chicago, IL 60612, United States,Department of Pharmacy Practice, University of Illinois-Chicago College of Pharmacy, 833 S Wood Street, Chicago, IL 60612, United States,Corresponding author at: Department of Emergency Medicine, Jesse Brown Veterans Affairs Medical Center, 820 S Damen Avenue, Chicago, IL 60612, United States
| | - Richard Doyle
- Department of Emergency Medicine, Jesse Brown Veterans Affairs Medical Center, 820 S Damen Avenue, Chicago, IL 60612, United States
| | - Lisa Young
- Department of Emergency Medicine, Jesse Brown Veterans Affairs Medical Center, 820 S Damen Avenue, Chicago, IL 60612, United States
| | - Mark Knaub
- Department of Emergency Medicine, Jesse Brown Veterans Affairs Medical Center, 820 S Damen Avenue, Chicago, IL 60612, United States
| | - Travis Yamanaka
- Department of Pulmonary and Critical Care, Jesse Brown Veterans Affairs Medical Center, 820 S Damen Avenue, Chicago, IL 60612, United States
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Wang M, Liu Z, Wang Z, Li K, Tian Y, Lu W, Hong J, Peng X, Shi J, Zhang Z, Mei G. Clinical characteristics of 1139 mild cases of the SARS-CoV-2 Omicron variant infected patients in Shanghai. J Med Virol 2023; 95:e28224. [PMID: 36238984 PMCID: PMC9874495 DOI: 10.1002/jmv.28224] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/21/2022] [Accepted: 10/11/2022] [Indexed: 01/27/2023]
Abstract
In March 2022, the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surged during the Coronavirus Disease 2019 (COVID-19) pandemic in Shanghai, but over 90% of patients were mild. This study included 1139 COVID-19 patients mildly infected with the Omicron variant of SARS-CoV-2 in Shanghai from May 1 to 10, 2022, aiming to clarify the demographic characteristics and clinical symptoms of patients with mild Omicron infection. The clinical phenotypes of Omicron infection were identified by model-based cluster analysis to explore the features of different clusters. The median age of the patients was 41.0 years [IQR: 31.0-52.0 years] and 73.0% were male. The top three clinical manifestations are cough (57.5%), expectoration (48.3%), and nasal congestion and runny nose (43.4%). The prevalence of nasal congestion and runny nose varied significantly across the doses of vaccinations, with 23.1% in the unvaccinated population and 30%, 45.9%, and 44.3% in the 1-dose, 2-dose and 3-dose vaccinated populations, respectively. In addition, there were significant differences for fever (23.1%, 26.0%, 28.6%, 18.4%), head and body heaviness (15.4%, 14.0%, 26.7%, 22.4%), and loss of appetite (25.6%, 30.0%, 33.6%, 27.7%). The unvaccinated population had a lower incidence of symptoms than the vaccinated population. Cluster analysis revealed that all four clusters had multisystemic symptoms and were dominated by both general and respiratory symptoms. The more severe the degree of the symptoms was, the higher the prevalence of multisystemic symptoms will be. The Omicron variant produced a lower incidence of symptoms in mildly infected patients than previous SARS-CoV-2 variants, but the clinical symptoms caused by the Omicron variant are more complex, so that it needs to be differentiated from influenza.
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Affiliation(s)
- Miao Wang
- Department of Internal Medicine of Traditional Chinese Medicine, Longhua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Zhidong Liu
- Department of Internal Medicine of Traditional Chinese Medicine, Longhua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Zengliang Wang
- Department of Epidemiology, School of Public Health, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Ke Li
- Department of Epidemiology and Health Statistics, School of Public HealthFudan UniversityShanghaiChina
| | - Yu Tian
- Department of Internal Medicine of Traditional Chinese Medicine, Longhua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Wei Lu
- Department of Nursing, Longhua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Jie Hong
- Department of Epidemiology and Health Statistics, School of Public HealthFudan UniversityShanghaiChina
| | - Xinwei Peng
- Department of Epidemiology and Health Statistics, School of Public HealthFudan UniversityShanghaiChina
| | - Jin Shi
- Department of Epidemiology and Health Statistics, School of Public HealthFudan UniversityShanghaiChina
| | - Zhijie Zhang
- Department of Epidemiology and Health Statistics, School of Public HealthFudan UniversityShanghaiChina
| | - Guojiang Mei
- Department of Internal Medicine of Traditional Chinese Medicine, Longhua HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
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Li L, Cui J, Tang J, Shi J, Deng X, Zheng X, Fan Q, Liu Y, Yu H, Tang X, Hu F, Li F. High titers of neutralizing antibodies in the blood fail to eliminate SARS-CoV-2 viral RNA in the upper respiratory tract. J Med Virol 2023; 95:e28219. [PMID: 36229892 PMCID: PMC9874792 DOI: 10.1002/jmv.28219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 10/11/2022] [Indexed: 01/27/2023]
Abstract
Retest-positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA, as a unique phenomenon among discharged individuals, has been demonstrated to be safe in the community. Still, the underlying mechanism of viral lingering is less investigated. In this study, first, we find that the frequency of viral RNA-positive retesting differs among variants. Higher ratios of viral RNA-positive retest were more frequently observed among Delta (61.41%, 514 of 837 cases) and Omicron (39.53%, 119 of 301 cases) infections than among ancestral viral infection (7.27%, 21 of 289 cases). Second, the tissues where viral RNA reoccurred were altered. Delta RNA reoccurred mainly in the upper respiratory tract (90%), but ancestral virus RNA reoccurred mainly in the gastrointestinal tract (71%). Third, vaccination did not reduce the frequency of viral RNA-positive retests, despite high concentrations of viral-specific antibodies in the blood. Finally, 37 of 55 (67.27%) Delta-infected patients receiving neutralizing antibody therapy become viral RNA retest positive when high concentrations of neutralizing antibodies still patrol in the blood. Altogether, our findings suggest that the presentence of high titers of neutralizing antibodies in the blood is incompetent in clearing residual viral RNA in the upper respiratory tract.
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Affiliation(s)
- Lu Li
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Jianping Cui
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Jingyan Tang
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Jingrong Shi
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Xilong Deng
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Xiaowen Zheng
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Qinghong Fan
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Ying Liu
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Haisheng Yu
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Xiaoping Tang
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
- Guangzhou LaboratoryBio‐IslandGuangzhouChina
| | - Fengyu Hu
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
- Guangzhou LaboratoryBio‐IslandGuangzhouChina
| | - Feng Li
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
- Guangzhou LaboratoryBio‐IslandGuangzhouChina
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42
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Choi G, Lim AY, Choi S, Park K, Lee SY, Kim JH. Viral shedding patterns of symptomatic SARS-CoV-2 infections by periods of variant predominance and vaccination status in Gyeonggi Province, Korea. Epidemiol Health 2022; 45:e2023008. [PMID: 36596734 PMCID: PMC10581894 DOI: 10.4178/epih.e2023008] [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: 10/17/2022] [Accepted: 12/21/2022] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES We compared the viral cycle threshold (Ct) values of infected patients to better understand viral kinetics by vaccination status during different periods of variant predominance in Gyeonggi Province, Korea. METHODS We obtained case-specific data from the coronavirus disease 2019 (COVID-19) surveillance system, Gyeonggi in-depth epidemiological report system, and Health Insurance Review & Assessment Service from January 2020 to January 2022. We defined periods of variant predominance and explored Ct values by analyzing viral sequencing test results. Using a generalized additive model, we performed a nonlinear regression analysis to determine viral kinetics over time. RESULTS Cases in the Delta variant's period of predominance had higher viral shedding patterns than cases in other periods. The temporal change of viral shedding did not vary by vaccination status in the Omicron-predominant period, but viral shedding decreased in patients who had completed their third vaccination in the Delta-predominant period. During the Delta-predominant and Omicron-predominant periods, the time from symptom onset to peak viral shedding based on the E gene was approximately 2.4 days (95% confidence interval [CI], 2.2 to 2.5) and 2.1 days (95% CI, 2.0 to 2.1), respectively. CONCLUSIONS In one-time tests conducted to diagnose COVID-19 in a large population, although no adjustment for individual characteristics was conducted, it was confirmed that viral shedding differed by the predominant strain and vaccination history. These results show the value of utilizing hundreds of thousands of test data produced at COVID-19 screening test centers.
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Affiliation(s)
- Gawon Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Ah-Young Lim
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Sojin Choi
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Kunhee Park
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
| | - Soon Young Lee
- Department of Preventive Medicine and Public Health, Ajou University School of Medicine, Suwon, Korea
| | - Jong-Hun Kim
- Gyeonggi Infectious Disease Control Center, Health Bureau, Gyeonggi Provincial Government, Suwon, Korea
- Department of Social and Preventive Medicine, Sungkyunkwan University School of Medicine, Suwon, Korea
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Zhang Q, Zhang M, Hu J, He G, Zhou Y, Chen X, Zhuang Y, Rong Z, Yin L, Zhao J, Huang Z, Zeng W, Li X, Zhu Z, Tang Y, Quan Y, Li Y, Zhang L, Fu D, Li Y, Xiao J. Spatial-temporal clustering of an outbreak of SARS-CoV-2 Delta VOC in Guangzhou, China in 2021. Front Public Health 2022; 10:1050096. [PMID: 36568757 PMCID: PMC9780675 DOI: 10.3389/fpubh.2022.1050096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Background In May 2021, the SARS-CoV-2 Delta variant led to the first local outbreak in China in Guangzhou City. We explored the epidemiological characteristics and spatial-temporal clustering of this outbreak. Methods Based on the 153 cases in the SARS-CoV-2 Delta variant outbreak, the Knox test was used to analyze the spatial-temporal clustering of the outbreak. We further explored the spatial-temporal clustering by gender and age groups, as well as compared the changes of clustering strength (S) value between the two outbreaks in Guangzhou. Results The result of the Knox analysis showed that the areas at short distances and brief periods presented a relatively high risk. The strength of clustering of male-male pairs was higher. Age groups showed that clustering was concentrated in cases aged ≤ 18 years matched to 18-59 years and cases aged 60+ years. The strength of clustering of the outbreak declined after the implementation of public health measures. The change of strength of clustering at time intervals of 1-5 days decreased greater in 2021 (S = 129.19, change rate 38.87%) than that in 2020 (S = 83.81, change rate 30.02%). Conclusions The outbreak of SARS-CoV-2 Delta VOC in Guangzhou has obvious spatial-temporal clustering. The timely intervention measures are essential role to contain this outbreak of high transmission.
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Affiliation(s)
- Qian Zhang
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Meng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou, China
| | - Jianxiong Hu
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guanhao He
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Yan Zhou
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Southern Medical University, Guangzhou, China
| | - Xuguang Chen
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou, China
| | - Yali Zhuang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou, China
| | - Zuhua Rong
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lihua Yin
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Jianguo Zhao
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Zitong Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Weilin Zeng
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Xing Li
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Zhihua Zhu
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Yerong Tang
- School of Public Health, Sun Yat-sen University, Guangzhou, China,Arboviral Disease Prevention Department, Yunnan Institute of Parasitic Diseases, Puer, China
| | - Yi Quan
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Southern Medical University, Guangzhou, China
| | - Yihan Li
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Southern Medical University, Guangzhou, China
| | - Li Zhang
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Southern Medical University, Guangzhou, China
| | - Di Fu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou, China,*Correspondence: Yan Li
| | - Jianpeng Xiao
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Jianpeng Xiao
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Alisoltani A, Jaroszewski L, Godzik A, Iranzadeh A, Simons LM, Dean TJ, Lorenzo-Redondo R, Hultquist JF, Ozer EA. ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes. Viruses 2022; 14:v14122714. [PMID: 36560718 PMCID: PMC9781208 DOI: 10.3390/v14122714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased the demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. The majority of the currently available tools either require computational expertise to deploy them or limit user input to preselected subsets of SARS-CoV-2 genomes. To address these limitations, we developed ViralVar, a publicly available, point-and-click webtool that gives users the freedom to investigate and visualize user-selected subsets of SARS-CoV-2 genomes obtained from the GISAID public database. ViralVar has two primary features that enable: (1) the visualization of the spatiotemporal dynamics of SARS-CoV-2 lineages and (2) a structural/functional analysis of genomic mutations. As proof-of-principle, ViralVar was used to explore the evolution of the SARS-CoV-2 pandemic in the USA in pediatric, adult, and elderly populations (n > 1.7 million genomes). Whereas the spatiotemporal dynamics of the variants did not differ between these age groups, several USA-specific sublineages arose relative to the rest of the world. Our development and utilization of ViralVar to provide insights on the evolution of SARS-CoV-2 in the USA demonstrates the importance of developing accessible tools to facilitate and accelerate the large-scale surveillance of circulating pathogens.
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Affiliation(s)
- Arghavan Alisoltani
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Correspondence: (A.A.); (E.A.O.)
| | - Lukasz Jaroszewski
- Biosciences Division, School of Medicine, University of California Riverside, Riverside, CA 92507, USA
| | - Adam Godzik
- Biosciences Division, School of Medicine, University of California Riverside, Riverside, CA 92507, USA
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lacy M. Simons
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Taylor J. Dean
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Correspondence: (A.A.); (E.A.O.)
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45
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Guo F, Han R, Sun Y, Sun L, Luo T, Zheng L, Gao C. The associations between COVID-19 vaccination and psychological disorders among healthcare workers in China. J Affect Disord 2022; 318:40-47. [PMID: 36031006 PMCID: PMC9420003 DOI: 10.1016/j.jad.2022.08.080] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/26/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022]
Abstract
INTRODUCTION COVID-19 has caused an unprecedented psychological affection that might impact the nationwide vaccination program in China. This study was to explore the association between COVID-19 vaccination and psychological disorders among healthcare workers. METHODS The study included 1571 healthcare workers from an anonymous online survey. Participants' sociodemographic characteristics, uptake data for the COVID-19 vaccine, and scores of the Depression, Anxiety, and Stress Scale (DASS-21) were collected. Nonparametric tests were conducted to compare the mean scores of DASS-21 between different subgroups. The potential factors related to psychological disorders of healthcare workers were analyzed using logistic regression. RESULTS The vaccination rate was 69.6 %, the incidence of vaccine-related adverse events was 35.13 %, and the prevalence of depression, anxiety, and stress were 24.8 %, 32 %, and 33.4 % in this study, respectively. Compared to vaccinated participants (single-dose and double-dose vaccines), unvaccinated participants got significantly higher mean scores of DASS-21 (p < 0.05 for all). Vaccinated participants who suffered no adverse events scored significantly lower than those who suffered 1-2 or ≥3 adverse events (p < 0.05 for all). Vaccination was negatively associated with higher depression, anxiety, and stress, however, the number of vaccine-related adverse events was positively associated with them. LIMITATIONS As this is a cross-sectional study, we could only speculate on the causality. CONCLUSIONS An obvious impact of the psychological disorders on the COVID-19 vaccine coverage and related adverse events was detected in this study. Public health agencies should attach great importance to the psychological states of our citizens before getting vaccinated.
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Affiliation(s)
- Fei Guo
- Department of Anesthesiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, People's Republic of China
| | - Ruili Han
- Department of Anesthesiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, People's Republic of China
| | - Yiwei Sun
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Li Sun
- Department of Anesthesiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, People's Republic of China
| | - Ting Luo
- Department of Obstetrics and Gynecology, the Second Xiangya Hospital of Central South University, Changsha, People's Republic of China
| | - Lanlan Zheng
- Department of Anesthesiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, People's Republic of China
| | - Changjun Gao
- Department of Anesthesiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, People's Republic of China.
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Sun Y, Wang M, Lin W, Dong W, Xu J. "Mutation blacklist" and "mutation whitelist" of SARS-CoV-2. JOURNAL OF BIOSAFETY AND BIOSECURITY 2022; 4:114-120. [PMID: 35845149 PMCID: PMC9273572 DOI: 10.1016/j.jobb.2022.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 01/26/2023] Open
Abstract
Over the past two years, scientists throughout the world have completed more than 6 million SARS-CoV-2 genome sequences. Today, the number of SARS-CoV-2 genomes exceeds the total number of all other viral genomes. These genomes are a record of the evolution of SARS-CoV-2 in the human host, and provide information on the emergence of mutations. In this study, analysis of these sequenced genomes identified 296,728 de novo mutations (DNMs), and found that six types of base substitutions reached saturation in the sequenced genome population. Based on this analysis, a "mutation blacklist" of SARS-CoV-2 was compiled. The loci on the "mutation blacklist" are highly conserved, and these mutations likely have detrimental effects on virus survival, replication, and transmission. This information is valuable for SARS-CoV-2 research on gene function, vaccine design, and drug development. Through association analysis of DNMs and viral transmission rates, we identified 185 DNMs that positively correlated with the SARS-CoV-2 transmission rate, and these DNMs where classified as the "mutation whitelist" of SARS-CoV-2. The mutations on the "mutation whitelist" are beneficial for SARS-CoV-2 transmission and could therefore be used to evaluate the transmissibility of new variants. The occurrence of mutations and the evolution of viruses are dynamic processes. To more effectively monitor the mutations and variants of SARS-CoV-2, we built a SARS-CoV-2 mutation and variant monitoring and pre-warning system (MVMPS), which can monitor the occurrence and development of mutations and variants of SARS-CoV-2, as well as provide pre-warning for the prevention and control of SARS-CoV-2 (https://www.omicx.cn/). Additionally, this system could be used in real-time to update the "mutation whitelist" and "mutation blacklist" of SARS-CoV-2.
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Affiliation(s)
- Yamin Sun
- Research Institute of Public Health, Nankai University, Tianjin, PR China
- Research Center for Functional Genomics and Biochip, Tianjin, PR China
| | - Min Wang
- Research Center for Functional Genomics and Biochip, Tianjin, PR China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, PR China
| | - Wenchao Lin
- Research Center for Functional Genomics and Biochip, Tianjin, PR China
| | - Wei Dong
- Research Center for Functional Genomics and Biochip, Tianjin, PR China
| | - Jianguo Xu
- Research Institute of Public Health, Nankai University, Tianjin, PR China
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 202206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
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47
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Cai J, Yang J, Deng X, Peng C, Chen X, Wu Q, Liu H, Zhang J, Zheng W, Zou J, Zhao Z, Ajelli M, Yu H. Assessing the transition of COVID-19 burden towards the young population while vaccines are rolled out in China. Emerg Microbes Infect 2022; 11:1205-1214. [PMID: 35380100 PMCID: PMC9045766 DOI: 10.1080/22221751.2022.2063073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 infection causes most cases of severe illness and fatality in older age groups. Over 92% of the Chinese population aged ≥12 years has been fully vaccinated against COVID-19 (albeit with vaccines developed against historical lineages). At the end of October 2021, the vaccination programme has been extended to children aged 3–11 years. Here, we aim to assess whether, in this vaccination landscape, the importation of Delta variant infections could shift COVID-19 burden from adults to children. We developed an age-structured susceptible-infectious-removed model of SARS-CoV-2 transmission to simulate epidemics triggered by the importation of Delta variant infections and project the age-specific incidence of SARS-CoV-2 infections, cases, hospitalizations, intensive care unit admissions, and deaths. In the context of the vaccination programme targeting individuals aged ≥12 years, and in the absence of non-pharmaceutical interventions, the importation of Delta variant infections could have led to widespread transmission and substantial disease burden in mainland China, even with vaccination coverage as high as 89% across the eligible age groups. Extending the vaccination roll-out to include children aged 3–11 years (as it was the case since the end of October 2021) is estimated to dramatically decrease the burden of symptomatic infections and hospitalizations within this age group (39% and 68%, respectively, when considering a vaccination coverage of 87%), but would have a low impact on protecting infants. Our findings highlight the importance of including children among the target population and the need to strengthen vaccination efforts by increasing vaccine effectiveness.
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Affiliation(s)
- Jun Cai
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China.,Department of Infectious Diseases, Huashan Hospital, School of Public Health, Fudan University, Shanghai, People's Republic of China.,Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People's Republic of China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Cheng Peng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Xinhua Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Qianhui Wu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Hengcong Liu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China.,Department of Infectious Diseases, Huashan Hospital, School of Public Health, Fudan University, Shanghai, People's Republic of China.,Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People's Republic of China
| | - Wen Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Junyi Zou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Zeyao Zhao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Marco Ajelli
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China.,Department of Infectious Diseases, Huashan Hospital, School of Public Health, Fudan University, Shanghai, People's Republic of China.,Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People's Republic of China
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Yang J, Hu X, Wang W, Yang Y, Zhang X, Fang W, Zhang L, Li S, Gu B. RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Emerg Microbes Infect 2022; 11:978-987. [PMID: 35293849 PMCID: PMC8982466 DOI: 10.1080/22221751.2022.2054368] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The highly infectious Delta variant strain of SARS-CoV-2 remains globally dominant and undermines COVID-19 vaccines. Rapid detection of the Delta variant is crucial for the identification and quarantine of infected individuals. In this study, our aim was to design and validate a genotyping RT-LAMP method to detect Delta variants specifically. R203M in the N gene of SARS-CoV-2 was chosen as the Delta variant-specific mutation for genotyping. To target the R203M-harboring region and the conserved sequence of the N gene, two sets of primers were designed, and a Cq (quantification cycle) ratio-based RT-LAMP for SARS-CoV-2 and R203M detection was developed by analyzing the significant discrepancy in amplification efficiency of the two sets of primers. We validated the RT-LAMP method on 498 clinical specimens in parallel with RT-qPCR, and 84 Delta variants from 198 positive samples were determined by sequencing. Compared with traditional RT-qPCR analyses, RT-LAMP appears to be 100% accurate in detecting SARS-CoV-2 clinical samples. RT-LAMP has a good ability to distinguish between Delta and non-Delta variants under a Cq ratio threshold of 1.80. Furthermore, the AUC (area under the curve) of this method was 1.00; the sensitivity, specificity and accuracy were all 100%. In summary, we have proposed a rapid, accurate and cost-effective RT-LAMP method to detect SARS-CoV-2 and Delta variants, which may facilitate the surveillance of COVID-19.
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Affiliation(s)
- Jianing Yang
- MOE International Joint Laboratory for Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Xuejiao Hu
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou 510000, P.R. China
| | - Wenzhuo Wang
- MOE International Joint Laboratory for Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China.,NMPA Key Laboratory for Quality Control of Blood Products, Guangdong Institute for Drug Control, Guangzhou 510663, P.R. China
| | - Yujing Yang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou 510000, P.R. China
| | - Xinqiang Zhang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou 510000, P.R. China
| | - Wei Fang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou 510000, P.R. China
| | - Lei Zhang
- MOE International Joint Laboratory for Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China.,NMPA Key Laboratory for Quality Control of Blood Products, Guangdong Institute for Drug Control, Guangzhou 510663, P.R. China
| | - Shan Li
- MOE International Joint Laboratory for Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Bing Gu
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou 510000, P.R. China
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The compartmentalized upper respiratory mucosa needs time to rally a sufficient immune force for SARS-CoV-2 clearance. Cell Mol Immunol 2022; 19:1425-1428. [PMID: 36220995 PMCID: PMC9552153 DOI: 10.1038/s41423-022-00931-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/07/2022] Open
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50
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Wei H, Shao Z, Tai J, Fu F, Lv C, Guo Z, Wu Y, Chen L, Bai Y, Wu Q, Yu X, Mu X, Shao F, Wang M. Analysis of CT signs, radiomic features and clinical characteristics for delta variant COVID-19 patients with different vaccination status. BMC Med Imaging 2022; 22:209. [PMID: 36447133 PMCID: PMC9832212 DOI: 10.1186/s12880-022-00937-9] [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: 07/14/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE To explore the characteristics of peripheral blood, high resolution computed tomography (HRCT) imaging and the radiomics signature (RadScore) in patients infected with delta variant virus under different coronavirus disease (COVID-19) vaccination status. METHODS 123 patients with delta variant virus infection collected from November 1, 2021 to March 1, 2022 were analyzed retrospectively. According to COVID-19 vaccination Status, they were divided into three groups: Unvaccinated group, partially vaccinated group and full vaccination group. The peripheral blood, chest HRCT manifestations and RadScore of each group were analyzed and compared. RESULTS The mean lymphocyte count 1.22 ± 0.49 × 10^9/L, CT score 7.29 ± 3.48, RadScore 0.75 ± 0.63 in the unvaccinated group; The mean lymphocyte count 1.55 ± 0.70 × 10^9/L, CT score 5.27 ± 2.72, RadScore 1.03 ± 0.46 in the partially vaccinated group; The mean lymphocyte count 1.87 ± 0.70 × 10^9/L, CT score 3.59 ± 3.14, RadScore 1.23 ± 0.29 in the fully vaccinated group. There were significant differences in lymphocyte count, CT score and RadScore among the three groups (all p < 0.05); Compared with the other two groups, the lung lesions in the unvaccinated group were more involved in multiple lobes, of which 26 cases involved the whole lung. CONCLUSIONS Through the analysis of clinical features, pulmonary imaging features and radiomics, we confirmed the positive effect of COVID-19 vaccine on pulmonary inflammatory symptoms and lymphocyte count (immune system) during delta mutant infection.
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Affiliation(s)
- Huanhuan Wei
- grid.414011.10000 0004 1808 090XAcademy of Medical Sciences, The People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China
| | - Zehua Shao
- grid.414011.10000 0004 1808 090XHeart Center of Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, 450003 Henan People’s Republic of China
| | - Jianqing Tai
- grid.417239.aThe First People’s Hospital of Zhengzhou, 56 East Street, Zhengzhou, 450004 Henan China
| | - Fangfang Fu
- grid.414011.10000 0004 1808 090XDepartment of Medical Imaging, Henan Provincial People’s Hospital & the People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China
| | - Chuanjian Lv
- grid.414011.10000 0004 1808 090XDepartment of Medical Imaging, Henan Provincial People’s Hospital & the People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China
| | - Zhiping Guo
- grid.417239.aThe First People’s Hospital of Zhengzhou, 56 East Street, Zhengzhou, 450004 Henan China
| | - Yaping Wu
- grid.414011.10000 0004 1808 090XDepartment of Medical Imaging, Henan Provincial People’s Hospital & the People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China
| | - Lijuan Chen
- grid.414011.10000 0004 1808 090XDepartment of Medical Imaging, Henan Provincial People’s Hospital & the People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China
| | - Yan Bai
- grid.414011.10000 0004 1808 090XDepartment of Medical Imaging, Henan Provincial People’s Hospital & the People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China
| | - Qingxia Wu
- Beijing United Imaging Research Institute of Intelligent Imaging, Beijing, 100089 China
| | - Xuan Yu
- grid.414011.10000 0004 1808 090XDepartment of Medical Imaging, Henan Provincial People’s Hospital & the People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China
| | - Xinling Mu
- grid.417239.aThe First People’s Hospital of Zhengzhou, 56 East Street, Zhengzhou, 450004 Henan China
| | - Fengmin Shao
- grid.414011.10000 0004 1808 090XDepartment of Medical Imaging, Henan Provincial People’s Hospital & the People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China
| | - Meiyun Wang
- grid.414011.10000 0004 1808 090XAcademy of Medical Sciences, The People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China ,grid.414011.10000 0004 1808 090XDepartment of Medical Imaging, Henan Provincial People’s Hospital & the People’s Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450003 Henan China
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