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Nazir F, John Kombe Kombe A, Khalid Z, Bibi S, Zhang H, Wu S, Jin T. SARS-CoV-2 replication and drug discovery. Mol Cell Probes 2024; 77:101973. [PMID: 39025272 DOI: 10.1016/j.mcp.2024.101973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to wreak havoc across the globe. This sudden and deadly pandemic emphasizes the necessity for anti-viral drug development that can be rapidly administered to reduce morbidity, mortality, and virus propagation. Thus, lacking efficient anti-COVID-19 treatment, and especially given the lengthy drug development process as well as the critical death tool that has been associated with SARS-CoV-2 since its outbreak, drug repurposing (or repositioning) constitutes so far, the ideal and ready-to-go best approach in mitigating viral spread, containing the infection, and reducing the COVID-19-associated death rate. Indeed, based on the molecular similarity approach of SARS-CoV-2 with previous coronaviruses (CoVs), repurposed drugs have been reported to hamper SARS-CoV-2 replication. Therefore, understanding the inhibition mechanisms of viral replication by repurposed anti-viral drugs and chemicals known to block CoV and SARS-CoV-2 multiplication is crucial, and it opens the way for particular treatment options and COVID-19 therapeutics. In this review, we highlighted molecular basics underlying drug-repurposing strategies against SARS-CoV-2. Notably, we discussed inhibition mechanisms of viral replication, involving and including inhibition of SARS-CoV-2 proteases (3C-like protease, 3CLpro or Papain-like protease, PLpro) by protease inhibitors such as Carmofur, Ebselen, and GRL017, polymerases (RNA-dependent RNA-polymerase, RdRp) by drugs like Suramin, Remdesivir, or Favipiravir, and proteins/peptides inhibiting virus-cell fusion and host cell replication pathways, such as Disulfiram, GC376, and Molnupiravir. When applicable, comparisons with SARS-CoV inhibitors approved for clinical use were made to provide further insights to understand molecular basics in inhibiting SARS-CoV-2 replication and draw conclusions for future drug discovery research.
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Affiliation(s)
- Farah Nazir
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China
| | - Arnaud John Kombe Kombe
- Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zunera Khalid
- Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Shaheen Bibi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Anhui, China
| | - Hongliang Zhang
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China
| | - Songquan Wu
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China.
| | - Tengchuan Jin
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China; Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Anhui, China; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science & Technology of China, Hefei, 230027, China; Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230001, China.
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Siragam V, Maltseva M, Castonguay N, Galipeau Y, Srinivasan MM, Soto JH, Dankar S, Langlois MA. Seasonal human coronaviruses OC43, 229E, and NL63 induce cell surface modulation of entry receptors and display host cell-specific viral replication kinetics. Microbiol Spectr 2024; 12:e0422023. [PMID: 38864599 PMCID: PMC11218498 DOI: 10.1128/spectrum.04220-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/25/2024] [Indexed: 06/13/2024] Open
Abstract
The emergence of the COVID-19 pandemic prompted an increased interest in seasonal human coronaviruses. OC43, 229E, NL63, and HKU1 are endemic seasonal coronaviruses that cause the common cold and are associated with generally mild respiratory symptoms. In this study, we identified cell lines that exhibited cytopathic effects (CPE) upon infection by three of these coronaviruses and characterized their viral replication kinetics and the effect of infection on host surface receptor expression. We found that NL63 produced CPE in LLC-MK2 cells, while OC43 produced CPE in MRC-5, HCT-8, and WI-38 cell lines, while 229E produced CPE in MRC-5 and WI-38 by day 3 post-infection. We observed a sharp increase in nucleocapsid and spike viral RNA (vRNA) from day 3 to day 5 post-infection for all viruses; however, the abundance and the proportion of vRNA copies measured in the supernatants and cell lysates of infected cells varied considerably depending on the virus-host cell pair. Importantly, we observed modulation of coronavirus entry and attachment receptors upon infection. Infection with 229E and OC43 led to a downregulation of CD13 and GD3, respectively. In contrast, infection with NL63 and OC43 leads to an increase in ACE2 expression. Attempts to block entry of NL63 using either soluble ACE2 or anti-ACE2 monoclonal antibodies demonstrated the potential of these strategies to greatly reduce infection. Overall, our results enable a better understanding of seasonal coronaviruses infection kinetics in permissive cell lines and reveal entry receptor modulation that may have implications in facilitating co-infections with multiple coronaviruses in humans.IMPORTANCESeasonal human coronavirus is an important cause of the common cold associated with generally mild upper respiratory tract infections that can result in respiratory complications for some individuals. There are no vaccines available for these viruses, with only limited antiviral therapeutic options to treat the most severe cases. A better understanding of how these viruses interact with host cells is essential to identify new strategies to prevent infection-related complications. By analyzing viral replication kinetics in different permissive cell lines, we find that cell-dependent host factors influence how viral genes are expressed and virus particles released. We also analyzed entry receptor expression on infected cells and found that these can be up- or down-modulated depending on the infecting coronavirus. Our findings raise concerns over the possibility of infection enhancement upon co-infection by some coronaviruses, which may facilitate genetic recombination and the emergence of new variants and strains.
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MESH Headings
- Humans
- Virus Replication
- Coronavirus NL63, Human/physiology
- Coronavirus NL63, Human/genetics
- Coronavirus 229E, Human/physiology
- Coronavirus 229E, Human/genetics
- Coronavirus OC43, Human/physiology
- Coronavirus OC43, Human/genetics
- Cell Line
- Virus Internalization
- Seasons
- Kinetics
- Receptors, Virus/metabolism
- Receptors, Virus/genetics
- Common Cold/virology
- Common Cold/metabolism
- SARS-CoV-2/physiology
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- RNA, Viral/metabolism
- RNA, Viral/genetics
- Animals
- COVID-19/virology
- COVID-19/metabolism
- Coronavirus/physiology
- Coronavirus/genetics
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Affiliation(s)
- Vinayakumar Siragam
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Mariam Maltseva
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Nicolas Castonguay
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Yannick Galipeau
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Mrudhula Madapuji Srinivasan
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Justino Hernandez Soto
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Samar Dankar
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- The Center for Infection, Immunity, and Inflammation (CI3), University of Ottawa, Ottawa, Canada
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3
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Heiskanen A, Galipeau Y, Little J, Langlois M, Cooper CL. Reduced seasonal coronavirus incidence in high-risk population groups during the COVID-19 pandemic. Immun Inflamm Dis 2024; 12:e1342. [PMID: 39023424 PMCID: PMC11256882 DOI: 10.1002/iid3.1342] [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: 01/02/2024] [Revised: 06/03/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Epidemiological data on seasonal coronaviruses (sCoVs) may provide insight on transmission patterns and demographic factors that favor coronaviruses (CoVs) with greater disease severity. This study describes the incidence of CoVs in several high-risk groups in Ottawa, Canada, from October 2020 to March 2022. METHODS Serological assays quantified IgG and IgM antibodies to SARS-CoV-2, HCoV-OC43, HCoV-NL63, HCoV-HKU1, and HCoV-229E. Incident infections were compared between four population groups: individuals exposed to children, transit users, immunocompromised, and controls. Associations between antibody prevalence indicative of natural infection and demographic variables were assessed using regression analyses. RESULTS Transit users and those exposed to children were at no greater risk of infection compared to the control group. Fewer infections were detected in the immunocompromised group (p = .03). SARS-CoV-2 seroprevalence was greater in individuals with low income and within ethnic minorities. CONCLUSIONS Our findings suggest that nonpharmaceutical interventions intended to reduce SAR-CoV-2 transmission protected populations at high risk of exposure. The re-emergence of sCoVs and other common respiratory viruses alongside SARS-CoV-2 may alter infection patterns and increase the risk in vulnerable populations.
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Affiliation(s)
- Aliisa Heiskanen
- School of Epidemiology and Public Health, Faculty of MedicineUniversity of OttawaOttawaOntarioCanada
| | - Yannick Galipeau
- Department of Biochemistry, Microbiology & Immunology, Faculty of MedicineUniversity of OttawaOttawaOntarioCanada
| | - Julian Little
- School of Epidemiology and Public Health, Faculty of MedicineUniversity of OttawaOttawaOntarioCanada
| | - Marc‐André Langlois
- Department of Biochemistry, Microbiology & Immunology, Faculty of MedicineUniversity of OttawaOttawaOntarioCanada
- Centre for Infection, Immunity and Inflammation (CI3)University of OttawaOttawaOntarioCanada
| | - Curtis L. Cooper
- School of Epidemiology and Public Health, Faculty of MedicineUniversity of OttawaOttawaOntarioCanada
- Ottawa Hospital Research InstituteOttawaOntarioCanada
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Gerardo RM, Guiomar HG, Ander GS, Carlos Andrés GC, Coral AC. Dynamics of endemic human coronavirus and SARS-CoV-2 in a hospital of Madrid, Spain. Retrospective study from June 2020 to July 2023. APMIS 2024. [PMID: 38873951 DOI: 10.1111/apm.13446] [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: 12/13/2023] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
An observational and retrospective study was carried out to analyse HCoV positivity from a multiplex PCR respiratory panel and RT-PCR for SARS-CoV-2 in respiratory samples from 1 June 2020 to 31 July 2023 at the Príncipe de Asturias University Hospital (HUPA) in Alcalá de Henares, Madrid, Spain. Out of 2802 respiratory panels, 1258 (44.8%) turned out positive. HCoV was detected in 114 (4%) cases (range 0-23; median 1.5; IQR 0-3.75) with positivity rates ranging from 0% to 14%. All four variants of HCoV circulated, and OC-43 was the most common in 62.3% of cases. After the onset of the pandemic, the HCoV season was delayed 22 weeks, with a peak positivity of 9% in the summer of 2021, showing an inverse relationship with the alpha and delta waves of SARS-CoV-2. In the two subsequent autumn-winter seasons, HCoV positivity increased (11-14%) with a reduction in the summer of 2022 and 2023 following the emergence of the omicron variant and the relaxation of social distancing measures. The seasonal spread pattern of endemic HCoV might be returning to normal in our region and likely in other temperate zones of the northern hemisphere after 3 years of the pandemic.
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Affiliation(s)
- Rojo-Marcos Gerardo
- Department of Internal Medicine, "Príncipe de Asturias" University Hospital, Alcalá de Henares, Madrid, Spain
- Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - Hernández-García Guiomar
- Department of Internal Medicine, "Príncipe de Asturias" University Hospital, Alcalá de Henares, Madrid, Spain
| | - González-Sarria Ander
- Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
- Department of Clinical Microbiology and Parasitology, "Príncipe de Asturias" University Hospital, Alcalá de Henares, Madrid, Spain
| | | | - Arévalo-Cañas Coral
- Department of Internal Medicine, "Príncipe de Asturias" University Hospital, Alcalá de Henares, Madrid, Spain
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Wang X, Zhang J, Liu M, Guo Y, Guo P, Yang X, Shang B, Li M, Tian J, Zhang T, Wang X, Jin R, Zhou J, Gao GF, Liu J. Nonconserved epitopes dominate reverse preexisting T cell immunity in COVID-19 convalescents. Signal Transduct Target Ther 2024; 9:160. [PMID: 38866784 PMCID: PMC11169541 DOI: 10.1038/s41392-024-01876-3] [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: 10/05/2023] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024] Open
Abstract
The herd immunity against SARS-CoV-2 is continuously consolidated across the world during the ongoing pandemic. However, the potential function of the nonconserved epitopes in the reverse preexisting cross-reactivity induced by SARS-CoV-2 to other human coronaviruses is not well explored. In our research, we assessed T cell responses to both conserved and nonconserved peptides shared by SARS-CoV-2 and SARS-CoV, identifying cross-reactive CD8+ T cell epitopes using enzyme-linked immunospot and intracellular cytokine staining assays. Then, in vitro refolding and circular dichroism were performed to evaluate the thermal stability of the HLA/peptide complexes. Lastly, single-cell T cell receptor reservoir was analyzed based on tetramer staining. Here, we discovered that cross-reactive T cells targeting SARS-CoV were present in individuals who had recovered from COVID-19, and identified SARS-CoV-2 CD8+ T cell epitopes spanning the major structural antigens. T cell responses induced by the nonconserved peptides between SARS-CoV-2 and SARS-CoV were higher and played a dominant role in the cross-reactivity in COVID-19 convalescents. Cross-T cell reactivity was also observed within the identified series of CD8+ T cell epitopes. For representative immunodominant peptide pairs, although the HLA binding capacities for peptides from SARS-CoV-2 and SARS-CoV were similar, the TCR repertoires recognizing these peptides were distinct. Our results could provide beneficial information for the development of peptide-based universal vaccines against coronaviruses.
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Affiliation(s)
- Xin Wang
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Jie Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, P.R. China
| | - Maoshun Liu
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yuanyuan Guo
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Peipei Guo
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Xiaonan Yang
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Bingli Shang
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Min Li
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Jinmin Tian
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ting Zhang
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xi Wang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, P.R. China
| | - Ronghua Jin
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, P.R. China
| | - Jikun Zhou
- Shijiazhuang Fifth Hospital, Shijiazhuang, 050011, China.
| | - George F Gao
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jun Liu
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
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Kim J, Hickerson BT, Ilyushina NA. Coinfection of Influenza A and B and Human OC43 Coronavirus in Normal Human Bronchial Epithelial Cells. Influenza Other Respir Viruses 2024; 18:e13279. [PMID: 38556468 PMCID: PMC10982074 DOI: 10.1111/irv.13279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Influenza viruses and seasonal coronaviruses are pathogens transmitted via an airborne route that can cause respiratory diseases in humans that have similar symptoms such as fever, cough, and pneumonia. These two viruses can infect similar human tissues, such as the respiratory tract and nasal, bronchial, and alveolar epithelial cells. Influenza virus and seasonal coronavirus coinfections are poorly understood. METHODS Here, we coinfected normal human bronchial epithelial (NHBE) cells with influenza A/California/04/09 (IAV) or B/Victoria/504/2000 (IBV) strains and the seasonal human beta-coronavirus OC43 and evaluated viral replication capacities. We also examined changes in the expression of various cytokines/chemokines by qPCR and Luminex assay. RESULTS We observed that the replication of IAV and IBV was not affected by coinfection with OC43. However, coinfection reduced OC43 titers (~3-fold) compared with infection with OC43 alone. Select cytokine/chemokine expression was increased in coinfected cells compared with all single infections with greater differences seen between coinfected cells and cells infected with OC43 alone compared with IAV- or IBV-infected cells. In addition, IL-8 and IL-1RA showed the highest expression among a panel of 22 cytokines by Luminex. CONCLUSIONS As the rate of influenza and seasonal coronavirus coinfection continue to increase, our findings may help set guidelines for the treatments of the individuals coinfected with both viruses.
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Affiliation(s)
- JungHyun Kim
- Division of Biotechnology Review and Research IIFood and Drug AdministrationSilver SpringMarylandUSA
| | - Brady T. Hickerson
- Division of Biotechnology Review and Research IIFood and Drug AdministrationSilver SpringMarylandUSA
| | - Natalia A. Ilyushina
- Division of Biotechnology Review and Research IIFood and Drug AdministrationSilver SpringMarylandUSA
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7
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Lidenge SJ, Yalcin D, Bennett SJ, Ngalamika O, Kweyamba BB, Mwita CJ, Tso FY, Mwaiselage J, West JT, Wood C. Viral Epitope Scanning Reveals Correlation between Seasonal HCoVs and SARS-CoV-2 Antibody Responses among Cancer and Non-Cancer Patients. Viruses 2024; 16:448. [PMID: 38543814 PMCID: PMC10975915 DOI: 10.3390/v16030448] [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: 01/27/2024] [Revised: 02/23/2024] [Accepted: 03/09/2024] [Indexed: 04/01/2024] Open
Abstract
Seasonal coronaviruses (HCoVs) are known to contribute to cross-reactive antibody (Ab) responses against SARS-CoV-2. While these responses are predictable due to the high homology between SARS-CoV-2 and other CoVs, the impact of these responses on susceptibility to SARS-CoV-2 infection in cancer patients is unclear. To investigate the influence of prior HCoV infection on anti-SARS-CoV-2 Ab responses among COVID-19 asymptomatic individuals with cancer and controls without cancers, we utilized the VirScan technology in which phage immunoprecipitation and sequencing (PhIP-seq) of longitudinal plasma samples was performed to investigate high-resolution (i.e., epitope level) humoral CoV responses. Despite testing positive for anti-SARS-CoV-2 Ab in the plasma, a majority of the participants were asymptomatic for COVID-19 with no prior history of COVID-19 diagnosis. Although the magnitudes of the anti-SARS-CoV-2 Ab responses were lower in individuals with Kaposi sarcoma (KS) compared to non-KS cancer individuals and those without cancer, the HCoV Ab repertoire was similar between individuals with and without cancer independent of age, sex, HIV status, and chemotherapy. The magnitudes of the anti-spike HCoV responses showed a strong positive association with those of the anti-SARS-CoV-2 spike in cancer patients, and only a weak association in non-cancer patients, suggesting that prior infection with HCoVs might play a role in limiting SARS-CoV-2 infection and COVID-19 disease severity.
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Affiliation(s)
- Salum J. Lidenge
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam P.O. Box 65001, Tanzania
| | - Dicle Yalcin
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
| | - Sydney J. Bennett
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68516, USA
| | - Owen Ngalamika
- Dermatology and Venereology Division, University Teaching Hospital, University of Zambia School of Medicine, Lusaka P.O. Box 50001, Zambia;
| | - Brenda B. Kweyamba
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
| | - Chacha J. Mwita
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
| | - For Yue Tso
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
| | - Julius Mwaiselage
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam P.O. Box 65001, Tanzania
| | - John T. West
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
| | - Charles Wood
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68516, USA
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Ocaña Gutiérrez VR, González Ramírez RA, Ocaña Aguilar VA, Ocaña Aguilar NG, Holguín Mauricci CE. The weekly P25 of the age of the influenza-like illness shows a higher correlation with COVID-19 mortality than rapid tests and could predict the evolution of COVID-19 pandemics in sentinel surveillance, Piura, Perú, 2021. PLoS One 2024; 19:e0295309. [PMID: 38452053 PMCID: PMC10919873 DOI: 10.1371/journal.pone.0295309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/20/2023] [Indexed: 03/09/2024] Open
Abstract
GOAL To describe the dynamics of syndromic surveillance of ILI cases in seasonal and COVID-19 pandemic scenarios. METHODOLOGY A descriptive study of the epidemiological behavior of ILI in the seasonal and COVID-19 pandemic scenarios. Of a sample of 16,231 cases of ILI from 2013 to 2021, the features of cases from 68 weeks before and during the pandemic were selected and compared; weekly endemic channels were built; data fluctuations on the trend of ILI cases were analyzed; and estimated weekly correlations between weekly P25 age, cases confirmed by rapid tests, and mortality from COVID-19. To analyze clinical-epidemiological and mortality data, Student's t test, Mann-Whitney U, Chi2, Spearman's Ro, polynomial, and multinomial regression with a 95% confidence interval were used. RESULTS During the COVID-19 pandemic, those most affected with ILI were: adults and the elderly; higher median age; autochthonous cases predominated; a lower proportion of other syndromes; delays in seeking care; and a higher rate of pneumonia attack than in the seasonal period (p< 0.01). Rapid tests (serological and antigenic) confirmed 52.7% as COVID-19. Two ILI pandemic waves were seasonally consistent with confirmed COVID-19 cases and district mortality with robust correlation (p<0.01) before and during the pandemic, especially the ILI weekly P25 age, which has a more robust correlation with mortality than ILI and rapid tests (p<0.01) whose endemic channels describe and could predict the evolution of the pandemic (p<0.01). CONCLUSIONS The pandemic changed the clinical and epidemiological behavior of ILI, and the weekly P25 of age is a more robust indicator to monitor the COVID-19 pandemic than a rapid test and could predict its evolution.
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Affiliation(s)
| | - Rodolfo Arturo González Ramírez
- School of Medicine, Cesar Vallejo University, Piura, Perú
- Department of Public Health, School of Medicine, National University of Cajamarca, Cajamarca, Perú
| | - Víctor Alexander Ocaña Aguilar
- School of Medicine, Cesar Vallejo University, Piura, Perú
- Department of Public Health, School of Medicine, National University of Cajamarca, Cajamarca, Perú
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9
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Collins CP, Longo DL, Murphy WJ. The immunobiology of SARS-CoV-2 infection and vaccine responses: potential influences of cross-reactive memory responses and aging on efficacy and off-target effects. Front Immunol 2024; 15:1345499. [PMID: 38469293 PMCID: PMC10925677 DOI: 10.3389/fimmu.2024.1345499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Immune responses to both SARS-CoV-2 infection and its associated vaccines have been highly variable within the general population. The increasing evidence of long-lasting symptoms after resolution of infection, called post-acute sequelae of COVID-19 (PASC) or "Long COVID," suggests that immune-mediated mechanisms are at play. Closely related endemic common human coronaviruses (hCoV) can induce pre-existing and potentially cross-reactive immunity, which can then affect primary SARS-CoV-2 infection, as well as vaccination responses. The influence of pre-existing immunity from these hCoVs, as well as responses generated from original CoV2 strains or vaccines on the development of new high-affinity responses to CoV2 antigenic viral variants, needs to be better understood given the need for continuous vaccine adaptation and application in the population. Due in part to thymic involution, normal aging is associated with reduced naïve T cell compartments and impaired primary antigen responsiveness, resulting in a reliance on the pre-existing cross-reactive memory cell pool which may be of lower affinity, restricted in diversity, or of shorter duration. These effects can also be mediated by the presence of down-regulatory anti-idiotype responses which also increase in aging. Given the tremendous heterogeneity of clinical data, utilization of preclinical models offers the greatest ability to assess immune responses under a controlled setting. These models should now involve prior antigen/viral exposure combined with incorporation of modifying factors such as age on immune responses and effects. This will also allow for mechanistic dissection and understanding of the different immune pathways involved in both SARS-CoV-2 pathogen and potential vaccine responses over time and how pre-existing memory responses, including potential anti-idiotype responses, can affect efficacy as well as potential off-target effects in different tissues as well as modeling PASC.
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Affiliation(s)
- Craig P. Collins
- Graduate Program in Immunology, University of California (UC) Davis, Davis, CA, United States
| | - Dan L. Longo
- Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - William J. Murphy
- Departments of Dermatology and Internal Medicine (Hematology/Oncology), University of California (UC) Davis School of Medicine, Sacramento, CA, United States
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10
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Ali MA, Caetano-Anollés G. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Spike Protein Variants. BIOLOGY 2024; 13:134. [PMID: 38534404 DOI: 10.3390/biology13030134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
The slow experimental acquisition of high-quality atomic structures of the rapidly changing proteins of the COVID-19 virus challenges vaccine and therapeutic drug development efforts. Fortunately, deep learning tools such as AlphaFold2 can quickly generate reliable models of atomic structure at experimental resolution. Current modeling studies have focused solely on definitions of mutant constellations of Variants of Concern (VOCs), leaving out the impact of haplotypes on protein structure. Here, we conduct a thorough comparative structural analysis of S-proteins belonging to major VOCs and corresponding latitude-delimited haplotypes that affect viral seasonal behavior. Our approach identified molecular regions of importance as well as patterns of structural recruitment. The S1 subunit hosted the majority of structural changes, especially those involving the N-terminal domain (NTD) and the receptor-binding domain (RBD). In particular, structural changes in the NTD were much greater than just translations in three-dimensional space, altering the sub-structures to greater extents. We also revealed a notable pattern of structural recruitment with the early VOCs Alpha and Delta behaving antagonistically by suppressing regions of structural change introduced by their corresponding haplotypes, and the current VOC Omicron behaving synergistically by amplifying or collecting structural change. Remarkably, haplotypes altering the galectin-like structure of the NTD were major contributors to seasonal behavior, supporting its putative environmental-sensing role. Our results provide an extensive view of the evolutionary landscape of the S-protein across the COVID-19 pandemic. This view will help predict important regions of structural change in future variants and haplotypes for more efficient vaccine and drug development.
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Affiliation(s)
- Muhammad Asif Ali
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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11
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Dos Santos Alves RP, Timis J, Miller R, Valentine K, Pinto PBA, Gonzalez A, Regla-Nava JA, Maule E, Nguyen MN, Shafee N, Landeras-Bueno S, Olmedillas E, Laffey B, Dobaczewska K, Mikulski Z, McArdle S, Leist SR, Kim K, Baric RS, Ollmann Saphire E, Elong Ngono A, Shresta S. Human coronavirus OC43-elicited CD4 + T cells protect against SARS-CoV-2 in HLA transgenic mice. Nat Commun 2024; 15:787. [PMID: 38278784 PMCID: PMC10817949 DOI: 10.1038/s41467-024-45043-2] [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: 08/18/2023] [Accepted: 01/10/2024] [Indexed: 01/28/2024] Open
Abstract
SARS-CoV-2-reactive T cells are detected in some healthy unexposed individuals. Human studies indicate these T cells could be elicited by the common cold coronavirus OC43. To directly test this assumption and define the role of OC43-elicited T cells that are cross-reactive with SARS-CoV-2, we develop a model of sequential infections with OC43 followed by SARS-CoV-2 in HLA-B*0702 and HLA-DRB1*0101 Ifnar1-/- transgenic mice. We find that OC43 infection can elicit polyfunctional CD8+ and CD4+ effector T cells that cross-react with SARS-CoV-2 peptides. Furthermore, pre-exposure to OC43 reduces subsequent SARS-CoV-2 infection and disease in the lung for a short-term in HLA-DRB1*0101 Ifnar1-/- transgenic mice, and a longer-term in HLA-B*0702 Ifnar1-/- transgenic mice. Depletion of CD4+ T cells in HLA-DRB1*0101 Ifnar1-/- transgenic mice with prior OC43 exposure results in increased viral burden in the lung but no change in virus-induced lung damage following infection with SARS-CoV-2 (versus CD4+ T cell-sufficient mice), demonstrating that the OC43-elicited SARS-CoV-2 cross-reactive T cell-mediated cross-protection against SARS-CoV-2 is partially dependent on CD4+ T cells. These findings contribute to our understanding of the origin of pre-existing SARS-CoV-2-reactive T cells and their effects on SARS-CoV-2 clinical outcomes, and also carry implications for development of broadly protective betacoronavirus vaccines.
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Affiliation(s)
| | - Julia Timis
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Robyn Miller
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kristen Valentine
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Andrew Gonzalez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Microbiology and Pathology, University Center for Health Science (CUCS), University of Guadalajara, Guadalajara, 44340, Mexico
| | - Erin Maule
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Michael N Nguyen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Norazizah Shafee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara Landeras-Bueno
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Brett Laffey
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Katarzyna Dobaczewska
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara McArdle
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth Kim
- Histopathology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Annie Elong Ngono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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12
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Benede N, Tincho MB, Walters A, Subbiah V, Ngomti A, Baguma R, Butters C, Hahnle L, Mennen M, Skelem S, Adriaanse M, Facey-Thomas H, Scott C, Day J, Spracklen TF, van Graan S, Balla SR, Moyo-Gwete T, Moore PL, MacGinty R, Botha M, Workman L, Johnson M, Goldblatt D, Zar HJ, Ntusi NA, Zühlke L, Webb K, Riou C, Burgers WA, Keeton RS. Distinct T cell polyfunctional profile in SARS-CoV-2 seronegative children associated with endemic human coronavirus cross-reactivity. iScience 2024; 27:108728. [PMID: 38235336 PMCID: PMC10792240 DOI: 10.1016/j.isci.2023.108728] [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: 07/10/2023] [Revised: 10/19/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
SARS-CoV-2 infection in children typically results in asymptomatic or mild disease. There is a paucity of studies on SARS-CoV-2 antiviral immunity in African children. We investigated SARS-CoV-2-specific T cell responses in 71 unvaccinated asymptomatic South African children who were seropositive or seronegative for SARS-CoV-2. SARS-CoV-2-specific CD4+ T cell responses were detectable in 83% of seropositive and 60% of seronegative children. Although the magnitude of the CD4+ T cell response did not differ significantly between the two groups, their functional profiles were distinct, with SARS-CoV-2 seropositive children exhibiting a higher proportion of polyfunctional T cells compared to their seronegative counterparts. The frequency of SARS-CoV-2-specific CD4+ T cells in seronegative children was associated with the endemic human coronavirus (HCoV) HKU1 IgG response. Overall, the presence of SARS-CoV-2-responding T cells in seronegative children may result from cross-reactivity to endemic coronaviruses and could contribute to the relative protection from disease observed in SARS-CoV-2-infected children.
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Affiliation(s)
- Ntombi Benede
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Marius B. Tincho
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Avril Walters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Vennesa Subbiah
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Amkele Ngomti
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Claire Butters
- Division of Paediatric Rheumatology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Observatory, South Africa
| | - Lina Hahnle
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Marguerite Adriaanse
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Heidi Facey-Thomas
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Christiaan Scott
- Division of Paediatric Rheumatology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Observatory, South Africa
| | - Jonathan Day
- Division of Paediatric Rheumatology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Observatory, South Africa
| | - Timothy F. Spracklen
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
| | - Strauss van Graan
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sashkia R. Balla
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Rae MacGinty
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Maresa Botha
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Marina Johnson
- Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London, UK
| | - Heather J. Zar
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Ntobeko A.B. Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Liesl Zühlke
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
| | - Kate Webb
- Division of Paediatric Rheumatology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Observatory, South Africa
- Crick African Network, The Francis Crick Institute, London, UK
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Roanne S. Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
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13
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Johnson NV, Wall SC, Kramer KJ, Holt CM, Periasamy S, Richardson S, Suryadevara N, Andreano E, Paciello I, Pierleoni G, Piccini G, Huang Y, Ge P, Allen JD, Uno N, Shiakolas AR, Pilewski KA, Nargi RS, Sutton RE, Abu-Shmais AA, Parks R, Haynes BF, Carnahan RH, Crowe JE, Montomoli E, Rappuoli R, Bukreyev A, Ross TM, Sautto GA, McLellan JS, Georgiev IS. Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575741. [PMID: 38293237 PMCID: PMC10827111 DOI: 10.1101/2024.01.15.575741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Three coronaviruses have spilled over from animal reservoirs into the human population and caused deadly epidemics or pandemics. The continued emergence of coronaviruses highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using LIBRA-seq, we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these antibodies, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryo-EM structure of 54043-5 bound to the pre-fusion S2 subunit of the SARS-CoV-2 spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses, including ADCC and ADCP. In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.
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Affiliation(s)
- Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Steven C. Wall
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Kevin J. Kramer
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Clinton M. Holt
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Simone Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | - Giulio Pierleoni
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | | | - Ying Huang
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Pan Ge
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - James D. Allen
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Naoko Uno
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
| | - Andrea R. Shiakolas
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Kelsey A. Pilewski
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Rachel S. Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Rachel E. Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Alexandria A. Abu-Shmais
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
- Departments of Medicine and Immunology, Duke University, Durham, NC 27710, USA
| | - Robert H. Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
- Department of Pediatrics, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Emanuele Montomoli
- VisMederi Research S.r.l., Siena 53100, Italy
- VisMederi S.r.l, Siena 53100, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena 53100, Italy
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Ted M. Ross
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Giuseppe A. Sautto
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ivelin S. Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Computer Science, Vanderbilt University; Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University; Nashville, TN 37232, USA
- Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
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14
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Zaidi AK, Bajpai S, Dehgani-Mobaraki P. B cell responses to SARS-CoV-2. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 202:155-181. [PMID: 38237985 DOI: 10.1016/bs.pmbts.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter provides an overview of B cell responses in COVID-19, highlighting the structure of SARS-CoV-2 and its impact on B cell immunity. It explores the production and maturation of SARS-CoV-2-specific B cells, with a focus on the two distinct phases of the humoral immune response: the extrafollicular (EF) phase and the germinal center (GC) phase. Furthermore, the interplay between B cells, follicular T helper cells, CD4+ T cells, and plasma cells is discussed, emphasizing their collaborative role in mounting an effective humoral immune response against SARS-CoV-2. The concept of immunological memory is explored, highlighting the roles of plasma cells and B memory cells in providing long-term protection. The chapter delves into the antibody response during SARS-CoV-2 infection, categorizing the types of antibodies generated. This includes a detailed analysis of neutralizing antibodies, such as those directed against the receptor-binding domain (RBD) and the N-terminal domain (NTD), as well as non-neutralizing antibodies. The role of mucosal antibodies, cross-reactive antibodies, and auto-reactive antibodies is also discussed. Factors influencing the dynamics of anti-SARS-CoV-2 antibodies are examined, including the duration and strength of the humoral response. Additionally, the chapter highlights the impact of the Omicron variant on humoral immune responses and its implications for vaccine efficacy and antibody-mediated protection.
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Affiliation(s)
| | - Sanchit Bajpai
- Consultant ENT & Head and Neck Surgeon at TSM Medical College and Multispeciality Hospital, Lucknow, India.
| | - Puya Dehgani-Mobaraki
- Founder and President, Associazione Naso Sano, Ringgold Institution ID 567754, San Mariano, Italy
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15
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Cecchini E, Schino S, Gambadoro N, Ricciardi L, Trio O, Biondi-Zoccai G, Sangiorgi G. Facing the pandemic with a smile: the case of Memedical and its impact on cardiovascular professionals. Minerva Cardiol Angiol 2023; 71:475-484. [PMID: 36305775 DOI: 10.23736/s2724-5683.22.06079-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Since its outbreak, the Coronavirus disease 2019 (COVID-19) has profoundly changed the world we were acquainted with. After the first known contact with humankind in Wuhan, China, in December 2019, the reckless spread of such pathogen put the healthcare system to the test, leading to harmful consequences affecting human lives in every aspect. As of February 2022, the death toll amounts to almost 6 million deaths, but the pathogenic profile of SARS-CoV-2 goes way beyond the mere biological interaction between the viral particle and our organism. People had to deal with the severe psychological impact caused by the only available weapon to fight this infection, i.e., social distancing. The human psychological profile has been strained with repercussions we still are unaware of nowadays. Healthcare professionals were among the most hit categories, not only because of the quarantine but above all for the situations they had to bear every day, constantly facing desperation, death, isolation, and rage. In such circumstances, social media represented a powerful shelter, giving people the ability to keep in contact and to feel connected even if miles apart. In our country, the power of communication was strongly emphasized by launching an Italian Facebook group called "Memedical," where members can share ironic memes to feel closer and give a glimmer of happiness in such a challenging moment. Our review highlights the severity of this pandemic's impact, deteriorating the global population's physical and mental health, and shows how wise use of social media can benefit the quality of life.
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Affiliation(s)
| | - Sofia Schino
- Division of Cardiology, Tor Vergata University, Rome, Italy
| | - Nicola Gambadoro
- Division of Cardiology, G. Fogliani Hospital, Milazzo, Messina, Italy
| | - Luca Ricciardi
- Division of Neurosurgery, Department of NESMOS, S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Olimpia Trio
- Division of Cardiology, University Hospital Gaetano Martino, Messina, Italy
| | - Giuseppe Biondi-Zoccai
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University, Latina, Italy
- Mediterranea Cardiocentro, Naples, Italy
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16
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Song W, Fang Z, Ma F, Li J, Huang Z, Zhang Y, Li J, Chen K. The role of SARS-CoV-2 N protein in diagnosis and vaccination in the context of emerging variants: present status and prospects. Front Microbiol 2023; 14:1217567. [PMID: 37675423 PMCID: PMC10478715 DOI: 10.3389/fmicb.2023.1217567] [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: 05/15/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Despite many countries rapidly revising their strategies to prevent contagions, the number of people infected with Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to surge. The emergent variants that can evade the immune response significantly affect the effectiveness of mainstream vaccines and diagnostic products based on the original spike protein. Therefore, it is essential to focus on the highly conserved nature of the nucleocapsid protein as a potential target in the field of vaccines and diagnostics. In this regard, our review initially discusses the structure, function, and mechanism of action of N protein. Based on this discussion, we summarize the relevant research on the in-depth development and application of diagnostic methods and vaccines based on N protein, such as serology and nucleic acid detection. Such valuable information can aid in designing more efficient diagnostic and vaccine tools that could help end the SARS-CoV-2 pandemic.
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Affiliation(s)
- Wanchen Song
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhongbiao Fang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Feike Ma
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiaxuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Zhiwei Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yanjun Zhang
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jianhua Li
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
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17
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Xiong R, Li X. Geospatial analysis in the United States reveals the changing roles of temperature on COVID-19 transmission. GEOSPATIAL HEALTH 2023; 18. [PMID: 37470265 DOI: 10.4081/gh.2023.1213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/30/2023] [Indexed: 07/21/2023]
Abstract
Environmental factors are known to affect outbreak patterns of infectious disease, but their impacts on the spread of COVID-19 along with the evolution of this relationship over time intervals and in different regions are unclear. This study utilized 3 years of data on COVID-19 cases in the continental United States from 2020 to 2022 and the corresponding weather data. We used regression analysis to investigate weather impacts on COVID-19 spread in the mainland United States and estimate the changes of these impacts over space and time. Temperature exhibited a significant and moderately strong negative correlation for most of the US while relative humidity and precipitation experienced mixed relationships. By regressing temperature factors with the spreading rate of waves, we found temperature change can explain over 20% of the spatial-temporal variation in the COVID-19 spreading, with a significant and negative response between temperature change and spreading rate. The pandemic in the continental United States during 2020-2022 was characterized by seven waves, with different transmission rates and wave peaks concentrated in seven time periods. When repeating the analysis for waves in the seven periods and nine climate zones, we found temperature impacts evolve over time and space, possibly due to virus mutation, changes in population susceptibility, social behavior, and control measures. Temperature impacts became weaker in 6 of 9 climate zones from the beginning of the epidemic to the end of 2022, suggesting that COVID-19 has increasingly adapted to wider weather conditions.
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Affiliation(s)
| | - Xiaolong Li
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL.
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18
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Mah MG, Linster M, Low DHW, Zhuang Y, Jayakumar J, Samsudin F, Wong FY, Bond PJ, Mendenhall IH, Su YCF, Smith GJD. Spike-Independent Infection of Human Coronavirus 229E in Bat Cells. Microbiol Spectr 2023; 11:e0348322. [PMID: 37199653 PMCID: PMC10269751 DOI: 10.1128/spectrum.03483-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/17/2023] [Indexed: 05/19/2023] Open
Abstract
Bats are the reservoir for numerous human pathogens, including coronaviruses. Despite many coronaviruses having descended from bat ancestors, little is known about virus-host interactions and broader evolutionary history involving bats. Studies have largely focused on the zoonotic potential of coronaviruses with few infection experiments conducted in bat cells. To determine genetic changes derived from replication in bat cells and possibly identify potential novel evolutionary pathways for zoonotic virus emergence, we serially passaged six human 229E isolates in a newly established Rhinolophus lepidus (horseshoe bat) kidney cell line. Here, we observed extensive deletions within the spike and open reading frame 4 (ORF4) genes of five 229E viruses after passaging in bat cells. As a result, spike protein expression and infectivity of human cells was lost in 5 of 6 viruses, but the capability to infect bat cells was maintained. Only viruses that expressed the spike protein could be neutralized by 229E spike-specific antibodies in human cells, whereas there was no neutralizing effect on viruses that did not express the spike protein inoculated on bat cells. However, one isolate acquired an early stop codon, abrogating spike expression but maintaining infection in bat cells. After passaging this isolate in human cells, spike expression was restored due to acquisition of nucleotide insertions among virus subpopulations. Spike-independent infection of human coronavirus 229E may provide an alternative mechanism for viral maintenance in bats that does not rely on the compatibility of viral surface proteins and known cellular entry receptors. IMPORTANCE Many viruses, including coronaviruses, originated from bats. Yet, we know little about how these viruses switch between hosts and enter human populations. Coronaviruses have succeeded in establishing in humans at least five times, including endemic coronaviruses and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In an approach to identify requirements for host switches, we established a bat cell line and adapted human coronavirus 229E viruses by serial passage. The resulting viruses lost their spike protein but maintained the ability to infect bat cells, but not human cells. Maintenance of 229E viruses in bat cells appears to be independent of a canonical spike receptor match, which in turn might facilitate cross-species transmission in bats.
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Affiliation(s)
- Marcus G. Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dolyce H. W. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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19
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Benede NSB, Tincho MB, Walters A, Subbiah V, Ngomti A, Baguma R, Butters C, Mennen M, Skelem S, Adriaanse M, van Graan S, Balla SR, Moyo-Gwete T, Moore PL, Botha M, Workman L, Zar HJ, Ntusi NAB, Zühlke L, Webb K, Riou C, Burgers WA, Keeton RS. Distinct T cell functional profiles in SARS-CoV-2 seropositive and seronegative children associated with endemic human coronavirus cross-reactivity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.16.23290059. [PMID: 37292954 PMCID: PMC10246143 DOI: 10.1101/2023.05.16.23290059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
SARS-CoV-2 infection in children typically results in asymptomatic or mild disease. There is a paucity of studies on antiviral immunity in African children. We investigated SARS-CoV-2-specific T cell responses in 71 unvaccinated asymptomatic South African children who were seropositive or seronegative for SARS-CoV-2. SARS-CoV-2-specific CD4+ T cell responses were detectable in 83% of seropositive and 60% of seronegative children. Although the magnitude of the CD4+ T cell response did not differ significantly between the two groups, their functional profiles were distinct, with SARS-CoV-2 seropositive children exhibiting a higher proportion of polyfunctional T cells compared to their seronegative counterparts. The frequency of SARS-CoV-2-specific CD4+ T cells in seronegative children was associated with the endemic human coronavirus (HCoV) HKU1 IgG response. Overall, the presence of SARS-CoV-2-responding T cells in seronegative children may result from cross-reactivity to endemic coronaviruses and could contribute to the relative protection from disease observed in SARS-CoV-2-infected children.
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Affiliation(s)
- Ntombi S. B. Benede
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Marius B. Tincho
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Avril Walters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Vennesa Subbiah
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Amkele Ngomti
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Claire Butters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Marguerite Adriaanse
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Strauss van Graan
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sashkia R. Balla
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Maresa Botha
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Ntobeko A. B. Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Liesl Zühlke
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
| | - Kate Webb
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
- Crick African Network, The Francis Crick Institute, London, United Kingdom
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Roanne S. Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
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20
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Devaux CA, Fantini J. Unravelling Antigenic Cross-Reactions toward the World of Coronaviruses: Extent of the Stability of Shared Epitopes and SARS-CoV-2 Anti-Spike Cross-Neutralizing Antibodies. Pathogens 2023; 12:713. [PMID: 37242383 PMCID: PMC10220573 DOI: 10.3390/pathogens12050713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The human immune repertoire retains the molecular memory of a very great diversity of target antigens (epitopes) and can recall this upon a second encounter with epitopes against which it has previously been primed. Although genetically diverse, proteins of coronaviruses exhibit sufficient conservation to lead to antigenic cross-reactions. In this review, our goal is to question whether pre-existing immunity against seasonal human coronaviruses (HCoVs) or exposure to animal CoVs has influenced the susceptibility of human populations to SARS-CoV-2 and/or had an impact upon the physiopathological outcome of COVID-19. With the hindsight that we now have regarding COVID-19, we conclude that although antigenic cross-reactions between different coronaviruses exist, cross-reactive antibody levels (titers) do not necessarily reflect on memory B cell frequencies and are not always directed against epitopes which confer cross-protection against SARS-CoV-2. Moreover, the immunological memory of these infections is short-term and occurs in only a small percentage of the population. Thus, in contrast to what might be observed in terms of cross-protection at the level of a single individual recently exposed to circulating coronaviruses, a pre-existing immunity against HCoVs or other CoVs can only have a very minor impact on SARS-CoV-2 circulation at the level of human populations.
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Affiliation(s)
- Christian A. Devaux
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM Institut Hospitalo-Universitaire—Méditerranée Infection, 13005 Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), 13009 Marseille, France
| | - Jacques Fantini
- Aix-Marseille Université, INSERM UMR_S 1072, 13015 Marseille, France
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21
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Murray SM, Ansari AM, Frater J, Klenerman P, Dunachie S, Barnes E, Ogbe A. The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses. Nat Rev Immunol 2023; 23:304-316. [PMID: 36539527 PMCID: PMC9765363 DOI: 10.1038/s41577-022-00809-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
Pre-existing cross-reactive immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins in infection-naive subjects have been described by several studies. In particular, regions of high homology between SARS-CoV-2 and common cold coronaviruses have been highlighted as a likely source of this cross-reactivity. However, the role of such cross-reactive responses in the outcome of SARS-CoV-2 infection and vaccination is currently unclear. Here, we review evidence regarding the impact of pre-existing humoral and T cell immune responses to outcomes of SARS-CoV-2 infection and vaccination. Furthermore, we discuss the importance of conserved coronavirus epitopes for the rational design of pan-coronavirus vaccines and consider cross-reactivity of immune responses to ancestral SARS-CoV-2 and SARS-CoV-2 variants, as well as their impact on COVID-19 vaccination.
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Affiliation(s)
- Sam M Murray
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Azim M Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Ane Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
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22
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Tomaszewski T, Ali MA, Caetano-Anollés K, Caetano-Anollés G. Seasonal effects decouple SARS-CoV-2 haplotypes worldwide. F1000Res 2023; 12:267. [PMID: 37069849 PMCID: PMC10105261 DOI: 10.12688/f1000research.131522.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Background: Variants of concern (VOCs) have been replacing each other during the still rampant COVID-19 pandemic. As a result, SARS-CoV-2 populations have evolved increasingly intricate constellations of mutations that often enhance transmissibility, disease severity, and other epidemiological characteristics. The origin and evolution of these constellations remain puzzling. Methods: Here we study the evolution of VOCs at the proteome level by analyzing about 12 million genomic sequences retrieved from GISAID on July 23, 2022. A total 183,276 mutations were identified and filtered with a relevancy heuristic. The prevalence of haplotypes and free-standing mutations was then tracked monthly in various latitude corridors of the world. Results: A chronology of 22 haplotypes defined three phases driven by protein flexibility-rigidity, environmental sensing, and immune escape. A network of haplotypes illustrated the recruitment and coalescence of mutations into major VOC constellations and seasonal effects of decoupling and loss. Protein interaction networks mediated by haplotypes predicted communications impacting the structure and function of proteins, showing the increasingly central role of molecular interactions involving the spike (S), nucleocapsid (N), and membrane (M) proteins. Haplotype markers either affected fusogenic regions while spreading along the sequence of the S-protein or clustered around binding domains. Modeling of protein structure with AlphaFold2 showed that VOC Omicron and one of its haplotypes were major contributors to the distortion of the M-protein endodomain, which behaves as a receptor of other structural proteins during virion assembly. Remarkably, VOC constellations acted cooperatively to balance the more extreme effects of individual haplotypes. Conclusions: Our study uncovers seasonal patterns of emergence and diversification occurring amid a highly dynamic evolutionary landscape of bursts and waves. The mapping of genetically-linked mutations to structures that sense environmental change with powerful ab initio modeling tools demonstrates the potential of deep-learning for COVID-19 predictive intelligence and therapeutic intervention.
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Affiliation(s)
- Tre Tomaszewski
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Muhammad Asif Ali
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | | | - Gustavo Caetano-Anollés
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- C. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
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23
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Kim MI, Lee C. Human Coronavirus OC43 as a Low-Risk Model to Study COVID-19. Viruses 2023; 15:v15020578. [PMID: 36851792 PMCID: PMC9965565 DOI: 10.3390/v15020578] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had irreversible and devastating impacts on every aspect of human life. To better prepare for the next similar pandemic, a clear understanding of coronavirus biology is a prerequisite. Nevertheless, the high-risk nature of the causative agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), requires the use of a cumbersome biosafety level-3 (BSL-3) confinement facility. To facilitate the development of preventive and therapeutic measures against SARS-CoV-2, one of the endemic strains of low-risk coronaviruses has gained attention as a useful research alternative: human coronavirus OC43 (HCoV-OC43). In this review, its history, classification, and clinical manifestations are first summarized. The characteristics of its viral genomes, genes, and evolution process are then further explained. In addition, the host factors necessary to support the life cycle of HCoV-OC43 and the innate, as well as adaptive, immunological responses to HCoV-OC43 infection are discussed. Finally, the development of in vitro and in vivo systems to study HCoV-OC43 and its application to the discovery of potential antivirals for COVID-19 by using HCoV-OC43 models are also presented. This review should serve as a concise guide for those who wish to use HCoV-OC43 to study coronaviruses in a low-risk research setting.
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Lafuente M, López FJ, Mateo PM, Cebrián AC, Asín J, Moler JA, Borque-Fernando Á, Esteban LM, Pérez-Palomares A, Sanz G. A multistate model and its standalone tool to predict hospital and ICU occupancy by patients with COVID-19. Heliyon 2023; 9:e13545. [PMID: 36776914 PMCID: PMC9899510 DOI: 10.1016/j.heliyon.2023.e13545] [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: 06/28/2022] [Revised: 01/28/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023] Open
Abstract
Objective This study aims to build a multistate model and describe a predictive tool for estimating the daily number of intensive care unit (ICU) and hospital beds occupied by patients with coronavirus 2019 disease (COVID-19). Material and methods The estimation is based on the simulation of patient trajectories using a multistate model where the transition probabilities between states are estimated via competing risks and cure models. The input to the tool includes the dates of COVID-19 diagnosis, admission to hospital, admission to ICU, discharge from ICU and discharge from hospital or death of positive cases from a selected initial date to the current moment. Our tool is validated using 98,496 cases positive for severe acute respiratory coronavirus 2 extracted from the Aragón Healthcare Records Database from July 1, 2020 to February 28, 2021. Results The tool demonstrates good performance for the 7- and 14-days forecasts using the actual positive cases, and shows good accuracy among three scenarios corresponding to different stages of the pandemic: 1) up-scenario, 2) peak-scenario and 3) down-scenario. Long term predictions (two months) also show good accuracy, while those using Holt-Winters positive case estimates revealed acceptable accuracy to day 14 onwards, with relative errors of 8.8%. Discussion In the era of the COVID-19 pandemic, hospitals must evolve in a dynamic way. Our prediction tool is designed to predict hospital occupancy to improve healthcare resource management without information about clinical history of patients. Conclusions Our easy-to-use and freely accessible tool (https://github.com/peterman65) shows good performance and accuracy for forecasting the daily number of hospital and ICU beds required for patients with COVID-19.
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Affiliation(s)
- Miguel Lafuente
- Department of Statistical Methods, Universidad de Zaragoza, C. Pedro Cerbuna 12, 50009 Zaragoza, Spain,Institute for Biocomputation and Physics of Complex Systems-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
| | - Francisco Javier López
- Department of Statistical Methods, Universidad de Zaragoza, C. Pedro Cerbuna 12, 50009 Zaragoza, Spain,Institute for Biocomputation and Physics of Complex Systems-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
| | - Pedro Mariano Mateo
- Department of Statistical Methods, Universidad de Zaragoza, C. Pedro Cerbuna 12, 50009 Zaragoza, Spain,Institute for Biocomputation and Physics of Complex Systems-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain,Centre Q-UPHS. Quantitative Methods for Uplifting the Performance of Health Services, Spain
| | - Ana Carmen Cebrián
- Department of Statistical Methods, Universidad de Zaragoza, C. Pedro Cerbuna 12, 50009 Zaragoza, Spain,Institute for Biocomputation and Physics of Complex Systems-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
| | - Jesús Asín
- Department of Statistical Methods, Universidad de Zaragoza, C. Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - José Antonio Moler
- Department of Statistics and Operational Research, Universidad Pública de Navarra, Campus Arrosadía S/n, 31006 Pamplona, Spain
| | - Ángel Borque-Fernando
- Department of Urology, Miguel Servet University Hospital and IIS Aragón, Paseo Isabel La Católica 1-3, 50009 Zaragoza, Spain
| | - Luis Mariano Esteban
- Institute for Biocomputation and Physics of Complex Systems-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain,Department of Applied Mathematics, Escuela Universitaria Politécnica de La Almunia, University of Zaragoza, C/ Mayor 5, 50100 La Almunia de Doña Godina, Spain,Corresponding author. Escuela Universitaria Politécnica de La Almunia, Universidad de Zaragoza, C. Mayor 5, 50100 La Almunia de Doña Godina, Spain
| | - Ana Pérez-Palomares
- Department of Statistical Methods, Universidad de Zaragoza, C. Pedro Cerbuna 12, 50009 Zaragoza, Spain,Department of Statistical Methods, Universidad de Zaragoza, C. Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Gerardo Sanz
- Department of Statistical Methods, Universidad de Zaragoza, C. Pedro Cerbuna 12, 50009 Zaragoza, Spain,Institute for Biocomputation and Physics of Complex Systems-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
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25
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Sonmezer MC, Sahin TK, Erul E, Dizman GT, Inkaya AC, Alp A, Alp S, Unal S. Prevalence of Common Human Coronaviruses (NL63, 229E, and OC43) in Adults before the COVID-19 Pandemic: a Single-Center Study from Turkey, 2015-2020. Jpn J Infect Dis 2023; 76:27-33. [PMID: 36047175 DOI: 10.7883/yoken.jjid.2022.255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Common Human Coronaviruses (HCoVs), such as NL63, HKU1, 229E, and OC43, induce respiratory tract infections worldwide. Epidemiological studies of HCoVs are of paramount importance because the disease burden and trajectory (in years) have not been well addressed in adults. Here, we aimed to describe the burden of HCoVs in a hospital setting over five years before the coronavirus disease 2019 pandemic. This was a retrospective study of patients (>18 years) between January 1, 2015, and January 1, 2020, whose respiratory specimens were tested by multiplex real-time polymerase chain reaction. In total, 7,861 respiratory samples (4,540 patients) were included, 38% of which tested positive for any respiratory virus. Of these, 212 (12.2%) samples were positive for HCoVs, and their co-infection with other respiratory viruses was 30.6%. Rhinovirus (27.6%) was the most common co-infection among all three HCoVs. The overall prevalence of HCoVs tended to be the highest in the winter (40.9%). Patients aged ≥60 years had the highest prevalence of overall HCoVs (39.7%). Given the duration and large sample size, this study from Turkey is one of the largest to date among adults in the literature. These epidemiological data and molecular surveillance of HCoVs have important implications for the control and prevention of respiratory infections.
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Affiliation(s)
- Meliha Cagla Sonmezer
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, Turkey
| | - Taha Koray Sahin
- Department of Internal Medicine, Hacettepe University Faculty of Medicine, Turkey
| | - Enes Erul
- Department of Internal Medicine, Hacettepe University Faculty of Medicine, Turkey
| | - Gulcin Telli Dizman
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, Turkey
| | - Ahmet Cagkan Inkaya
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, Turkey
| | - Alparslan Alp
- Department of Microbiology and Clinical Microbiology, Hacettepe University Faculty of Medicine, Turkey
| | - Sehnaz Alp
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, Turkey
| | - Serhat Unal
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University Faculty of Medicine, Turkey
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Hickerson BT, Sheikh F, Donnelly RP, Ilyushina NA. Comparison of the Antiviral Activity of Remdesivir, Chloroquine, and Interferon-β as Single or Dual Agents Against the Human Beta-Coronavirus OC43. J Interferon Cytokine Res 2023; 43:35-42. [PMID: 36651846 PMCID: PMC9885548 DOI: 10.1089/jir.2022.0210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The human beta-coronavirus strain, OC43, provides a useful model for testing the antiviral activity of various agents. We compared the activity of several antiviral drugs against OC43, including remdesivir, chloroquine, interferon (IFN)-β, IFN-λ1, and IFN-λ4, in two distinct cell types: human colorectal carcinoma cell line (HCT-8 cells) and normal human bronchial epithelial (NHBE) cells. We also tested whether these agents mediate additive, synergistic, or antagonistic activity against OC43 infection when used in combination. When used as single agents, remdesivir exhibited stronger antiviral activity than chloroquine, and IFN-β exhibited stronger activity than IFN-λ1 or IFN-λ4 against OC43 in both HCT-8 and NHBE cells. Anakinra (IL-1 inhibitor) and tocilizumab (IL-6 inhibitor) did not mediate any antiviral activity. The combination of IFN-β plus chloroquine or remdesivir resulted in higher synergy scores and higher expression of IFN-stimulated genes than did IFN-β alone. In contrast, the combination of remdesivir plus chloroquine resulted in an antagonistic interaction in NHBE cells. Our findings indicate that the combined use of IFN-β plus remdesivir or chloroquine induces maximal antiviral activity against human coronavirus strain OC43 in primary human respiratory epithelial cells. Furthermore, our experimental OC43 virus infection model provides an excellent method for evaluating the biological activity of antiviral drugs.
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Affiliation(s)
- Brady T. Hickerson
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Faruk Sheikh
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Raymond P. Donnelly
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Natalia A. Ilyushina
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA.,Address correspondence to: Dr. Natalia A. Ilyushina, Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
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27
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Frutos AM, Balmaseda A, Vydiswaran N, Patel M, Ojeda S, Brouwer A, Tutino R, Cai S, Bakker K, Sanchez N, Lopez R, Kuan G, Gordon A. Burden and seasonality of primary and secondary symptomatic common cold coronavirus infections in Nicaraguan children. Influenza Other Respir Viruses 2023; 17:e13078. [PMID: 36494188 PMCID: PMC9835451 DOI: 10.1111/irv.13086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The current SARS-CoV-2 pandemic highlights the need for an increased understanding of coronavirus epidemiology. In a pediatric cohort in Nicaragua, we evaluate the seasonality and burden of common cold coronavirus (ccCoV) infection and evaluate likelihood of symptoms in reinfections. METHODS Children presenting with symptoms of respiratory illness were tested for each of the four ccCoVs (NL63, 229E, OC43, and HKU1). Annual blood samples collected before ccCoV infection were tested for antibodies against each ccCoV. Seasonality was evaluated using wavelet and generalized additive model (GAM) analyses, and age-period effects were investigated using a Poisson model. We also evaluate the risk of symptom presentation between primary and secondary infections. RESULTS In our cohort of 2576 children from 2011 to 2016, we observed 595 ccCoV infections and 107 cases of ccCoV-associated lower respiratory infection (LRI). The overall incidence rate was 61.1 per 1000 person years (95% confidence interval (CI): 56.3, 66.2). Children under two had the highest incidence of ccCoV infections and associated LRI. ccCoV incidence rapidly decreases until about age 6. Each ccCoV circulated throughout the year and demonstrated annual periodicity. Peaks of NL63 typically occurred 3 months before 229E peaks and 6 months after OC43 peaks. Approximately 69% of symptomatic ccCoV infections were secondary infections. There was slightly lower risk (rate ratio (RR): 0.90, 95% CI: 0.83, 0.97) of LRI between secondary and primary ccCoV infections among participants under the age of 5. CONCLUSIONS ccCoV spreads annually among children with the greatest burden among ages 0-1. Reinfection is common; prior infection is associated with slight protection against LRI among the youngest children.
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Affiliation(s)
- Aaron M. Frutos
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Angel Balmaseda
- Health Center Sócrates Flores VivasMinistry of HealthManaguaNicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnósticoy ReferenciaMinistry of HealthManaguaNicaragua
| | - Nivea Vydiswaran
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Mayuri Patel
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | | | - Andrew Brouwer
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Rebecca Tutino
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Shuwei Cai
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Kevin Bakker
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | | | - Roger Lopez
- Laboratorio Nacional de Virología, Centro Nacional de Diagnósticoy ReferenciaMinistry of HealthManaguaNicaragua
- Sustainable Sciences InstituteManaguaNicaragua
| | - Guillermina Kuan
- Health Center Sócrates Flores VivasMinistry of HealthManaguaNicaragua
- Sustainable Sciences InstituteManaguaNicaragua
| | - Aubree Gordon
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
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28
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Hernandez N, Caetano-Anollés G. Worldwide Correlations Support COVID-19 Seasonal Behavior and Impact of Global Change. Evol Bioinform Online 2023; 19:11769343231169377. [PMID: 37155556 PMCID: PMC10113908 DOI: 10.1177/11769343231169377] [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: 12/26/2022] [Accepted: 03/14/2023] [Indexed: 05/10/2023] Open
Abstract
Many viral diseases exhibit seasonal behavior and can be affected by environmental stressors. Using time-series correlation charts extrapolated from worldwide data, we provide strong support for the seasonal development of COVID-19 regardless of the immunity of the population, behavioral changes, and the periodic appearance of new variants with higher rates of infectivity and transmissibility. Statistically significant latitudinal gradients were also observed with indicators of global change. Using the Environmental Protection Index (EPI) and State of Global Air (SoGA) metrics, a bilateral analysis of environmental health and ecosystem vitality effects showed associations with COVID-19 transmission. Air quality, pollution emissions, and other indicators showed strong correlations with COVID-19 incidence and mortality. Remarkably, EPI category and performance indicators also correlated with latitude, suggesting cultural and psychological diversity in human populations not only impact wealth and happiness but also planetary health at latitudinal level. Looking forward, we conclude there will be a need to disentangle the seasonal and global change effects of COVID-19 noting that countries that go against the health of the planet affect health in general.
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Affiliation(s)
| | - Gustavo Caetano-Anollés
- Gustavo Caetano-Anollés, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 332 NSRC, 1101W Peabody Drive, Urbana, IL 61801, USA.
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29
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Shah MM, Winn A, Dahl RM, Kniss KL, Silk BJ, Killerby ME. Seasonality of Common Human Coronaviruses, United States, 2014-2021 1. Emerg Infect Dis 2022; 28:1970-1976. [PMID: 36007923 PMCID: PMC9514339 DOI: 10.3201/eid2810.220396] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 4 common types of human coronaviruses (HCoVs)-2 alpha (HCoV-NL63 and HCoV-229E) and 2 beta (HCoV-HKU1 and HCoV-OC43)-generally cause mild upper respiratory illness. Seasonal patterns and annual variation in predominant types of HCoVs are known, but parameters of expected seasonality have not been defined. We defined seasonality of HCoVs during July 2014-November 2021 in the United States by using a retrospective method applied to National Respiratory and Enteric Virus Surveillance System data. In the 6 HCoV seasons before 2020-21, season onsets occurred October 21-November 12, peaks January 6-February 13, and offsets April 18-June 27; most (>93%) HCoV detection was within the defined seasonal onsets and offsets. The 2020-21 HCoV season onset was 11 weeks later than in prior seasons, probably associated with COVID-19 mitigation efforts. Better definitions of HCoV seasonality can be used for clinical preparedness and for determining expected patterns of emerging coronaviruses.
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30
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Kaur A, Singh N, Singh K, Sidhu SK, Kaur H, Jain P, Kaur M, Jairath M. SARS-CoV-2 IgG Antibody Seroprevalence in Children from the Amritsar District of Punjab. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2022. [DOI: 10.15324/kjcls.2022.54.3.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Amandeep Kaur
- The Viral Research and Diagnostic Laboratory, Government Medical College, Amritsar, India
| | - Narinder Singh
- Department of Pediatrics, Government Medical College, Amritsar, India
| | - Kanwardeep Singh
- Department of Microbiology, Government Medical College, Amritsar, India
| | | | - Harleen Kaur
- The Viral Research and Diagnostic Laboratory, Government Medical College, Amritsar, India
| | - Poonam Jain
- The Viral Research and Diagnostic Laboratory, Government Medical College, Amritsar, India
| | - Manmeet Kaur
- Department of Pediatrics, Government Medical College, Amritsar, India
| | - Mohan Jairath
- The Viral Research and Diagnostic Laboratory, Government Medical College, Amritsar, India
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31
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Vojdani A, Vojdani E, Melgar AL, Redd J. Reaction of SARS-CoV-2 antibodies with other pathogens, vaccines, and food antigens. Front Immunol 2022; 13:1003094. [PMID: 36211404 PMCID: PMC9537454 DOI: 10.3389/fimmu.2022.1003094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
It has been shown that SARS-CoV-2 shares homology and cross-reacts with vaccines, other viruses, common bacteria and many human tissues. We were inspired by these findings, firstly, to investigate the reaction of SARS-CoV-2 monoclonal antibody with different pathogens and vaccines, particularly DTaP. Additionally, since our earlier studies have shown immune reactivity by antibodies made against pathogens and autoantigens towards different food antigens, we also studied cross-reaction between SARS-CoV-2 and common foods. For this, we reacted monoclonal and polyclonal antibodies against SARS-CoV-2 spike protein and nucleoprotein with 15 different bacterial and viral antigens and 2 different vaccines, BCG and DTaP, as well as with 180 different food peptides and proteins. The strongest reaction by SARS-CoV-2 antibodies were with DTaP vaccine antigen, E. faecalis, roasted almond, broccoli, soy, cashew, α+β casein and milk, pork, rice endochitinase, pineapple bromelain, and lentil lectin. Because the immune system tends to form immune responses towards the original version of an antigen that it has encountered, this cross-reactivity may have its advantages with regards to immunity against SARS-CoV-2, where the SARS-CoV-2 virus may elicit a “remembered” immune response because of its structural similarity to a pathogen or food antigen to which the immune system was previously exposed. Our findings indicate that cross-reactivity elicited by DTaP vaccines in combination with common herpesviruses, bacteria that are part of our normal flora such as E. faecalis, and foods that we consume on a daily basis should be investigated for possible cross-protection against COVID-19. Additional experiments would be needed to clarify whether or not this cross-protection is due to cross-reactive antibodies or long-term memory T and B cells in the blood.
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Affiliation(s)
- Aristo Vojdani
- Immunosciences Lab, Los Angeles, CA, United States
- Cyrex Laboratories, Limited Liability Company (LLC), Phoenix, AZ, United States
- *Correspondence: Aristo Vojdani,
| | | | | | - Joshua Redd
- RedRiver Health and Wellness, South Jordan, UT, United States
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32
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Shen DP, Vermeulen F, Debeer A, Lagrou K, Smits A. Impact of COVID-19 on viral respiratory infection epidemiology in young children: A single-center analysis. Front Public Health 2022; 10:931242. [PMID: 36203684 PMCID: PMC9530989 DOI: 10.3389/fpubh.2022.931242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/22/2022] [Indexed: 01/24/2023] Open
Abstract
Background The COVID-19 pandemic impacts different health aspects. Concomitant with the adoption of non-pharmaceutical interventions (NPIs) to reduce the spread of SARS-CoV-2, global surveillance studies reported a reduction in occurrence of respiratory pathogens like influenza A and B virus (IAV & IBV) and respiratory syncytial virus (RSV). We hypothesized to observe this collateral benefit on viral respiratory infection epidemiology in young children. Methods Respiratory samples of children aged below 6 years, presenting at the outpatient clinic, emergency department, or pediatric infectious diseases department of the University Hospitals Leuven, between April 2017 and April 2021 were retrospectively analyzed. The occurrence (positivity rate), and seasonal patterns of viral respiratory infections were described. Chi-squared or Fisher's exact test (and Bonferroni correction) were used to explore differences in occurrence between 2020-2021 and previous 12-month (April to April) periods. Results We included 3020 samples (453 respiratory panels, 2567 single SARS-CoV-2 PCR tests). IAV and IBV were not detected from March and January 2020, respectively. For IAV, positivity rate in 2020-2021 (0%, n = 0) was significantly different from 2018-2019 (12.4%, n = 17) (p < 0.001) and 2019-2020 (15.4%, n = 19) (p < 0.001). IBV positivity rate in 2020-2021 (0%, n = 0) was not significantly different from previous periods. RSV occurrence was significantly lower in 2020-2021 (3.2%, n = 3), compared to 2017-2018 (15.0%, n = 15) (p = 0.006), 2018-2019 (16.1%, n = 22) (p = 0.002) and 2019-2020 (22.8%, n = 28) (p < 0.001). The RSV (winter) peak was absent and presented later (March-April 2021). Positivity rate of parainfluenza virus 3 (PIV-3) was significantly higher in 2020-2021 (11.8%, n = 11) than 2017-2018 (1%, n = 1) (p = 0.002). PIV-3 was absent from April 2020 to January 2021, whereas no clear seasonal pattern was distinguished the other years. For the other viruses tested, no significant differences in occurrence were observed between 2020-2021 and previous periods. From March 2020 onwards, 20 cases (0.7%) of SARS-CoV-2 were identified. Conclusion These findings reinforce the hypothesis of NPIs impacting the epidemiology of influenza viruses and RSV in young children. Compared to previous periods, no IAV and IBV cases were observed in the 2020-2021 study period, and the RSV peak occurred later. Since the pandemic is still ongoing, continuation of epidemiological surveillance, even on a larger scale, is indicated.
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Affiliation(s)
| | - François Vermeulen
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Anne Debeer
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium,Neonatal Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - Katrien Lagrou
- Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Anne Smits
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium,Neonatal Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium,L-C&Y, KU Leuven Child & Youth Institute, Leuven, Belgium,*Correspondence: Anne Smits
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Yu ED, Narowski TM, Wang E, Garrigan E, Mateus J, Frazier A, Weiskopf D, Grifoni A, Premkumar L, da Silva Antunes R, Sette A. Immunological memory to common cold coronaviruses assessed longitudinally over a three-year period pre-COVID19 pandemic. Cell Host Microbe 2022; 30:1269-1278.e4. [PMID: 35932763 PMCID: PMC9296686 DOI: 10.1016/j.chom.2022.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/12/2022] [Accepted: 07/15/2022] [Indexed: 12/01/2022]
Abstract
The immune memory to common cold coronaviruses (CCCs) influences SARS-CoV-2 infection outcome, and understanding its effect is crucial for pan-coronavirus vaccine development. We performed a longitudinal analysis of pre-COVID19-pandemic samples from 2016-2019 in young adults and assessed CCC-specific CD4+ T cell and antibody responses. Notably, CCC responses were commonly detected with comparable frequencies as with other common antigens and were sustained over time. CCC-specific CD4+ T cell responses were associated with low HLA-DR+CD38+ signals, and their magnitude did not correlate with yearly CCC infection prevalence. Similarly, CCC-specific and spike RBD-specific IgG responses were stable in time. Finally, high CCC-specific CD4+ T cell reactivity, but not antibody titers, was associated with pre-existing SARS-CoV-2 immunity. These results provide a valuable reference for understanding the immune response to endemic coronaviruses and suggest that steady and sustained CCC responses are likely from a stable pool of memory CD4+ T cells due to repeated earlier exposures and possibly occasional reinfections.
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Affiliation(s)
- Esther Dawen Yu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Tara M Narowski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Eric Wang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Emily Garrigan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
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34
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Kiseleva I, Musaeva T, Ksenafontov A. SARS-CoV-2 Invasion: What Happens to Other Respiratory Viruses? Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2206100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This letter briefly presents the relationships between respiratory viruses in the years prior to and during the COVID-19 pandemic. Viral common colds are self-limiting infections that typically resolve within a few days. However, when well-established epidemiological relationships are disrupted during a pandemic, they behave differently. For instance, during the 2009 influenza pandemic, while the majority of seasonal respiratory viruses lost ground under the pressure of a new pandemic strain, some others (for instance, human rhinoviruses) continued to circulate along with the pandemic pathogen and in some cases, even delayed its spread. With the arrival of the COVID-19 pandemic, the degree of circulation of many respiratory viruses has changed dramatically. Along with a significant reduction in the circulation of many seasonal respiratory pathogens, rhinoviruses, respiratory syncytial virus and non-COVID-19 coronaviruses—being the most frequently identified respiratory pathogens—have shown their unique capability to compete with SARS-CoV-2.
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Khare K, Pandey R. Cellular heterogeneity in disease severity and clinical outcome: Granular understanding of immune response is key. Front Immunol 2022; 13:973070. [PMID: 36072602 PMCID: PMC9441806 DOI: 10.3389/fimmu.2022.973070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 07/26/2022] [Indexed: 12/15/2022] Open
Abstract
During an infectious disease progression, it is crucial to understand the cellular heterogeneity underlying the differential immune response landscape that will augment the precise information of the disease severity modulators, leading to differential clinical outcome. Patients with COVID-19 display a complex yet regulated immune profile with a heterogeneous array of clinical manifestation that delineates disease severity sub-phenotypes and worst clinical outcomes. Therefore, it is necessary to elucidate/understand/enumerate the role of cellular heterogeneity during COVID-19 disease to understand the underlying immunological mechanisms regulating the disease severity. This article aims to comprehend the current findings regarding dysregulation and impairment of immune response in COVID-19 disease severity sub-phenotypes and relate them to a wide array of heterogeneous populations of immune cells. On the basis of the findings, it suggests a possible functional correlation between cellular heterogeneity and the COVID-19 disease severity. It highlights the plausible modulators of age, gender, comorbidities, and hosts' genetics that may be considered relevant in regulating the host response and subsequently the COVID-19 disease severity. Finally, it aims to highlight challenges in COVID-19 disease that can be achieved by the application of single-cell genomics, which may aid in delineating the heterogeneity with more granular understanding. This will augment our future pandemic preparedness with possibility to identify the subset of patients with increased diseased severity.
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Affiliation(s)
- Kriti Khare
- Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Pandey
- Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Pelegri‐Martinez E, Guruceaga X, Martin‐Souto L, Abad‐Diaz‐de‐Cerio A, Rementeria A, Dominguez A, Gallego M, Martinez O, Arana‐Arri E, Aranzamendi M, Ramirez‐Garcia A. Flexible multiplex
PCR
to detect
SARS‐CoV
‐2, coronavirus
OC43
and influenza A virus in nasopharyngeal swab samples. J Appl Microbiol 2022; 133:3534-3545. [PMID: 35988051 PMCID: PMC9537992 DOI: 10.1111/jam.15788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Eduardo Pelegri‐Martinez
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology University of the Basque Country (UPV/EHU) Barrio Sarriena s/n,48940 Leioa Spain
| | - Xabier Guruceaga
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology University of the Basque Country (UPV/EHU) Barrio Sarriena s/n,48940 Leioa Spain
| | - Leire Martin‐Souto
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology University of the Basque Country (UPV/EHU) Barrio Sarriena s/n,48940 Leioa Spain
| | - Ana Abad‐Diaz‐de‐Cerio
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology University of the Basque Country (UPV/EHU) Barrio Sarriena s/n,48940 Leioa Spain
| | - Aitor Rementeria
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology University of the Basque Country (UPV/EHU) Barrio Sarriena s/n,48940 Leioa Spain
| | - Alazne Dominguez
- Biocruces Bizkaia Health Research Institute Hospital Universitario Cruces Bilbao Spain
| | - Mikel Gallego
- Biocruces Bizkaia Health Research Institute Hospital Universitario Cruces Bilbao Spain
| | - Oscar Martinez
- Biocruces Bizkaia Health Research Institute Hospital Universitario Cruces Bilbao Spain
| | - Eunate Arana‐Arri
- Biocruces Bizkaia Health Research Institute Hospital Universitario Cruces Bilbao Spain
| | - Maitane Aranzamendi
- Biocruces Bizkaia Health Research Institute Hospital Universitario Cruces Bilbao Spain
| | - Andoni Ramirez‐Garcia
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology University of the Basque Country (UPV/EHU) Barrio Sarriena s/n,48940 Leioa Spain
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Solomon MD, Escobar GJ, Lu Y, Schlessinger D, Steinman JB, Steinman L, Lee C, Liu VX. Risk of severe COVID-19 infection among adults with prior exposure to children. Proc Natl Acad Sci U S A 2022; 119:e2204141119. [PMID: 35895714 PMCID: PMC9388132 DOI: 10.1073/pnas.2204141119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/27/2022] [Indexed: 12/14/2022] Open
Abstract
Susceptibility and severity of COVID-19 infection vary widely. Prior exposure to endemic coronaviruses, common in young children, may protect against SARS-CoV-2. We evaluated risk of severe COVID-19 among adults with and without exposure to young children in a large, integrated healthcare system. Adults with children 0-5 years were matched 1:1 to adults with children 6-11 years, 12-18 years, and those without children based upon a COVID-19 propensity score and risk factors for severe COVID-19. COVID-19 infections, hospitalizations, and need for intensive care unit (ICU) were assessed in 3,126,427 adults, of whom 24% (N = 743,814) had children 18 years or younger, and 8.8% (N = 274,316) had a youngest child 0-5 years. After 1:1 matching, propensity for COVID-19 infection and risk factors for severe COVID-19 were well balanced between groups. Rates of COVID-19 infection were slightly higher for adults with exposure to older children (incident risk ratio, 1.09, 95% confidence interval, [1.05-1.12] and IRR 1.09 [1.05-1.13] for adults with children 6-11 and 12-18, respectively), compared to those with children 0-5 years, although no difference in rates of COVID-19 illness requiring hospitalization or ICU admission was observed. However, adults without exposure to children had lower rates of COVID-19 infection (IRR 0.85, [0.83-0.87]) but significantly higher rates of COVID-19 hospitalization (IRR 1.49, [1.29-1.73]) and hospitalization requiring ICU admission (IRR 1.76, [1.19-2.58]) compared to those with children aged 0-5. In a large, real-world population, exposure to young children was associated with less severe COVID-19 illness. Endemic coronavirus cross-immunity may play a role in protection against severe COVID-19.
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Affiliation(s)
- Matthew D. Solomon
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612
- Department of Cardiology, Kaiser Oakland Medical Center, Oakland, CA 94611
| | - Gabriel J. Escobar
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612
| | - Yun Lu
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612
| | - David Schlessinger
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612
| | | | - Lawrence Steinman
- Department of Pediatrics, Stanford University, Stanford, CA 94305
- Department of Neurology, Stanford University, Stanford, CA 94305
- Department of Neurological Sciences, Stanford University, Stanford, CA 94305
| | - Catherine Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612
| | - Vincent X. Liu
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612
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38
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Chen D, Ou Z, Zhu J, Wang H, Ding P, Luo L, Ding X, Sun C, Lan T, Sahu SK, Wu W, Yuan Y, Wu W, Qiu J, Zhu Y, Yue Q, Jia Y, Wei Y, Qin Q, Li R, Zhao W, Lv Z, Pu M, Lv B, Yang S, Chang A, Wei X, Chen F, Yang T, Wei Z, Yang F, Zhang P, Guo G, Li Y, Hua Y, Liu H. Screening of cell-virus, cell-cell, gene-gene crosstalk among animal kingdom at single cell resolution. Clin Transl Med 2022; 12:e886. [PMID: 35917402 PMCID: PMC9345398 DOI: 10.1002/ctm2.886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The exact animal origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains obscure and understanding its host range is vital for preventing interspecies transmission. METHODS Herein, we applied single-cell sequencing to multiple tissues of 20 species (30 data sets) and integrated them with public resources (45 data sets covering 26 species) to expand the virus receptor distribution investigation. While the binding affinity between virus and receptor is essential for viral infectivity, understanding the receptor distribution could predict the permissive organs and tissues when infection occurs. RESULTS Based on the transcriptomic data, the expression profiles of receptor or associated entry factors for viruses capable of causing respiratory, blood, and brain diseases were described in detail. Conserved cellular connectomes and regulomes were also identified, revealing fundamental cell-cell and gene-gene cross-talks from reptiles to humans. CONCLUSIONS Overall, our study provides a resource of the single-cell atlas of the animal kingdom which could help to identify the potential host range and tissue tropism of viruses and reveal the host-virus co-evolution.
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Affiliation(s)
- Dongsheng Chen
- BGI‐ShenzhenShenzhenChina,Suzhou Institute of Systems MedicineSuzhouJiangsuChina
| | - Zhihua Ou
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen IdentificationBGI‐ShenzhenShenzhenChina
| | - Jiacheng Zhu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Haoyu Wang
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Peiwen Ding
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Lihua Luo
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Xiangning Ding
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Chengcheng Sun
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | | | - Weiying Wu
- The MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouChina
| | - Yuting Yuan
- Department of Physiology, School of Basic Medical SciencesBinzhou Medical UniversityYantaiChina
| | - Wendi Wu
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Jiaying Qiu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yixin Zhu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Qizhen Yue
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Yi Jia
- BGI‐ShenzhenShenzhenChina
| | - Yanan Wei
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Qiuyu Qin
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Runchu Li
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Wandong Zhao
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Zhiyuan Lv
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | - Mingyi Pu
- BGI‐ShenzhenShenzhenChina,School of Basic MedicineQingdao UniversityQingdaoChina
| | | | - Shangchen Yang
- College of Life SciencesZhejiang UniversityHangzhouChina
| | | | | | | | - Tao Yang
- China National GeneBankShenzhenChina
| | | | - Fan Yang
- China National GeneBankShenzhenChina
| | - Peijing Zhang
- Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouChina
| | - Guoji Guo
- Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouChina
| | | | - Yan Hua
- Guangdong Provincial Key Laboratory of SilvicultureProtection and UtilizationGuangdong Academy of ForestryGuangzhouChina
| | - Huan Liu
- BGI‐ShenzhenShenzhenChina,College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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39
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A Bayesian approach to infer recombination patterns in coronaviruses. Nat Commun 2022; 13:4186. [PMID: 35859071 PMCID: PMC9297283 DOI: 10.1038/s41467-022-31749-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/30/2022] [Indexed: 02/06/2023] Open
Abstract
As shown during the SARS-CoV-2 pandemic, phylogenetic and phylodynamic methods are essential tools to study the spread and evolution of pathogens. One of the central assumptions of these methods is that the shared history of pathogens isolated from different hosts can be described by a branching phylogenetic tree. Recombination breaks this assumption. This makes it problematic to apply phylogenetic methods to study recombining pathogens, including, for example, coronaviruses. Here, we introduce a Markov chain Monte Carlo approach that allows inference of recombination networks from genetic sequence data under a template switching model of recombination. Using this method, we first show that recombination is extremely common in the evolutionary history of SARS-like coronaviruses. We then show how recombination rates across the genome of the human seasonal coronaviruses 229E, OC43 and NL63 vary with rates of adaptation. This suggests that recombination could be beneficial to fitness of human seasonal coronaviruses. Additionally, this work sets the stage for Bayesian phylogenetic tracking of the spread and evolution of SARS-CoV-2 in the future, even as recombinant viruses become prevalent. Genetic recombination can confound standard phylogenetic approaches. Here, the authors present a method to reconstruct virus recombination networks, and show the importance of recombination in shaping the ongoing evolution of SARS-like, MERS and 3 human seasonal coronaviruses.
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40
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Rodriguez-Nava G, Egoryan G, Dong T, Zhang Q, Hyser E, Poudel B, Yanez-Bello MA, Trelles-Garcia DP, Chung CW, Pyakuryal B, Imani-Ramos T, Trelles-Garcia VP, Bustamante-Soliz DS, Stake JJ. Comparison of clinical characteristics and outcomes of hospitalized patients with seasonal coronavirus infection and COVID-19: a retrospective cohort study. BMC Infect Dis 2022; 22:618. [PMID: 35840902 PMCID: PMC9284965 DOI: 10.1186/s12879-022-07555-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/20/2022] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Unlike SARS-CoV and MERS-C0V, SARS-CoV-2 has the potential to become a recurrent seasonal infection; hence, it is essential to compare the clinical spectrum of COVID-19 to the existent endemic coronaviruses. We conducted a retrospective cohort study of hospitalized patients with seasonal coronavirus (sCoV) infection and COVID-19 to compare their clinical characteristics and outcomes. METHODS A total of 190 patients hospitalized with any documented respiratory tract infection and a positive respiratory viral panel for sCoV from January 1, 2011, to March 31, 2020, were included. Those patients were compared with 190 hospitalized adult patients with molecularly confirmed symptomatic COVID-19 admitted from March 1, 2020, to May 25, 2020. RESULTS Among 190 patients with sCoV infection, the Human Coronavirus-OC93 was the most common coronavirus with 47.4% of the cases. When comparing demographics and baseline characteristics, both groups were of similar age (sCoV: 74 years vs. COVID-19: 69 years) and presented similar proportions of two or more comorbidities (sCoV: 85.8% vs. COVID-19: 81.6%). More patients with COVID-19 presented with severe disease (78.4% vs. 67.9%), sepsis (36.3% vs. 20.5%), and developed ARDS (15.8% vs. 2.6%) compared to patients with sCoV infection. Patients with COVID-19 had an almost fourfold increased risk of in-hospital death than patients with sCoV infection (OR 3.86, CI 1.99-7.49; p < .001). CONCLUSION Hospitalized patients with COVID-19 had similar demographics and baseline characteristics to hospitalized patients with sCoV infection; however, patients with COVID-19 presented with higher disease severity, had a higher case-fatality rate, and increased risk of death than patients with sCoV. Clinical findings alone may not help confirm or exclude the diagnosis of COVID-19 during high acute respiratory illness seasons. The respiratory multiplex panel by PCR that includes SARS-CoV-2 in conjunction with local epidemiological data may be a valuable tool to assist clinicians with management decisions.
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Affiliation(s)
- Guillermo Rodriguez-Nava
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, 355 Ridge Ave, Evanston, IL, 60202, USA.
| | - Goar Egoryan
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, 355 Ridge Ave, Evanston, IL, 60202, USA
| | - Tianyu Dong
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, 355 Ridge Ave, Evanston, IL, 60202, USA
| | - Qishuo Zhang
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, 355 Ridge Ave, Evanston, IL, 60202, USA
| | - Elise Hyser
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, 355 Ridge Ave, Evanston, IL, 60202, USA
| | - Bidhya Poudel
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, 355 Ridge Ave, Evanston, IL, 60202, USA
| | - Maria Adriana Yanez-Bello
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, 355 Ridge Ave, Evanston, IL, 60202, USA
| | | | - Chul Won Chung
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, 355 Ridge Ave, Evanston, IL, 60202, USA
| | - Bimatshu Pyakuryal
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, 355 Ridge Ave, Evanston, IL, 60202, USA
| | - Taraz Imani-Ramos
- Department of Internal Medicine, AMITA Health Saint Joseph Hospital, Chicago, IL, USA
| | | | | | - Jonathan J Stake
- Department of Infection Prevention, AMITA Health Saint Francis Hospital, Evanston, IL, USA
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41
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Otieno JR, Cherry JL, Spiro DJ, Nelson MI, Trovão NS. Origins and Evolution of Seasonal Human Coronaviruses. Viruses 2022; 14:1551. [PMID: 35891531 PMCID: PMC9320361 DOI: 10.3390/v14071551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses. The recombination rate was highest for 229E and OC43 whereas substitutions per recombination event were highest in NL63 and HKU1. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors. 229E may have origins in a bat, camel, or an unsampled intermediate host. HKU1 had the earliest common ancestor (1809-1899) but fell into two distinct clades (genotypes A and B), possibly representing two independent transmission events from murine-origin CoVs that appear to be a single introduction due to large gaps in the sampling of CoVs in animals. In fact, genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.
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Affiliation(s)
- James R. Otieno
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
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42
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The Cellular Characterization of SARS-CoV-2 Spike Protein in Virus-Infected Cells Using the Receptor Binding Domain Binding Specific Human Monoclonal Antibodies. J Virol 2022; 96:e0045522. [PMID: 35727030 PMCID: PMC9278116 DOI: 10.1128/jvi.00455-22] [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] [Indexed: 11/20/2022] Open
Abstract
A human monoclonal antibody panel (PD4, PD5, PD7, SC23, and SC29) was isolated from the B cells of convalescent patients and used to examine the S protein in SARS-CoV-2-infected cells. While all five antibodies bound conformational-specific epitopes within SARS-CoV-2 spike (S) protein, only PD5, PD7, and SC23 were able to bind to the receptor binding domain (RBD). Immunofluorescence microscopy was used to examine the S protein RBD in cells infected with the Singapore isolates SARS-CoV-2/0334 and SARS-CoV-2/1302. The RBD-binders exhibited a distinct cytoplasmic staining pattern that was primarily localized within the Golgi complex and was distinct from the diffuse cytoplasmic staining pattern exhibited by the non-RBD-binders (PD4 and SC29). These data indicated that the S protein adopted a conformation in the Golgi complex that enabled the RBD recognition by the RBD-binders. The RBD-binders also recognized the uncleaved S protein, indicating that S protein cleavage was not required for RBD recognition. Electron microscopy indicated high levels of cell-associated virus particles, and multiple cycle virus infection using RBD-binder staining provided evidence for direct cell-to-cell transmission for both isolates. Although similar levels of RBD-binder staining were demonstrated for each isolate, SARS-CoV-2/1302 exhibited slower rates of cell-to-cell transmission. These data suggest that a conformational change in the S protein occurs during its transit through the Golgi complex that enables RBD recognition by the RBD-binders and suggests that these antibodies can be used to monitor S protein RBD formation during the early stages of infection. IMPORTANCE The SARS-CoV-2 spike (S) protein receptor binding domain (RBD) mediates the attachment of SARS-CoV-2 to the host cell. This interaction plays an essential role in initiating virus infection, and the S protein RBD is therefore a focus of therapeutic and vaccine interventions. However, new virus variants have emerged with altered biological properties in the RBD that can potentially negate these interventions. Therefore, an improved understanding of the biological properties of the RBD in virus-infected cells may offer future therapeutic strategies to mitigate SARS- CoV-2 infection. We used physiologically relevant antibodies that were isolated from the B cells of convalescent COVID-19 patients to monitor the RBD in cells infected with SARS-CoV-2 clinical isolates. These immunological reagents specifically recognize the correctly folded RBD and were used to monitor the appearance of the RBD in SARS-CoV-2-infected cells and identified the site where the RBD first appears.
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43
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Balloux F, Tan C, Swadling L, Richard D, Jenner C, Maini M, van Dorp L. The past, current and future epidemiological dynamic of SARS-CoV-2. OXFORD OPEN IMMUNOLOGY 2022; 3:iqac003. [PMID: 35872966 PMCID: PMC9278178 DOI: 10.1093/oxfimm/iqac003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron variants of concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterized by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunization are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good-circulation of a fifth endemic 'common cold' coronavirus of potentially low virulence, the bad-a situation roughly comparable with seasonal flu, and the ugly-extensive diversification into serotypes with long-term high-level endemicity.
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Affiliation(s)
- François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 138672 Singapore, Singapore
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Damien Richard
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Charlotte Jenner
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Mala Maini
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
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44
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Cohen LE, Spiro DJ, Viboud C. Projecting the SARS-CoV-2 transition from pandemicity to endemicity: Epidemiological and immunological considerations. PLoS Pathog 2022; 18:e1010591. [PMID: 35771775 PMCID: PMC9246171 DOI: 10.1371/journal.ppat.1010591] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In this review, we discuss the epidemiological dynamics of different viral infections to project how the transition from a pandemic to endemic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) might take shape. Drawing from theories of disease invasion and transmission dynamics, waning immunity in the face of viral evolution and antigenic drift, and empirical data from influenza, dengue, and seasonal coronaviruses, we discuss the putative periodicity, severity, and age dynamics of SARS-CoV-2 as it becomes endemic. We review recent studies on SARS-CoV-2 epidemiology, immunology, and evolution that are particularly useful in projecting the transition to endemicity and highlight gaps that warrant further research.
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Affiliation(s)
- Lily E. Cohen
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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45
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Metcalf CJE, Paireau J, O'Driscoll M, Pivette M, Hubert B, Pontais I, Nickbakhsh S, Cummings DAT, Cauchemez S, Salje H. Comparing the age and sex trajectories of SARS-CoV-2 morbidity and mortality with other respiratory pathogens. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211498. [PMID: 35719888 PMCID: PMC9198511 DOI: 10.1098/rsos.211498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/27/2022] [Indexed: 05/03/2023]
Abstract
Comparing age and sex differences in SARS-CoV-2 hospitalization and mortality with MERS-CoV, seasonal coronaviruses, influenza and other health outcomes opens the way to generating hypotheses as to underlying mechanisms driving disease risk. Using 60-year-olds as a reference age group, we find that relative rates of hospitalization and mortality associated with the emergent coronaviruses are lower during childhood and start to increase earlier (around puberty) as compared with influenza and seasonal coronaviruses. The changing distribution of disease risk by age for emerging pathogens appears to broadly track the gradual deterioration of the immune system (immunosenescence), which starts around puberty. By contrast, differences in severe disease risk by age from endemic pathogens are more decoupled from the immune ageing process. Intriguingly, age-specific sex differences in hospitalizations are largely similar across endemic and emerging infections. We discuss potential mechanisms that may be associated with these patterns.
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Affiliation(s)
- C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - Juliette Paireau
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, CNRS, UMR2000, Paris, France
- Santé publique France, French national public health agency, Saint Maurice, France
| | | | - Mathilde Pivette
- Santé publique France, French national public health agency, Saint Maurice, France
| | - Bruno Hubert
- Santé publique France, French national public health agency, Saint Maurice, France
| | - Isabelle Pontais
- Santé publique France, French national public health agency, Saint Maurice, France
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Sema Nickbakhsh
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, CNRS, UMR2000, Paris, France
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK
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46
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Rodríguez Díaz C, Lafuente-Gómez N, Coutinho C, Pardo D, Alarcón-Iniesta H, López-Valls M, Coloma R, Milán-Rois P, Domenech M, Abreu M, Cantón R, Galán JC, Bocanegra R, Campos LA, Miranda R, Castellanos M, Somoza Á. Development of colorimetric sensors based on gold nanoparticles for SARS-CoV-2 RdRp, E and S genes detection. Talanta 2022; 243:123393. [PMID: 35325745 PMCID: PMC8923713 DOI: 10.1016/j.talanta.2022.123393] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/20/2022]
Abstract
We present a fast, reliable and easy to scale-up colorimetric sensor based on gold nanoparticles (AuNPs) to detect the sequences coding for the RdRp, E, and S proteins of SARS-CoV-2. The optimization of the system (so-called “the sensor”) includes the evaluation of different sizes of nanoparticles, sequences of oligonucleotides and buffers. It is stable for months without any noticeable decrease in its activity, allowing the detection of SARS-CoV-2 sequences by the naked eye in 15 min. The efficiency and selectivity of detection, in terms of significative colorimetric changes in the solution upon target recognition, are qualitatively (visually) and quantitatively (absorbance measurements) assessed using synthetic samples and samples derived from infected cells and patients. Furthermore, an easy and affordable amplification approach is implemented to increase the system's sensitivity for detecting high and medium viral loads (≥103 - 104 viral RNA copies/μl) in patient samples. The whole process (amplification and detection) takes 2.5 h. Due to the ease of use, stability and minimum equipment requirements, the proposed approach can be a valuable tool for the detection of SARS-CoV-2 at facilities with limited resources.
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47
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Metcalf CJE, Paireau J, O'Driscoll M, Pivette M, Hubert B, Pontais I, Nickbakhsh S, Cummings DAT, Cauchemez S, Salje H. Comparing the age and sex trajectories of SARS-CoV-2 morbidity and mortality with other respiratory pathogens. ROYAL SOCIETY OPEN SCIENCE 2022. [PMID: 35719888 DOI: 10.6084/m9.figshare.c.6032507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Comparing age and sex differences in SARS-CoV-2 hospitalization and mortality with MERS-CoV, seasonal coronaviruses, influenza and other health outcomes opens the way to generating hypotheses as to underlying mechanisms driving disease risk. Using 60-year-olds as a reference age group, we find that relative rates of hospitalization and mortality associated with the emergent coronaviruses are lower during childhood and start to increase earlier (around puberty) as compared with influenza and seasonal coronaviruses. The changing distribution of disease risk by age for emerging pathogens appears to broadly track the gradual deterioration of the immune system (immunosenescence), which starts around puberty. By contrast, differences in severe disease risk by age from endemic pathogens are more decoupled from the immune ageing process. Intriguingly, age-specific sex differences in hospitalizations are largely similar across endemic and emerging infections. We discuss potential mechanisms that may be associated with these patterns.
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Affiliation(s)
- C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - Juliette Paireau
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, CNRS, UMR2000, Paris, France
- Santé publique France, French national public health agency, Saint Maurice, France
| | | | - Mathilde Pivette
- Santé publique France, French national public health agency, Saint Maurice, France
| | - Bruno Hubert
- Santé publique France, French national public health agency, Saint Maurice, France
| | - Isabelle Pontais
- Santé publique France, French national public health agency, Saint Maurice, France
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, CNRS, UMR2000, Paris, France
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK
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48
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Sechan F, Grobben M, Edridge AWD, Jebbink MF, Loens K, Ieven M, Goossens H, van Hemert-Glaubitz S, van Gils MJ, van der Hoek L. Atypical Antibody Dynamics During Human Coronavirus HKU1 Infections. Front Microbiol 2022; 13:853410. [PMID: 35572703 PMCID: PMC9093712 DOI: 10.3389/fmicb.2022.853410] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/10/2022] [Indexed: 11/29/2022] Open
Abstract
Human coronavirus HKU1 (HCoV-HKU1) is one of the four endemic coronaviruses. It has been suggested that there is a difference in incidence, with PCR-confirmed HCoV-NL63 and HCoV-OC43 infections occurring more commonly, whereas HCoV-HKU1 is the least seen. Lower incidence of HCoV-HKU1 infection has also been observed in serological studies. The current study aimed to investigate antibody dynamics during PCR-confirmed HCoV-HKU1 infections using serum collected during infection and 1 month later. We expressed a new HCoV-HKU1 antigen consisting of both the linker and carboxy-terminal domain of the viral nucleocapsid protein and implemented it in ELISA. We also applied a spike-based Luminex assay on serum samples from PCR-confirmed infections by the four endemic HCoVs. At least half of HCoV-HKU1-infected subjects consistently showed no antibody rise via either assay, and some subjects even exhibited substantial antibody decline. Investigation of self-reported symptoms revealed that HCoV-HKU1-infected subjects rated their illness milder than subjects infected by other HCoVs. In conclusion, HCoV-HKU1 infections reported in this study displayed atypical antibody dynamics and milder symptoms when compared to the other endemic HCoVs.
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Affiliation(s)
- Ferdyansyah Sechan
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Marloes Grobben
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Arthur W D Edridge
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Katherine Loens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerpen, Belgium.,Department of Microbiology, University Hospital Antwerp, Edegem, Belgium
| | - Margareta Ieven
- Department of Microbiology, University Hospital Antwerp, Edegem, Belgium
| | - Herman Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerpen, Belgium.,Department of Microbiology, University Hospital Antwerp, Edegem, Belgium
| | - Susan van Hemert-Glaubitz
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, Utrecht, Netherlands
| | - Marit J van Gils
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
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49
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Tomaszewski T, Gurtler V, Caetano-Anollés K, Caetano-Anollés G. The emergence of SARS-CoV-2 variants of concern in Australia by haplotype coalescence reveals a continental link to COVID-19 seasonality. METHODS IN MICROBIOLOGY 2022; 50:233-268. [PMID: 38013929 PMCID: PMC9110064 DOI: 10.1016/bs.mim.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
SARS-CoV-2 continues to evolve, even after implementation of public-wide vaccination, as can be observed by an increasing number of mutations over time. Compared to responses by the United States and European countries, the disease mitigation strategies employed by the Australian government have been swift and effective. This provides a unique opportunity to study the emergence of variants of concern (VOCs) at many latitude levels in a country that has been able to control infection for the majority of the pandemic. In the present study, we explored the occurrence and accumulation of major mutations typical of VOCs in different regions of Australia and the effects that latitude has on the establishment of VOC-induced disease. We also studied the constellation of mutations characteristic of VOCs to determine if the mutation sets acted as haplotypes. Our goal was to explore processes behind the emergence of VOCs as the viral disease progresses towards becoming endemic. Most reported COVID-19 cases were in largest cities located within a -30°S to - 50°S latitude corridor previously identified to be associated with seasonal behavior. Accumulation plots of individual amino acid variants of major VOCs showed that the first major haplotypes reported worldwide were also present in Australia. A classification of accumulation plots revealed the existence of 18 additional haplotypes associated with VOCs alpha, delta and omicron. Core mutant constellations for these VOCs and curve overlaps for variants in each set of haplotypes demonstrated significant decoupling patterns, suggesting processes of emergence. Finally, construction of a "haplotype network" that describes the viral population landscape of Australia throughout the COVID-19 pandemic revealed significant and unanticipated seasonal patterns of emergence and diversification. These results provide a unique window into our evolutionary understanding of a human pathogen of great significance. They may guide future research into mitigation and prediction strategies for future VOCs.
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Affiliation(s)
- Tre Tomaszewski
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | | | | | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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50
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Gomes MGM, Ferreira MU, Corder RM, King JG, Souto-Maior C, Penha-Gonçalves C, Gonçalves G, Chikina M, Pegden W, Aguas R. Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold. J Theor Biol 2022; 540:111063. [PMID: 35189135 PMCID: PMC8855661 DOI: 10.1016/j.jtbi.2022.111063] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/21/2022]
Abstract
Individual variation in susceptibility and exposure is subject to selection by natural infection, accelerating the acquisition of immunity, and reducing herd immunity thresholds and epidemic final sizes. This is a manifestation of a wider population phenomenon known as "frailty variation". Despite theoretical understanding, public health policies continue to be guided by mathematical models that leave out considerable variation and as a result inflate projected disease burdens and overestimate the impact of interventions. Here we focus on trajectories of the coronavirus disease (COVID-19) pandemic in England and Scotland until November 2021. We fit models to series of daily deaths and infer relevant epidemiological parameters, including coefficients of variation and effects of non-pharmaceutical interventions which we find in agreement with independent empirical estimates based on contact surveys. Our estimates are robust to whether the analysed data series encompass one or two pandemic waves and enable projections compatible with subsequent dynamics. We conclude that vaccination programmes may have contributed modestly to the acquisition of herd immunity in populations with high levels of pre-existing naturally acquired immunity, while being crucial to protect vulnerable individuals from severe outcomes as the virus becomes endemic.
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Affiliation(s)
- M Gabriela M Gomes
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK; Centro de Matemática e Aplicações, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marcelo U Ferreira
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal
| | - Rodrigo M Corder
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jessica G King
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Caetano Souto-Maior
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Guilherme Gonçalves
- Unidade Multidisciplinar de Investigação Biomédica, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh, Pittburgh, PA, USA
| | - Wesley Pegden
- Department of Mathematical Sciences, Carnegie Mellon University, Pittburgh, PA, USA
| | - Ricardo Aguas
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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