1
|
Tang CY, Li T, Haynes TA, McElroy JA, Ritter D, Hammer RD, Sampson C, Webby R, Hang J, Wan XF. Rural populations facilitated early SARS-CoV-2 evolution and transmission in Missouri, USA. NPJ VIRUSES 2023; 1:7. [PMID: 38186942 PMCID: PMC10769004 DOI: 10.1038/s44298-023-00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/20/2023] [Indexed: 01/09/2024]
Abstract
In the United States, rural populations comprise 60 million individuals and suffered from high COVID-19 disease burdens. Despite this, surveillance efforts are biased toward urban centers. Consequently, how rurally circulating SARS-CoV-2 viruses contribute toward emerging variants remains poorly understood. In this study, we aim to investigate the role of rural communities in the evolution and transmission of SARS-CoV-2 during the early pandemic. We collected 544 urban and 435 rural COVID-19-positive respiratory specimens from an overall vaccine-naïve population in Southwest Missouri between July and December 2020. Genomic analyses revealed 53 SARS-CoV-2 Pango lineages in our study samples, with 14 of these lineages identified only in rural samples. Phylodynamic analyses showed that frequent bi-directional diffusions occurred between rural and urban communities in Southwest Missouri, and that four out of seven Missouri rural-origin lineages spread globally. Further analyses revealed that the nucleocapsid protein (N):R203K/G204R paired substitutions, which were detected disproportionately across multiple Pango lineages, were more associated with urban than rural sequences. Positive selection was detected at N:204 among rural samples but was not evident in urban samples, suggesting that viruses may encounter distinct selection pressures in rural versus urban communities. This study demonstrates that rural communities may be a crucial source of SARS-CoV-2 evolution and transmission, highlighting the need to expand surveillance and resources to rural populations for COVID-19 mitigation.
Collapse
Affiliation(s)
- Cynthia Y. Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tricia A. Haynes
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jane A. McElroy
- Family and Community Medicine, University of Missouriś, Columbia, MO, USA
| | - Detlef Ritter
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | - Richard D. Hammer
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | | | - Richard Webby
- Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA
| |
Collapse
|
2
|
Chen HF, Wang WJ, Chen CY, Chang WC, Hsueh PR, Peng SL, Wu CS, Chen Y, Huang HY, Shen WJ, Wang SC, Hung MC. The natural tannins oligomeric proanthocyanidins and punicalagin are potent inhibitors of infection by SARS-CoV-2. eLife 2023; 12:e84899. [PMID: 37642993 PMCID: PMC10465125 DOI: 10.7554/elife.84899] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 07/17/2023] [Indexed: 08/31/2023] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) pandemic continues to infect people worldwide. While the vaccinated population has been increasing, the rising breakthrough infection persists in the vaccinated population. For living with the virus, the dietary guidelines to prevent virus infection are worthy of and timely to develop further. Tannic acid has been demonstrated to be an effective inhibitor of coronavirus and is under clinical trial. Here we found that two other members of the tannins family, oligomeric proanthocyanidins (OPCs) and punicalagin, are also potent inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection with different mechanisms. OPCs and punicalagin showed inhibitory activity against omicron variants of SARS-CoV-2 infection. The water extractant of the grape seed was rich in OPCs and also exhibited the strongest inhibitory activities for viral entry of wild-type and other variants in vitro. Moreover, we evaluated the inhibitory activity of grape seed extractants (GSE) supplementation against SARS-CoV-2 viral entry in vivo and observed that serum samples from the healthy human subjects had suppressive activity against different variants of SARS-CoV-2 Vpp infection after taking GSE capsules. Our results suggest that natural tannins acted as potent inhibitors against SARS-CoV-2 infection, and GSE supplementation could serve as healthy food for infection prevention.
Collapse
Affiliation(s)
- Hsiao-Fan Chen
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
| | - Wei-Jan Wang
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
- Department of Biological Science and Technology, College of Life Sciences, China Medical UniversityTaichungTaiwan
| | - Chung-Yu Chen
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
| | - Wei-Chao Chang
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichungTaiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical UniversityTaichungTaiwan
| | - Shin-Lei Peng
- Department of Biomedical Imaging and Radiological Science, China Medical UniversityTaichungTaiwan
- Neuroscience and Brain Disease Center, China Medical UniversityTaichungTaiwan
| | - Chen-Shiou Wu
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
| | - Yeh Chen
- Department of Biological Science and Technology, College of Life Sciences, China Medical UniversityTaichungTaiwan
- Institute of New Drug Development, China Medical UniversityTaichungTaiwan
| | - Hsin-Yu Huang
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
| | - Wan-Jou Shen
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichungTaiwan
- Cancer Biology and Precision Therapeutics Center, China Medical UniversityTaichungTaiwan
- Department of Biotechnology, Asia UniversityTaichungTaiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichungTaiwan
- Cancer Biology and Precision Therapeutics Center, China Medical UniversityTaichungTaiwan
- Department of Biotechnology, Asia UniversityTaichungTaiwan
- Institute of Biochemistry and Molecular Biology, China Medical UniversityTaichungTaiwan
| |
Collapse
|
3
|
Bufetova A, Vishnyakov A, Gorelov E, Leushina E, Utenkova E. Vaccination of children against COVID-19: foreign experience (literature review). CHILDREN INFECTIONS 2023. [DOI: 10.22627/2072-8107-2023-22-1-45-49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
|
4
|
Salvatore PP, Lee CC, Sleweon S, McCormick DW, Nicolae L, Knipe K, Dixon T, Banta R, Ogle I, Young C, Dusseau C, Salmonson S, Ogden C, Godwin E, Ballom T, Rhodes T, Wynn NT, David E, Bessey TK, Kim G, Suppiah S, Tamin A, Harcourt JL, Sheth M, Lowe L, Browne H, Tate JE, Kirking HL, Hagan LM. Transmission potential of vaccinated and unvaccinated persons infected with the SARS-CoV-2 Delta variant in a federal prison, July-August 2021. Vaccine 2023; 41:1808-1818. [PMID: 36572604 PMCID: PMC9744684 DOI: 10.1016/j.vaccine.2022.11.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/19/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND The extent to which vaccinated persons who become infected with SARS-CoV-2 contribute to transmission is unclear. During a SARS-CoV-2 Delta variant outbreak among incarcerated persons with high vaccination rates in a federal prison, we assessed markers of viral shedding in vaccinated and unvaccinated persons. METHODS Consenting incarcerated persons with confirmed SARS-CoV-2 infection provided mid-turbinate nasal specimens daily for 10 consecutive days and reported symptom data via questionnaire. Real-time reverse transcription-polymerase chain reaction (RT-PCR), viral whole genome sequencing, and viral culture was performed on these nasal specimens. Duration of RT-PCR positivity and viral culture positivity was assessed using survival analysis. RESULTS A total of 957 specimens were provided by 93 participants, of whom 78 (84 %) were vaccinated and 17 (16 %) were unvaccinated. No significant differences were detected in duration of RT-PCR positivity among vaccinated participants (median: 13 days) versus those unvaccinated (median: 13 days; p = 0.50), or in duration of culture positivity (medians: 5 days and 5 days; p = 0.29). Among vaccinated participants, overall duration of culture positivity was shorter among Moderna vaccine recipients versus Pfizer (p = 0.048) or Janssen (p = 0.003) vaccine recipients. In post-hoc analyses, Moderna vaccine recipients demonstrated significantly shorter duration of culture positivity compared to unvaccinated participants (p = 0.02). When restricted to participants without reported prior infection, the difference between Moderna vaccine recipients and unvaccinated participants was more pronounced (medians: 3 days and 6 days, p = 0.002). CONCLUSIONS Infectious periods for vaccinated and unvaccinated persons who become infected with SARS-CoV-2 are similar and can be highly variable, though some vaccinated persons are likely infectious for shorter durations. These findings are critically important, especially in congregate settings where viral transmission can lead to large outbreaks. In such settings, clinicians and public health practitioners should consider vaccinated, infected persons to be no less infectious than unvaccinated, infected persons.
Collapse
Affiliation(s)
- Phillip P Salvatore
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States; United States Public Health Service, Rockville, MD, United States.
| | - Christine C Lee
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States; Laboratory Leadership Service, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sadia Sleweon
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - David W McCormick
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States; United States Public Health Service, Rockville, MD, United States; Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lavinia Nicolae
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Kristen Knipe
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tom Dixon
- Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - Robert Banta
- United States Public Health Service, Rockville, MD, United States; Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - Isaac Ogle
- United States Public Health Service, Rockville, MD, United States; Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - Cristen Young
- Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - Charles Dusseau
- United States Public Health Service, Rockville, MD, United States; Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - Shawn Salmonson
- Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - Charles Ogden
- United States Public Health Service, Rockville, MD, United States; Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - Eric Godwin
- Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - TeCora Ballom
- United States Public Health Service, Rockville, MD, United States; Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - Tara Rhodes
- United States Public Health Service, Rockville, MD, United States; Bureau of Prisons, U.S. Department of Justice, Washington, DC, United States
| | - Nhien Tran Wynn
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Ebenezer David
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Theresa K Bessey
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gimin Kim
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Suganthi Suppiah
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Azaibi Tamin
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jennifer L Harcourt
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Mili Sheth
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Luis Lowe
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Hannah Browne
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jacqueline E Tate
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States; United States Public Health Service, Rockville, MD, United States
| | - Hannah L Kirking
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States; United States Public Health Service, Rockville, MD, United States
| | - Liesl M Hagan
- COVID-19 Pandemic Response Team, Centers for Disease Control and Prevention, Atlanta, GA, United States
| |
Collapse
|
5
|
Muacevic A, Adler JR, Taw MJ, Sharma A, Rajbongshi G, Chamuah K, Henbi N, Barman RK, Chingtham S, Brahma D, Sarmah K, Baruah P, Nath K, Choudhury PD, Mazumder D, Sarmah A, Sharma A, Hazarika B, Choudhury MK, Baishya AC. Understanding the Demographic, Clinical, and Real-Time Polymerase Chain Reaction Profiles of COVID-19 Patients in a Tertiary Care Hospital in Northeast India. Cureus 2023; 15:e35426. [PMID: 36860823 PMCID: PMC9970726 DOI: 10.7759/cureus.35426] [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] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Introduction and aims The demographic and clinical profile and dynamics of real-time polymerase chain reaction (RT-PCR) in coronavirus disease 2019 (COVID-19) patients are not well understood. The study aimed to analyze the demographic, clinical, and RT-PCR profiles of COVID-19 patients. Methodology The study was a retrospective, observational study conducted at a COVID-19 care facility, and the study period was from April 2020 to March 2021. Patients with laboratory-confirmed COVID-19 by real-time polymerase chain reaction (RT-PCR) were enrolled in the study. Patients with incomplete details or with only single PCR tests were excluded. Demographic and clinical details and the results of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RT-PCR collected at different time points were retrieved from the records. The statistical software Minitab version 17.1.0 package (Minitab, LLC, State College, PA, USA) and Rstudio version 1.3.959 (Rstudio, Boston, MA, USA) were used for the statistical analysis. Results The mean duration from symptom onset to the last positive RT-PCR was 14.2 ± 4.2 days. The proportions of positive RT-PCR tests were 100%, 40.6%, 7.5%, and 0% at the end of the first, second, third, and fourth weeks of illness. The median duration of days to first negative RT-PCR in the asymptomatic patients was 8 ± 4 days, and 88.2% of asymptomatic patients were RT-PCR-negative within 14 days. A total of 16 symptomatic patients had prolonged positive test results even after three weeks of symptom onset. Older patients were associated with prolonged RT-PCR positivity. Conclusion This study revealed that the average period of RT-PCR positivity from the onset of symptoms is >2 weeks in symptomatic COVID-19 patients. Prolonged observation in the elderly population and repeat RT-PCR before discharge or discontinuation of quarantine is required.
Collapse
|
6
|
Ahmed MIM, Diepers P, Janke C, Plank M, Eser TM, Rubio-Acero R, Fuchs A, Baranov O, Castelletti N, Kroidl I, Olbrich L, Bauer B, Wang D, Prelog M, Liese JG, Reinkemeyer C, Hoelscher M, Steininger P, Überla K, Wieser A, Geldmacher C. Enhanced Spike-specific, but attenuated Nucleocapsid-specific T cell responses upon SARS-CoV-2 breakthrough versus non-breakthrough infections. Front Immunol 2022; 13:1026473. [PMID: 36582222 PMCID: PMC9792977 DOI: 10.3389/fimmu.2022.1026473] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 vaccine breakthrough infections frequently occurred even before the emergence of Omicron variants. Yet, relatively little is known about the impact of vaccination on SARS-CoV-2-specific T cell and antibody response dynamics upon breakthrough infection. We have therefore studied the dynamics of CD4 and CD8 T cells targeting the vaccine-encoded Spike and the non-encoded Nucleocapsid antigens during breakthrough infections (BTI, n=24) and in unvaccinated control infections (non-BTI, n=30). Subjects with vaccine breakthrough infection had significantly higher CD4 and CD8 T cell responses targeting the vaccine-encoded Spike during the first and third/fourth week after PCR diagnosis compared to non-vaccinated controls, respectively. In contrast, CD4 T cells targeting the non-vaccine encoded Nucleocapsid antigen were of significantly lower magnitude in BTI as compared to non-BTI. Hence, previous vaccination was linked to enhanced T cell responses targeting the vaccine-encoded Spike antigen, while responses against the non-vaccine encoded Nucleocapsid antigen were significantly attenuated.
Collapse
Affiliation(s)
- Mohamed Ibraheem Mahmoud Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Paulina Diepers
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Christian Janke
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Michael Plank
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Tabea M. Eser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Anna Fuchs
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Olga Baranov
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany,Oxford Vaccine Group, Department of Paediatrics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Bernadette Bauer
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Danni Wang
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Martina Prelog
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Johannes G. Liese
- Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Christina Reinkemeyer
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Philipp Steininger
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Klaus Überla
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany,*Correspondence: Christof Geldmacher,
| |
Collapse
|
7
|
Johnson KE, Pasco R, Woody S, Lachmann M, Johnson-Leon M, Bhavnani D, Klima J, Paltiel AD, Fox SJ, Meyers LA. Optimizing COVID-19 testing strategies on college campuses: evaluation of the health and economic costs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.12.04.22283074. [PMID: 36523405 PMCID: PMC9753781 DOI: 10.1101/2022.12.04.22283074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Colleges and universities in the US struggled to provide safe in-person education throughout the COVID-19 pandemic. Testing coupled with isolation is a nimble intervention strategy that can be tailored to mitigate health and economic costs, as the virus and our arsenal of medical countermeasures continue to evolve. We developed a decision-support tool to aid in the design of university-based testing strategies using a mathematical model of SARS-CoV-2 transmission. Applying this framework to a large public university reopening in the fall of 2021 with a 60% student vaccination rate, we find that the optimal strategy, in terms of health and economic costs, is twice weekly antigen testing of all students. This strategy provides a 95% guarantee that, throughout the fall semester, case counts would not exceed the CDC's original high transmission threshold of 100 cases per 100k persons over 7 days. As the virus and our medical armament continue to evolve, testing will remain a flexible tool for managing risks and keeping campuses open. We have implemented this model as an online tool to facilitate the design of testing strategies that adjust for COVID-19 conditions, university-specific parameters, and institutional goals.
Collapse
Affiliation(s)
- Kaitlyn E. Johnson
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- The Pandemic Prevention Institute, The Rockefeller Foundation, New York, New York
| | - Remy Pasco
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Spencer Woody
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Michael Lachmann
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Maureen Johnson-Leon
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Darlene Bhavnani
- Department of Population Health, Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Jessica Klima
- Office of the Vice President for Research, The University of Texas at Austin, Austin, Texas
| | - A. David Paltiel
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut
| | - Spencer J. Fox
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Epidemiology & Biostatistics, The University of Georgia, Athens, Georgia
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| |
Collapse
|
8
|
Zhu J, Li Y, Liang J, Mubareka S, Slutsky AS, Zhang H. The Potential Protective Role of GS-441524, a Metabolite of the Prodrug Remdesivir, in Vaccine Breakthrough SARS-CoV-2 Infections. INTENSIVE CARE RESEARCH 2022; 2:49-60. [PMID: 36407474 PMCID: PMC9645326 DOI: 10.1007/s44231-022-00021-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Cases of vaccine breakthrough, especially in variants of concern (VOCs) infections, are emerging in coronavirus disease (COVID-19). Due to mutations of structural proteins (SPs) (e.g., Spike proteins), increased transmissibility and risk of escaping from vaccine-induced immunity have been reported amongst the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Remdesivir was the first to be granted emergency use authorization but showed little impact on survival in patients with severe COVID-19. Remdesivir is a prodrug of the nucleoside analogue GS-441524 which is converted into the active nucleotide triphosphate to disrupt viral genome of the conserved non-structural proteins (NSPs) and thus block viral replication. GS-441524 exerts a number of pharmacological advantages over Remdesivir: (1) it needs fewer conversions for bioactivation to nucleotide triphosphate; (2) it requires only nucleoside kinase, while Remdesivir requires several hepato-renal enzymes, for bioactivation; (3) it is a smaller molecule and has a potency for aerosol and oral administration; (4) it is less toxic allowing higher pulmonary concentrations; (5) it is easier to be synthesized. The current article will focus on the discussion of interactions between GS-441524 and NSPs of VOCs to suggest potential application of GS-441524 in breakthrough SARS-CoV-2 infections. Supplementary Information The online version contains supplementary material available at 10.1007/s44231-022-00021-4.
Collapse
Affiliation(s)
- JiaYi Zhu
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON Canada
- Department of Physiology, University of Toronto, Toronto, ON Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Yuchong Li
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON Canada
- The State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jady Liang
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON Canada
- Department of Physiology, University of Toronto, Toronto, ON Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
- Department of Medical Microbiology and Infectious Disease, Sunnybrook Health Science Centre, Toronto, ON Canada
| | - Arthur S. Slutsky
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON Canada
- The State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, ON Canada
| | - Haibo Zhang
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON Canada
- Department of Physiology, University of Toronto, Toronto, ON Canada
- The State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, ON Canada
- Department of Anaesthesiology and Pain Medicine, University of Toronto, Toronto, ON Canada
| |
Collapse
|
9
|
The Receptor Binding Domain of SARS-CoV-2 Lambda Variant Has a Better Chance Than the Delta Variant in Evading BNT162b2 COVID-19 mRNA Vaccine-Induced Humoral Immunity. Int J Mol Sci 2022; 23:ijms231911325. [PMID: 36232627 PMCID: PMC9569855 DOI: 10.3390/ijms231911325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/07/2022] [Accepted: 09/20/2022] [Indexed: 12/04/2022] Open
Abstract
The SARS-CoV-2 Delta and Lambda variants had been named variants of concern (VOC) and variants of interest (VOI), respectively, by the World Health Organization (WHO). Both variants have two mutations in the spike receptor binding domain (RBD) region, with L452R and T478K mutations in the Delta variant, and L452Q and F490S mutations in the Lambda variant. We used surface plasmon resonance (SPR)-based technology to evaluate the effect of these mutations on human angiotensin-converting enzyme 2 (ACE2) and Bamlanivimab binding. The affinity for the RBD ligand, ACE2, of the Delta RBD is approximately twice as strong as that of the wild type RBD, an increase that accounts for the increased infectivity of the Delta variant. On the other hand, in spite of its amino acid changes, the Lambda RBD has similar affinity to ACE2 as the wild type RBD. The protective anti-wild type RBD antibody Bamlanivimab binds very poorly to the Delta RBD and not at all to the Lambda RBD. Nevertheless, serum antibodies from individuals immunized with the BNT162b2 vaccine were found to bind well to the Delta RBD, but less efficiently to the Lambda RBD in contrast. As a result, the blocking ability of ACE2 binding by serum antibodies was decreased more by the Lambda than the Delta RBD. Titers of sera from BNT162b2 mRNA vaccinated individuals dropped 3-fold within six months of vaccination regardless of whether the target RBD was wild type, Delta or Lambda. This may account partially for the fall off with time in the protective effect of vaccines against any variant.
Collapse
|
10
|
Vass WB, Lednicky JA, Shankar SN, Fan ZH, Eiguren-Fernandez A, Wu CY. Viable SARS-CoV-2 Delta variant detected in aerosols in a residential setting with a self-isolating college student with COVID-19. JOURNAL OF AEROSOL SCIENCE 2022; 165:106038. [PMID: 35774447 PMCID: PMC9217630 DOI: 10.1016/j.jaerosci.2022.106038] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 05/08/2023]
Abstract
The B.1.617.2 (Delta) variant of SARS-CoV-2 emerged in India in October of 2020 and spread widely to over 145 countries, comprising over 99% of genome sequence-confirmed virus in COVID-19 cases of the United States (US) by September 2021. The rise in COVID-19 cases due to the Delta variant coincided with a return to in-person school attendance, straining COVID-19 mitigation plans implemented by educational institutions. Some plans required sick students to self-isolate off-campus, resulting in an unintended consequence: exposure of co-inhabitants of dwellings used by the sick person during isolation. We assessed air and surface samples collected from the bedroom of a self-isolating university student with mild COVID-19 for the presence of SARS-CoV-2. That virus' RNA was detected by real-time reverse-transcription quantitative polymerase chain reaction (rRT-qPCR) in air samples from both an isolation bedroom and a distal, non-isolation room of the same dwelling. SARS-CoV-2 was detected and viable virus was isolated in cell cultures from aerosol samples as well as from the surface of a mobile phone. Genomic sequencing revealed that the virus was a Delta variant SARS-CoV-2 strain. Taken together, the results of this work confirm the presence of viable SARS-CoV-2 within a residential living space of a person with COVID-19 and show potential for transportation of virus-laden aerosols beyond a designated isolation suite to other areas of a single-family home.
Collapse
Affiliation(s)
- William B Vass
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - John A Lednicky
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Sripriya Nannu Shankar
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Z Hugh Fan
- Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL, 32611, USA
- Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | | | - Chang-Yu Wu
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| |
Collapse
|
11
|
Langel SN, Johnson S, Martinez CI, Tedjakusuma SN, Peinovich N, Dora EG, Kuehl PJ, Irshad H, Barrett EG, Werts A, Tucker SN. Adenovirus type 5 SARS-CoV-2 vaccines delivered orally or intranasally reduced disease severity and transmission in a hamster model. Sci Transl Med 2022; 14:eabn6868. [PMID: 35511920 PMCID: PMC9097881 DOI: 10.1126/scitranslmed.abn6868] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/27/2022] [Indexed: 01/07/2023]
Abstract
Transmission-blocking strategies that slow the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and protect against coronavirus disease 2019 (COVID-19) are needed. We have developed an orally delivered adenovirus type 5-vectored SARS-CoV-2 vaccine candidate that expresses the spike protein. Here, we demonstrated that hamsters vaccinated by the oral or intranasal route had robust and cross-reactive antibody responses. We then induced a postvaccination infection by inoculating vaccinated hamsters with SARS-CoV-2. Orally or intranasally vaccinated hamsters had decreased viral RNA and infectious virus in the nose and lungs and experienced less lung pathology compared to mock-vaccinated hamsters after SARS-CoV-2 challenge. Naïve hamsters exposed in a unidirectional air flow chamber to mucosally vaccinated, SARS-CoV-2-infected hamsters also had lower nasal swab viral RNA and exhibited fewer clinical symptoms than control animals, suggesting that the mucosal route reduced viral transmission. The same platform encoding the SARS-CoV-2 spike and nucleocapsid proteins elicited mucosal cross-reactive SARS-CoV-2-specific IgA responses in a phase 1 clinical trial (NCT04563702). Our data demonstrate that mucosal immunization is a viable strategy to decrease SARS-CoV-2 disease and airborne transmission.
Collapse
Affiliation(s)
- Stephanie N. Langel
- Duke Center for Human Systems Immunology and Department of Surgery, Durham, NC 27710, USA
| | | | | | | | | | | | - Philip J. Kuehl
- Lovelace Biomedical Research Institute, Albuquerque, NM 87108, USA
| | - Hammad Irshad
- Lovelace Biomedical Research Institute, Albuquerque, NM 87108, USA
| | | | - Adam Werts
- Lovelace Biomedical Research Institute, Albuquerque, NM 87108, USA
| | | |
Collapse
|
12
|
Williams A, Zhan CG. Fast Prediction of Binding Affinities of SARS-CoV-2 Spike Protein and Its Mutants with Antibodies through Intermolecular Interaction Modeling-Based Machine Learning. J Phys Chem B 2022; 126:5194-5206. [PMID: 35817617 PMCID: PMC9301770 DOI: 10.1021/acs.jpcb.2c02123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Indexed: 11/30/2022]
Abstract
Since the introduction of the novel SARS-CoV-2 virus (COVID-19) in late 2019, various new variants have appeared with mutations that confer resistance to the vaccines and monoclonal antibodies that were developed in response to the wild-type virus. As we continue through the pandemic, an accurate and efficient methodology is needed to help predict the effects certain mutations will have on both our currently produced therapeutics and those that are in development. Using published cryo-electron microscopy and X-ray crystallography structures of the spike receptor binding domain region with currently known antibodies, in the present study, we created and cross-validated an intermolecular interaction modeling-based multi-layer perceptron machine learning approach that can accurately predict the mutation-caused shifts in the binding affinity between the spike protein (wild-type or mutant) and various antibodies. This validated artificial intelligence (AI) model was used to predict the binding affinity (Kd) of reported SARS-CoV-2 antibodies with various variants of concern, including the most recently identified "Deltamicron" (or "Deltacron") variant. This AI model may be employed in the future to predict the Kd of developed novel antibody therapeutics to overcome the challenging antibody resistance issue and develop structural bases for the effects of both current and new mutants of the spike protein. In addition, the similar AI strategy and approach based on modeling of the intermolecular interactions may be useful in development of machine learning models predicting binding affinities for other protein-protein binding systems, including other antibodies binding with their antigens.
Collapse
Affiliation(s)
- Alexander
H. Williams
- Molecular
Modeling and Biopharmaceutical Center, University
of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Chang-Guo Zhan
- Molecular
Modeling and Biopharmaceutical Center, University
of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| |
Collapse
|
13
|
Effect of vaccination on household transmission of SARS-CoV-2 Delta variant of concern. Nat Commun 2022; 13:3764. [PMID: 35773247 PMCID: PMC9244879 DOI: 10.1038/s41467-022-31494-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Effective vaccines protect individuals by not only reducing the susceptibility to infection, but also reducing the infectiousness of breakthrough infections in vaccinated cases. To disentangle the vaccine effectiveness against susceptibility to infection (VES) and vaccine effectiveness against infectiousness (VEI), we took advantage of Danish national data comprising 24,693 households with a primary case of SARS-CoV-2 infection (Delta Variant of Concern, 2021) including 53,584 household contacts. In this setting, we estimated VES as 61% (95%-CI: 59-63), when the primary case was unvaccinated, and VEI as 31% (95%-CI: 26-36), when the household contact was unvaccinated. Furthermore, unvaccinated secondary cases with an infection exhibited a three-fold higher viral load compared to fully vaccinated secondary cases with a breakthrough infection. Our results demonstrate that vaccinations reduce susceptibility to infection as well as infectiousness, which should be considered by policy makers when seeking to understand the public health impact of vaccination against transmission of SARS-CoV-2. COVID-19 vaccines may reduce the susceptibility of an individual to infection and/or the infectiousness of breakthrough infections. Here, the authors use data from Denmark and estimate that vaccine effectiveness was 61% for susceptibility and 31% for infectiousness during a period of Delta variant dominance.
Collapse
|
14
|
Kamle S, Ma B, Lee CM, Schor G, Zhou Y, Lee CG, Elias JA. Host chitinase 3-like-1 is a universal therapeutic target for SARS-CoV-2 viral variants in COVID-19. eLife 2022; 11:e78273. [PMID: 35735790 PMCID: PMC9273216 DOI: 10.7554/elife.78273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/19/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is the disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2; SC2), which has caused a worldwide pandemic with striking morbidity and mortality. Evaluation of SC2 strains demonstrated impressive genetic variability, and many of these viral variants are now defined as variants of concern (VOC) that cause enhanced transmissibility, decreased susceptibility to antibody neutralization or therapeutics, and/or the ability to induce severe disease. Currently, the delta (δ) and omicron (ο) variants are particularly problematic based on their impressive and unprecedented transmissibility and ability to cause breakthrough infections. The delta variant also accumulates at high concentrations in host tissues and has caused waves of lethal disease. Because studies from our laboratory have demonstrated that chitinase 3-like-1 (CHI3L1) stimulates ACE2 and Spike (S) priming proteases that mediate SC2 infection, studies were undertaken to determine if interventions that target CHI3L1 are effective inhibitors of SC2 viral variant infection. Here, we demonstrate that CHI3L1 augments epithelial cell infection by pseudoviruses that express the alpha, beta, gamma, delta, or omicron S proteins and that the CHI3L1 inhibitors anti-CHI3L1 and kasugamycin inhibit epithelial cell infection by these VOC pseudovirus moieties. Thus, CHI3L1 is a universal, VOC-independent therapeutic target in COVID-19.
Collapse
Affiliation(s)
- Suchitra Kamle
- Department of Molecular Microbiology and Immunology, Brown UniversityProvidenceUnited States
| | - Bing Ma
- Department of Molecular Microbiology and Immunology, Brown UniversityProvidenceUnited States
| | - Chang Min Lee
- Department of Molecular Microbiology and Immunology, Brown UniversityProvidenceUnited States
| | - Gail Schor
- Department of Molecular Microbiology and Immunology, Brown UniversityProvidenceUnited States
| | - Yang Zhou
- Department of Molecular Microbiology and Immunology, Brown UniversityProvidenceUnited States
| | - Chun Geun Lee
- Department of Molecular Microbiology and Immunology, Brown UniversityProvidenceUnited States
| | | |
Collapse
|
15
|
Kemp SA, Cheng MTK, Hamilton WL, Kamelian K, Singh S, Rakshit P, Agrawal A, Illingworth CJR, Gupta RK. Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers. Sci Rep 2022; 12:10492. [PMID: 35729228 PMCID: PMC9212198 DOI: 10.1038/s41598-022-14411-7] [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: 12/13/2021] [Accepted: 06/07/2022] [Indexed: 01/01/2023] Open
Abstract
Breakthrough infections with SARS-CoV-2 Delta variant have been reported in doubly-vaccinated recipients and as re-infections. Studies of viral spread within hospital settings have highlighted the potential for transmission between doubly-vaccinated patients and health care workers and have highlighted the benefits of high-grade respiratory protection for health care workers. However the extent to which vaccination is preventative of viral spread in health care settings is less well studied. Here, we analysed data from 118 vaccinated health care workers (HCW) across two hospitals in India, constructing two probable transmission networks involving six HCWs in Hospital A and eight HCWs in Hospital B from epidemiological and virus genome sequence data, using a suite of computational approaches. A maximum likelihood reconstruction of transmission involving known cases of infection suggests a high probability that doubly vaccinated HCWs transmitted SARS-CoV-2 between each other and highlights potential cases of virus transmission between individuals who had received two doses of vaccine. Our findings show firstly that vaccination may reduce rates of transmission, supporting the need for ongoing infection control measures even in highly vaccinated populations, and secondly we have described a novel approach to identifying transmissions that is scalable and rapid, without the need for an infection control infrastructure.
Collapse
Affiliation(s)
- Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mark T K Cheng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
| | | | - Kimia Kamelian
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Sujit Singh
- National Centre for Disease Control, Delhi, India
| | | | - Anurag Agrawal
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Christopher J R Illingworth
- Garscube Campus, MRC - University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK. .,MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge, UK. .,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK. .,Department of Medicine, University of Cambridge, Cambridge, UK. .,Africa Health Research Institute, Durban, South Africa. .,Jeffrey Cheah Biomedical Centre, Cambridge, CB5 8UB, UK.
| |
Collapse
|
16
|
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant transmits much more rapidly than prior SARS-CoV-2 viruses. The primary mode of transmission is via short range aerosols that are emitted from the respiratory tract of an index case. There is marked heterogeneity in the spread of this virus, with 10% to 20% of index cases contributing to 80% of secondary cases, while most index cases have no subsequent transmissions. Vaccination, ventilation, masking, eye protection, and rapid case identification with contact tracing and isolation can all decrease the transmission of this virus.
Collapse
Affiliation(s)
- Eric A Meyerowitz
- Montefiore Medical Center, 111 East 210th Street, Bronx, NY 10467, USA.
| | - Aaron Richterman
- Hospital of the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| |
Collapse
|
17
|
Yavuz SŞ, Tunçer G, Altuntaş-Aydın Ö, Aydın M, Pehlivanoğlu F, Tok Y, Mese S, Gündüz A, Güçlü CG, Özdoğan İ, Hemiş-Aydın B, Soğuksu P, Benli A, Başaran S, Midilli K, Eraksoy H. Comparison of the Clinical and Laboratory Findings and Outcomes of Hospitalized COVID-19 Patients Who Were Either Fully Vaccinated with Coronavac or Not: An Analytical, Cross Sectional Study. Vaccines (Basel) 2022; 10:vaccines10050733. [PMID: 35632489 PMCID: PMC9148084 DOI: 10.3390/vaccines10050733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/27/2023] Open
Abstract
COVID-19 vaccines are highly protective against severe disease; however, vaccine breakthrough infections resulting in hospitalization may still occur in a small percentage of vaccinated individuals. We investigated whether the clinical and microbiological features and outcomes were different between hospitalized COVID-19 patients who were either fully vaccinated with Coronovac or not. All hospitalized COVID-19 patients who had at least one dose of Coronavac were included in the study. The oldest unvaccinated patients with comorbidities, who were hospitalized during the same period, were chosen as controls. All epidemiologic, clinical and laboratory data of the patients were recorded and compared between the fully vaccinated and unvaccinated individuals. There were 69 and 217 patients who had been either fully vaccinated with Coronavac or not, respectively. All breakthrough infections occurred in the first 3 months of vaccination. Fully vaccinated patients were older and had more comorbidities than unvaccinated patients. There were minor differences between the groups in symptoms, physical and laboratory findings, anti-spike IgG positivity rate and level, the severity of COVID-19, complications, and clinical improvement rate. The mortality rate of fully vaccinated patients was higher than the mortality rate in unvaccinated patients in univariate analysis, which was attributed to the fact that vaccinated patients were older and had more comorbidities. The severity and clinical outcomes of hospitalized patients with breakthrough COVID-19 after Coronavac vaccination were similar to those of unvaccinated patients. Our findings suggest that the immune response elicited by Coronovac could be insufficient to prevent COVID-19-related severe disease and death within 3 months of vaccination among elderly people with comorbidities.
Collapse
Affiliation(s)
- Serap Şimşek Yavuz
- Department of Infectious Disease and Clinical Microbiology, İstanbul Faculty of Medicine, İstanbul University, İstanbul 34093, Turkey; (B.H.-A.); (A.B.); (S.B.); (H.E.)
- Correspondence:
| | - Gülşah Tunçer
- Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital, İstanbul 34093, Turkey; (G.T.); (F.P.); (C.G.G.)
| | - Özlem Altuntaş-Aydın
- Department of Infectious Diseases and Clinical Microbiology, Çam and Sakura City Hospital, İstanbul 34093, Turkey; (Ö.A.-A.); (A.G.)
| | - Mehtap Aydın
- Department of Infectious Diseases and Clinical Microbiology, Ümraniye Training and Research Hospital, İstanbul 34093, Turkey; (M.A.); (İ.Ö.)
| | - Filiz Pehlivanoğlu
- Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital, İstanbul 34093, Turkey; (G.T.); (F.P.); (C.G.G.)
| | - Yeşim Tok
- Department of Medical Microbiology, Cerrahpaşa Faculty of Medicine, Division of Virology, Istanbul Cerrahpaşa University, İstanbul 34093, Turkey; (Y.T.); (K.M.)
| | - Sevim Mese
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Division of Virology and Fundamental Immunology, Istanbul University, İstanbul 34093, Turkey; (S.M.); (P.S.)
| | - Alper Gündüz
- Department of Infectious Diseases and Clinical Microbiology, Çam and Sakura City Hospital, İstanbul 34093, Turkey; (Ö.A.-A.); (A.G.)
| | - Ceyda Geyiktepe Güçlü
- Department of Infectious Diseases and Clinical Microbiology, Haseki Training and Research Hospital, İstanbul 34093, Turkey; (G.T.); (F.P.); (C.G.G.)
| | - İklima Özdoğan
- Department of Infectious Diseases and Clinical Microbiology, Ümraniye Training and Research Hospital, İstanbul 34093, Turkey; (M.A.); (İ.Ö.)
| | - Börçe Hemiş-Aydın
- Department of Infectious Disease and Clinical Microbiology, İstanbul Faculty of Medicine, İstanbul University, İstanbul 34093, Turkey; (B.H.-A.); (A.B.); (S.B.); (H.E.)
| | - Pınar Soğuksu
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Division of Virology and Fundamental Immunology, Istanbul University, İstanbul 34093, Turkey; (S.M.); (P.S.)
| | - Aysun Benli
- Department of Infectious Disease and Clinical Microbiology, İstanbul Faculty of Medicine, İstanbul University, İstanbul 34093, Turkey; (B.H.-A.); (A.B.); (S.B.); (H.E.)
| | - Seniha Başaran
- Department of Infectious Disease and Clinical Microbiology, İstanbul Faculty of Medicine, İstanbul University, İstanbul 34093, Turkey; (B.H.-A.); (A.B.); (S.B.); (H.E.)
| | - Kenan Midilli
- Department of Medical Microbiology, Cerrahpaşa Faculty of Medicine, Division of Virology, Istanbul Cerrahpaşa University, İstanbul 34093, Turkey; (Y.T.); (K.M.)
| | - Haluk Eraksoy
- Department of Infectious Disease and Clinical Microbiology, İstanbul Faculty of Medicine, İstanbul University, İstanbul 34093, Turkey; (B.H.-A.); (A.B.); (S.B.); (H.E.)
| |
Collapse
|
18
|
Liu S, Kang M, Zhao N, Zhuang Y, Li S, Song T. Comprehensive narrative review of real-world COVID-19 vaccines: viewpoints and opportunities. MEDICAL REVIEW 2022; 2:169-196. [PMID: 35862507 PMCID: PMC9274757 DOI: 10.1515/mr-2021-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/03/2022] [Indexed: 12/15/2022]
Abstract
Currently, people all over the world have been affected by coronavirus disease 2019 (COVID-19). Fighting against COVID-19 is the top priority for all the countries and nations. The development of a safe and effective COVID-19 vaccine is considered the optimal way of ending the pandemic. Three hundred and 44 vaccines were in development, with 149 undergoing clinical research and 35 authorized for emergency use as to March 15 of 2022. Many studies have shown the effective role of COVID-19 vaccines in preventing SARS-CoV-2 infections as well as serious and fatal COVID-19 cases. However, tough challenges have arisen regarding COVID-19 vaccines, including long-term immunity, emerging COVID-19 variants, and vaccine inequalities. A systematic review was performed of recent COVID-19 vaccine studies, with a focus on vaccine type, efficacy and effectiveness, and protection against SARS-CoV-2 variants, breakthrough infections, safety, deployment and vaccine strategies used in the real-world. Ultimately, there is a need to establish a unified evaluation standard of vaccine effectiveness, monitor vaccine safety and effectiveness, along with the virological characteristics of SARS-CoV-2 variants; and determine the most useful booster schedule. These aspects must be coordinated to ensure timely responses to beneficial or detrimental situations. In the future, global efforts should be directed toward effective and immediate vaccine allocations, improving vaccine coverage, SARS-CoV-2 new variants tracking, and vaccine booster development.
Collapse
Affiliation(s)
- Shelan Liu
- Department of Infectious Diseases , Zhejiang Provincial Centre for Disease Control and Prevention , Hangzhou , Zhejiang Province , China
| | - Min Kang
- Guangdong Provincial Centre for Disease Control and Prevention , Guangzhou , Guangdong Province , China
| | - Na Zhao
- School of Ecology and Environment, Anhui Normal University , Wuhu , Anhui Province , China
| | - Yali Zhuang
- Guangdong Provincial Centre for Disease Control and Prevention , Guangzhou , Guangdong Province , China
| | - Shijian Li
- Department of Public Health, SUNY Old Westbury , New York , USA
| | - Tie Song
- Guangdong Provincial Centre for Disease Control and Prevention , Guangzhou , Guangdong Province , China
| |
Collapse
|
19
|
Law N, Chan J, Kelly C, Auffermann WF, Dunn DP. Incidence of pulmonary embolism in COVID-19 infection in the ED: ancestral, Delta, Omicron variants and vaccines. Emerg Radiol 2022; 29:625-629. [PMID: 35446000 PMCID: PMC9022402 DOI: 10.1007/s10140-022-02039-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE This retrospective review examines the incidence of pulmonary embolism (PE) during computed tomography pulmonary angiography (CTPA) exams performed in the emergency room setting of a tertiary care center over dominant periods of the ancestral, Delta, and Omicron variants of COVID-19. MATERIALS/METHODS Demographic information, patient comorbidities and risk factors, vaccination status, and COVID-19 infection status were collected from patient's charts. Incidence of PE in COVID positive patients was compared between variant waves. Subgroup analysis of vaccination effect was performed. RESULTS CTPA was ordered in 18.3% of COVID-19 positive patients during the ancestral variant period, 18.3% during the Delta period and 17.3% during the Omicron wave. PE was seen in 15.0% of the ancestral COVID-19 variant cohort, 10.6% in the Delta COVID cohort and 9.23% of the Omicron cohort, reflecting a 41% and 60% increased risk of PE with ancestral variants compared to Delta and Omicron periods respectively. The study however was underpowered and the difference in rate of PE did not reach statistically significance (p = 0.43 and p = 0.22). Unvaccinated patients had an 2.75-fold increased risk of COVID-associated PE during the Delta and Omicron periods (p = .02) compared to vaccinated or recovered patients. CONCLUSION Vaccination reduces the risk of COVID-19 associated PE. Patients infected with the Delta and Omicron COVID-19 variants may have a lower incidence of pulmonary embolism, though a larger or multi-institution study is needed to prove definitively.
Collapse
Affiliation(s)
- Nicole Law
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT, USA
| | - Jessica Chan
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT, USA
| | - Christopher Kelly
- Division of Emergency Medicine, University of Utah, Salt Lake City, UT, USA
| | - William F Auffermann
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT, USA
| | - Dell P Dunn
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
20
|
Using high-resolution contact networks to evaluate SARS-CoV-2 transmission and control in large-scale multi-day events. Nat Commun 2022; 13:1956. [PMID: 35414056 PMCID: PMC9005731 DOI: 10.1038/s41467-022-29522-y] [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: 11/03/2021] [Accepted: 03/11/2022] [Indexed: 11/12/2022] Open
Abstract
The emergence of highly transmissible SARS-CoV-2 variants has created a need to reassess the risk posed by increasing social contacts as countries resume pre-pandemic activities, particularly in the context of resuming large-scale events over multiple days. To examine how social contacts formed in different activity settings influences interventions required to control Delta variant outbreaks, we collected high-resolution data on contacts among passengers and crew on cruise ships and combined the data with network transmission models. We found passengers had a median of 20 (IQR 10-36) unique close contacts per day, and over 60% of their contact episodes were made in dining or sports areas where mask wearing is typically limited. In simulated outbreaks, we found that vaccination coverage and rapid antigen tests had a larger effect than mask mandates alone, indicating the importance of combined interventions against Delta to reduce event risk in the vaccine era.
Collapse
|
21
|
Duong BV, Larpruenrudee P, Fang T, Hossain SI, Saha SC, Gu Y, Islam MS. Is the SARS CoV-2 Omicron Variant Deadlier and More Transmissible Than Delta Variant? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084586. [PMID: 35457468 PMCID: PMC9032753 DOI: 10.3390/ijerph19084586] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 12/20/2022]
Abstract
Genetic variants of severe acute respiratory syndrome coronavirus (SARS-CoV-2) have been globally surging and devastating many countries around the world. There are at least eleven reported variants dedicated with inevitably catastrophic consequences. In 2021, the most dominant Delta and Omicron variants were estimated to lead to more severity and deaths than other variants. Furthermore, these variants have some contagious characteristics involving high transmissibility, more severe illness, and an increased mortality rate. All outbreaks caused by the Delta variant have been rapidly skyrocketing in infection cases in communities despite tough restrictions in 2021. Apart from it, the United States, the United Kingdom and other high-rate vaccination rollout countries are still wrestling with this trend because the Delta variant can result in a significant number of breakthrough infections. However, the pandemic has changed since the latest SARS-CoV-2 variant in late 2021 in South Africa, Omicron. The preliminary data suggest that the Omicron variant possesses 100-fold greater than the Delta variant in transmissibility. Therefore, this paper aims to review these characteristics based on the available meta-data and information from the first emergence to recent days. Australia and the five most affected countries, including the United States, India, Brazil, France, as well as the United Kingdom, are selected in order to review the transmissibility, severity and fatality due to Delta and Omicron variants. Finally, the vaccination programs for each country are also reviewed as the main factor in prevention.
Collapse
Affiliation(s)
- Bao V. Duong
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia; (B.V.D.); (P.L.); (T.F.); (S.C.S.)
| | - Puchanee Larpruenrudee
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia; (B.V.D.); (P.L.); (T.F.); (S.C.S.)
| | - Tianxin Fang
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia; (B.V.D.); (P.L.); (T.F.); (S.C.S.)
| | - Sheikh I. Hossain
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Suvash C. Saha
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia; (B.V.D.); (P.L.); (T.F.); (S.C.S.)
| | - Yuantong Gu
- School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Mohammad S. Islam
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia; (B.V.D.); (P.L.); (T.F.); (S.C.S.)
- Correspondence:
| |
Collapse
|
22
|
Goyal A, Reeves DB, Schiffer JT. Multi-scale modelling reveals that early super-spreader events are a likely contributor to novel variant predominance. J R Soc Interface 2022; 19:20210811. [PMID: 35382576 PMCID: PMC8984334 DOI: 10.1098/rsif.2021.0811] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The emergence of new SARS-CoV-2 variants of concern (VOC) has hampered international efforts to contain the COVID-19 pandemic. VOCs have been characterized to varying degrees by higher transmissibility, worse infection outcomes and evasion of vaccine and infection-induced immunologic memory. VOCs are hypothesized to have originated from animal reservoirs, communities in regions with low surveillance and/or single individuals with poor immunologic control of the virus. Yet, the factors dictating which variants ultimately predominate remain incompletely characterized. Here we present a multi-scale model of SARS-CoV-2 dynamics that describes population spread through individuals whose viral loads and numbers of contacts (drawn from an over-dispersed distribution) are both time-varying. This framework allows us to explore how super-spreader events (SSE) (defined as greater than five secondary infections per day) contribute to variant emergence. We find stochasticity remains a powerful determinant of predominance. Variants that predominate are more likely to be associated with higher infectiousness, an SSE early after variant emergence and ongoing decline of the current dominant variant. Additionally, our simulations reveal that most new highly infectious variants that infect one or a few individuals do not achieve permanence in the population. Consequently, interventions that reduce super-spreading may delay or mitigate emergence of VOCs.
Collapse
Affiliation(s)
- Ashish Goyal
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Daniel B Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Medicine, University of Washington, Seattle, WA 98195, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| |
Collapse
|
23
|
Pajon R, Paila YD, Girard B, Dixon G, Kacena K, Baden LR, El Sahly HM, Essink B, Mullane KM, Frank I, Denhan D, Kerwin E, Zhao X, Ding B, Deng W, Tomassini JE, Zhou H, Leav B, Schödel F. Initial analysis of viral dynamics and circulating viral variants during the mRNA-1273 Phase 3 COVE trial. Nat Med 2022; 28:823-830. [PMID: 35145311 PMCID: PMC9018421 DOI: 10.1038/s41591-022-01679-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022]
Abstract
The mRNA-1273 vaccine for coronavirus disease 2019 (COVID-19) demonstrated 93.2% efficacy in reduction of symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in the blinded portion of the Phase 3 Coronavirus Efficacy (COVE) trial. While mRNA-1273 demonstrated high efficacy in prevention of COVID-19, including severe disease, its effect on the viral dynamics of SARS-CoV-2 infections is not understood. Here, in exploratory analyses, we assessed the impact of mRNA-1273 vaccination in the ongoing COVE trial (number NCT04470427) on SARS-CoV-2 copy number and shedding, burden of disease and infection, and viral variants. Viral variants were sequenced in all COVID-19 and adjudicated COVID-19 cases (n = 832), from July 2020 in the blinded part A of the study to May 2021 of the open-label part B of the study, in which participants in the placebo arm started to receive the mRNA-1273 vaccine after US Food and Drug Administration emergency use authorization of mRNA-1273 in December 2020. mRNA-1273 vaccination significantly reduced SARS-CoV-2 viral copy number (95% confidence interval) by 100-fold on the day of diagnosis compared with placebo (4.1 (3.4-4.8) versus 6.2 (6.0-6.4) log10 copies per ml). Median times to undetectable viral copies were 4 days for mRNA-1273 and 7 days for placebo. Vaccination also substantially reduced the burden of disease and infection scores. Vaccine efficacies (95% confidence interval) against SARS-CoV-2 variants circulating in the United States during the trial assessed in this post hoc analysis were 82.4% (40.4-94.8%) for variants Epsilon and Gamma and 81.2% (36.1-94.5%) for Epsilon. The detection of other, non-SARS-CoV-2, respiratory viruses during the trial was similar between groups. While additional study is needed, these data show that in SARS-CoV-2-infected individuals, vaccination reduced both the viral copy number and duration of detectable viral RNA, which may be markers for the risk of virus transmission.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ian Frank
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Edward Kerwin
- Criscor Clinical Research Institute, Medford, OR, USA
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Dal-Ré R, Camps V. [August 2021 and the Delta variant: is mandatory vaccination of individuals against SARS-CoV-2 acceptable?]. Med Clin (Barc) 2022; 158:233-236. [PMID: 34895889 PMCID: PMC8585632 DOI: 10.1016/j.medcli.2021.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Rafael Dal-Ré
- Unidad de Epidemiología, Instituto de Investigación Sanitaria-Hospital Universitario Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, España.
| | - Victoria Camps
- Departamento de Filosofía, Universidad Autónoma de Barcelona, Barcelona, España
| |
Collapse
|
25
|
Li H, Lin H, Chen X, Li H, Li H, Lin S, Huang L, Chen G, Zheng G, Wang S, Hu X, Huang H, Tu H, Li X, Ji Y, Zhong W, Li Q, Fang J, Lin Q, Yu R, Xie B. Unvaccinated Children Are an Important Link in the Transmission of SARS-CoV-2 Delta Variant (B1.617.2): Comparative Clinical Evidence From a Recent Community Surge. Front Cell Infect Microbiol 2022; 12:814782. [PMID: 35350438 PMCID: PMC8957884 DOI: 10.3389/fcimb.2022.814782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/11/2022] [Indexed: 01/08/2023] Open
Abstract
Objective To evaluate the necessity of Covid-19 vaccination in children aged < 12 y by comparing the clinical characteristics between unvaccinated children aged < 12 y and vaccinated patients aged ≥ 12y during the Delta surge (B.1.617.2) in Putian, Fujian, China. Methods A total of 226 patients with SARS-Cov-2 Delta variant (B.1.167.2; confirmed by Real-time PCR positivity and sequencing) were enrolled from Sep 10th to Oct 20th, 2021, including 77 unvaccinated children (aged < 12y) and 149 people aged ≥ 12y, mostly vaccinated. The transmission route was explored and the clinical data of two groups were compared; The effect factors for the time of the nucleic acid negativization (NAN) were examined by R statistical analysis. Results The Delta surge in Putian spread from children in schools to factories, mostly through family contact. Compared with those aged ≥ 12y, patients aged < 12y accounted for 34.07% of the total and showed milder fever, less cough and fatigue; they reported higher peripheral blood lymphocyte counts [1.84 (1.32, 2.71)×10^9/L vs. 1.31 (0.94, 1.85)×10^9/L; p<0.05), higher normal CRP rate (92.21% vs. 57.72%), lower IL-6 levels [5.28 (3.31, 8.13) vs. 9.10 (4.37, 15.14); p<0.05]. Upon admission, their COVID19 antibodies (IgM and IgG) and IgG in convalescence were lower [0.13 (0.00, 0.09) vs. 0.12 (0.03, 0.41), p<0.05; 0.02 (0.00, 0.14) vs. 1.94 (0.54, 6.40), p<0.05; 5.46 (2.41, 9.26) vs. 73.63 (54.63, 86.55), p<0.05, respectively], but longer NAN time (18 days vs. 16 days, p=0.13). Conclusion Unvaccinated children may be an important link in the transmission of SARS-CoV-2 delta variant (B1.617.2), which indicated an urgent need of vaccination for this particular population.
Collapse
Affiliation(s)
- Hongru Li
- Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fujian Shengli Medical College, Fujian Medical University, Fuzhou, China
| | - Haibin Lin
- Department of Orthopaedics, Affiliated Hospital of Fujian Putian University, Putian, China
| | - Xiaoping Chen
- College of Mathematics and Statistics, Fujian Normal University, Fuzhou, China
| | - Hang Li
- Department of Orthopaedics, Affiliated Hospital of Fujian Putian University, Putian, China
| | - Hong Li
- Nursing Department, Fujian Provincial Hospital, Fuzhou, China
| | - Sheng Lin
- Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fujian Shengli Medical College, Fujian Medical University, Fuzhou, China
| | - Liping Huang
- Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fujian Shengli Medical College, Fujian Medical University, Fuzhou, China
| | - Gongping Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Guilin Zheng
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Putian University, Putian, China
| | - Shibiao Wang
- Department of Pediatrics, Fujian Maternal and Child Health Hospital, Fuzhou, China
| | - Xiaowei Hu
- Fujian Hospital of Shanghai Children’s Medical Center, Fuzhou, China
| | - Handong Huang
- Department of Internal Critical Medicine, Affiliated Hospital of Putian University, Putian, China
| | - Haijian Tu
- Department of Laboratory Medicine, Affiliated Hospital of Putian University, Putian, China
| | - Xiaoqin Li
- Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fujian Shengli Medical College, Fujian Medical University, Fuzhou, China
| | - Yuejiao Ji
- College of Mathematics and Statistics, Fujian Normal University, Fuzhou, China
| | - Wen Zhong
- Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fujian Shengli Medical College, Fujian Medical University, Fuzhou, China
| | - Qing Li
- Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fujian Shengli Medical College, Fujian Medical University, Fuzhou, China
| | - Jiabin Fang
- Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fujian Shengli Medical College, Fujian Medical University, Fuzhou, China
| | - Qunying Lin
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Putian University, Putian, China
- *Correspondence: Baosong Xie, ; Rongguo Yu, ; Qunying Lin,
| | - Rongguo Yu
- Department of Surgical Critical Medicine, Fujian Provincial Hospital, Fuzhou, China
- *Correspondence: Baosong Xie, ; Rongguo Yu, ; Qunying Lin,
| | - Baosong Xie
- Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fujian Shengli Medical College, Fujian Medical University, Fuzhou, China
- *Correspondence: Baosong Xie, ; Rongguo Yu, ; Qunying Lin,
| |
Collapse
|
26
|
Dal-Ré R, Camps V. August 2021 and the Delta variant: is mandatory vaccination of individuals against SARS-CoV-2 acceptable? MEDICINA CLÍNICA (ENGLISH EDITION) 2022; 158:233-236. [PMID: 35165659 PMCID: PMC8818404 DOI: 10.1016/j.medcle.2021.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
27
|
Zimmermann P, Pittet LF, Finn A, Pollard AJ, Curtis N. Should children be vaccinated against COVID-19? Arch Dis Child 2022; 107:e1. [PMID: 34732388 DOI: 10.1136/archdischild-2021-323040] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022]
Abstract
Whether all children under 12 years of age should be vaccinated against COVID-19 remains an ongoing debate. The relatively low risk posed by acute COVID-19 in children, and uncertainty about the relative harms from vaccination and disease mean that the balance of risk and benefit of vaccination in this age group is more complex. One of the key arguments for vaccinating healthy children is to protect them from long-term consequences. Other considerations include population-level factors, such as reducing community transmission, vaccine supply, cost, and the avoidance of quarantine, school closures and other lockdown measures. The emergence of new variants of concern necessitates continual re-evaluation of the risks and benefits. In this review, we do not argue for or against vaccinating children against COVID-19 but rather outline the points to consider and highlight the complexity of policy decisions on COVID-19 vaccination in this age group.
Collapse
Affiliation(s)
- Petra Zimmermann
- Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland .,Department of Paediatrics, Fribourg Hospital HFR, Fribourg, Switzerland.,Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Laure F Pittet
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Pediatric Infectious Diseases Unit, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Adam Finn
- Bristol Vaccine Centre, School of Clinical Sciences and School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK.,Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Nigel Curtis
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
28
|
Kamle S, Ma B, Lee CM, Schor G, Zhou Y, Lee CG, Elias JA. Host Chitinase 3-like-1 is a Universal Therapeutic Target for SARS-CoV-2 Viral Variants in COVID 19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.21.477274. [PMID: 35118470 PMCID: PMC8811903 DOI: 10.1101/2022.01.21.477274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
COVID 19 is the disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2; SC2) which has caused a world-wide pandemic with striking morbidity and mortality. Evaluation of SC2 strains demonstrated impressive genetic variability and many of these viral variants are now defined as variants of concern (VOC) that cause enhanced transmissibility, decreased susceptibility to antibody neutralization or therapeutics and or the ability to induce severe disease. Currently, the delta (δ) and omicron (o) variants are particularly problematic based on their impressive and unprecedented transmissibility and ability to cause break through infections. The delta variant also accumulates at high concentrations in host tissues and has caused waves of lethal disease. Because studies from our laboratory have demonstrated that chitinase 3-like-1 (CHI3L1) stimulates ACE2 and Spike (S) priming proteases that mediate SC2 infection, studies were undertaken to determine if interventions that target CHI3L1 are effective inhibitors of SC2 viral variant infection. Here we demonstrate that CHI3L1 augments epithelial cell infection by pseudoviruses that express the alpha, beta, gamma, delta or omicron S proteins and that the CHI3L1 inhibitors anti-CHI3L1 and kasugamycin inhibit epithelial cell infection by these VOC pseudovirus moieties. Thus, CHI3L1 is a universal, VOC-independent therapeutic target in COVID 19.
Collapse
|
29
|
Kumar N, Quadri S, AlAwadhi AI, AlQahtani M. COVID-19 Recovery Patterns Across Alpha (B.1.1.7) and Delta (B.1.617.2) Variants of SARS-CoV-2. Front Immunol 2022; 13:812606. [PMID: 35237265 PMCID: PMC8882843 DOI: 10.3389/fimmu.2022.812606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background B.1.1.7 (alpha) and B.1.617.2 (delta) variants of concern for SARS-CoV-2 have been reported to have differential infectivity and pathogenicity. Difference in recovery patterns across these variants and the interaction with vaccination status has not been reported in population-based studies. Objective The objective of this research was to study the length of stay and temporal trends in RT-PCR cycle times (Ct) across alpha and delta variants of SARS-CoV-2 between vaccinated and unvaccinated individuals. Methods Participants consisted of patients admitted to national COVID-19 treatment facilities if they had a positive RT-PCR test for SARS-CoV-2, and analysis of variants was performed (using whole genome sequencing). Information on vaccination status, age, sex, cycle times (Ct) for four consecutive RT-PCR tests conducted during hospital stay, and total length of hospital stay for each participant were ascertained from electronic medical records. Results Patients infected with the delta variant were younger (mean age = 35years vs 39 years for alpha, p<0.001) and had lesser vaccination coverage (54% vs 72% for alpha, p<0.001). RT-PCR Ct values were similar for both variants at the baseline test; however by the fourth test, delta variant patients had significantly lower Ct values (27 vs 29, p=0.05). Length of hospital stay was higher in delta variant patients in vaccinated (3 days vs 2.9 days for alpha variant) as well as in unvaccinated patients (5.2 days vs 4.4 days for alpha variant, p<0.001). Hazards of hospital discharge after adjusting for vaccination status, age, and sex was higher for alpha variant infections (HR=1.2, 95% CI: 1.01-1.41, p=0.029). Conclusion Patients infected with the delta variant of SARS-CoV-2 were found to have a slower recovery as indicated by longer length of stay and higher shedding of the virus compared to alpha variant infections, and this trend was consistent in both vaccinated and unvaccinated patients.
Collapse
Affiliation(s)
- Nitya Kumar
- Department of Medicine, Royal College of Surgeons in Ireland –Bahrain, Muharraq, Bahrain
| | - Suha Quadri
- Department of Medicine, Royal College of Surgeons in Ireland –Bahrain, Muharraq, Bahrain
| | | | - Manaf AlQahtani
- Department of Medicine, Royal College of Surgeons in Ireland –Bahrain, Muharraq, Bahrain
- Department of Pathology, Bahrain Defense Force Hospital–Royal Medical Services, Riffa, Bahrain
| |
Collapse
|
30
|
Christensen PA, Olsen RJ, Long SW, Subedi S, Davis JJ, Hodjat P, Walley DR, Kinskey JC, Ojeda Saavedra M, Pruitt L, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Mangham R, Pena S, Trinh T, Yerramilli P, Nguyen M, Olson R, Snehal R, Gollihar J, Musser JM. Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas. THE AMERICAN JOURNAL OF PATHOLOGY 2022. [PMID: 34774517 DOI: 10.1101/2021.07.19.21260808] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have repeatedly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Delta variants are now the focus of intense international attention because they are causing widespread COVID-19 globally and are associated with vaccine breakthrough cases. We sequenced 16,965 SARS-CoV-2 genomes from samples acquired March 15, 2021, through September 20, 2021, in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared with all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared with 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold value (a proxy for high virus load). This value was similar to the median cycle threshold value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe COVID-19, hospitalizations, and deaths.
Collapse
Affiliation(s)
- Paul A Christensen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - S Wesley Long
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Sishir Subedi
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - James J Davis
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Parsa Hodjat
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Debbie R Walley
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jacob C Kinskey
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Matthew Ojeda Saavedra
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Regan Mangham
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Sindy Pena
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Trina Trinh
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Prasanti Yerramilli
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Robert Olson
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Richard Snehal
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jimmy Gollihar
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; DEVCOM Army Research Laboratory-South, Austin, Texas
| | - James M Musser
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
| |
Collapse
|
31
|
Poopalasingam N, Korenkov M, Ashurov A, Strobel J, Fish I, Hellmich M, Gruell H, Lehmann C, Heger E, Klein F. Determining the reliability of rapid SARS-CoV-2 antigen detection in fully vaccinated individuals. J Clin Virol 2022; 148:105119. [PMID: 35248992 PMCID: PMC8858005 DOI: 10.1016/j.jcv.2022.105119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 12/22/2022]
Abstract
Background Rapid antigen detection tests (RADT) are commonly used as SARS-CoV-2 diagnostic tests both by medical professionals and laypeople. However, the performance of RADT in vaccinated individuals has not been fully investigated. Objectives RT-qPCR and rapid antigen detection testing were performed to evaluate the performance of the Standard Q COVID-19 Ag Test in detecting SARS-CoV-2 breakthrough infections in vaccinated individuals. Study design Two swab specimens, one for RT-qPCR and one for RADT, were collected from vaccinated individuals in an outpatient clinic. For comparison of RADT performance in vaccinated and unvaccinated individuals, a dataset already published by this group was used as reference. Results During the delta wave, a total of 696 samples were tested with both RT-qPCR and RADT that included 692 (99.4%) samples from vaccinated individuals. Of these, 76 (11.0%) samples were detected SARS-CoV-2 positive by RT-qPCR and 45 (6.5%) samples by the Standard Q COVID-19 Ag test. Stratified by Ct values, sensitivity of the RADT was 100.0%, 94.4% and 81.1% for Ct ≤ 20 (n=18), Ct ≤ 25 (n=36) and Ct ≤ 30 (n=53), respectively. Samples with Ct values ≥ 30 (n=23) were not detected. Overall RADT specificity was 99.7% and symptom status did not affect RADT performance. Notably, RADT detected 4 out of 4 samples of probable Omicron variant infection based on single nucleotide polymorphism analysis. Conclusion Our results show that RADT testing remains a valuable tool in detecting breakthrough infections with high viral RNA loads.
Collapse
Affiliation(s)
- Nareshkumar Poopalasingam
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Michael Korenkov
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Artem Ashurov
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Janina Strobel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Irina Fish
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Martin Hellmich
- Institute of Medical Statistics, Informatics and Epidemiology, Faculty of Medicine, University of Cologne, Robert-Koch-Str. 10, 50931 Cologne, Germany
| | - Henning Gruell
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Clara Lehmann
- German Center for Infection Research, Partner Site Bonn-Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
| | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935 Cologne, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Fürst-Pückler-Straße 56, 50935 Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, Kerpener Str. 62, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany.
| |
Collapse
|
32
|
Greaney AM, Raredon MSB, Kochugaeva MP, Niklason LE, Levchenko A. SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.29.478335. [PMID: 35132420 PMCID: PMC8820667 DOI: 10.1101/2022.01.29.478335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite much concerted effort to better understand SARS-CoV-2 viral infection, relatively little is known about the dynamics of early viral entry and infection in the airway. Here we analyzed a single-cell RNA sequencing dataset of early SARS-CoV-2 infection in a humanized in vitro model, to elucidate key mechanisms by which the virus triggers a cell-systems-level response in the bronchial epithelium. We find that SARS-CoV-2 virus preferentially enters the tissue via ciliated cell precursors, giving rise to a population of infected mature ciliated cells, which signal to basal cells, inducing further rapid differentiation. This feed-forward loop of infection is mitigated by further cell-cell communication, before interferon signaling begins at three days post-infection. These findings suggest hijacking by the virus of potentially beneficial tissue repair mechanisms, possibly exacerbating the outcome. This work both elucidates the interplay between barrier tissues and viral infections, and may suggest alternative therapeutic approaches targeting non-immune response mechanisms.
Collapse
|
33
|
Jiang Y, Wu Q, Song P, You C. The Variation of SARS-CoV-2 and Advanced Research on Current Vaccines. Front Med (Lausanne) 2022; 8:806641. [PMID: 35118097 PMCID: PMC8804231 DOI: 10.3389/fmed.2021.806641] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022] Open
Abstract
Over the past 2 years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) and rapidly spread worldwide. In the process of evolution, new mutations of SARS-CoV-2 began to appear to be more adaptable to the diverse changes of various cellular environments and hosts. Generally, the emerging SARS-CoV-2 variants are characterized by high infectivity, augmented virulence, and fast transmissibility, posing a serious threat to the prevention and control of the global epidemic. At present, there is a paucity of effective measurements to cure COVID-19. It is extremely crucial to develop vaccines against SARS-CoV-2 and emerging variants to enhance individual immunity, but it is not yet known whether they are approved by the authority. Therefore, we systematically reviewed the main characteristics of the emerging various variants of SARS-CoV-2, including their distribution, mutations, transmissibility, severity, and susceptibility to immune responses, especially the Delta variant and the new emerging Omicron variant. Furthermore, we overviewed the suitable crowd, the efficacy, and adverse events (AEs) of current vaccines.
Collapse
Affiliation(s)
| | | | | | - Chongge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, China
| |
Collapse
|
34
|
Stein M, Ashkenazi-Hoffnung L, Greenberg D, Dalal I, Livni G, Chapnick G, Stein-Zamir C, Ashkenazi S, Hecht-Sagie L, Grossman Z. The Burden of COVID-19 in Children and Its Prevention by Vaccination: A Joint Statement of the Israeli Pediatric Association and the Israeli Society for Pediatric Infectious Diseases. Vaccines (Basel) 2022; 10:81. [PMID: 35062742 PMCID: PMC8781684 DOI: 10.3390/vaccines10010081] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 01/27/2023] Open
Abstract
As of October 2021, SARS-CoV-2 infections were reported among 512,613 children and adolescents in Israel (~33% of all COVID-19 cases). The 5-11-year age group accounted for about 43% (223,850) of affected children and adolescents. In light of the availability of the Pfizer-BioNTech BNT162b2 vaccine against COVID-19 for children aged 5-11 years, we aimed to write a position paper for pediatricians, policymakers and families regarding the clinical aspects of COVID-19 and the vaccination of children against COVID-19. The first objective of this review was to describe the diverse facets of the burden of COVID-19 in children, including the direct effects of hospitalization during the acute phase of the disease, multisystem inflammatory syndrome in children, long COVID and the indirect effects of social isolation and interruption in education. In addition, we aimed to provide an update regarding the efficacy and safety of childhood mRNA COVID-19 vaccination and to instill confidence in pediatricians regarding the benefits of vaccinating children against COVID-19. We reviewed up-to-date Israeli and international epidemiological data and literature regarding COVID-19 morbidity and its sequelae in children, vaccine efficacy in reducing COVID-19-related morbidity and SARS-CoV-2 transmission and vaccine safety data. We conducted a risk-benefit analysis regarding the vaccination of children and adolescents. We concluded that vaccines are safe and effective and are recommended for all children aged 5 to 11 years to protect them from COVID-19 and its complications and to reduce community transmissions. Based on these data, after weighing the benefits of vaccination versus the harm, the Israeli Ministry of Health decided to recommend vaccination for children aged 5-11 years.
Collapse
Affiliation(s)
- Michal Stein
- Infectious Diseases and Infection Control Unit, Hillel Yaffe Medical Center, Hadera 3810101, Israel
- Rappaport Faculty of Medicine, Technion—Israel Institute of Technology, Haifa 3109601, Israel
| | - Liat Ashkenazi-Hoffnung
- Department of Day Care Hospitalization, Schneider Children’s Medical Center, Petah Tikva 4920235, Israel;
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel; (I.D.); (G.L.)
| | - David Greenberg
- The Pediatric Infectious Disease Unit, Soroka Medical Center, Be’er Sheva 8458900, Israel;
- The Faculty of Health Sciences, Joyce & Irving Goldman Medical School at Ben Gurion University of the Negev, Be’er Sheva 8410501, Israel
| | - Ilan Dalal
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel; (I.D.); (G.L.)
- Pediatric Department, E. Wolfson Medical Center, Holon 5822012, Israel
| | - Gilat Livni
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel; (I.D.); (G.L.)
- Department of Pediatrics A, Schneider Children’s Medical Center, Petah Tikva 4920245, Israel
| | - Gil Chapnick
- Maccabi Healthcare Services, Tel Aviv-Yafo 6812509, Israel; (G.C.); (L.H.-S.); (Z.G.)
| | - Chen Stein-Zamir
- Jerusalem District Health Office, Jerusalem 9137001, Israel;
- Braun School of Public Health and Community Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Shai Ashkenazi
- Schneider Children’s Medical Center, Petah Tikva 4920235, Israel;
- Adelson School of Medicine, Ariel University, Ari’el 4070000, Israel
| | - Lior Hecht-Sagie
- Maccabi Healthcare Services, Tel Aviv-Yafo 6812509, Israel; (G.C.); (L.H.-S.); (Z.G.)
| | - Zachi Grossman
- Maccabi Healthcare Services, Tel Aviv-Yafo 6812509, Israel; (G.C.); (L.H.-S.); (Z.G.)
- Adelson School of Medicine, Ariel University, Ari’el 4070000, Israel
| |
Collapse
|
35
|
Mistry P, Barmania F, Mellet J, Peta K, Strydom A, Viljoen IM, James W, Gordon S, Pepper MS. SARS-CoV-2 Variants, Vaccines, and Host Immunity. Front Immunol 2022; 12:809244. [PMID: 35046961 PMCID: PMC8761766 DOI: 10.3389/fimmu.2021.809244] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new beta coronavirus that emerged at the end of 2019 in the Hubei province of China. SARS-CoV-2 causes coronavirus disease 2019 (COVID-19) and was declared a pandemic by the World Health Organization (WHO) on 11 March 2020. Herd or community immunity has been proposed as a strategy to protect the vulnerable, and can be established through immunity from past infection or vaccination. Whether SARS-CoV-2 infection results in the development of a reservoir of resilient memory cells is under investigation. Vaccines have been developed at an unprecedented rate and 7 408 870 760 vaccine doses have been administered worldwide. Recently emerged SARS-CoV-2 variants are more transmissible with a reduced sensitivity to immune mechanisms. This is due to the presence of amino acid substitutions in the spike protein, which confer a selective advantage. The emergence of variants therefore poses a risk for vaccine effectiveness and long-term immunity, and it is crucial therefore to determine the effectiveness of vaccines against currently circulating variants. Here we review both SARS-CoV-2-induced host immune activation and vaccine-induced immune responses, highlighting the responses of immune memory cells that are key indicators of host immunity. We further discuss how variants emerge and the currently circulating variants of concern (VOC), with particular focus on implications for vaccine effectiveness. Finally, we describe new antibody treatments and future vaccine approaches that will be important as we navigate through the COVID-19 pandemic.
Collapse
Affiliation(s)
- Priyal Mistry
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Fatima Barmania
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Kimberly Peta
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Adéle Strydom
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Ignatius M. Viljoen
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - William James
- James and Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Siamon Gordon
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City, Taiwan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Michael S. Pepper
- Department of Immunology, Institute for Cellular and Molecular Medicine, University of Pretoria, Pretoria, South Africa
- South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
36
|
Kriegel M, Hartmann A, Buchholz U, Seifried J, Baumgarte S, Gastmeier P. SARS-CoV-2 Aerosol Transmission Indoors: A Closer Look at Viral Load, Infectivity, the Effectiveness of Preventive Measures and a Simple Approach for Practical Recommendations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 19:220. [PMID: 35010484 PMCID: PMC8750733 DOI: 10.3390/ijerph19010220] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
There is uncertainty about the viral loads of infectious individuals required to transmit COVID-19 via aerosol. In addition, there is a lack of both quantification of the influencing parameters on airborne transmission and simple-to-use models for assessing the risk of infection in practice, which furthermore quantify the influence of non-medical preventive measures. In this study, a dose-response model was adopted to analyze 25 documented outbreaks at infection rates of 4-100%. We show that infection was only possible if the viral load was higher than 108 viral copies/mL. Based on mathematical simplifications of our approach to predict the probable situational attack rate (PARs) of a group of persons in a room, and valid assumptions, we provide simplified equations to calculate, among others, the maximum possible number of persons and the person-related virus-free air supply flow necessary to keep the number of newly infected persons to less than one. A comparison of different preventive measures revealed that testing contributes the most to the joint protective effect, besides wearing masks and increasing ventilation. In addition, we conclude that absolute volume flow rate or person-related volume flow rate are more intuitive parameters for evaluating ventilation for infection prevention than air exchange rate.
Collapse
Affiliation(s)
- Martin Kriegel
- Hermann-Rietschel-Institut, Technical University of Berlin, 10623 Berlin, Germany;
| | - Anne Hartmann
- Hermann-Rietschel-Institut, Technical University of Berlin, 10623 Berlin, Germany;
| | - Udo Buchholz
- Department for Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany; (U.B.); (J.S.)
| | - Janna Seifried
- Department for Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany; (U.B.); (J.S.)
| | | | - Petra Gastmeier
- Institute for Hygiene and Environmental Medicine, Charité-University Medicine Berlin, 12203 Berlin, Germany;
| |
Collapse
|
37
|
Duerr R, Dimartino D, Marier C, Zappile P, Levine S, François F, Iturrate E, Wang G, Dittmann M, Lighter J, Elbel B, Troxel AB, Goldfeld KS, Heguy A. Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.12.07.21267431. [PMID: 34909779 PMCID: PMC8669846 DOI: 10.1101/2021.12.07.21267431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In 2021, Delta has become the predominant SARS-CoV-2 variant worldwide. While vaccines effectively prevent COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occur. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contribute to increased rates of breakthrough infections compared to unvaccinated controls. Here, we show a steep and near complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25, its spike mutation S112L, and nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthroughs increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Our data indicate a limited impact of vaccine escape in favor of Delta's increased epidemic growth in times of waning vaccine protection.
Collapse
Affiliation(s)
- Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | - Paul Zappile
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | | | | | | | - Guiqing Wang
- Department of Pathology, NYU Grossman School of Medicine
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine
| | - Jennifer Lighter
- Department of Pediatric Infectious Diseases, NYU Grossman School of Medicine
| | - Brian Elbel
- Department of Population Health, NYU Grossman School of Medicine
- NYU Wagner Graduate School of Public Service
| | - Andrea B. Troxel
- Department of Population Health, NYU Grossman School of Medicine
| | | | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health
- Department of Pathology, NYU Grossman School of Medicine
| |
Collapse
|
38
|
Guo K, Barrett BS, Mickens KL, Vladar EK, Morrison JH, Hasenkrug KJ, Poeschla EM, Santiago ML. Interferon Resistance of Emerging SARS-CoV-2 Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.20.436257. [PMID: 33758840 PMCID: PMC7986999 DOI: 10.1101/2021.03.20.436257] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The emergence of SARS-CoV-2 variants with enhanced transmissibility, pathogenesis and resistance to vaccines presents urgent challenges for curbing the COVID-19 pandemic. While Spike mutations that enhance virus infectivity or neutralizing antibody evasion may drive the emergence of these novel variants, studies documenting a critical role for interferon responses in the early control of SARS-CoV-2 infection, combined with the presence of viral genes that limit these responses, suggest that interferons may also influence SARS-CoV-2 evolution. Here, we compared the potency of 17 different human interferons against multiple viral lineages sampled during the course of the global outbreak, including ancestral and four major variants of concern. Our data reveal increased interferon resistance in emerging SARS-CoV-2 variants, suggesting that evasion of innate immunity may be a significant, ongoing driving force for SARS-CoV-2 evolution. These findings have implications for the increased lethality of emerging variants and highlight the interferon subtypes that may be most successful in the treatment of early infections.
Collapse
Affiliation(s)
- Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Bradley S. Barrett
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Kaylee L. Mickens
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Ezster K. Vladar
- Division of Pulmonary Sciences and Critical Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - James H. Morrison
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Kim J. Hasenkrug
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Eric M. Poeschla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| |
Collapse
|
39
|
Gunadi, Hakim MS, Wibawa H, Marcellus, Setiawaty V, Slamet, Trisnawati I, Supriyati E, El Khair R, Iskandar K, Afiahayati, Siswanto, Irene, Anggorowati N, Daniwijaya EW, Nugrahaningsih DAA, Puspadewi Y, Puspitarani DA, Tania I, Vujira KA, Ardlyamustaqim MB, Gabriela GC, Eryvinka LS, Nirmala BC, Geometri ET, Darutama AA, Kuswandani AA, Lestari, Irianingsih SH, Khoiriyah S, Lestari I, Ananda NR, Arguni E, Nuryastuti T, Wibawa T. Is the Infection of the SARS-CoV-2 Delta Variant Associated With the Outcomes of COVID-19 Patients? Front Med (Lausanne) 2021; 8:780611. [PMID: 34957154 PMCID: PMC8695874 DOI: 10.3389/fmed.2021.780611] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) has been responsible for the current increase in Coronavirus disease 2019 (COVID-19) infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java provinces, Indonesia. Methods: In this cross-sectional study, we ascertained 161 patients, 69 with the Delta variant and 92 with the non-Delta variant. The Illumina MiSeq next-generation sequencer was used to perform the whole-genome sequences of SARS-CoV-2. Results: The mean age of patients with the Delta variant and the non-Delta variant was 27.3 ± 20.0 and 43.0 ± 20.9 (p = 3 × 10-6). The patients with Delta variant consisted of 23 males and 46 females, while the patients with the non-Delta variant involved 56 males and 36 females (p = 0.001). The Ct value of the Delta variant (18.4 ± 2.9) was significantly lower than that of the non-Delta variant (19.5 ± 3.8) (p = 0.043). There was no significant difference in the hospitalization and mortality of patients with Delta and non-Delta variants (p = 0.80 and 0.29, respectively). None of the prognostic factors were associated with the hospitalization, except diabetes with an OR of 3.6 (95% CI = 1.02-12.5; p = 0.036). Moreover, the patients with the following factors have been associated with higher mortality rate than the patients without the factors: age ≥65 years, obesity, diabetes, hypertension, and cardiovascular disease with the OR of 11 (95% CI = 3.4-36; p = 8 × 10-5), 27 (95% CI = 6.1-118; p = 1 × 10-5), 15.6 (95% CI = 5.3-46; p = 6 × 10-7), 12 (95% CI = 4-35.3; p = 1.2 × 10-5), and 6.8 (95% CI = 2.1-22.1; p = 0.003), respectively. Multivariate analysis showed that age ≥65 years, obesity, diabetes, and hypertension were the strong prognostic factors for the mortality of COVID-19 patients with the OR of 3.6 (95% CI = 0.58-21.9; p = 0.028), 16.6 (95% CI = 2.5-107.1; p = 0.003), 5.5 (95% CI = 1.3-23.7; p = 0.021), and 5.8 (95% CI = 1.02-32.8; p = 0.047), respectively. Conclusions: We show that the patients infected by the SARS-CoV-2 Delta variant have a lower Ct value than the patients infected by the non-Delta variant, implying that the Delta variant has a higher viral load, which might cause a more transmissible virus among humans. However, the Delta variant does not affect the COVID-19 outcomes in our patients. Our study also confirms that older age and comorbidity increase the mortality rate of patients with COVID-19.
Collapse
Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Marcellus
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Vivi Setiawaty
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Slamet
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Ika Trisnawati
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riat El Khair
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Siswanto
- Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Irene
- Balai Besar Teknik Kesehatan Lingkungan dan Pengendalian Penyakit, Yogyakarta, Indonesia
| | - Nungki Anggorowati
- Department of Anatomical Pathology/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Aris Agung Nugrahaningsih
- Department of Pharmacology and Therapy/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yunika Puspadewi
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Dyah Ayu Puspitarani
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Irene Tania
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Muhammad Buston Ardlyamustaqim
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Gita Christy Gabriela
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Bunga Citta Nirmala
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Esensi Tarian Geometri
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Abirafdi Amajida Darutama
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Anisa Adityarini Kuswandani
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Lestari
- Disease Investigation Center, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | | | | | | | - Nur Rahmi Ananda
- Pulmonology Division, Department of Internal Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| |
Collapse
|
40
|
Focosi D, Franchini M, Pirofski LA, Maggi F, Casadevall A. Is SARS-CoV-2 viral clearance in nasopharyngeal swabs an appropriate surrogate marker for clinical efficacy of neutralising antibody-based therapeutics? Rev Med Virol 2021; 32:e2314. [PMID: 34861088 DOI: 10.1002/rmv.2314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022]
Abstract
Viral clearance is likely the best way to assess the efficacy of antibody-based therapies. Although antibodies can mediate a variety of effects that include modulation of inflammation, the demonstration of viral clearance provides an accessible and measurable parameter that can be used to evaluate efficacy and determine dosing. Therefore, it is important to ascertain the ability of monoclonal antibodies and convalescent plasma to effect viral clearance. For COVID-19, which is caused by the respiratory virus SARS-CoV-2, the most common assay to assess viral clearance is via a nasopharyngeal swab (NPS). However, assessment of antibody efficacy by sampling this site may be misleading because it may not be as accessible to serum antibodies as respiratory secretions or circulating blood. Adding to the complexity of assessing the efficacy of administered antibody, particularly in randomised controlled trials (RCTs) that enroled patients at different times after the onset of COVID-19 symptoms, viral clearance may also be mediated by endogenous antibody. In this article we critically review available data on viral clearance in RCTs, matched control studies, case series and case reports of antibody therapies in an attempt to identify variables that contribute to antibody efficacy and suggest optimal strategies for future studies.
Collapse
Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Massimo Franchini
- Division of Transfusion Medicine, Carlo Poma Hospital, Mantua, Italy
| | - Liise-Anne Pirofski
- Division of Infectious Diseases, Departments of Medicine, Microbiology and Immunology, Albert Einstein College of Medicine and Montefiore Medical Center, New York City, New York, USA
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Laboratory of Microbiology, ASST Sette Laghi, Varese, Italy
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
41
|
Pouwels KB, Pritchard E, Matthews PC, Stoesser N, Eyre DW, Vihta KD, House T, Hay J, Bell JI, Newton JN, Farrar J, Crook D, Cook D, Rourke E, Studley R, Peto TEA, Diamond I, Walker AS. Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK. Nat Med 2021; 27:2127-2135. [PMID: 34650248 PMCID: PMC8674129 DOI: 10.1038/s41591-021-01548-7] [Citation(s) in RCA: 327] [Impact Index Per Article: 109.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022]
Abstract
The effectiveness of the BNT162b2 and ChAdOx1 vaccines against new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections requires continuous re-evaluation, given the increasingly dominant B.1.617.2 (Delta) variant. In this study, we investigated the effectiveness of these vaccines in a large, community-based survey of randomly selected households across the United Kingdom. We found that the effectiveness of BNT162b2 and ChAdOx1 against infections (new polymerase chain reaction (PCR)-positive cases) with symptoms or high viral burden is reduced with the B.1.617.2 variant (absolute difference of 10-13% for BNT162b2 and 16% for ChAdOx1) compared to the B.1.1.7 (Alpha) variant. The effectiveness of two doses remains at least as great as protection afforded by prior natural infection. The dynamics of immunity after second doses differed significantly between BNT162b2 and ChAdOx1, with greater initial effectiveness against new PCR-positive cases but faster declines in protection against high viral burden and symptomatic infection with BNT162b2. There was no evidence that effectiveness varied by dosing interval, but protection was higher in vaccinated individuals after a prior infection and in younger adults. With B.1.617.2, infections occurring after two vaccinations had similar peak viral burden as those in unvaccinated individuals. SARS-CoV-2 vaccination still reduces new infections, but effectiveness and attenuation of peak viral burden are reduced with B.1.617.2.
Collapse
Affiliation(s)
- Koen B Pouwels
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| | - Emma Pritchard
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nicole Stoesser
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - David W Eyre
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Karina-Doris Vihta
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Department of Engineering, University of Oxford, Oxford, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK
- IBM Research, Hartree Centre, Sci-Tech Daresbury, UK
| | - Jodie Hay
- Glasgow Lighthouse Laboratory, Glasgow, UK
- University of Glasgow, Glasgow, UK
| | - John I Bell
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
| | - John N Newton
- Health Improvement Directorate, Public Health England, London, UK
| | | | - Derrick Crook
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | | | - Tim E A Peto
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | - A Sarah Walker
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- MRC Clinical Trials Unit at UCL, University College London, London, UK
| |
Collapse
|
42
|
Abstract
Waning vaccine-induced immunity coupled with the emergence of SARS-CoV-2 variants has led to increases in breakthrough infections, prompting consideration for vaccine booster doses. Boosters have been reported to be safe and increase SARS-CoV-2-specific neutralizing antibody levels, but how these doses impact the trajectory of the global pandemic and herd immunity is unknown. Information on immunology, epidemiology, and equitable vaccine distribution should be considered when deciding the timing and eligibility for COVID-19 vaccine boosters.
Collapse
|
43
|
Au J. Higher Vaccination Rate Predicts Reduction in SARS-CoV-2 Transmission across the United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.11.14.21266325. [PMID: 34816265 PMCID: PMC8609904 DOI: 10.1101/2021.11.14.21266325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began proliferating widely throughout the world in late 2019/early 2020, creating a global pandemic and health crisis. Although vaccines became available to the public approximately one year after the onset of the pandemic, there still remains much hesitancy surrounding vaccination even two years into the pandemic. One key concern comes from reports of breakthrough infections among the vaccinated that show comparable levels of peak viral load as the unvaccinated, calling into question the ability of vaccines to slow or prevent transmission. Therefore young, healthy individuals who are at low risk of serious complications themselves have little incentive to receive a vaccine that they are not convinced will protect others around them. To address this important concern, this article analyzes COVID-19 incidence in the United States as a function of each state's vaccination rate. Results show that states with higher percentages of fully vaccinated individuals report fewer new cases among the remaining unvaccinated population. These data add to accumulating evidence that COVID-19 vaccinations can indeed slow the spread of SARS-CoV-2, and are an important tool in society's arsenal to put this pandemic behind us.
Collapse
Affiliation(s)
- Jacky Au
- School of Education, University of California, Irvine, Irvine CA, 92697, USA
| |
Collapse
|
44
|
Bai W, Gu Y, Liu H, Zhou L. Epidemiology Features and Effectiveness of Vaccination and Non-Pharmaceutical Interventions of Delta and Lambda SARS-CoV-2 Variants. China CDC Wkly 2021; 3:977-982. [PMID: 34804631 PMCID: PMC8598544 DOI: 10.46234/ccdcw2021.216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/04/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- Wenqing Bai
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yue Gu
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haoliang Liu
- Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Zhou
- Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
45
|
Bošnjak B, Odak I, Barros-Martins J, Sandrock I, Hammerschmidt SI, Permanyer M, Patzer GE, Greorgiev H, Gutierrez Jauregui R, Tscherne A, Schwarz JH, Kalodimou G, Ssebyatika G, Ciurkiewicz M, Willenzon S, Bubke A, Ristenpart J, Ritter C, Tuchel T, Meyer zu Natrup C, Shin DL, Clever S, Limpinsel L, Baumgärtner W, Krey T, Volz A, Sutter G, Förster R. Intranasal Delivery of MVA Vector Vaccine Induces Effective Pulmonary Immunity Against SARS-CoV-2 in Rodents. Front Immunol 2021; 12:772240. [PMID: 34858430 PMCID: PMC8632543 DOI: 10.3389/fimmu.2021.772240] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/25/2021] [Indexed: 01/08/2023] Open
Abstract
Antigen-specific tissue-resident memory T cells (Trms) and neutralizing IgA antibodies provide the most effective protection of the lungs from viral infections. To induce those essential components of lung immunity against SARS-CoV-2, we tested various immunization protocols involving intranasal delivery of a novel Modified Vaccinia virus Ankara (MVA)-SARS-2-spike vaccine candidate. We show that a single intranasal MVA-SARS-CoV-2-S application in mice strongly induced pulmonary spike-specific CD8+ T cells, albeit restricted production of neutralizing antibodies. In prime-boost protocols, intranasal booster vaccine delivery proved to be crucial for a massive expansion of systemic and lung tissue-resident spike-specific CD8+ T cells and the development of Th1 - but not Th2 - CD4+ T cells. Likewise, very high titers of IgG and IgA anti-spike antibodies were present in serum and broncho-alveolar lavages that possessed high virus neutralization capacities to all current SARS-CoV-2 variants of concern. Importantly, the MVA-SARS-2-spike vaccine applied in intramuscular priming and intranasal boosting treatment regimen completely protected hamsters from developing SARS-CoV-2 lung infection and pathology. Together, these results identify intramuscular priming followed by respiratory tract boosting with MVA-SARS-2-S as a promising approach for the induction of local, respiratory as well as systemic immune responses suited to protect from SARS-CoV-2 infections.
Collapse
Affiliation(s)
- Berislav Bošnjak
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Ivan Odak
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | - Inga Sandrock
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | - Marc Permanyer
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | - Hristo Greorgiev
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | - Alina Tscherne
- Division of Virology, Department of Veterinary Sciences, Ludwig Maximilian University (LMU) Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Jan Hendrik Schwarz
- Division of Virology, Department of Veterinary Sciences, Ludwig Maximilian University (LMU) Munich, Munich, Germany
| | - Georgia Kalodimou
- Division of Virology, Department of Veterinary Sciences, Ludwig Maximilian University (LMU) Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - George Ssebyatika
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | | | | | - Anja Bubke
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | | | - Tamara Tuchel
- Institute for Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | | | - Dai-Lun Shin
- Institute for Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Sabrina Clever
- Institute for Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Leonard Limpinsel
- Division of Virology, Department of Veterinary Sciences, Ludwig Maximilian University (LMU) Munich, Munich, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Thomas Krey
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, Lübeck, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Asisa Volz
- Division of Virology, Department of Veterinary Sciences, Ludwig Maximilian University (LMU) Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Institute for Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Gerd Sutter
- Division of Virology, Department of Veterinary Sciences, Ludwig Maximilian University (LMU) Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover, Hannover, Germany
| |
Collapse
|
46
|
Rzymski P, Camargo CA, Fal A, Flisiak R, Gwenzi W, Kelishadi R, Leemans A, Nieto JJ, Ozen A, Perc M, Poniedziałek B, Sedikides C, Sellke F, Skirmuntt EC, Stashchak A, Rezaei N. COVID-19 Vaccine Boosters: The Good, the Bad, and the Ugly. Vaccines (Basel) 2021; 9:1299. [PMID: 34835230 PMCID: PMC8623745 DOI: 10.3390/vaccines9111299] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/06/2023] Open
Abstract
Pursuing vaccinations against COVID-19 brings hope to limit the spread of SARS-CoV-2 and remains the most rational decision under pandemic conditions. However, it does not come without challenges, including temporary shortages in vaccine doses, significant vaccine inequity, and questions regarding the durability of vaccine-induced immunity that remain unanswered. Moreover, SARS-CoV-2 has undergone evolution with the emergence of its novel variants, characterized by enhanced transmissibility and ability to at least partially evade neutralizing antibodies. At the same time, serum antibody levels start to wane within a few months after vaccination, ultimately increasing the risk of breakthrough infections. This article discusses whether the administration of booster doses of COVID-19 vaccines is urgently needed to control the pandemic. We conclude that, at present, optimizing the immunity level of wealthy populations cannot come at the expense of low-income regions that suffer from vaccine unavailability. Although the efficiency of vaccination in protecting from infection may decrease over time, current data show that efficacy against severe disease, hospitalization, and death remains at a high level. If vaccine coverage continues at extremely low levels in various regions, including African countries, SARS-CoV-2 may sooner or later evolve into variants better adapted to evade natural and vaccine-induced immunity, ultimately bringing a global threat that, of course, includes wealthy populations. We offer key recommendations to increase vaccination rates in low-income countries. The pandemic is, by definition, a major epidemiological event and requires looking beyond one's immediate self-interest; otherwise, efforts to contain it will be futile.
Collapse
Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland;
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
| | - Carlos A. Camargo
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Andrzej Fal
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- Collegium Medicum, Warsaw Faculty of Medicine, Cardinal Stefan Wyszyński University, 01-938 Warsaw, Poland
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, 15-540 Białystok, Poland;
| | - Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, Department of Agricultural and Biosystems Engineering, University of Zimbabwe, Mount Pleasant, Harare P.O. Box MP167, Zimbabwe;
| | - Roya Kelishadi
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- Department of Pediatrics, Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan 8174673441, Iran
| | - Alexander Leemans
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- PROVIDI Lab, Image Sciences Institute, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Juan J. Nieto
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- Instituto de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ahmet Ozen
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- Department of Pediatric Allergy and Immunology, Marmara University School of Medicine, 34854 Istanbul, Turkey
| | - Matjaž Perc
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- Faculty of Natural Sciences and Mathematics, University of Maribor, 2000 Maribor, Slovenia
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 404332, Taiwan
| | - Barbara Poniedziałek
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland;
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
| | - Constantine Sedikides
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- Center for Research on Self and Identity, School of Psychology, University of Southampton, Southampton SO17 1BJ, UK
| | - Frank Sellke
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- Alpert Medical School of Brown University, Division of Cardiothoracic Surgery, Rhode Island Hospital, Providence, RI 02905, USA
| | - Emilia C. Skirmuntt
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford OX1 3SY, UK;
| | - Anzhela Stashchak
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- International Relations Office, Kharkiv National Medical University, 61000 Kharkiv, Ukraine
| | - Nima Rezaei
- Universal Scientific Education and Research Network (USERN), https://usern.tums.ac.ir, Tehran 1417614411, Iran; (C.A.C.J.); (A.F.); (R.K.); (A.L.); (J.J.N.); (A.O.); (M.P.); (C.S.); (F.S.); (A.S.)
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran 1417614411, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| |
Collapse
|
47
|
McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen LE, Dang HV, De Marco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D. Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. SCIENCE (NEW YORK, N.Y.) 2021; 374:1621-1626. [PMID: 34751595 DOI: 10.1126/science.abl8506] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Ha V Dang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicholas Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jennifer Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Margaret Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | | | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
48
|
Deb P, Molla MMA, Saif-Ur-Rahman KM, Das MC, Das D. A review of epidemiology, clinical features and disease course, transmission dynamics, and neutralization efficacy of SARS-CoV-2 variants. THE EGYPTIAN JOURNAL OF BRONCHOLOGY 2021. [PMCID: PMC8571979 DOI: 10.1186/s43168-021-00090-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background After the first detection in November 2019, SARS-CoV-2 has spread rapidly over the continents and started the pandemic of the millennium. In addition to several novels and repurposed monoclonal antibodies (mAbs) as a therapeutic option against COVID-19, scientists from across the world have developed several candidate vaccines, developed mainly targeting the Wuhan strain, with very promising results to combat this pandemic. Unfortunately like any RNA viruses, SARS CoV-2 has also gone through the accumulation of hundreds and thousands of mutations in their genome lead to the development of several variants of concerns (VOC) and variants of interests (VOI), resulting in increased transmissibility and virulence of the virus, along with their capacity to escape cross-protection. Seemingly, the main hindrance of containing this pandemic right now is the effectiveness of currently available vaccines and mAbs against newly emerging variants. Therefore, it is important to monitor variants epidemiology, transmission dynamics, clinical characteristics, as well as their immune evasion capacity to implement appropriate vaccine strategy and other containment measures. Body In this review, we tried to focus on variants characteristics and to what extent they can escape immunity, provided by both available vaccinated sera and convalescent sera. A stringent literature review was performed using various databases, mentioned in the methodology portion. The current geographical distribution of these variants of SARS CoV-2 has been presented using a heat map. Findings from published articles comparing these variants, in terms of genome epidemiology, transmissibility, viral load dynamics, and association with different waves have been described briefly. Due strength was given while describing variants neutralization potency against current vaccines, mAbs, and also against convalescent sera. Data from both clinical trials and in vitro/ex-vivo studies have been discussed here. Comparative findings from several articles were brought into one concise paper. After careful reviewing of all the available data, it was clear that, without hesitation, we should strengthen our vaccination strategy, because the severity of COVID 19 is reasonably lower, irrespective of variants and vaccine used. Conclusion We hope that many falsified myths and beliefs regarding vaccine immunity and emerging variants will be clarified in light of this available evidence, which we summarized in our paper.
Collapse
|
49
|
Rzymski P, Poniedziałek B, Fal A. Willingness to Receive the Booster COVID-19 Vaccine Dose in Poland. Vaccines (Basel) 2021; 9:1286. [PMID: 34835217 PMCID: PMC8624071 DOI: 10.3390/vaccines9111286] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/18/2021] [Accepted: 11/03/2021] [Indexed: 12/29/2022] Open
Abstract
COVID-19 vaccinations are essential to mitigate the pandemic and prevent severe SARS-CoV-2 infections. However, the serum antibody levels in vaccinated individuals gradually decrease over time, while SARS-CoV-2 is undergoing an evolution toward more transmissible variants, such as B.1.617.2, ultimately increasing the risk of breakthrough infections and further virus spread. This cross-sectional online study of adult Poles (n = 2427) was conducted in September 2021 (before a general recommendation to administer a booster COVID-19 vaccine dose in Poland was issued) to assess the attitude of individuals who completed the current vaccination regime toward a potential booster dose of the COVID-19 vaccine and identify potential factors that may influence it. Overall, 71% of participants declared willingness to receive a booster COVID-19 dose, with a low median level of fear of receiving it of 1.0 (measured by the 10-point Likert-type scale), which was increased particularly in those having a worse experience (in terms of severity of side effects and associated fear) with past COVID-19 vaccination. The lowest frequency of willingness to receive a booster dose (26.7%) was seen in the group previously vaccinated with Ad26.COV2.S. The majority of individuals vaccinated previously with mRNA vaccines wished to receive the same vaccine, while in the case of AZD1222, such accordance was observed only in 9.1%. The main reasons against accepting a booster COVID-19 dose included the side effects experienced after previous doses, the opinion that further vaccination is unnecessary, and safety uncertainties. Women, older individuals (≥50 years), subjects with obesity, chronic diseases, and pre-vaccination and post-vaccination SARS-CoV-2 infections, and those with a history of vaccination against influenza were significantly more frequently willing to receive a booster COVID-19 dose. Moreover, the majority of immunosuppressed individuals (88%) were willing to receive an additional dose. The results emphasize some hesitancy toward potential further COVID-19 vaccination in the studied group of Poles and indicate the main groups to be targeted with effective science communication regarding the booster doses.
Collapse
Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland;
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznań, Poland
| | - Barbara Poniedziałek
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland;
| | - Andrzej Fal
- Collegium Medicum, Warsaw Faculty of Medicine, Cardinal Stefan Wyszyński University, 01-938 Warsaw, Poland;
| |
Collapse
|
50
|
Viral loads of Delta-variant SARS-CoV-2 breakthrough infections after vaccination and booster with BNT162b2. Nat Med 2021; 27:2108-2110. [PMID: 34728830 DOI: 10.1038/s41591-021-01575-4] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/08/2021] [Indexed: 11/08/2022]
Abstract
The effectiveness of the coronavirus disease 2019 (COVID-19) BNT162b2 vaccine in preventing disease and reducing viral loads of breakthrough infections (BTIs) has been decreasing, concomitantly with the rise of the Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, it is unclear whether the observed decreased effectiveness of the vaccine in reducing viral loads is inherent to the Delta variant or is dependent on time from immunization. By analyzing viral loads of over 16,000 infections during the current, Delta-variant-dominated pandemic wave in Israel, we found that BTIs in recently fully vaccinated individuals have lower viral loads than infections in unvaccinated individuals. However, this effect starts to decline 2 months after vaccination and ultimately vanishes 6 months or longer after vaccination. Notably, we found that the effect of BNT162b2 on reducing BTI viral loads is restored after a booster dose. These results suggest that BNT162b2 might decrease the infectiousness of BTIs even with the Delta variant, and that, although this protective effect declines with time, it can be restored, at least temporarily, with a third, booster, vaccine dose.
Collapse
|