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Van Nam L, Dien TC, Bang LVN, Thach PN, Van Duyet L. Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam. IJID Reg 2024; 11:100348. [PMID: 38601946 PMCID: PMC11004080 DOI: 10.1016/j.ijregi.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Objectives We investigated the genetic variations in the Alpha, Delta, and Omicron variants of SARS-CoV-2 and their association with clinical status and treatment outcomes in patients with COVID-19. Methods MiSeq was used to sequence the Alpha, Delta, and Omicron genomes, and MEGA 6.6 was used to define the nucleotide variations. We determined the association between clinical severity and treatment outcomes for the SARS-CoV-2 variants. Results The BA.1.1 and BA.2 lineages of the Omicron variant had 57-59 mutations, which is 2-2.7-fold higher than that of the B.1.1.7 (Alpha), B.1.617.2, and AY.57 (Delta) lineages. We found distinct mutations in SARS-CoV-2: five in Alpha (C26305T, G26558T, G7042T, C14120T, and C27509T); seven in Delta (C26408T, C1403T, C5184T, C9891T, T11418C, C11514T, and C22227T); and three in Omicron (C26408T, C8991T, and C25810T). Patients with the Delta variant had a severe rate of 23.8%, a critical rate of 53.7%, and a mortality rate of 38.9%, which were significantly higher than those with the Omicron and Alpha variants. Conclusions The Alpha, Delta, and Omicron variants in this study had genetic diversity and differed from the strains reported in other countries, with the Delta variant producing significantly more clinical severity and mortality than the Alpha and Omicron variants.
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Affiliation(s)
- Le Van Nam
- Departments of Infectious Disease, Military Hospital, Hanoi, Vietnam
| | - Trinh Cong Dien
- Departments of Infectious Disease, Military Hospital, Hanoi, Vietnam
| | | | - Pham Ngoc Thach
- Micobiology and Molecular Biology Department, National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Le Van Duyet
- Micobiology and Molecular Biology Department, National Hospital for Tropical Diseases, Hanoi, Vietnam
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Sadeghi F, Halaji M, Shirafkan H, Pournajaf A, Ghorbani H, Babazadeh S, Ezami N, Fallhpour K, Fakhraie F, Gorjinejad S, Amoli SS, Amiri FH, Baghershiroodi M, Ahmadnia Z, Salehi M, Tourani M, Jafarzadeh J, Tabari FS, Ahmadian SR, Mohammadi Abandansari R, Jafarian F, Rouhi S, Zabihollahi A, Mostafanezhad S, Saeedi F, Ebrahimian A, Deldar Z, Zavareh MSH, Bayani M, Broun MB, Shirzad M, Sabbaghi S, Mohammadi M, Rahmani R, Yahyapour Y. Characteristics, outcome, duration of hospitalization, and cycle threshold of patients with COVID-19 referred to four hospitals in Babol City: a multicenter retrospective observational study on the fourth, fifth, and sixth waves. BMC Infect Dis 2024; 24:55. [PMID: 38184533 PMCID: PMC10771668 DOI: 10.1186/s12879-023-08939-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND The aim of the present study was to compare the epidemiological patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infections, hospitalizations, deaths, and duration of hospitalization during the fourth, fifth and sixth epidemic waves of coronavirus disease 2019 (COVID-19) in Iran. METHODS A multicenter retrospective observational study was conducted on hospitalized patients in four hospitals in the Babol district of northern Iran. The study periods were during the fourth, fifth, and sixth waves of the epidemic in Iran, (March 2021 to March 2022). A total of 13,312 patients with suspected COVID-19 were included. Patient demographics, medical history, length of hospital stay, and clinical outcomes were obtained from the hospital information system. Data on the cycle threshold (Ct) and SARS-CoV2 variant were collected for SARS-CoV2-positive cases. RESULTS The highest number of hospitalized patients was reported during the fifth (Delta) wave (5231; 39.3%), while the lowest number of hospitalized patients was reported during the sixth (Omicron) wave (2143; 16.1%). In total, 6459 (48.5%) out of 13,312 hospitalized patients with suspected COVID-19 had a positive rRT-PCR result. The fifth (Delta) wave had the highest number of SARS-CoV2 rRT-PCR-positive hospitalized patients (3573, 55.3%), while the sixth (Omicron) wave had the lowest number (835, 12.9%). Moreover, 238 (3.7%) patients with laboratory-confirmed COVID-19 died. The hospital mortality rate was 6.8% in the fourth (Alpha) wave, which reduced to 2.7 and 3.5% in the fifth (Delta) and sixth (Omicron) waves, respectively (p < 0.001). CONCLUSIONS This is the most comprehensive study evaluating the epidemiologic characteristics of laboratory-confirmed SARS-CoV2 cases in Iran during the Alpha, Delta, and Omicron waves. The highest number of SARS-CoV2-positive hospitalized patients was in the fifth wave of COVID-19 (dominance of the Delta variant), while the sixth wave (dominance of the Omicron variant) had the lowest number. Comorbidities were similar, and cardiovascular disease, diabetes, kidney disease, and hypertension were the main risk factors in all waves.
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Affiliation(s)
- Farzin Sadeghi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Hoda Shirafkan
- Social Determinants of Health Research Center, Health Research Institute, Babol University of Medical Science, Babol, Iran
| | - Abazar Pournajaf
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Hossein Ghorbani
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Sara Babazadeh
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
- Department of Pathology, Ayatollah Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Nafiseh Ezami
- Part of Medical Records, Ayatollah Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Kobra Fallhpour
- Part of Infectious Control, Shahid Beheshti Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Fakhraie
- Part of Infectious Control, Shahid Yahyanejad Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Shahrbano Gorjinejad
- Part of Infectious Control, Amirkola Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Saghar Saber Amoli
- Department of Medical Microbiology and Biotechnology Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Hejazi Amiri
- Department of Medical Microbiology and Biotechnology Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mahnaz Baghershiroodi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Zahra Ahmadnia
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Maryam Salehi
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Mehdi Tourani
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Jalal Jafarzadeh
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Farzane Shanehbandpour Tabari
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Seyed Raheleh Ahmadian
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | | | - Farzaneh Jafarian
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Samaneh Rouhi
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Arezoo Zabihollahi
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Sarina Mostafanezhad
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Saeedi
- Department of Pathology, Ayatollah Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Arefeh Ebrahimian
- Department of Medical Microbiology and Biotechnology Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Zeinab Deldar
- Department of Medical Microbiology and Biotechnology Faculty of Medicine Guilan, University of Medical Sciences, City, Ondo, Nigeria
| | - Mahmoud Sadeghi Haddad Zavareh
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Masoumeh Bayani
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mana Bazi Broun
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Moein Shirzad
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Siamak Sabbaghi
- Clinical Research Development Unit of Rouhani Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Mohsen Mohammadi
- Non-Communicable Pediatric Diseases Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Rabeae Rahmani
- MSc. in Cellular and Molecular Biology, Education of Amol Teacher, Amol, Iran
| | - Yousef Yahyapour
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
- Biomedical and Microbial Advanced Technologies Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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Brehm TT, Heyer A, Woo MS, Fischer M, van der Meirschen M, Wichmann D, Jarczak D, Roedl K, Schmiedel S, Addo MM, Lütgehetmann M, Christner M, Huber S, Lohse AW, Kluge S, Schulze Zur Wiesch J. Comparative analysis of characteristics and outcomes in hospitalized COVID-19 patients infected with different SARS-CoV-2 variants between January 2020 and April 2022 - A retrospective single-center cohort study. J Infect Public Health 2023; 16:1806-1812. [PMID: 37741015 DOI: 10.1016/j.jiph.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/31/2023] [Accepted: 08/14/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, the roll-out of vaccines and therapeutic agents, as well as the emergence of novel SARS-CoV-2 variants, have shown significant effects on disease severity. METHODS Patients hospitalized at our center between January 2020 and April 2022 were attributed to subgroups depending on which SARS-CoV-2 variant was predominantly circulating in Germany: (i) Wild-type: January 1, 2020, to March 7, 2021, (ii) Alpha variant: August 3, 2021, to June 27, 2021, (iii) Delta variant: June 28, 2021, to December 26, 2021, and (iv) Omicron variant: December 27, 2021, to April 30, 2022. RESULTS Between January 2020 and April 2022, 1500 patients with SARS-CoV-2 infections were admitted to the University Medical Center Hamburg-Eppendorf. The rate of patients who were admitted to the intensive care unit (ICU) decreased from 31.2% (n = 223) in the wild-type group, 28.5% (n = 72) in the Alpha variant group, 18.8% (n = 67) in the Delta variant group, and 13.4% (n = 135) in the Omicron variant group. Also, in-hospital mortality decreased from 20.6% (n = 111) in the wild-type group, 17.5% (n = 30) in the Alpha variant group, 16.8% (n = 33) in the Delta variant group, and 6.6% (n = 39) in the Omicron variant group. The median duration of hospitalization was similar in all subgroups and ranged between 11 and 15 days throughout the pandemic. CONCLUSIONS In-hospital mortality and rate of ICU admission among hospitalized COVID-19 patients steadily decreased throughout the pandemic. However, the practically unchanged duration of hospitalization demonstrates the persistent burden of COVID-19 on the healthcare system.
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Affiliation(s)
- Thomas Theo Brehm
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Andreas Heyer
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marcel S Woo
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Neuroimmunology and Multiple Sclerosis (INIMS), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marlene Fischer
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marc van der Meirschen
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Dominic Wichmann
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Dominik Jarczak
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Kevin Roedl
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Stefan Schmiedel
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Marylyn M Addo
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany; Institute for Infection Research and Vaccine Development (IIRVD), University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Martin Christner
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Samuel Huber
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Ansgar W Lohse
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Stefan Kluge
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Julian Schulze Zur Wiesch
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany.
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Pascall DJ, Vink E, Blacow R, Bulteel N, Campbell A, Campbell R, Clifford S, Davis C, da Silva Filipe A, El Sakka N, Fjodorova L, Forrest R, Goldstein E, Gunson R, Haughney J, Holden MTG, Honour P, Hughes J, James E, Lewis T, MacLean O, McHugh M, Mollett G, Nyberg T, Onishi Y, Parcell B, Ray S, Robertson DL, Seaman SR, Shabaan S, Shepherd JG, Smollett K, Templeton K, Wastnedge E, Wilkie C, Williams T, Thomson EC. Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. J Infect 2023; 87:128-135. [PMID: 37270070 PMCID: PMC10234362 DOI: 10.1016/j.jinf.2023.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023]
Abstract
OBJECTIVES To determine how the intrinsic severity of successively dominant SARS-CoV-2 variants changed over the course of the pandemic. METHODS A retrospective cohort analysis in the NHS Greater Glasgow and Clyde (NHS GGC) Health Board. All sequenced non-nosocomial adult COVID-19 cases in NHS GGC with relevant SARS-CoV-2 lineages (B.1.177/Alpha, Alpha/Delta, AY.4.2 Delta/non-AY.4.2 Delta, non-AY.4.2 Delta/Omicron, and BA.1 Omicron/BA.2 Omicron) during analysis periods were included. Outcome measures were hospital admission, ICU admission, or death within 28 days of positive COVID-19 test. We report the cumulative odds ratio; the ratio of the odds that an individual experiences a severity event of a given level vs all lower severity levels for the resident and the replacement variant after adjustment. RESULTS After adjustment for covariates, the cumulative odds ratio was 1.51 (95% CI: 1.08-2.11) for Alpha versus B.1.177, 2.09 (95% CI: 1.42-3.08) for Delta versus Alpha, 0.99 (95% CI: 0.76-1.27) for AY.4.2 Delta versus non-AY.4.2 Delta, 0.49 (95% CI: 0.22-1.06) for Omicron versus non-AY.4.2 Delta, and 0.86 (95% CI: 0.68-1.09) for BA.2 Omicron versus BA.1 Omicron. CONCLUSIONS The direction of change in intrinsic severity between successively emerging SARS-CoV-2 variants was inconsistent, reminding us that the intrinsic severity of future SARS-CoV-2 variants remains uncertain.
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Affiliation(s)
- David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom; Joint Universities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom.
| | - Elen Vink
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Lothian, Edinburgh EH1 3EG, United Kingdom.
| | - Rachel Blacow
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | | | | | | | | | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | | | | | - Emily Goldstein
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Rory Gunson
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - John Haughney
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Matthew T G Holden
- Public Health Scotland, Edinburgh EH12 9EB, United Kingdom; School of Medicine, University of St Andrews, St Andrews KY16 9TF, United Kingdom.
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | - Tim Lewis
- NHS Lothian, Edinburgh EH1 3EG, United Kingdom.
| | - Oscar MacLean
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | - Guy Mollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Tommy Nyberg
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom.
| | | | - Ben Parcell
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
| | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, Glasgow G12 8TA, United Kingdom.
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Shaun R Seaman
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom.
| | - Sharif Shabaan
- Public Health Scotland, Edinburgh EH12 9EB, United Kingdom.
| | - James G Shepherd
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | | | - Craig Wilkie
- School of Mathematics and Statistics, University of Glasgow, Glasgow G12 8TA, United Kingdom.
| | - Thomas Williams
- NHS Lothian, Edinburgh EH1 3EG, United Kingdom; Royal Hospital for Children and Young People, University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom.
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom; London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.
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Rezaei Z, Asaei S, Sepehrpour S, Jamalidoust M, Namayandeh M, Norouzi F, Pourabbas B. SARS-CoV-2 variants circulating in the Fars province, southern Iran, December 2020-March 2021: A cross-sectional study. Health Sci Rep 2023; 6:e1373. [PMID: 37383927 PMCID: PMC10293940 DOI: 10.1002/hsr2.1373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/03/2023] [Accepted: 06/11/2023] [Indexed: 06/30/2023] Open
Affiliation(s)
- Zahra Rezaei
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Sadaf Asaei
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Shima Sepehrpour
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Marzieh Jamalidoust
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Mandana Namayandeh
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
| | - Fatemeh Norouzi
- Department of Microbiology, School of MedicineFasa University of Medical SciencesFasaIran
| | - Bahman Pourabbas
- Professor Alborzi Clinical Microbiology Research CenterShiraz University of Medical SciencesShirazIran
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Nichols JH, Williams EP, Parvathareddy J, Cao X, Kong Y, Fitzpatrick E, Webby RJ, Jonsson CB. Upper Respiratory Infection Drives Clinical Signs and Inflammatory Responses Following Heterologous Challenge of SARS-CoV-2 Variants of Concern in K18 Mice. Viruses 2023; 15:v15040946. [PMID: 37112926 PMCID: PMC10144791 DOI: 10.3390/v15040946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the emergence of several variants of concern (VOC) with increased immune evasion and transmissibility. This has motivated studies to assess protection conferred by earlier strains following infection or vaccination to each new VOC. We hypothesized that while NAbs play a major role in protection against infection and disease, a heterologous reinfection or challenge may gain a foothold in the upper respiratory tract (URT) and result in a self-limited viral infection accompanied by an inflammatory response. To test this hypothesis, we infected K18-hACE2 mice with SARS-CoV-2 USA-WA1/2020 (WA1) and, after 24 days, challenged with WA1, Alpha, or Delta. While NAb titers against each virus were similar across all cohorts prior to challenge, the mice challenged with Alpha and Delta showed weight loss and upregulation of proinflammatory cytokines in the URT and lower RT (LRT). Mice challenged with WA1 showed complete protection. We noted increased levels of viral RNA transcripts only in the URT of mice challenged with Alpha and Delta. In conclusion, our results suggested self-limiting breakthrough infections of Alpha or Delta in the URT, which correlated with clinical signs and a significant inflammatory response in mice.
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Affiliation(s)
- Jacob H Nichols
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan P Williams
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Xueyuan Cao
- Department of Health Promotion and Disease Prevention, College of Nursing, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ying Kong
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Elizabeth Fitzpatrick
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Richard J Webby
- St. Jude Children's Research Hospital, Memphis, TN 38163, USA
| | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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7
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Tam NT, Anh NT, Tung TS, Thach PN, Dung NT, Trang VD, Hung LM, Dien TC, Ngoc NM, Van Duyet L, Cuong PM, Phuong HVM, Thai PQ, Tung NLN, Man DNH, Phong NT, Quang VM, Thoa PTN, Truong NT, Thao TNP, Linh DP, Tai NT, Bao HT, Vuong VT, Nhung HTK, Hong PND, Hanh LTP, Chung LT, Nhan NTT, Thanh TT, Hung DT, Mai HK, Long TH, Trang NT, Thuong NTH, Hong NTT, Nhu LNT, Ny NTH, Thuy CT, Thanh LK, Nguyet LA, Mai LTQ, Thuong TC, Nga LH, Thanh TT, Thwaites G, Rogier van Doorn H, Chau NVV, Kesteman T, Van Tan L. Spatiotemporal Evolution of SARS-CoV-2 Alpha and Delta Variants during Large Nationwide Outbreak of COVID-19, Vietnam, 2021. Emerg Infect Dis 2023; 29:1002-1006. [PMID: 37015283 PMCID: PMC10124647 DOI: 10.3201/eid2905.221787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
We analyzed 1,303 SARS-CoV-2 whole-genome sequences from Vietnam, and found the Alpha and Delta variants were responsible for a large nationwide outbreak of COVID-19 in 2021. The Delta variant was confined to the AY.57 lineage and caused >1.7 million infections and >32,000 deaths. Viral transmission was strongly affected by nonpharmaceutical interventions.
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Heinrich F, Huter T, Mertens S, Lange P, Vering J, Heinemann A, Nörz DS, Hoffmann A, Aepfelbacher M, Ondruschka B, Krasemann S, Lütgehetmann M. New Postmortem Perspective on Emerging SARS-CoV-2 Variants of Concern, Germany. Emerg Infect Dis 2023; 29:652-656. [PMID: 36787498 PMCID: PMC9973696 DOI: 10.3201/eid2903.221297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
We performed autopsies on persons in Germany who died from COVID-19 and observed higher nasopharyngeal SARS-CoV-2 viral loads for variants of concern (VOC) compared with non-VOC lineages. Pulmonary inflammation and damage appeared higher in non-VOC than VOC lineages until adjusted for vaccination status, suggesting COVID-19 vaccination may mitigate pulmonary damage.
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9
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Doi A, Iwata K, Nakamura T, Oh K, Isome K, Hasegawa K, Kuroda H, Hasuike T, Seo R, Kosai H, Nakanishi N, Nomoto R, Fujiyama R, Kusunoki N, Iwamoto T, Nishioka H, Tomii K, Kihara Y. Clinical outcomes of COVID-19 caused by the Alpha variant compared with one by wild type in Kobe, Japan. A multi-center nested case-control study. J Infect Chemother 2023; 29:289-93. [PMID: 36494058 DOI: 10.1016/j.jiac.2022.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/02/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The emergence of the Alpha variant of novel coronavirus 2019 (SARS-CoV-2) is a concerning issue but their clinical implications have not been investigated fully. METHODS We conducted a nested case-control study to compare severity and mortality caused by the Alpha variant (B.1.1.7) with the one caused by the wild type as a control from December 2020 to March 2021, using whole-genome sequencing. 28-day mortality and other clinically important outcomes were evaluated. RESULTS Infections caused by the Alpha variant were associated with an increase in the use of oxygen (43.4% vs 26.3%. p = 0.017), high flow nasal cannula (21.2% vs 4.0%, p = 0.0007), mechanical ventilation (16.2% vs 6.1%, p = 0.049), ICU care (30.3% vs 14.1%, p = 0.01) and the length of hospital stay (17 vs 10 days, p = 0.031). More patients with the Alpha variant received medications such as dexamethasone. However, the duration of each modality did not differ between the 2 groups. Likewise, there was no difference in 28-day mortality between the 2 groups (12% vs 8%, p = 0.48), even after multiple sensitivity analyses, including propensity score analysis. CONCLUSION The Alpha variant was associated with a severe form of COVID-19, compared with the non-Alpha wild type, but might not be associated with higher mortality.
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10
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Janezic S, Mahnic A, Kuhar U, Kovač J, Jenko Bizjan B, Koritnik T, Tesovnik T, Šket R, Krapež U, Slavec B, Malovrh T, Battelino T, Rupnik M, Zohar Cretnik T. SARS-CoV-2 molecular epidemiology in Slovenia, January to September 2021. Euro Surveill 2023; 28:2200451. [PMID: 36820641 PMCID: PMC9951254 DOI: 10.2807/1560-7917.es.2023.28.8.2200451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
BackgroundSequencing of SARS-CoV-2 PCR-positive samples was introduced in Slovenia in January 2021. Our surveillance programme comprised three complementary schemes: (A) non-targeted sequencing of at least 10% of samples, (B) sequencing of samples positive after PCR screening for variants of concern (VOC) and (C) sequencing as per epidemiological indication.AimWe present the analysis of cumulative data of the non-targeted surveillance of SARS-CoV-2 and variant-dependent growth kinetics for the five most common variants in Slovenia for the first 9 months of 2021.MethodsSARS-CoV-2 PCR-positive samples, from January to September 2021, were selected for sequencing according to the national surveillance plan. Growth kinetics studies were done on Vero E6 cells.ResultsAltogether 15,175 genomes were sequenced and 64 variants were detected, of which three successively prevailed. Variant B.1.258.17 was detected in ca 80% of samples in January and was replaced, within 9 weeks, by the Alpha variant. The number of cases decreased substantially during the summer of 2021. However, the introduction of the Delta variant caused a fourth wave and completely outcompeted other variants. Other VOC were only detected in small numbers. Infection of Vero E6 cells showed higher replication rates for the variants Alpha and Delta, compared with B.1.258.17, B.1.258, and B.1.1.70, which dominated in Slovenia before the introduction of the Alpha and Delta variants.ConclusionInformation on SARS-CoV-2 variant diversity provided context to the epidemiological data of PCR-positive cases, contributed to control of the initial spread of known VOC and influenced epidemiological measures.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food, Maribor, Slovenia
| | - Aleksander Mahnic
- National Laboratory for Health, Environment and Food, Maribor, Slovenia
| | - Urška Kuhar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Kovač
- Clinical Institute of Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Clinical Institute of Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tom Koritnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia
| | - Tine Tesovnik
- Clinical Institute of Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Robert Šket
- Clinical Institute of Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Uroš Krapež
- Institute for Poultry, Birds, Small Mammals, and Reptiles, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Brigita Slavec
- Institute for Poultry, Birds, Small Mammals, and Reptiles, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tadej Malovrh
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tadej Battelino
- Clinical Institute of Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia
| | | | | | - CISLD NGS team
- Members of the CISLD NGS team, UMC Ljubljana are listed under Collaborators
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11
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Trobajo-Sanmartín C, Miqueleiz A, Guevara M, Fernández-Huerta M, Burgui C, Casado I, Baigorria F, Navascués A, Ezpeleta C, Castilla J. Comparison of the Risk of Hospitalization and Severe Disease Among Co-circulating Severe Acute Respiratory Syndrome Coronavirus 2 Variants. J Infect Dis 2023; 227:332-338. [PMID: 36179126 DOI: 10.1093/infdis/jiac385] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/18/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND We compare the risk of coronavirus disease 2019 (COVID-19) outcomes among co-circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants between January 2021 and May 2022 in Navarra, Spain. METHODS We compared the frequency of hospitalization and severe disease (intensive care unit admission or death) due to COVID-19 among the co-circulating variants. Variants analyzed were nonvariants of concern (non-VOCs), Alpha, Delta, Omicron BA.1, and Omicron BA.2. Logistic regression models were used to estimate adjusted odds ratio (aOR). RESULTS The Alpha variant had a higher risk of hospitalization (aOR, 1.86 [95 confidence interval {CI}, 1.282.71]) and severe disease (aOR, 2.40 [95 CI, 1.314.40]) than non-VOCs. The Delta variant did not show a significantly different risk of hospitalization (aOR, 0.73 [95 CI, .401.30]) and severe disease (aOR, 3.04 [95 CI, .5716.22]) compared to the Alpha variant. The Omicron BA.1 significantly reduced both risks relative to the Delta variant (aORs, 0.28 [95 CI, .16.47] and 0.23 [95 CI, .12.46], respectively). The Omicron BA.2 reduced the risk of hospitalization compared to BA.1 (aOR, 0.52 [95 CI, .29.95]). CONCLUSIONS The Alpha and Delta variants showed an increased risk of hospitalization and severe disease, which decreased considerably with the Omicron BA.1 and BA.2. Surveillance of variants can lead to important differences in severity.
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Affiliation(s)
- Camino Trobajo-Sanmartín
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | - Ana Miqueleiz
- Navarra Institute for Health Research, Pamplona, Spain
- Clinical Microbiology Department, Hospital Universitario de Navarra, Pamplona, Spain
| | - Marcela Guevara
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | - Miguel Fernández-Huerta
- Navarra Institute for Health Research, Pamplona, Spain
- Clinical Microbiology Department, Hospital Universitario de Navarra, Pamplona, Spain
| | - Cristina Burgui
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | - Itziar Casado
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | | | - Ana Navascués
- Navarra Institute for Health Research, Pamplona, Spain
- Clinical Microbiology Department, Hospital Universitario de Navarra, Pamplona, Spain
| | - Carmen Ezpeleta
- Navarra Institute for Health Research, Pamplona, Spain
- Clinical Microbiology Department, Hospital Universitario de Navarra, Pamplona, Spain
| | - Jesús Castilla
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
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12
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Hognon C, Bignon E, Monari A, Marazzi M, Garcia-Iriepa C. Revealing the Molecular Interactions between Human ACE2 and the Receptor Binding Domain of the SARS-CoV-2 Wild-Type, Alpha and Delta Variants. Int J Mol Sci 2023; 24:ijms24032517. [PMID: 36768842 PMCID: PMC9916449 DOI: 10.3390/ijms24032517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
After a sudden and first spread of the pandemic caused by the novel SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) wild-type strain, mutants have emerged which have been associated with increased infectivity, inducing surges in the contagions. The first of the so-called variants of concerns, was firstly isolated in the United Kingdom and later renamed Alpha variant. Afterwards, in the middle of 2021, a new variant appeared called Delta. The latter is characterized by the presence of point mutations in the Spike protein of SARS-CoV-2, especially in the Receptor Binding Domain (RBD). When in its active conformation, the RBD can interact with the human receptor Angiotensin-Converting Enzyme 2 (ACE2) to allow the entry of the virions into cells. In this contribution, by using extended all-atom molecular dynamic simulations, complemented with machine learning post-processing, we analyze the changes in the molecular interaction network induced by these different strains in comparison with the wild-type. On one hand, although relevant variations are evidenced, only limited changes in the global stability indicators and in the flexibility profiles have been observed. On the other hand, key differences were obtained by tracking hydrophilic and hydrophobic molecular interactions, concerning both positioning at the ACE2/RBD interface and formation/disruption dynamic behavior.
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Affiliation(s)
- Cécilia Hognon
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
| | - Emmanuelle Bignon
- UMR 7019 LPCT, Université de Lorraine and CNRS, F-5400 Nancy, France
| | - Antonio Monari
- ITODYS, Université Paris Cité and CNRS, F-75006 Paris, France
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
- Correspondence: (M.M.); (C.G.-I.)
| | - Cristina Garcia-Iriepa
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
- Correspondence: (M.M.); (C.G.-I.)
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13
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Shimada N, Shinoda M, Takei H, Yoshida Y, Nishimura M, Kousaka M, Morikawa M, Sato T, Matsuse H, Shinkai M. A case of reinfection with a different variant of SARS-CoV-2: case report. Egypt J Intern Med 2023; 35:13. [PMID: 36785595 PMCID: PMC9907179 DOI: 10.1186/s43162-023-00194-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) was previously thought to have a low reinfection rate, but there are concerns that the reinfection rate will increase with the emergence and spread of mutant variants. This report describes the case of a 36-year-old, non-immunosuppressed man who was infected twice by two different variants of COVID-19 within a relatively short period. Case presentation A 36-year-old Japanese man with no comorbidities was infected with the E484K variant (R.1 lineage) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptoms were mild and improved with symptomatic treatment alone. About four months later he presented to another outpatient department with high fever and headache. We diagnosed him as infected with the Alpha variant (B.1.1.7) of SARS-CoV-2 based on SARS-CoV-2 real-time reverse transcription polymerase chain reaction testing (RT-PCR). The patient was hospitalized with high fever. The patient received treatment in the form of anti-inflammatory therapy with corticosteroid and antibacterial chemotherapy. The patient improved without developing severe disease. Conclusion Concerns have been raised that the reinfection rate of COVID-19 will increase with the emergence of mutant variants. Particularly in mild cases, adequate amounts of neutralizing antibodies may not be produced, and reinfection may thus occur. Continued attention to sufficient infection control is thus essential.
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Affiliation(s)
- Nagashige Shimada
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan ,grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masahiro Shinoda
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Hiroaki Takei
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan ,grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Yuto Yoshida
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan ,grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masashi Nishimura
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Mio Kousaka
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Miwa Morikawa
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Takashi Sato
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Hiroto Matsuse
- grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masaharu Shinkai
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
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14
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Essaidi-Laziosi M, Alvarez C, Puhach O, Sattonnet-Roche P, Torriani G, Tapparel C, Kaiser L, Eckerle I. Sequential infections with rhinovirus and influenza modulate the replicative capacity of SARS-CoV-2 in the upper respiratory tract. Emerg Microbes Infect 2022; 11:412-423. [PMID: 34931581 PMCID: PMC8803056 DOI: 10.1080/22221751.2021.2021806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/19/2021] [Indexed: 01/07/2023]
Abstract
Although frequently reported since the beginning of the pandemic, questions remain regarding the impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) interaction with circulating respiratory viruses in coinfected patients. We here investigated dual infections involving early-pandemic SARS-CoV-2 and the Alpha variant and three of the most prevalent respiratory viruses, rhinovirus (RV) and Influenza A and B viruses (IAV and IBV), in reconstituted respiratory airway epithelial cells cultured at air-liquid interface. We found that SARS-CoV-2 replication was impaired by primary, but not secondary, rhino- and influenza virus infection. In contrast, SARS-CoV-2 had no effect on the replication of these seasonal respiratory viruses. Inhibition of SARS-CoV-2 correlated better with immune response triggered by RV, IAV and IBV than the virus entry. Using neutralizing antibody against type I and III interferons, SARS-CoV-2 blockade in dual infections could be partly prevented. Altogether, these data suggested that SARS-CoV-2 interaction with seasonal respiratory viruses would be modulated by interferon induction and could impact SARS-CoV-2 epidemiology when circulation of other respiratory viruses is restored.
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Affiliation(s)
- Manel Essaidi-Laziosi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Catia Alvarez
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Olha Puhach
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pascale Sattonnet-Roche
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Giulia Torriani
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Kaiser
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, University of Geneva, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Isabella Eckerle
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
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15
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Munnink BBO, Nijhuis RHT, Worp N, Boter M, Weller B, Verstrepen BE, GeurtsvanKessel C, Corsten MF, Russcher A, Koopmans M. Highly Divergent SARS-CoV-2 Alpha Variant in Chronically Infected Immunocompromised Person. Emerg Infect Dis 2022; 28:1920-1923. [PMID: 35925013 PMCID: PMC9423911 DOI: 10.3201/eid2809.220875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We detected a highly divergent SARS-CoV-2 Alpha variant in an immunocompromised person several months after the latest detection of the Alpha variant in the Netherlands. The patient was infected for 42 weeks despite several treatment regimens and disappearance of most clinical symptoms. We identified several potential immune escape mutations in the spike protein.
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16
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Onianwa O, Garratt I, Carter J, Spencer A, Verlander NQ, Pottage T, Bennett AM. Comparison of Surface Persistence of SARS-CoV-2 Alpha and Delta Variants on Stainless Steel at 4°C and 24°C. Appl Environ Microbiol 2022; 88:e0076422. [PMID: 35867558 DOI: 10.1128/aem.00764-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most studies on surface persistence of SARS-CoV-2 have been conducted at temperatures between 20°C and 30°C. There is limited data on the survival of SARS-CoV-2 at low temperatures. In this study, the stability of SARS-CoV-2 Alpha and Delta variants on stainless steel was investigated at two temperatures (4°C and 24°C). The results show that both variants decayed more rapidly at 24°C compared with 4°C. At 24°C, Alpha and Delta variants showed reductions of 0.33 log10 and 1.02 log10, respectively, within the first 2.5 h. However, at 4°C, Alpha variant showed a reduction of 0.16 log10 within the first 2.5 h while no reduction was observed with Delta variant. After remaining in situ for 24 h at 24°C, log10 reductions of 2.66 (Alpha) and 3.11 (Delta) were observed. No viable Alpha and Delta variant was recovered after 48 h and 72 h, respectively. After 24 h in a refrigerated environment (4°C) log10 reductions of 1.16 (Alpha) and 0.95 (Delta) were observed. Under these experimental conditions, both viruses survived on stainless steel for at least 1 week. No viable Alpha and Delta variant was recovered after 10 days. These findings support the potential for increased fomite transmission of SARS-CoV-2 during winter months in colder regions worldwide and in some industrial sectors. IMPORTANCE Human transmission is believed to occur primarily through direct transfer of infectious droplets or aerosols. However, fomite transmission through contact with contaminated surfaces may also play an important role. This study provides novel evidence comparing the stability of Alpha and Delta variants on stainless steel surfaces at 4°C and 24°C. At 4°C both variants were found to be still detectable for up to 7 days. At 24°C Delta variant could be recovered over 2 days compared with Alpha variant which could not be recovered after 2 days. This has implications for fomite transmission interventions for people living and working in cold environments.
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17
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Fourati S, Gautier G, Chovelon M, Soulier A, N'Debi M, Demontant V, Kennel C, Rodriguez C, Pawlotsky JM. Persistent SARS-CoV-2 Alpha Variant Infection in Immunosuppressed Patient, France, February 2022. Emerg Infect Dis 2022; 28:1512-1515. [PMID: 35514025 PMCID: PMC9239896 DOI: 10.3201/eid2807.220467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe persistent circulation of SARS-CoV-2 Alpha variant in an immunosuppressed patient in France during February 2022. The virus had a new pattern of mutation accumulation. The ongoing circulation of previous variants of concern could lead to reemergence of variants with the potential to propagate future waves of infection.
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18
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Chaki SP, Kahl-McDonagh MM, Neuman BW, Zuelke KA. Receptor-Binding-Motif-Targeted Sanger Sequencing: a Quick and Cost-Effective Strategy for Molecular Surveillance of SARS-CoV-2 Variants. Microbiol Spectr 2022; 10:e0066522. [PMID: 35638906 DOI: 10.1128/spectrum.00665-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequencing (WGS) is the gold standard for characterizing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and identification of new variants. However, the cost involved and time needed for WGS prevent routine, rapid clinical use. This study aimed to develop a quick and cost-effective surveillance strategy for SARS-CoV-2 variants in saliva and nasal swab samples by spike protein receptor-binding-motif (RBM)-targeted Sanger sequencing. Saliva and nasal swabs prescreened for the presence of the nucleocapsid (N) gene of SARS-CoV-2 were subjected to RBM-specific single-amplicon generation and Sanger sequencing. Sequences were aligned by CLC Sequence Viewer 8, and variants were identified based upon specific mutation signature. Based on this strategy, the present study identified Alpha, Beta/Gamma, Delta, and Omicron variants in a quick and cost-effective manner. IMPORTANCE The coronavirus disease 2019 (COVID-19) pandemic resulted in 427 million infections and 5.9 million deaths globally as of 21 February 2022. SARS-CoV-2, the causative agent of the COVID-19 pandemic, frequently mutates and has developed into variants of major public health concerns. Following the Alpha variant (B.1.1.7) infection wave, the Delta variant (B.1.617.2) became prevalent, and now the recently identified Omicron (B.1.1.529) variant is spreading rapidly and forming BA.1, BA.1.1, BA.2, BA.3, BA.4, and BA.5 lineages of concern. Prompt identification of mutational changes in SARS-CoV-2 variants is challenging but critical to managing the disease spread and vaccine/therapeutic modifications. Considering the cost involved and resource limitation of WGS globally, an RBM-targeted Sanger sequencing strategy is adopted in this study for quick molecular surveillance of SARS-CoV-2 variants.
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19
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Inui S, Fujikawa A, Gonoi W, Kawano S, Sakurai K, Uchida Y, Ishida M, Abe O. Comparison of CT findings of coronavirus disease 2019 (COVID-19) pneumonia caused by different major variants. Jpn J Radiol 2022; 40:1246-1256. [PMID: 35763239 PMCID: PMC9244322 DOI: 10.1007/s11604-022-01301-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022]
Abstract
Purpose To explore the CT findings and pneumonnia progression pattern of the Alpha and Delta variants of SARS-CoV-2 by comparing them with the pre-existing wild type. Method In this retrospective comparative study, a total of 392 patients with COVID-19 were included: 118 patients with wild type (70 men, 56.8 ± 20.7 years), 137 with Alpha variant (93 men, 49.4 ± 17.0 years), and 137 with Delta variant (94 men, 45.4 ± 12.4). Chest CT evaluation included opacities and repairing changes as well as lesion distribution and laterality. Chest CT severity score was also calculated. These parameters were statistically compared across the variants. Results Ground glass opacity (GGO) with consolidation and repairing changes were more frequent in the order of Delta variant, Alpha variant, and wild type throughout the disease course. Delta variant showed GGO with consolidation more conspicuously than did the other two on days 1–4 (vs. wild type, Bonferroni corrected p = 0.01; vs. Alpha variant, Bonferroni corrected p = 0.003) and days 5–8 (vs. wild type, Bonferroni corrected p < 0.001; vs. Alpha variant, Bonferroni corrected-p = 0.003). Total lung CT severity scores of Delta variant were higher than those of wild type on days 1–4 and 5–8 (Bonferroni corrected p = 0.01 and Bonferroni corrected p = 0.005, respectively) and that of Alpha variant on days 1–4 (Bonferroni corrected p = 0.002). There was no difference in the CT findings between wild type and Alpha variant. Conclusions Pneumonia progression of Delta variant may be more rapid and severe in the early stage than in the other two.
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Affiliation(s)
- Shohei Inui
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
- Department of Radiology, Japan Self-Defense Forces Central Hospital, 1-2-24, Ikejiri, Setagaya-ku, Tokyo, 154-0001, Japan.
| | - Akira Fujikawa
- Department of Radiology, Japan Self-Defense Forces Central Hospital, 1-2-24, Ikejiri, Setagaya-ku, Tokyo, 154-0001, Japan
| | - Wataru Gonoi
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shuichi Kawano
- Department of Respiratory Medicine, Japan Self-Defense Forces Central Hospital, 1-2-24, Ikejiri, Setagaya-ku, Tokyo, 154-0001, Japan
| | - Keita Sakurai
- Department of Radiology, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, Aichi, 474-8511, Japan
| | - Yuto Uchida
- Department of Neurology, Graduate School of Medicine, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8601, Japan
| | - Masanori Ishida
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Osamu Abe
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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20
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Riddell AC, Kele B, Harris K, Bible J, Murphy M, Dakshina S, Storey N, Owoyemi D, Pade C, Gibbons JM, Harrington D, Alexander E, McKnight Á, Cutino-Moguel T. Generation of Novel Severe Acute Respiratory Syndrome Coronavirus 2 Variants on the B.1.1.7 Lineage in 3 Patients With Advanced Human Immunodeficiency Virus-1 Disease. Clin Infect Dis 2022; 75:2016-2018. [PMID: 35616095 PMCID: PMC9213850 DOI: 10.1093/cid/ciac409] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Indexed: 01/17/2023] Open
Abstract
The emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is of public health concern in case of vaccine escape. Described are 3 patients with advanced human immunodeficiency virus (HIV)-1 and chronic SARS-CoV-2 infection in whom there is evidence of selection and persistence of novel mutations that are associated with increased transmissibility and immune escape.
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Affiliation(s)
- Anna C Riddell
- Correspondence: A. C. Riddell, Department of Infection, 3rd Floor Pathology and Pharmacy Building, Royal London Hospital, 80 Newark Street, London, UK, E1 2ES ()
| | - Beatrix Kele
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Kathryn Harris
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Jon Bible
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Maurice Murphy
- Department of Infection and Immunity, Barts Health NHS Trust, London, United Kingdom
| | - Subathira Dakshina
- Department of Infection and Immunity, Barts Health NHS Trust, London, United Kingdom
| | - Nathaniel Storey
- Microbiology, Virology, and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Dola Owoyemi
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Corinna Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Joseph M Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - David Harrington
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Eliza Alexander
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
| | - Áine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Teresa Cutino-Moguel
- Virology Department, Division of Infection, Barts Health NHS Trust, London, United Kingdom
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21
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Tanaka H, Ogata T, Shibata T, Nagai H, Takahashi Y, Kinoshita M, Matsubayashi K, Hattori S, Taniguchi C. Shorter Incubation Period among COVID-19 Cases with the BA.1 Omicron Variant. Int J Environ Res Public Health 2022; 19. [PMID: 35627870 DOI: 10.3390/ijerph19106330] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 01/27/2023]
Abstract
We aimed to elucidate the range of the incubation period in patients infected with the SARS-CoV-2 Omicron variant in comparison with the Alpha variant. Contact tracing data from three Japanese public health centers (total residents, 1.06 million) collected following the guidelines of the Infectious Diseases Control Law were reviewed for 1589 PCR-confirmed COVID-19 cases diagnosed in January 2022. We identified 77 eligible symptomatic patients for whom the date and setting of transmission were known, in the absence of any other probable routes of transmission. The observed incubation period was 3.03 ± 1.35 days (mean ± SDM). In the log-normal distribution, 5th, 50th and 95th percentile values were 1.3 days (95% CI: 1.0−1.6), 2.8 days (2.5−3.1) and 5.8 days (4.8−7.5), significantly shorter than among the 51 patients with the Alpha variant diagnosed in April and May in 2021 (4.94 days ± 2.19, 2.1 days (1.5−2.7), 4.5 days (4.0−5.1) and 9.6 days (7.4−13.0), p < 0.001). As this incubation period, mainly of sublineage BA.1, is even shorter than that in the Delta variant, it is thought to partially explain the variant replacement occurring in late 2021 to early 2022 in many countries.
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22
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Brosh-Nissimov T, Maor Y, Elbaz M, Lipman-Arens S, Wiener-Well Y, Hussein K, Orenbuch-Harroch E, Cohen R, Zimhony O, Chazan B, Nesher L, Rahav G, Zayyad H, Hershman-Sarafov M, Weinberger M, Najjar-Debbiny R, Chowers M. Hospitalised patients with breakthrough COVID-19 following vaccination during two distinct waves in Israel, January to August 2021: a multicentre comparative cohort study. Euro Surveill 2022; 27. [PMID: 35593161 PMCID: PMC9121662 DOI: 10.2807/1560-7917.es.2022.27.20.2101026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Background Changing patterns of vaccine breakthrough can clarify vaccine effectiveness. Aim To compare breakthrough infections during a SARS-CoV-2 Delta wave vs unvaccinated inpatients, and an earlier Alpha wave. Methods In an observational multicentre cohort study in Israel, hospitalised COVID-19 patients were divided into three cohorts: breakthrough infections in Comirnaty-vaccinated patients (VD; Jun–Aug 2021) and unvaccinated cases during the Delta wave (ND) and breakthrough infections during an earlier Alpha wave (VA; Jan–Apr 2021). Primary outcome was death or ventilation. Results We included 343 VD, 162 ND and 172 VA patients. VD were more likely older (OR: 1.06; 95% CI: 1.05–1.08), men (OR: 1.6; 95% CI: 1.0–2.5) and immunosuppressed (OR: 2.5; 95% CI: 1.1–5.5) vs ND. Median time between second vaccine dose and admission was 179 days (IQR: 166–187) in VD vs 41 days (IQR: 28–57.5) in VA. VD patients were less likely to be men (OR: 0.6; 95% CI: 0.4–0.9), immunosuppressed (OR: 0.3; 95% CI: 0.2–0.5) or have congestive heart failure (OR: 0.6; 95% CI: 0.3–0.9) vs VA. The outcome was similar between all cohorts and affected by age and immunosuppression and not by vaccination, variant or time from vaccination. Conclusions Vaccination was protective during the Delta variant wave, as suggested by older age and greater immunosuppression in vaccinated breakthrough vs unvaccinated inpatients. Nevertheless, compared with an earlier post-vaccination period, breakthrough infections 6 months post-vaccination occurred in healthier patients. Thus, waning immunity increased vulnerability during the Delta wave, which suggests boosters as a countermeasure.
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Affiliation(s)
- Tal Brosh-Nissimov
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheba, Israel.,Infectious Diseases Unit, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Yasmin Maor
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Infectious Disease Unit, Wolfson Medical Center, Holon, Israel
| | - Meital Elbaz
- Department of Infectious Diseases, Tel Aviv Sourasky Medical Center.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shelly Lipman-Arens
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Infectious Disease and Infection Control Unit, Hillel Yaffe Medical Center, Hadera, Israel
| | - Yonit Wiener-Well
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,Shaare Zedek Medical Center, Jerusalem, Israel
| | - Khetam Hussein
- Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Efrat Orenbuch-Harroch
- Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Regev Cohen
- Infectious Diseases Unit, Sanz Medical Center, Laniado Hospital, Netanya, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Oren Zimhony
- Infectious Diseases Unit, Kaplan Medical Center, Rehovot, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bibiana Chazan
- Infectious Diseases Unit, Emek Medical Center, Afula, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lior Nesher
- Infectious Disease Institute, Soroka Medical Center, Beer Sheba, Israel.,Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheba, Israel
| | - Galia Rahav
- Infectious Diseases Unit, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hiba Zayyad
- The Azrieli Faculty of Medicine in the Galilee, Bar Ilan university, Safed, Israel.,Infectious Disease Unit, The Baruch Padeh Medical Center, Tiberias, Israel
| | - Mirit Hershman-Sarafov
- Bnai Zion Medical Center, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Miriam Weinberger
- Shamir (Assaf Harofe) Medical Center, Zerifin, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronza Najjar-Debbiny
- Carmel Medical Center, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Michal Chowers
- Meir Medical Center, Kfar Saba, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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23
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Trobajo-Sanmartín C, Martínez-Baz I, Miqueleiz A, Fernández-Huerta M, Burgui C, Casado I, Baigorría F, Navascués A, Castilla J, Ezpeleta C. Differences in Transmission between SARS-CoV-2 Alpha (B.1.1.7) and Delta (B.1.617.2) Variants. Microbiol Spectr 2022;:e0000822. [PMID: 35412379 DOI: 10.1128/spectrum.00008-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The present study aimed to compare the susceptibility and infectivity between the Alpha and Delta variants of SARS-CoV-2 and to investigate characteristics of the index case and the contact that may affect transmission. The risk of SARS-CoV-2 infection was compared between close contacts of COVID-19 cases with Alpha and Delta variants during June 2021 to August 2021. In index cases, Spike gene target failure (TaqPath) was used as a proxy of Alpha variant and the L452R mutation (TaqMan) for Delta variant. Cox regression models were used to estimate adjusted relative risks (RR). We compared close contacts of index cases with Alpha (n = 2139) and Delta variants (n = 5439). Delta variant was more transmissible overall (relative risk [RR] 1.32, 95% CI = 1.13 to 1.53), and in non-household contacts (RR 1.71, 95% CI = 1.35 to 2.16), but not in household contacts (RR 1.10, 95% CI = 0.91 to 1.34; Pinteraction < 0.001). Delta variant excess transmission was observed when the index cases were 12 to 39 years old (RR 1.51, 95% CI = 1.27 to 1.79) and the close contacts were 18 to 39 years old (RR 1.62, 95% CI = 1.29 to 2.03), but not among those younger or older than such ages. Differences in transmissibility between variants disappeared with vaccination of the index case (RR 0.68, 95% CI = 0.46 to 1.02), but not with vaccination of the close contact. This report shows that the Delta variant is more transmissible than Alpha variant mainly among young adults. Vaccination of the index cases reduced the excess transmission, which reinforces the recommendation of vaccination to reduce transmission of the Delta variant. IMPORTANCE The higher transmissibility of the Delta variant of SARS-CoV-2 in comparison with the Alpha variant has been reported. We compared the transmission of the Alpha and Delta variants by characteristics and COVID-19 vaccination status of index cases and their close contacts. Interestingly, the Delta variant showed increased transmissibility when the index case was an adolescent or young adult and when the close contact was a young adult; however, in index cases and close contacts of other age groups, transmission did not differ between variants. This may explain the increased proportion of young people who have been infected in the surges due to the Delta variant. The Delta variant was more transmissible than the Alpha variant when the index cases were unvaccinated against COVID-19, and their vaccination equaled the transmissibility of both variants, which suggests a higher impact of vaccination in controlling transmission of the Delta variant.
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24
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Ye C, Lv Y, Kuang W, Yang L, Lu Y, Gu J, Ding F, Shen H, Yang Y. Inactivated vaccines prevent severe COVID-19 in patients infected with the Delta variant: a comparative study of the Delta and Alpha variants from China. J Med Virol 2022; 94:3613-3624. [PMID: 35365888 PMCID: PMC9088567 DOI: 10.1002/jmv.27759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/21/2022]
Abstract
The Delta variant has gradually replaced the Alpha variant as the major strain of SARS‐COV‐2 infection worldwide. We extracted the clinical characteristics and outcomes information about 381 hospitalized patients infected with Delta variant and compared them with 856 patients diagnosed with Alpha variant infection in Zhejiang Province. The majority (85.3%) of patients infected with the Delta variant had received inactivated vaccine. The patients' condition was generally mild. Most of them were mild (35.7%) and common (62.7%) types. Only six patients (1.5%) were severe/critical types. During the follow‐up period, patients infected with the Delta variant had longer hospital stays than the Alpha variant (24 [21–26] vs. 18 [14–24], p < 0.001). In addition, the unvaccinated patients infected with the Delta variant had a higher proportion of severe/critical cases than vaccinated patients (11.11% vs. 0.92%, p = 0.024) and a higher usage rate of glucocorticoids (38.89 vs. 14.77%, p = 0.017) and antibiotics (55.56% vs. 32.31%, p = 0.042) during hospitalization. The vaccine's efficacy against severe COVID‐19 did not diminish over time for patients who received two doses of the inactivated vaccine. The disease types and clinical manifestations were generally mild in patients infected with the Delta variant, possibly associated with widespread vaccination with inactivated vaccines in China.
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Affiliation(s)
- Chanyuan Ye
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University
| | - Yan Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University
| | - Wei Kuang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University
| | - Lisha Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University
| | - Yingfeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University
| | - Jueqing Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University
| | - Feng Ding
- Affiliated Hospital of Shaoxing University, Department of Infectious Diseases
| | - Huajiang Shen
- Affiliated Hospital of Shaoxing University, Department of Infectious Diseases
| | - Yida Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University
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25
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Ogata T, Tanaka H, Nozawa Y, Mukouyama K, Tanaka E, Osaki N, Noguchi E, Seo K, Wada K. Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. Int J Environ Res Public Health 2022; 19:ijerph19073889. [PMID: 35409572 PMCID: PMC8997792 DOI: 10.3390/ijerph19073889] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023]
Abstract
This study aimed to elucidate the household secondary attack rate (HSAR) of the Delta variant in comparison to the Alpha variant, and evaluate the risk factors among unvaccinated household contacts of patients with coronavirus disease 2019 (COVID-19). We studied household contacts of index cases of COVID-19 infected with Delta (L452R mutation), Alpha (N501Y mutation), and wild strain from December 2020 through November 2021 in Itako, Japan. The HSARs of the entire household contact, and the contact of index case with Delta variant were calculated and compared across the risk factors. We used a generalized estimating equation regression model for the multivariate analysis. We enrolled 1257 unvaccinated contacts from 580 households. The HSAR was higher in household contacts of index patients with Delta (48.5%) than with Alpha variant (21.7%) (aOR = 3.34, p = 0.000). In Delta variants, the HSAR was higher in household contacts with spousal relationships to index patients (63.4%) than contacts with other relationships (45.5%) (aOR 1.94, p = 0.026), and was lower in household contacts of index patients aged ≤19 (33.1%) than for contacts of index cases aged 20–59 years (52.6%) (aOR = 0.50, p = 0.027). The result of our study can be used to devise informed strategy to prevent transmission within households.
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Affiliation(s)
- Tsuyoshi Ogata
- Itako Public Health Center of Ibaraki Prefectural Government, Itako 311-2422, Japan; (Y.N.); (K.M.); (E.T.); (N.O.); (E.N.); (K.S.)
- Correspondence:
| | - Hideo Tanaka
- Fujiidera Public Health Center of Osaka Prefectural Government, Fujiidera 583-0024, Japan;
| | - Yumiko Nozawa
- Itako Public Health Center of Ibaraki Prefectural Government, Itako 311-2422, Japan; (Y.N.); (K.M.); (E.T.); (N.O.); (E.N.); (K.S.)
| | - Kazue Mukouyama
- Itako Public Health Center of Ibaraki Prefectural Government, Itako 311-2422, Japan; (Y.N.); (K.M.); (E.T.); (N.O.); (E.N.); (K.S.)
| | - Emiko Tanaka
- Itako Public Health Center of Ibaraki Prefectural Government, Itako 311-2422, Japan; (Y.N.); (K.M.); (E.T.); (N.O.); (E.N.); (K.S.)
| | - Natsumi Osaki
- Itako Public Health Center of Ibaraki Prefectural Government, Itako 311-2422, Japan; (Y.N.); (K.M.); (E.T.); (N.O.); (E.N.); (K.S.)
| | - Etsuko Noguchi
- Itako Public Health Center of Ibaraki Prefectural Government, Itako 311-2422, Japan; (Y.N.); (K.M.); (E.T.); (N.O.); (E.N.); (K.S.)
| | - Kayoko Seo
- Itako Public Health Center of Ibaraki Prefectural Government, Itako 311-2422, Japan; (Y.N.); (K.M.); (E.T.); (N.O.); (E.N.); (K.S.)
| | - Koji Wada
- Department of Public Health, Faculty of Medicine and Graduate School of Public Health, International University of Health and Welfare, Tokyo 107-8402, Japan;
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26
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Mosselhy DA, Kareinen L, Kivistö I, Virtanen J, Loikkanen E, Ge Y, Maunula L, Sironen T. Inhibition of SARS-CoV-2 Alpha Variant and Murine Noroviruses on Copper-Silver Nanocomposite Surfaces. Nanomaterials (Basel) 2022; 12:nano12071037. [PMID: 35407155 PMCID: PMC9000483 DOI: 10.3390/nano12071037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 02/05/2023]
Abstract
With the continued scenario of the COVID-19 pandemic, the world is still seeking out-of-the-box solutions to break its transmission cycle and contain the pandemic. There are different transmission routes for viruses, including indirect transmission via surfaces. To this end, we used two relevant viruses in our study. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the pandemic and human norovirus (HuNV), both known to be transmitted via surfaces. Several nanoformulations have shown attempts to inhibit SARS-CoV-2 and other viruses. However, a rigorous, similar inactivation scheme to inactivate the cords of two tedious viruses (SARS-CoV-2 Alpha variant and HuNV) is lacking. The present study demonstrates the inactivation of the SARS-CoV-2 Alpha variant and the decrease in the murine norovirus (MNV, a surrogate to HuNV) load after only one minute of contact to surfaces including copper-silver (Cu-Ag) nanocomposites. We thoroughly examined the physicochemical characteristics of such plated surfaces using diverse microscopy tools and found that Cu was the dominanting element in the tested three different surfaces (~56, ~59, and ~48 wt%, respectively), hence likely playing the major role of Alpha and MNV inactivation followed by the Ag content (~28, ~13, and ~11 wt%, respectively). These findings suggest that the administration of such surfaces within highly congested places (e.g., schools, public transportations, public toilets, and hospital and live-stock reservoirs) could break the SARS-CoV-2 and HuNV transmission. We suggest such an administration after an in-depth examination of the in vitro (especially on skin cells) and in vivo toxicity of the nanocomposite formulations and surfaces while also standardizing the physicochemical parameters, testing protocols, and animal models.
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Affiliation(s)
- Dina A. Mosselhy
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (L.K.); (I.K.); (J.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (D.A.M.); (T.S.)
| | - Lauri Kareinen
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (L.K.); (I.K.); (J.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Ilkka Kivistö
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (L.K.); (I.K.); (J.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Jenni Virtanen
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (L.K.); (I.K.); (J.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Emil Loikkanen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland; (E.L.); (L.M.)
| | - Yanling Ge
- VTT Technical Research Center of Finland Ltd., 02044 Espoo, Finland;
| | - Leena Maunula
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland; (E.L.); (L.M.)
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (L.K.); (I.K.); (J.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (D.A.M.); (T.S.)
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Acer Ö, Bahçe YG, Özüdoğru O. Association of viral load with age, gender, disease severity and death in SARS-CoV-2 variants. J Med Virol 2022; 94:3063-3069. [PMID: 35212012 DOI: 10.1002/jmv.27677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/02/2022] [Accepted: 02/21/2022] [Indexed: 11/12/2022]
Abstract
In the current study, the relationship between viral load, demographic characteristics, and disease information in 1007(48.5%) patients with Delta variant (B.1.617.2), and 1070 (51.5%) patients with Alpha variant (B1.1.7) mutations was investigated. We found that there was a significant difference in viral load between patients who died from the Alpha variant and those who were discharged (p<0.05). Nevertheless, no significant difference was observed in patients with Delta variant. The viral load in patients who died from the Alpha variant was significantly higher than those who were discharged (p<0.05). The viral load was found to be higher in females in patients with Delta variant, whereas it was very close in males and females in patients with Alpha variant (p>0.05). No significant difference was detected between the cycle threshold values (Ct) and disease severity. In terms of the mean Ct values, statistical differences were observed in patients with Delta and Alpha variant. The Alpha variant was found to have a higher viral load than the Delta variant. Furthermore, Delta variant was found to be higher in the 40-year-old and under-age group than in the Alpha variant, whereas the Alpha variant was higher in the 40-year-old and older group. While the rate of moderate and severe patients in Alpha variant was found to be higher, the rate of mild survivors was found to be higher in Delta variant. In conclusion, The increase in vaccination prior to the appearance of the Delta variant in our region may have influenced the viral load and clinical status of the patients. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ömer Acer
- Siirt University, Medical Faculty, Department of Medical Microbiology, 56100, Siirt, Turkey
| | - Yasemin Genç Bahçe
- Siirt Training and Research Hospital, Microbiology Laboratory, 56100, Siirt, Turkey
| | - Osman Özüdoğru
- Siirt University, Medical Faculty, Department of Internal Medicine, 56100, Siirt, Turkey
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Kislaya I, Rodrigues EF, Borges V, Gomes JP, Sousa C, Almeida JP, Peralta-Santos A, Nunes B. Comparative Effectiveness of Coronavirus Vaccine in Preventing Breakthrough Infections among Vaccinated Persons Infected with Delta and Alpha Variants. Emerg Infect Dis 2022; 28:331-337. [PMID: 34876242 PMCID: PMC8798697 DOI: 10.3201/eid2802.211789] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We developed a case-case study to compare mRNA vaccine effectiveness against Delta versus Alpha coronavirus variants. We used data on 2,097 case-patients with PCR-positive severe acute respiratory syndrome coronavirus 2 infections reported in Portugal during May-July 2021. We estimated the odds of vaccine breakthrough infection in Delta-infected versus Alpha-infected patients by using conditional logistic regression adjusted for age group and sex and matched by the week of diagnosis. We compared reverse-transcription PCR cycle threshold values by vaccination status and variant as an indirect measure of viral load. We found significantly higher odds of vaccine breakthrough infection in Delta-infected patients than in Alpha-infected patients (odds ratio 1.96 [95% CI 1.22-3.14]), suggesting lower effectiveness of the mRNA vaccines in preventing infection with the Delta variant. We estimated lower mean cycle threshold values for the Delta cases (mean difference -2.10 [95% CI -2.74 to -1.47]), suggesting higher infectiousness than the Alpha variant.
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Affiliation(s)
| | | | - Vítor Borges
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - João P. Gomes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - Carlos Sousa
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - José P. Almeida
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - André Peralta-Santos
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - Baltazar Nunes
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
| | - PT-COVID-19 Group2
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal (I. Kislaya, V. Borges, J.P. Gomes, B. Nunes)
- Direção-Geral da Saúde, Lisbon (E.F. Rodrigues, A. Peralta-Santos)
- Unilabs, Porto, Portugal (C. Sousa, J.P. Almeida)
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29
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Seadawy MG, Gad AF, Abo-Elmaaty SA, Hassan MG. Genome sequencing of SARS-CoV-2 reveals the prevalence of variant B 1.1.7 in Egypt. Infect Genet Evol 2022; 97:105191. [PMID: 34923158 PMCID: PMC8677423 DOI: 10.1016/j.meegid.2021.105191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/12/2022]
Abstract
Recently, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) resulted in Coronavirus Disease 2019 (COVID-19) outbreak. A new SARS-CoV-2 strain is expected to emerge in late 2020, including B.1.1.7. The high transmission rate of SARS-CoV-2 B.1.1.7 has raised public health concerns in several countries. Hence, in this study, we assessed the sequencing of SARS-COV2 to reveals the prevalence of the SARS-CoV-2 Alpha variant (B 1.1.7) in Egypt. We found that the viral transmission of the alpha variant is expanding. Moreover, based on hospitalizations and case fatality rates, there is a potential for increasing severity. There was no effect on susceptibility to Emergency Use Authorization monoclonal antibody treatments. However, there was minimal impact on neutralization by convalescent and post-vaccination sera. Samples have been clustered into the 20D sub clade for the majority of them. The eight samples shown in our study are considered the first recorded samples with the Alpha variant in Egypt. Therefore, The Egyptian government, represented by the Ministry of Health, must take all measures to examine the compatibility of the currently used vaccines with this new strain and the feasibility of the treatment protocol presently used with such strains developed in the Arab Republic of Egypt.
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Affiliation(s)
| | - Ahmed F Gad
- Biological Prevention Department, Egypt Army, Egypt.
| | - Sabah A Abo-Elmaaty
- Botany and Microbiology Department, Faculty of Science, Benha University, Egypt
| | - Mervat G Hassan
- Botany and Microbiology Department, Faculty of Science, Benha University, Egypt
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30
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Huang ACC, Lin SM, Chiu TH, Chang KW, Huang TH, Yang TH, Shiao YH, Lee CS, Chung FT, Chiu CH. Comparison of Clinical Characteristics and Outcomes of Hospitalized Patients Infected with the D614G Strain or Alpha Variant of COVID-19 in Taiwan: A Multi-Center Cohort Study. Int J Med Sci 2022; 19:1912-1919. [PMID: 36438919 PMCID: PMC9682515 DOI: 10.7150/ijms.76725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022] Open
Abstract
Objective: Direct comparison of the clinical traits of coronavirus disease 2019 (COVID-19) in strain D614G, which originated from Wuhan, China, and the Alpha variant, which contains 17 mutations, infected patients could help physicians distinguish between strains and make clinical decisions accordingly. This study sought to compare the clinical characteristics and outcomes of the D614G strain and Alpha variant of SARS-COV-2 and identify the predictors for viral RNA clearance and in-hospital mortality in patients with COVID-19. Methods: This study recruited consecutive patients from four hospitals between March 1, 2020, and July 31, 2021. Demographic characteristics, laboratory results, and clinical outcomes were determined. Results: Among the 239 enrolled patients, 11.2% (27/239) were infected with strain D614G and 88.7% (212/239) were infected with the Alpha variant. There were no significant differences in disease progression, rate of respiratory failure, subsequent development of acute respiratory distress syndrome (ARDS), acute kidney injury, cardiac injury, duration of stay in the intensive care unit or hospital, discharge rate, mortality rate, or viral RNA clearance time between the two groups. Multivariate Cox regression revealed that antibiotic therapy reduced the risk of delayed viral RNA clearance (hazard ratio [HR], 0.26; 95% confidence interval [CI], 0.13-0.55), while autoimmune disease increased the risk of delayed viral RNA clearance (HR, 3.98; 95% CI, 1.21-13.04). Elderly patients (age > 65 years) and patients with a history of cerebrovascular accident (CVA) were at increased risk of in-hospital mortality (HR, 5.14; 95% CI, 1.06-24.72 and HR, 3.62; 95% CI, 1.25-10.42, respectively). Conclusions: There were no significant differences between the D614G strain and Alpha variant of COVID-19 in terms of clinical characteristics and outcomes. However, factors affecting viral RNA clearance and the risk of in-hospital mortality were identified. These results could help to inform the future prioritization of resource allocation and identify patients in need of intense monitoring.
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Affiliation(s)
- Allen Chung-Cheng Huang
- Department of Thoracic Medicine, Chang Gung Memorial Hospital, Chang Gung University, School of Medicine, Taoyuan, Taiwan
| | - Shu-Min Lin
- Department of Thoracic Medicine, Chang Gung Memorial Hospital, Chang Gung University, School of Medicine, Taoyuan, Taiwan
| | - Tzu-Hsuan Chiu
- Department of Thoracic Medicine, Chang Gung Memorial Hospital, Chang Gung University, School of Medicine, Taoyuan, Taiwan
| | - Ko-Wei Chang
- Department of Thoracic Medicine, Chang Gung Memorial Hospital, Chang Gung University, School of Medicine, Taoyuan, Taiwan
| | - Tse-Hung Huang
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan.,School of Traditional Chinese Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Health Industry Technology, Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan, Taiwan.,Department & Graduate Institute of Chemical Engineering & Graduate Institute of Biochemical Engineering, Ming Chi University of Technology, New Taipei, Taiwan.,School of Nursing, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
| | - Tsung-Hsien Yang
- Department of Traditional Chinese Medicine, New Taipei Municipal Tucheng Hospital, New Taipei City, Taiwan
| | - Yi-Hsien Shiao
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Chung-Shu Lee
- Department of Thoracic Medicine, Chang Gung Memorial Hospital, Chang Gung University, School of Medicine, Taoyuan, Taiwan.,Department of Pulmonary and Critical Care Medicine, New Taipei Municipal Tucheng Hospital, New Taipei City, Taiwan
| | - Fu-Tsai Chung
- Department of Thoracic Medicine, Chang Gung Memorial Hospital, Chang Gung University, School of Medicine, Taoyuan, Taiwan.,Department of Pulmonary and Critical Care Medicine, New Taipei Municipal Tucheng Hospital, New Taipei City, Taiwan
| | - Cheng-Hsun Chiu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
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31
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Mukhopadhyay L, Gupta N, Yadav PD, Aggarwal N. Neutralization assays for SARS-CoV-2: Implications for assessment of protective efficacy of COVID-19 vaccines. Indian J Med Res 2022; 155:105-122. [PMID: 35859437 PMCID: PMC9552365 DOI: 10.4103/ijmr.ijmr_2544_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The WHO emergency use-listed (EUL) COVID-19 vaccines were developed against early strains of SARS-CoV-2. With the emergence of SARS-CoV-2 variants of concern (VOCs) - Alpha, Beta, Gamma, Delta and Omicron, it is necessary to assess the neutralizing activity of these vaccines against the VOCs. PubMed and preprint platforms were searched for literature on neutralizing activity of serum from WHO EUL vaccine recipients, against the VOCs, using appropriate search terms till November 30, 2021. Our search yielded 91 studies meeting the inclusion criteria. The analysis revealed a drop of 0-8.9-fold against Alpha variant, 0.3-42.4-fold against Beta variant, 0-13.8-fold against Gamma variant and 1.35-20-fold against Delta variant in neutralization titres of serum from the WHO EUL COVID-19 vaccine recipients, as compared to early SARS-CoV-2 isolates. The wide range of variability was due to differences in the choice of virus strains selected for neutralization assays (pseudovirus or live virus), timing of serum sample collection after the final dose of vaccine (day 0 to 8 months) and sample size (ranging from 5 to 470 vaccinees). The reasons for this variation have been discussed and the possible way forward to have uniformity across neutralization assays in different laboratories have been described, which will generate reliable data. Though in vitro neutralization studies are a valuable tool to estimate the performance of vaccines against the backdrop of emerging variants, the results must be interpreted with caution and corroborated with field-effectiveness studies.
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Affiliation(s)
- Labanya Mukhopadhyay
- Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Nivedita Gupta
- Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Pragya D Yadav
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Neeraj Aggarwal
- Virology Unit, Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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32
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Hu X, Liu Z, Liang J, Song X, Wang Z, Gao R, Jiang F. Environmental contamination of a quarantine hotel via SARS-CoV-2 positive travellers. J Travel Med 2021; 28:6377253. [PMID: 34581412 PMCID: PMC8500083 DOI: 10.1093/jtm/taab148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/12/2021] [Accepted: 09/14/2021] [Indexed: 01/12/2023]
Abstract
We report on the extent of environmental contamination of a quarantine hotel in China via two SARS-CoV-2 VOCs positive travellers.
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Affiliation(s)
- Xiaowen Hu
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong Province, China
| | - Ziran Liu
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong Province, China
| | - Jiwei Liang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong Province, China
| | - Xin Song
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong Province, China
| | - Zhaoguo Wang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong Province, China
| | - Ruqin Gao
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong Province, China
| | - Fachun Jiang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao, Shandong Province, China
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Muñoz M, Patiño LH, Ballesteros N, Castañeda S, Luna N, Delgado L, Hernandez-Pereira C, Shaban MV, Muñoz SA, Paniz-Mondolfi A, Ramírez JD. Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources. One Health 2021; 14:100363. [PMID: 34931174 PMCID: PMC8673956 DOI: 10.1016/j.onehlt.2021.100363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/18/2022] Open
Abstract
Due to the necessity to control human-to-human spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the overwhelming majority of the generated data on this virus was solely related to the genomic characteristics of strains infecting humans; conversely, this work aimed to recover and analyze the diversity of viral genomes from non-human sources. From a set of 3595 publicly available SARS-CoV-2 genome sequences, 128 lineages were identified in non-human hosts, the majority represented by the variants of concern Delta (n = 1105, 30.7%) and Alpha (n = 466, 12.9%), followed by B.1.1.298 lineage (n = 458, 12.7%). Environment, Neovison vison, Odocoileus virginianus and Felis catus were the non-human sources with the highest number of lineages (14, 12 and 10, respectively). Phylogenomic analyses showed viral clusters from environmental sources, N. vison, O. virginianus, Panthera tigris, and Panthera leo. These clusters were collectively related to human viruses as well as all other non-human sources that were heterogeneously distributed in the phylogenetic tree. Further, the genetic details of viral genomes from bats and pangolins were independently investigated owing to their high divergence, revealing five distinct clusters. Cluster 4 exclusively included bat-sourced genomes and the SARS-CoV-2 reference strain Wuhan-01. In summary, this study identified new genetic landmarks of SARS-CoV-2 evolution. We propose potential interspecies transmission routes of SARS-CoV-2 between animals and humans, which should be considered in order to establish better pathogen surveillance and containment strategies.
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Affiliation(s)
- Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nicolás Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Lourdes Delgado
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Carlos Hernandez-Pereira
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Maryia V Shaban
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Shirly Alexandra Muñoz
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Bogotá, Colombia.,Unidad de Salud de Ibagué (USI) E.S.E., Ibagué, Colombia
| | - Alberto Paniz-Mondolfi
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela.,Microbiology Division, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.,Microbiology Division, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
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34
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Luong Ngyen LB, Bauer R, Lesieur Z, Galtier F, Duval X, Vanhems P, Lainé F, Tattevin P, Durier C, Launay O. Vaccine effectiveness against COVID-19 hospitalization in adults in France: A test negative case control study. Infect Dis Now 2021; 52:40-43. [PMID: 34920180 PMCID: PMC8673927 DOI: 10.1016/j.idnow.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/18/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
Background Measuring vaccine effectiveness (VE) using real-life data is critical to confirm the effectiveness of licensed vaccine, which could strengthen vaccination adherence. Methods We measured VE against adult COVID-19 hospitalization in five hospitals in France using a test negative design. We compared the odds of vaccinated patients hospitalized with COVID-19 with the odds of vaccinated patients hospitalized for the same symptoms with a negative test. Results A total of 853 patients (463 cases and 390 controls) were included, with a total of 170 patients vaccinated (104 with one dose, 65 with two doses, and one with three doses). There were four cases of breakthrough infections, all in immunocompromised patients. The VE was 84.0% (CI0.95 = [72.6; 90.6]) for one dose and 96.2% (CI0.95 = [86.8; 98.9]) for two doses. Conclusion Our results confirm the high VE of COVID-19 vaccine in France to prevent hospitalizations due to the alpha variant.
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Affiliation(s)
| | | | | | - Florence Galtier
- Inserm, CIC 1411, CHU de Montpellier, Saint-Éloi Hospital, Montpellier, France
| | - Xavier Duval
- Inserm, CIC 1425, AP-HP, Hôpital Bichat, Paris, France
| | - Philippe Vanhems
- Service d'hygiène, épidémiologie, infectiovigilance et prévention, hospices civils de Lyon, Lyon, France
| | | | - Pierre Tattevin
- Services de maladies infectieuses et réanimation médicale, hôpital Pontchaillou, CHU de Rennes, Rennes, France
| | | | - Odile Launay
- Inserm, CIC 1417, Hôpital Cochin, AP-HP, Paris, France; Inserm, F-CRIN I-REIVAC, Paris, France
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35
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Boshier FAT, Venturini C, Stirrup O, Guerra-Assunção JA, Alcolea-Medina A, Becket AH, Byott M, Charalampous T, Filipe ADS, Frampton D, Glaysher S, Khan T, Kulasegara-Shylini R, Kele B, Monahan IM, Mollett G, Parker M, Pelosi E, Randell P, Roy S, Taylor JF, Weller SJ, Wilson-Davies E, Wade P, Williams R, Copas AJ, Cutino-Moguel T, Freemantle N, Hayward AC, Holmes A, Hughes J, Mahungu TW, Nebbia G, Nastouli E, Partridge DG, Pope CF, Price JR, Robson SC, Saeed K, Shin GY, de Silva TI, Snell LB, Thomson EC, Witney AA, Breuer J. The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. J Infect 2021; 83:693-700. [PMID: 34610391 PMCID: PMC8487101 DOI: 10.1016/j.jinf.2021.09.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals. METHODS We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-CoV-2 infections, sampled from 16th November 2020 to 10th January 2021, from nine hospitals participating in the COG-UK HOCI study. Outbreaks were identified using ward information, lineage and pairwise genetic differences between viral sequences. RESULTS Mixed effects logistic regression analysis of 4184 sequences showed healthcare-acquired infections were no more likely to be identified as the Alpha variant than community acquired infections. Nosocomial outbreaks were investigated based on overlapping ward stay and SARS-CoV-2 genome sequence similarity. There was no significant difference in the number of patients involved in outbreaks caused by the Alpha variant compared to outbreaks caused by other lineages. CONCLUSIONS We find no evidence to support it causing more nosocomial transmission than previous lineages. This suggests that the stringent infection prevention measures already in place in UK hospitals contained the spread of the Alpha variant as effectively as other less transmissible lineages, providing reassurance of their efficacy against emerging variants of concern.
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Affiliation(s)
- Florencia A T Boshier
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Cristina Venturini
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Oliver Stirrup
- Institute for Global Health, University College London, London, United Kingdom
| | - José Afonso Guerra-Assunção
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Infection Sciences, Viapath, London, United Kingdom
| | - Angela H Becket
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom; School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Matthew Byott
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Dan Frampton
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; Division of Infection and Immunity, University College London, London, United Kingdom
| | - Sharon Glaysher
- Portsmouth Hospitals University NHS Trust, Queen Alexandra Hospital, Portsmouth PO6 3LY, United Kingdom
| | - Tabassum Khan
- Division of Infection, The Royal London Hospital, Barts Health, United Kingdom
| | | | - Beatrix Kele
- Division of Infection, The Royal London Hospital, Barts Health, United Kingdom
| | - Irene M Monahan
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
| | - Guy Mollett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Matthew Parker
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, United Kingdom; Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom; Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, United Kingdom
| | - Emanuela Pelosi
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Paul Randell
- Department of Infection and Immunity, North West London Pathology, London, United Kingdom
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Joshua F Taylor
- Department of Microbiology, South West London Pathology, Jenner Wing, St. George's Hospital, Blackshaw Road, London SW17 0QT, United Kingdom
| | - Sophie J Weller
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Eleri Wilson-Davies
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Phillip Wade
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Rachel Williams
- Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Andrew J Copas
- Institute for Global Health, University College London, London, United Kingdom
| | | | - Nick Freemantle
- Institute for Clinical Trials and Methodology, University College London, London, United Kingdom
| | - Andrew C Hayward
- Institute of Epidemiology and Health Care, University College London, London, United Kingdom
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, United Kingdom; Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Tabitha W Mahungu
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, United Kingdom
| | - Eleni Nastouli
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Cassie F Pope
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom; Infection Care Group, St George's University Hospitals NHS Foundation Trust, Blackshaw Road, London SW17 0QT, United Kingdom
| | - James R Price
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Samuel C Robson
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom; School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom; School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Kordo Saeed
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, United Kingdom; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Tremona Road, Southampton, United Kingdom
| | - Gee Yen Shin
- Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
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Julin CH, Robertson AH, Hungnes O, Tunheim G, Bekkevold T, Laake I, Aune IF, Killengreen MF, Strand TR, Rykkvin R, Dorenberg DH, Stene-Johansen K, Berg ES, Bodin JE, Oftung F, Steens A, Næss LM. Household Transmission of SARS-CoV-2: A Prospective Longitudinal Study Showing Higher Viral Load and Increased Transmissibility of the Alpha Variant Compared to Previous Strains. Microorganisms 2021; 9:2371. [PMID: 34835495 PMCID: PMC8622435 DOI: 10.3390/microorganisms9112371] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/23/2022] Open
Abstract
We studied the secondary attack rate (SAR), risk factors, and precautionary practices of household transmission in a prospective, longitudinal study. We further compared transmission between the Alpha (B.1.1.7) variant and non-Variant of Concern (non-VOC) viruses. From May 2020 throughout April 2021, we recruited 70 confirmed COVID-19 cases with 146 household contacts. Participants donated biological samples eight times over 6 weeks and answered questionnaires. SARS-CoV-2 infection was detected by real-time RT-PCR. Whole genome sequencing and droplet digital PCR were used to establish virus variant and viral load. SARS-CoV-2 transmission occurred in 60% of the households, and the overall SAR for household contacts was 50%. The SAR was significantly higher for the Alpha variant (78%) compared with non-VOC viruses (43%) and was associated with a higher viral load. SAR was higher in household contacts aged ≥40 years (69%) than in younger contacts (40-47%), and for contacts of primary cases with loss of taste/smell. Children had lower viral loads and were more often asymptomatic than adults. Sleeping separately from the primary case reduced the risk of transmission. In conclusion, we found substantial household transmission, particularly for the Alpha variant. Precautionary practices seem to reduce SAR, but preventing household transmission may become difficult with more contagious variants, depending on vaccine use and effectiveness.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lisbeth Meyer Næss
- Division of Infection Control, Norwegian Institute of Public Health, P.O. Box 222 Skøyen, 0213 Oslo, Norway; (C.H.J.); (A.H.R.); (O.H.); (G.T.); (T.B.); (I.L.); (I.F.A.); (M.F.K.); (T.R.S.); (R.R.); (D.H.D.); (K.S.-J.); (E.S.B.); (J.E.B.); (F.O.); (A.S.)
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37
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Erster O, Mendelson E, Levy V, Kabat A, Mannasse B, Asraf H, Azar R, Ali Y, Shirazi R, Bucris E, Bar-Ilan D, Mor O, Mandelboim M, Sofer D, Fleishon S, Zuckerman NS. Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Microbiol Spectr 2021; 9:e0050621. [PMID: 34612692 PMCID: PMC8510166 DOI: 10.1128/spectrum.00506-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/19/2021] [Indexed: 11/20/2022] Open
Abstract
Emerging SARS-CoV-2 (SC-2) variants with increased infectivity and vaccine resistance are of major concern. Rapid identification of such variants is important for the public health decision making and to provide valuable data for epidemiological and policy decision making. We developed a multiplex reverse transcriptase quantitative PCR (RT-qPCR) assay that can specifically identify and differentiate between the emerging B.1.1.7 and B.1.351 SC-2 variants. In a single assay, we combined four reactions-one that detects SC-2 RNA independently of the strain, one that detects the D3L mutation, which is specific to variant B.1.1.7, one that detects the 242 to 244 deletion, which is specific to variant B.1.351, and the fourth reaction, which identifies the human RNAseP gene, serving as an endogenous control for RNA extraction integrity. We show that the strain-specific reactions target mutations that are strongly associated with the target variants and not with other major known variants. The assay's specificity was tested against a panel of respiratory pathogens (n = 16), showing high specificity toward SC-2 RNA. The assay's sensitivity was assessed using both in vitro transcribed RNA and clinical samples and was determined to be between 20 and 40 viral RNA copies per reaction. The assay performance was corroborated with Sanger and whole-genome sequencing, showing complete agreement with the sequencing results. The new assay is currently implemented in the routine diagnostic work at the Central Virology Laboratory, and may be used in other laboratories to facilitate the diagnosis of these major worldwide-circulating SC-2 variants. IMPORTANCE This study describes the design and utilization of a multiplex reverse transcriptase quantitative PCR (RT-qPCR) to identify SARS-COV-2 (SC2) RNA in general and, specifically, to detect whether it is of lineage B.1.1.7 or B.1.351. Implementation of this method in diagnostic and research laboratories worldwide may help the efforts to contain the COVID-19 pandemic. The method can be easily scaled up and be used in high-throughput laboratories, as well as small ones. In addition to immediate help in diagnostic efforts, this method may also help in epidemiological studies focused on the spread of emerging SC-2 lineages.
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Affiliation(s)
- Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Virginia Levy
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Areej Kabat
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Batya Mannasse
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Hadar Asraf
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Yaniv Ali
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Rachel Shirazi
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dana Bar-Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Shai Fleishon
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Neta S. Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
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38
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Erster O, Mendelson E, Levy V, Kabat A, Mannasse B, Asraf H, Azar R, Ali Y, Shirazi R, Bucris E, Bar-Ilan D, Mor O, Mandelboim M, Sofer D, Fleishon S, Zuckerman NS. Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Microbiol Spectr 2021; 9:e0050621. [PMID: 34612692 DOI: 10.1101/2021.05.19.21257439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Emerging SARS-CoV-2 (SC-2) variants with increased infectivity and vaccine resistance are of major concern. Rapid identification of such variants is important for the public health decision making and to provide valuable data for epidemiological and policy decision making. We developed a multiplex reverse transcriptase quantitative PCR (RT-qPCR) assay that can specifically identify and differentiate between the emerging B.1.1.7 and B.1.351 SC-2 variants. In a single assay, we combined four reactions-one that detects SC-2 RNA independently of the strain, one that detects the D3L mutation, which is specific to variant B.1.1.7, one that detects the 242 to 244 deletion, which is specific to variant B.1.351, and the fourth reaction, which identifies the human RNAseP gene, serving as an endogenous control for RNA extraction integrity. We show that the strain-specific reactions target mutations that are strongly associated with the target variants and not with other major known variants. The assay's specificity was tested against a panel of respiratory pathogens (n = 16), showing high specificity toward SC-2 RNA. The assay's sensitivity was assessed using both in vitro transcribed RNA and clinical samples and was determined to be between 20 and 40 viral RNA copies per reaction. The assay performance was corroborated with Sanger and whole-genome sequencing, showing complete agreement with the sequencing results. The new assay is currently implemented in the routine diagnostic work at the Central Virology Laboratory, and may be used in other laboratories to facilitate the diagnosis of these major worldwide-circulating SC-2 variants. IMPORTANCE This study describes the design and utilization of a multiplex reverse transcriptase quantitative PCR (RT-qPCR) to identify SARS-COV-2 (SC2) RNA in general and, specifically, to detect whether it is of lineage B.1.1.7 or B.1.351. Implementation of this method in diagnostic and research laboratories worldwide may help the efforts to contain the COVID-19 pandemic. The method can be easily scaled up and be used in high-throughput laboratories, as well as small ones. In addition to immediate help in diagnostic efforts, this method may also help in epidemiological studies focused on the spread of emerging SC-2 lineages.
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Affiliation(s)
- Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Virginia Levy
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Areej Kabat
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Batya Mannasse
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Hadar Asraf
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Yaniv Ali
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Rachel Shirazi
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dana Bar-Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Shai Fleishon
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
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Shoukat A, Vilches TN, Moghadas SM, Sah P, Schneider EC, Shaff J, Ternier A, Chokshi DA, Galvani AP. Lives saved and hospitalizations averted by COVID-19 vaccination in New York City: a modeling study. Lancet Reg Health Am 2021; 5:100085. [PMID: 34746912 PMCID: PMC8556548 DOI: 10.1016/j.lana.2021.100085] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/29/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Following the start of COVID-19 vaccination in New York City (NYC), cases have declined over 10-fold from the outbreak peak in January 2020, despite the emergence of highly transmissible variants. We evaluated the impact of NYC's vaccination campaign on saving lives as well as averting hospitalizations and cases. METHODS We used an age-stratified agent-based model of COVID-19 to include transmission dynamics of Alpha, Gamma, Delta and Iota variants as identified in NYC. The model was calibrated and fitted to reported incidence in NYC, accounting for the relative transmissibility of each variant and vaccination rollout data. We simulated COVID-19 outbreak in NYC under the counterfactual scenario of no vaccination and compared the resulting disease burden with the number of cases, hospitalizations and deaths reported under the actual pace of vaccination. FINDINGS We found that without vaccination, there would have been a spring-wave of COVID-19 in NYC due to the spread of Alpha and Delta variants. The COVID-19 vaccination campaign in NYC prevented such a wave, and averted 290,467 (95% CrI: 232,551 - 342,664) cases, 48,076 (95% CrI: 42,264 - 53,301) hospitalizations, and 8,508 (95% CrI: 7,374 - 9,543) deaths from December 14, 2020 to July 15, 2021. INTERPRETATION Our study demonstrates that the vaccination program in NYC was instrumental to substantially reducing the COVID-19 burden and suppressing a surge of cases attributable to more transmissible variants. As the Delta variant sweeps predominantly among unvaccinated individuals, our findings underscore the urgent need to accelerate vaccine uptake and close the vaccination coverage gaps. FUNDING This study was supported by The Commonwealth Fund.
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Affiliation(s)
- Affan Shoukat
- Center for Infectious Disease Modeling and Analysis (CIDMA), Yale School of Public Health, New Haven, Connecticut, USA
| | - Thomas N. Vilches
- Center for Infectious Disease Modeling and Analysis (CIDMA), Yale School of Public Health, New Haven, Connecticut, USA,Agent-Based Modelling Laboratory, York University, Toronto, Ontario, Canada
| | - Seyed M. Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, Ontario, Canada
| | - Pratha Sah
- Center for Infectious Disease Modeling and Analysis (CIDMA), Yale School of Public Health, New Haven, Connecticut, USA
| | | | - Jaimie Shaff
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Alexandra Ternier
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Dave A. Chokshi
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Alison P. Galvani
- Center for Infectious Disease Modeling and Analysis (CIDMA), Yale School of Public Health, New Haven, Connecticut, USA,Corresponding author: Alison P. Galvani. Yale University School of Public Health, Center for Infectious Disease Modeling and Analysis, 135 College, New Haven, Connecticut 06510, USA.
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40
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Mor O, Zuckerman NS, Hazan I, Fluss R, Ash N, Ginish N, Mendelson E, Alroy-Preis S, Freedman L, Huppert A. BNT162b2 vaccine effectiveness was marginally affected by the SARS-CoV-2 beta variant in fully vaccinated individuals. J Clin Epidemiol 2021; 142:38-44. [PMID: 34715314 PMCID: PMC8553421 DOI: 10.1016/j.jclinepi.2021.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 11/04/2022]
Abstract
Objective To evaluate the effectiveness of the Pfizer BNT162b2 vaccine against the SARS-Cov-2 Beta variant. Study Design and Setting Israel's mass vaccination program, using two doses of the Pfizer BNT162b2 vaccine, successfully curtailed the Alpha variant outbreak during winter 2020–2021, However, the virus may mutate and partially evade the immune system. To monitor this, sequencing of selected positive swab samples of interest was initiated. Comparing vaccinated with unvaccinated PCR positive persons, we estimated the odds ratio for a vaccinated case to have the Beta vs. the Alpha variant, using logistic regression, controlling for important confounders. Results There were 19 cases of Beta variant (3.2%) among those vaccinated more than 14 days before the positive sample and 79 (3.4%) among the unvaccinated. The estimated odds ratio was 1.26 (95% CI: 0.65–2.46). Assuming the effectiveness against the Alpha variant to be 95%, the estimated effectiveness against the Beta variant was 94% (95% CI: 88%–98%). Conclusion Despite concerns over the Beta variant, the BNT162b2 vaccine seemed to provide substantial immunity against both the Beta and the Alpha variants. From 14 days following the second vaccine dose, the effectiveness of BNT162b2 vaccine was at most marginally affected by the Beta variant.
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Affiliation(s)
- Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 5262100, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 5262100, Israel
| | - Itay Hazan
- Israel Ministry of Health, 39 Yirmiyahu Street, P.O.Box 1176, Jerusalem 9101002, Israel
| | - Ronen Fluss
- The Biostatistical and Biomathematical Unit, Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Ramat Gan 5265601, Israel
| | - Nachman Ash
- Israel Ministry of Health, 39 Yirmiyahu Street, P.O.Box 1176, Jerusalem 9101002, Israel
| | - Netanel Ginish
- Israel Ministry of Health, 39 Yirmiyahu Street, P.O.Box 1176, Jerusalem 9101002, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Tel-Hashomer 5262100, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Sharon Alroy-Preis
- Public Health Services, Israel Ministry of Health, 39 Yirmiyahu Street, P.O.Box 1176, Jerusalem 9101002, Israel
| | - Laurence Freedman
- The Biostatistical and Biomathematical Unit, Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Ramat Gan 5265601, Israel
| | - Amit Huppert
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel; The Biostatistical and Biomathematical Unit, Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Ramat Gan 5265601, Israel.
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41
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Johnson KE, Woody S, Lachmann M, Fox SJ, Klima J, Hines TS, Meyers LA. Real-Time Projections of SARS-CoV-2 B.1.1.7 Variant in a University Setting, Texas, USA. Emerg Infect Dis 2021; 27:3188-3190. [PMID: 34708684 PMCID: PMC8632165 DOI: 10.3201/eid2712.210652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We used the incidence of spike gene target failures identified during PCR testing to provide an early projection of the prevalence of severe acute respiratory syndrome coronavirus 2 variant B.1.1.7 in a university setting in Texas, USA, before sequencing results were available. Findings from a more recent evaluation validated those early projections.
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42
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Kant R, Nguyen PT, Blomqvist S, Erdin M, Alburkat H, Suvanto M, Zakham F, Salminen V, Olander V, Paloniemi M, Huhti L, Lehtinen S, Luukinen B, Jarva H, Kallio-Kokko H, Kurkela S, Lappalainen M, Liimatainen H, Hannula S, Halkilahti J, Ikonen J, Ikonen N, Helve O, Gunell M, Vuorinen T, Plyusnin I, Lindh E, Ellonen P, Sironen T, Savolainen-Kopra C, Smura T, Vapalahti O. Incidence Trends for SARS-CoV-2 Alpha and Beta Variants, Finland, Spring 2021. Emerg Infect Dis 2021; 27:3137-3141. [PMID: 34708686 PMCID: PMC8632157 DOI: 10.3201/eid2712.211631] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 Alpha and Beta variants became dominant in Finland in spring 2021 but had diminished by summer. We used phylogenetic clustering to identify sources of spreading. We found that outbreaks were mostly seeded by a few introductions, highlighting the importance of surveillance and prevention policies.
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43
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Graber TE, Mercier É, Bhatnagar K, Fuzzen M, D'Aoust PM, Hoang HD, Tian X, Towhid ST, Plaza-Diaz J, Eid W, Alain T, Butler A, Goodridge L, Servos M, Delatolla R. Near real-time determination of B.1.1.7 in proportion to total SARS-CoV-2 viral load in wastewater using an allele-specific primer extension PCR strategy. Water Res 2021; 205:117681. [PMID: 34619611 PMCID: PMC8459324 DOI: 10.1016/j.watres.2021.117681] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 05/02/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed millions of lives to date. Antigenic drift has resulted in viral variants with putatively greater transmissibility, virulence, or both. Early and near real-time detection of these variants of concern (VOC) and the ability to accurately follow their incidence and prevalence in communities is wanting. Wastewater-based epidemiology (WBE), which uses nucleic acid amplification tests to detect viral fragments, is a reliable proxy of COVID-19 incidence and prevalence, and thus offers the potential to monitor VOC viral load in a given population. Here, we describe and validate a primer extension PCR strategy targeting a signature mutation in the N gene of SARS-CoV-2. This allows quantification of B.1.1.7 versus non-B.1.1.7 allele frequency in wastewater without the need to employ quantitative RT-PCR standard curves. We show that the wastewater B.1.1.7 profile correlates with its clinical counterpart and benefits from a near real-time and facile data collection and reporting pipeline. This assay can be quickly implemented within a current SARS-CoV-2 WBE framework with minimal cost; allowing early and contemporaneous estimates of B.1.1.7 community transmission prior to, or in lieu of, clinical screening and identification. Our study demonstrates that this strategy can provide public health units with an additional and much needed tool to rapidly triangulate VOC incidence/prevalence with high sensitivity and lineage specificity.
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Affiliation(s)
- Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kamya Bhatnagar
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Xin Tian
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Syeda Tasneem Towhid
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Julio Plaza-Diaz
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Ainslie Butler
- Simcoe Muskoka District Health Unit, Barrie, Ontario, L4M 6K9, Canada
| | - Lawrence Goodridge
- Department of Food Science, Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mark Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada.
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Ballesteros N, Castañeda S, Muñoz M, Patiño LH, Méndez C, Oliveros C, Pérez J, Albarracín L, Márquez EK, Alvarado MT, Santos Ortiz FDL, Romero Y, Correa-Cárdenas CA, Duque MC, Gutíerrez-Riveros S, Paniz-Mondolfi A, Ramírez JD. Cluster characterization of SARS-CoV-2 in military personnel deployed to Egypt and subsequent introduction of B.1.1.7 and C.36 lineages to Colombia. J Travel Med 2021; 28:6354472. [PMID: 34409452 PMCID: PMC8499738 DOI: 10.1093/jtm/taab131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 11/14/2022]
Abstract
In April 2021, 126 active-duty militaries returned to Colombia after a mission in Egypt. Of 29 cases, 28 were B.1.1.7, and one C.36 (first description of this lineage in Colombia). We highlight the militaries as at-risk population and call for implementation of genomic surveillance to improve public health policies in military settings.
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Affiliation(s)
- Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz H Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Claudia Méndez
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Carolina Oliveros
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Julie Pérez
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Lorena Albarracín
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Elizabeth K Márquez
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - María Teresa Alvarado
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Frank de Los Santos Ortiz
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Yanira Romero
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Camilo A Correa-Cárdenas
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Maria Clara Duque
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Sergio Gutíerrez-Riveros
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Alberto Paniz-Mondolfi
- Department of Pathology, Molecular and Cell-Based Medicine, Laboratory of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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Liu Y, Rocklöv J. The reproductive number of the Delta variant of SARS-CoV-2 is far higher compared to the ancestral SARS-CoV-2 virus. J Travel Med 2021; 28:taab124. [PMID: 34369565 PMCID: PMC8436367 DOI: 10.1093/jtm/taab124] [Citation(s) in RCA: 312] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/21/2022]
Abstract
The Delta variant is now replacing all other SARS-CoV-2 variants. We found a mean R0 of 5.08, which is much higher than the R0 of the ancestral strain of 2.79. Rapidly ramping up vaccine coverage rates while enhancing public health and social measures is now even more urgent and important.
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Affiliation(s)
- Ying Liu
- School of International Business, Xiamen University Tan Kah Kee College, Zhangzhou 363105, China
| | - Joacim Rocklöv
- Section of Sustainable Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå SE-90187, Sweden
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46
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Lee BU. Why Does the SARS-CoV-2 Delta VOC Spread So Rapidly? Universal Conditions for the Rapid Spread of Respiratory Viruses, Minimum Viral Loads for Viral Aerosol Generation, Effects of Vaccination on Viral Aerosol Generation, and Viral Aerosol Clouds. Int J Environ Res Public Health 2021; 18:9804. [PMID: 34574724 PMCID: PMC8470664 DOI: 10.3390/ijerph18189804] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/16/2022]
Abstract
This study analyzes the reasons the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant of concern (VOC) spreads so rapidly. Novel topics such as universal conditions for the rapid spread of respiratory viruses, minimum viral loads for viral aerosol generation, effects of vaccination on viral aerosol generation, and viral aerosol clouds were studied. The analyses were based on experimental results and analytic model studies. Four universal conditions, namely asymptomatic host, high viral load, stability of viruses in air, and binding affinity of viruses to human cells, need to be satisfied for the rapid spread of respiratory viruses. SARS-CoV-2 and its variants such as the Alpha VOC and Delta VOC satisfy the four fundamental conditions. In addition, there is an original principle of aerosol generation of respiratory viruses. Assuming that the aerosol-droplet cutoff particle diameter for distinguishing potential aerosols from earthbound respiratory particles is 100 μm, the minimum viral load required in respiratory fluids to generate viral aerosols is ~106 copies mL-1, which is within the range of the reported viral loads in the Alpha VOC cases and the Delta VOC cases. The daily average viral loads of the Delta VOC in hosts have been reported to be between ~109 copies mL-1 and ~1010 copies mL-1 during the four days after symptom onset in 1848 cases of the Delta VOC infection. Owing to the high viral load, the SARS-CoV-2 Delta VOC has the potential to effectively spread through aerosols. COVID-19 vaccination can decrease aerosol transmission of the SARS-CoV-2 Alpha VOC by reducing the viral load. The viral load can explain the conundrum of viral aerosol spreading. The SARS-CoV-2 Delta VOC aerosol clouds have been assumed to be formed in restricted environments, resulting in a massive numbers of infected people in a very short period with a high spreading speed. Strong control methods against bioaerosols should be considered in this SARS-CoV-2 Delta VOC pandemic. Large-scale environmental monitoring campaigns of SARS-CoV-2 Delta VOC aerosols in public places in many countries are necessary, and these activities could contribute to controlling the coronavirus disease pandemic.
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Affiliation(s)
- Byung Uk Lee
- Aerosol and Bioengineering Laboratory, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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47
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Garcia Borrega J, Naendrup JH, Heindel K, Hamacher L, Heger E, Di Cristanziano V, Deppe AC, Dusse F, Wetsch WA, Eichenauer DA, Shimabukuro-Vornhagen A, Böll B, Kochanek M. Clinical Course and Outcome of Patients with SARS-CoV-2 Alpha Variant Infection Compared to Patients with SARS-CoV-2 Wild-Type Infection Admitted to the ICU. Microorganisms 2021; 9:1944. [PMID: 34576839 PMCID: PMC8470850 DOI: 10.3390/microorganisms9091944] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022] Open
Abstract
The alpha variant of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is associated with higher transmissibility and possibly higher mortality compared with wild-type SARS-CoV-2. However, few data are available on the clinical course of infections with the alpha variant compared with wild-type SARS-CoV-2 in critically ill patients in intensive care units (ICUs). Therefore, we retrospectively analyzed patients admitted to our ICU due to SARS-CoV-2 Alpha variant infection and compared characteristics and course to patients with SARS-CoV-2 wild-type infection. The median age of patients with Alpha variant infections was 57 years compared to 62 years in the wild-type group. ICU survival was 41/80 (51%) in the Alpha variant group and 35/80 (44%) in the wild-type group (p = 0.429). Results of a matched-pair analysis based on age and sex illustrated that 45/58 patients (77.6%) in the Alpha variant group and 38/58 (65.5%) patients in the wild-type group required mechanical ventilation (p = 0.217). ICU survival was documented for 28/58 patients (48.3%) in the Alpha variant group and 27/58 patients (46.6%) in the wild-type group (p = 1). Thus, ICU mortality among patients with SARS-CoV-2 infections remains high. Although the Alpha variant group included younger patients requiring mechanical ventilation, no significant differences between patients with the SARS-CoV-2 Alpha variant and the SARS-CoV-2 wild-type, respectively, were detected with respect to clinical course and ICU mortality. For future VOCs, we believe it would be important to obtain valid and rapid data on the clinical course of critically ill patients who test positive for COVID-19 in order to perform appropriate epidemiological planning of intensive care capacity.
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Affiliation(s)
- Jorge Garcia Borrega
- First Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Dusseldorf (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (J.G.B.); (J.-H.N.); (K.H.); (L.H.); (D.A.E.); (A.S.-V.); (B.B.)
| | - Jan-Hendrik Naendrup
- First Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Dusseldorf (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (J.G.B.); (J.-H.N.); (K.H.); (L.H.); (D.A.E.); (A.S.-V.); (B.B.)
| | - Katrin Heindel
- First Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Dusseldorf (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (J.G.B.); (J.-H.N.); (K.H.); (L.H.); (D.A.E.); (A.S.-V.); (B.B.)
| | - Laura Hamacher
- First Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Dusseldorf (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (J.G.B.); (J.-H.N.); (K.H.); (L.H.); (D.A.E.); (A.S.-V.); (B.B.)
| | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (E.H.); (V.D.C.)
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (E.H.); (V.D.C.)
| | - Antje-Christin Deppe
- Department of Cardiothoracic Surgery, ECMO Centre Cologne, Heart Centre, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Fabian Dusse
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany; (F.D.); (W.A.W.)
| | - Wolfgang Alois Wetsch
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany; (F.D.); (W.A.W.)
| | - Dennis Alexander Eichenauer
- First Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Dusseldorf (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (J.G.B.); (J.-H.N.); (K.H.); (L.H.); (D.A.E.); (A.S.-V.); (B.B.)
| | - Alexander Shimabukuro-Vornhagen
- First Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Dusseldorf (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (J.G.B.); (J.-H.N.); (K.H.); (L.H.); (D.A.E.); (A.S.-V.); (B.B.)
| | - Boris Böll
- First Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Dusseldorf (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (J.G.B.); (J.-H.N.); (K.H.); (L.H.); (D.A.E.); (A.S.-V.); (B.B.)
| | - Matthias Kochanek
- First Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Dusseldorf (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (J.G.B.); (J.-H.N.); (K.H.); (L.H.); (D.A.E.); (A.S.-V.); (B.B.)
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48
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Cetin M, Balci PO, Sivgin H, Cetin S, Ulgen A, Dörtok Demir H, Li W. Alpha variant (B.1.1.7) of SARS-CoV-2 increases fatality-rate for patients under age of 70 years and hospitalization risk overall. Acta Microbiol Immunol Hung 2021. [PMID: 34383706 DOI: 10.1556/030.2021.01524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/28/2021] [Indexed: 01/03/2023]
Abstract
The emergence of new SARS-CoV-2 variants is a challenge to the control of this pandemic. It is therefore important to collect and to analyze data related to the infection caused by different variants. We have obtained more than 3,700 COVID-19 patients between April 2020 and March 2021 from Tokat, Turkey (roughly 3,100 outpatients and close to 600 inpatients) where about 30% were infected with Alpha variant (B.1.1.7). Descriptive statistics was used to characterize different subgroups. Both logistic regression and cause-specific Cox survival analysis of competing-risk was run on inpatients, to examine the impact of Alpha variant on hospitalization, on mortality and on other factors. We observed that the Alpha variant is over-represented in inpatients than outpatients so infection by Alpha variant increases the chance for hospitalization. The impact of Alpha variant on mortality seems to depend on the patient's age. For patients under age of 70, the case-fatality-rate was 0.84% (5.3%) for patients without (with) Alpha variant (Fisher's test P-value = 2.4 × 10-10). For patients above age of 70, the trend is opposite: the case-fatality-rate is 31.5% (13.6%) for patients without (with) Alpha variant (Fisher's test P-value = 0.0016). The two opposite trends would cancel each other, making other analyses such as cause-specific Cox regression and logistic regression non-significant. The Alpha variant increases the risk for hospitalization, increases the case-fatality-rate for lower age group, and decreases the case-fatality-rate for the upper age group. If the increase of case-fatality-rate in not the most senior group holds true, it should provide useful information for a vaccination planning to counter the impact of Alpha variants.
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Affiliation(s)
- Meryem Cetin
- 1Department of Medical Microbiology, Faculty of Medicine, Amasya University, Amasya, Turkey
| | - Pervin Ozlem Balci
- 2Department of Medical Microbiology, Tokat State Hospital, Tokat, Turkey
| | - Hakan Sivgin
- 3Department of Internal Medicine, Tokat State Hospital, Tokat, Turkey
| | - Sirin Cetin
- 4Department of Biostatistics, Faculty of Medicine, Tokat Gaziosman Pasa University, Turkey
| | - Ayse Ulgen
- 5Department of Biostatistics, Faculty of Medicine, Girne American University, Karmi, Cyprus
| | - Hatice Dörtok Demir
- 6Department of Medical Biochemistry Faculty of Medicine, Amasya University, Amasya, Turkey
| | - Wentian Li
- 7The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
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49
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Tanaka H, Hirayama A, Nagai H, Shirai C, Takahashi Y, Shinomiya H, Taniguchi C, Ogata T. Increased Transmissibility of the SARS-CoV-2 Alpha Variant in a Japanese Population. Int J Environ Res Public Health 2021; 18:7752. [PMID: 34360046 PMCID: PMC8345780 DOI: 10.3390/ijerph18157752] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 11/24/2022]
Abstract
To assess the relative transmissibility of the SARS-CoV-2 Alpha variant compared to the pre-existing SARS-CoV-2 in Japan, we performed a cross-sectional study to determine the secondary attack rate of COVID-19 in household contacts before and after the Alpha variant became dominant in Osaka. We accessed 290 household contacts whose index cases were diagnosed between 1 and 20 December 2020 (the third epidemic group), at a time when Osaka was free of the Alpha variant. We also accessed 398 household contacts whose index cases were diagnosed between 20 April and 3 May 2021 (the fourth epidemic group), by which time the Alpha variant had become dominant. We identified 124 household contacts whose index case was determined positive for the Alpha variant (Alpha group) in this fourth group. The secondary attack rates in the fourth group (34.7%) and the Alpha group (38.7%) were significantly higher than that in the third group (19.3%, p < 0.001). Multivariable Poisson regression analysis with a robust error variance showed a significant excess risk in the fourth group (1.90, 95% CI = 1.47-2.48) and the Alpha group (2.34, 95% CI = 1.71-3.21). This finding indicates that the SARS-CoV-2 Alpha variant has an approximately 1.9-2.3-fold higher transmissibility than the pre-existing virus in the Japanese population.
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Affiliation(s)
- Hideo Tanaka
- Fujiidera Public Health Center of Osaka Prefectural Government, Fujiidera 583-0024, Japan;
| | - Atsushi Hirayama
- Department of Public Health and Medical Affairs, Osaka Prefectural Government, Osaka 540-8507, Japan;
| | - Hitomi Nagai
- Ibaraki Public Health Center of Osaka Prefectural Government, Ibaraki 567-8585, Japan;
| | - Chika Shirai
- Hirakata City of Public Health Center, Hirakata 573-8666, Japan;
| | - Yuki Takahashi
- Fujiidera Public Health Center of Osaka Prefectural Government, Fujiidera 583-0024, Japan;
| | - Hiroto Shinomiya
- Ehime Prefectural Institute of Public Health and Environmental Science, Matsuyama 790-0003, Japan;
| | - Chie Taniguchi
- College of Nursing, Aichi Medical University, Nagakute 480-1195, Japan;
| | - Tsuyoshi Ogata
- Itako Public Health Center of Ibaraki Prefectural Government, Itako 311-2422, Japan;
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50
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Yang CH, Li HC, Lee WH, Lo SY. Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. Pathogens 2021; 10:pathogens10070869. [PMID: 34358019 PMCID: PMC8308897 DOI: 10.3390/pathogens10070869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 12/03/2022] Open
Abstract
The COVID-19 pandemic was caused by SARS-CoV-2 infection. To prevent the spread of SARS-CoV-2, an effective vaccine is required. Two linear peptides from potential B-cell epitopes in the spike protein of SARS-CoV-2 (a.a. 440–460; a.a. 494–506) were synthesized and used to immunize rabbits. High-titer antibodies of IgG were produced, purified, and verified by Western blot analysis. Antibodies against these two epitopes could effectively neutralize SARS-CoV-2 pseudoviral particles with the spike proteins from not only the original strain (basal; wild-type), but also a strain with a single point mutation (D614G), and two other emerging variants (the Alpha and Beta variants) prevalent around the world, but not from SARS-CoV. In conclusion, antibodies against these two epitopes are protective. This information is important for the development of vaccines against SARS-CoV-2.
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Affiliation(s)
- Chee-Hing Yang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan; (C.-H.Y.); (W.-H.L.)
| | - Hui-Chun Li
- Department of Biochemistry, Tzu Chi University, Hualien 97004, Taiwan;
| | - Wen-Han Lee
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan; (C.-H.Y.); (W.-H.L.)
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan; (C.-H.Y.); (W.-H.L.)
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
- Correspondence: ; Tel.: +886-3-8565301 (ext. 2322)
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