1
|
Mwendwa F, Kanji A, Bukhari AR, Khan U, Sadiqa A, Mushtaq Z, Nasir N, Mahmood SF, Aamir UB, Hasan Z. Shift in SARS-CoV-2 variants of concern from Delta to Omicron was associated with reduced hospitalizations, increased risk of breakthrough infections but lesser disease severity. J Infect Public Health 2024; 17:1100-1107. [PMID: 38714122 PMCID: PMC11142923 DOI: 10.1016/j.jiph.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND COVID-19 epidemiology changed with the emergence of SARS-CoV-2 variants of concern (VOC). Pakistan administered mostly inactivated vaccines. We investigated the association between VOC and breakthrough infections in a mixed-vaccination-status population of Karachi. METHODS We investigated SARS-CoV-2 VOC tested in 392 respiratory specimens collected between May and December 2021. Data for age, sex, hospital admission, vaccinations, together with CT values of the diagnostic PCR test were analyzed. RESULTS The median age of COVID-19 cases tested was 40 (27-57) years and 43.4% were female. Delta variants were most common (56.4%) followed by Alpha (15.9%), Omicron (12.2%), Beta/Gamma (11.3%), and others (4.3%). Eighteen percent of cases were hospitalized whereby, predominant VOC were Beta/Gamma (40.8%), Alpha (35.2%) and Delta (22.5%). Overall, 55.4% of individuals were fully vaccinated, 7.4% were partially vaccinated and 37.2% were unvaccinated. Most (74.6%) inpatients were unvaccinated. Vaccines comprised inactivated (85.34%), single-shot vector (8.62%), two-shot vector (3.02%) and mRNA (3.02%) types. Omicron variants showed lower viral loads as compared to Alpha, Beta/Gamma, and Delta (p = 0.017). The risk of infection with Delta and Omicron variants was higher, 8 weeks after vaccination. The majority of those with breakthrough infections after receiving inactivated vaccines acquired COVID-19 within 4 months of vaccination. CONCLUSION Our data highlights the shifting of VOC from Delta to Omicron during 2021 and that COVID-19 vaccinations reduced both hospitalizations and viral transmission. It informs on the increased risk of breakthrough infection within 8 weeks of vaccination, indicating the need for booster vaccinations.
Collapse
Affiliation(s)
- Fridah Mwendwa
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Ali Raza Bukhari
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Unab Khan
- Department of Family Medicine, The Aga Khan University, Karachi, Pakistan
| | - Ayesha Sadiqa
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Zain Mushtaq
- Department of Family Medicine, The Aga Khan University, Karachi, Pakistan
| | - Nosheen Nasir
- Department of Family Medicine, The Aga Khan University, Karachi, Pakistan
| | | | | | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| |
Collapse
|
2
|
Saksena NK, Reddy SB, Miranda-Saksena M, Cardoso THS, Silva EMA, Ferreira JC, Rabeh WM. SARS-CoV-2 variants, its recombinants and epigenomic exploitation of host defenses. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166836. [PMID: 37549720 DOI: 10.1016/j.bbadis.2023.166836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
Since 2003, we have seen the emergence of novel viruses, such as SARS-CoV-1, MERS, ZIKA, swine flu virus H1N1, Marburg, Monkeypox, Ebola, and SARS-CoV-2, but none of them gained pandemic proportions similar to SARS-CoV-2. This could be attributed to unique viral traits, allowing its rapid global dissemination following its emergence in October 2019 in Wuhan, China, which appears to be primarily driven by the emergence of highly transmissible and virulent variants that also associate, in some cases, with severe disease and considerable mortality caused by fatal pneumonia, acute respiratory distress syndrome (ARDS) in infected individuals. Mechanistically, several factors are involved in viral pathogenesis, and epigenetic alterations take the front seat in host-virus interactions. The molecular basis of all viral infections, including SARS-CoV-2, tightly hinges on the transitory silencing of the host gene machinery via epigenetic modulation. SARS-CoV-2 also hijacks and subdues the host gene machinery, leading to epigenetic modulation of the critical host elements responsible for antiviral immunity. Epigenomics is a powerful, unexplored avenue that can provide a profound understanding of virus-host interactions and lead to the development of epigenome-based therapies and vaccines to counter viruses. This review discusses current developments in SARS-CoV-2 variation and its role in epigenetic modulation in infected hosts. This review provides an overview, especially in the context of emerging viral strains, their recombinants, and their possible roles in the epigenetic exploitation of host defense and viral pathogenesis. It provides insights into host-virus interactions at the molecular, genomic, and immunological levels and sheds light on the future of epigenomics-based therapies for SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Nitin K Saksena
- Victoria University, Footscray Campus, Melbourne, VIC. Australia.
| | - Srinivasa Bonam Reddy
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Thyago H S Cardoso
- OMICS Centre of Excellence, G42 Healthcare, Mazdar City, Abu Dhabi, United Arab Emirates.
| | - Edson M A Silva
- Science Division, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
3
|
Meyers E, Park J, Coen A, Raman L, Heytens S, Rhee J, Padalko E, Cools P. Evaluation of a smartphone-operated point-of-care device using loop-mediated isothermal amplification technology for rapid and remote detection of SARS-CoV-2. J Med Virol 2023; 95:e29158. [PMID: 37842790 DOI: 10.1002/jmv.29158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023]
Abstract
During the SARS-CoV-2 pandemic, rapid and sensitive detection of SARS-CoV-2 has been of high importance for outbreak control. Reverse transcriptase polymerase chain reaction (RT-PCR) is the current gold standard, however, the procedures require an equipped laboratory setting and personnel, which have been regularly overburdened during the pandemic. This often resulted in long waiting times for patients. In contrast, reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) is a simple, cost-efficient, and fast procedure, allowing for rapid and remote detection of SARS-CoV-2. In the current study, we performed a clinical evaluation of a new point-of-care test system based on LAMP-technology for SARS-CoV-2 detection, providing a result within 25 min (1copy™ COVID-19 MDx Kit Professional system). We tested 112 paired nasopharyngeal swabs, collected in the COVID-19 Ghent University Hospital test center, using the 1copy™ COVID-19 MDx Kit Professional system, and RT-PCR as the reference method. The test system was found to have a clinical sensitivity of 93.24% (69/74) (95% confidence interval [CI]: 84.93%-97.77%) and specificity of 97.37% (37/38) (95% CI: 86.19%-99.93%). Due to its easy smartphone operation and ready-to-use reagents, it ought to be easily applied in for instance general practices, pharmacies, nursing homes, schools, and companies. This would facilitate an efficient SARS-CoV-2 outbreak control and quarantine policy, as diagnosis can occur sooner in a near-patient setting.
Collapse
Affiliation(s)
- Eline Meyers
- Laboratory Bacteriology Research, Ghent University, Ghent, Belgium
| | | | - Anja Coen
- Department of Public Health and Primary Care, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Leen Raman
- Laboratory of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Stefan Heytens
- Department of Public Health and Primary Care, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | | | - Elizaveta Padalko
- Laboratory of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Piet Cools
- Laboratory Bacteriology Research, Ghent University, Ghent, Belgium
| |
Collapse
|
4
|
Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
Collapse
Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| |
Collapse
|
5
|
Fryer HR, Golubchik T, Hall M, Fraser C, Hinch R, Ferretti L, Thomson L, Nurtay A, Pellis L, House T, MacIntyre-Cockett G, Trebes A, Buck D, Piazza P, Green A, Lonie LJ, Smith D, Bashton M, Crown M, Nelson A, McCann CM, Adnan Tariq M, Elstob CJ, Nunes Dos Santos R, Richards Z, Xhang X, Hawley J, Lee MR, Carrillo-Barragan P, Chapman I, Harthern-Flint S, Bonsall D, Lythgoe KA. Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias. PLoS Pathog 2023; 19:e1011461. [PMID: 37578971 PMCID: PMC10449197 DOI: 10.1371/journal.ppat.1011461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 08/24/2023] [Accepted: 06/05/2023] [Indexed: 08/16/2023] Open
Abstract
In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burden, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. By analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior exposure, viral burden was 44% lower among Alpha variant infections, compared to those with the predecessor strain, B.1.177. Vaccination reduced viral burden by 67%, and among vaccinated individuals, viral burden was 286% higher among Delta variant, compared to Alpha variant, infections. In addition, viral burden increased by 17% for every 10-year age increment of the infected individual. In summary, within-host viral burden increases with age, is reduced by vaccination, and is influenced by the interplay of vaccination status and viral variant.
Collapse
Affiliation(s)
- Helen R. Fryer
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Robert Hinch
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Laura Thomson
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Anel Nurtay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Lorenzo Pellis
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
| | | | - Amy Trebes
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - David Buck
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Angie Green
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Lorne J Lonie
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Darren Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Matthew Crown
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Clare M. McCann
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Mohammed Adnan Tariq
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Claire J. Elstob
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Rui Nunes Dos Santos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Zack Richards
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Xin Xhang
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Joseph Hawley
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Mark R. Lee
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Priscilla Carrillo-Barragan
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Isobel Chapman
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Sarah Harthern-Flint
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | | | - David Bonsall
- Pandemic Sciences Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Katrina A. Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Department of Biology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
6
|
Trigo-Tasende N, Vallejo JA, Rumbo-Feal S, Conde-Pérez K, Vaamonde M, López-Oriona Á, Barbeito I, Nasser-Ali M, Reif R, Rodiño-Janeiro BK, Fernández-Álvarez E, Iglesias-Corrás I, Freire B, Tarrío-Saavedra J, Tomás L, Gallego-García P, Posada D, Bou G, López-de-Ullibarri I, Cao R, Ladra S, Poza M. Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27877-3. [PMID: 37286834 DOI: 10.1007/s11356-023-27877-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
Wastewater-based epidemiology has been widely used as a cost-effective method for tracking the COVID-19 pandemic at the community level. Here we describe COVIDBENS, a wastewater surveillance program running from June 2020 to March 2022 in the wastewater treatment plant of Bens in A Coruña (Spain). The main goal of this work was to provide an effective early warning tool based in wastewater epidemiology to help in decision-making at both the social and public health levels. RT-qPCR procedures and Illumina sequencing were used to weekly monitor the viral load and to detect SARS-CoV-2 mutations in wastewater, respectively. In addition, own statistical models were applied to estimate the real number of infected people and the frequency of each emerging variant circulating in the community, which considerable improved the surveillance strategy. Our analysis detected 6 viral load waves in A Coruña with concentrations between 103 and 106 SARS-CoV-2 RNA copies/L. Our system was able to anticipate community outbreaks during the pandemic with 8-36 days in advance with respect to clinical reports and, to detect the emergence of new SARS-CoV-2 variants in A Coruña such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529 and BA.2) in wastewater with 42, 30, and 27 days, respectively, before the health system did. Data generated here helped local authorities and health managers to give a faster and more efficient response to the pandemic situation, and also allowed important industrial companies to adapt their production to each situation. The wastewater-based epidemiology program developed in our metropolitan area of A Coruña (Spain) during the SARS-CoV-2 pandemic served as a powerful early warning system combining statistical models with mutations and viral load monitoring in wastewater over time.
Collapse
Affiliation(s)
- Noelia Trigo-Tasende
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Juan A Vallejo
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Soraya Rumbo-Feal
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Kelly Conde-Pérez
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Manuel Vaamonde
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Ángel López-Oriona
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Inés Barbeito
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Mohammed Nasser-Ali
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Rubén Reif
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), University of Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
| | - Bruno K Rodiño-Janeiro
- BFlow, University of Santiago de Compostela (USC) and Health Research Institute of Santiago de Compostela (IDIS), Campus Vida, 15706, Santiago de Compostela, A Coruña, Spain
| | - Elisa Fernández-Álvarez
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Iago Iglesias-Corrás
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Borja Freire
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Javier Tarrío-Saavedra
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
| | - Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
| | - David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain
| | - Germán Bou
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Ignacio López-de-Ullibarri
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Ricardo Cao
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Susana Ladra
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Margarita Poza
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain.
| |
Collapse
|
7
|
Gong X, Khan A, Wani MY, Ahmad A, Duse A. COVID-19: A state of art on immunological responses, mutations, and treatment modalities in riposte. J Infect Public Health 2023; 16:233-249. [PMID: 36603376 PMCID: PMC9798670 DOI: 10.1016/j.jiph.2022.12.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/25/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Over the last few years, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) unleashed a global public health catastrophe that had a substantial influence on human physical and mental health, the global economy, and socio-political dynamics. SARS-CoV-2 is a respiratory pathogen and the cause of ongoing COVID-19 pandemic, which testified how unprepared humans are for pandemics. Scientists and policymakers continue to face challenges in developing ideal therapeutic agents and vaccines, while at the same time deciphering the pathology and immunology of SARS-CoV-2. Challenges in the early part of the pandemic included the rapid development of diagnostic assays, vaccines, and therapeutic agents. The ongoing transmission of COVID-19 is coupled with the emergence of viral variants that differ in their transmission efficiency, virulence, and vaccine susceptibility, thus complicating the spread of the pandemic. Our understanding of how the human immune system responds to these viruses as well as the patient groups (such as the elderly and immunocompromised individuals) who are often more susceptible to serious illness have both been aided by this epidemic. COVID-19 causes different symptoms to occur at different stages of infection, making it difficult to determine distinct treatment regimens employed for the various clinical phases of the disease. Unsurprisingly, determining the efficacy of currently available medications and developing novel therapeutic strategies have been a process of trial and error. The global scientific community collaborated to research and develop vaccines at a neck-breaking speed. This review summarises the overall picture of the COVID-19 pandemic, different mutations in SARS-CoV-2, immune response, and the treatment modalities against SARS-CoV-2.
Collapse
Affiliation(s)
- Xiaolong Gong
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amber Khan
- Department of Clinical Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohmmad Younus Wani
- Department of Chemistry, College of Science, University of Jeddah, P.O. Box 80327, Jeddah 21589, Kingdom of Saudi Arabia
| | - Aijaz Ahmad
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Division of Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa,Corresponding author at: Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adriano Duse
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Division of Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa
| |
Collapse
|
8
|
Hopkins FR, Govender M, Svanberg C, Nordgren J, Waller H, Nilsdotter-Augustinsson Å, Henningsson AJ, Hagbom M, Sjöwall J, Nyström S, Larsson M. Major alterations to monocyte and dendritic cell subsets lasting more than 6 months after hospitalization for COVID-19. Front Immunol 2023; 13:1082912. [PMID: 36685582 PMCID: PMC9846644 DOI: 10.3389/fimmu.2022.1082912] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction After more than two years the Coronavirus disease-19 (COVID-19) pandemic continues to burden healthcare systems and economies worldwide, and it is evident that the effects on the immune system can persist for months post-infection. The activity of myeloid cells such as monocytes and dendritic cells (DC) is essential for correct mobilization of the innate and adaptive responses to a pathogen. Impaired levels and responses of monocytes and DC to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is likely to be a driving force behind the immune dysregulation that characterizes severe COVID-19. Methods Here, we followed a cohort of COVID-19 patients hospitalized during the early waves of the pandemic for 6-7 months. The levels and phenotypes of circulating monocyte and DC subsets were assessed to determine both the early and long-term effects of the SARS-CoV-2 infection. Results We found increased monocyte levels that persisted for 6-7 months, mostly attributed to elevated levels of classical monocytes. Myeloid derived suppressor cells were also elevated over this period. While most DC subsets recovered from an initial decrease, we found elevated levels of cDC2/cDC3 at the 6-7 month timepoint. Analysis of functional markers on monocytes and DC revealed sustained reduction in program death ligand 1 (PD-L1) expression but increased CD86 expression across almost all cell types examined. Finally, C-reactive protein (CRP) correlated positively to the levels of intermediate monocytes and negatively to the recovery of DC subsets. Conclusion By exploring the myeloid compartments, we show here that alterations in the immune landscape remain more than 6 months after severe COVID-19, which could be indicative of ongoing healing and/or persistence of viral antigens.
Collapse
Affiliation(s)
- Francis R. Hopkins
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Melissa Govender
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Cecilia Svanberg
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johan Nordgren
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Hjalmar Waller
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden,Department of Infectious Diseases, Linköping University, Linköping, Sweden
| | - Anna J. Henningsson
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden,Division of Clinical Microbiology, Department of Laboratory Medicine in Jönköping, Ryhov County Hospital, Jönköping, Sweden
| | - Marie Hagbom
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johanna Sjöwall
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden,Department of Infectious Diseases, Linköping University, Linköping, Sweden
| | - Sofia Nyström
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden,Department of Clinical Immunology and Transfusion Medicine, Linköping University, Linköping, Sweden
| | - Marie Larsson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden,*Correspondence: Marie Larsson,
| |
Collapse
|
9
|
Zhang H, Chen W, Ye X, Zhou Y, Zheng Y, Weng Z, Xie J, Zheng K, Su Z, Zhuang X, Yu X. Clinical characteristics of patients infected with novel coronavirus wild strain, Delta variant strain and Omicron variant strain in Quanzhou: A real‑world study. Exp Ther Med 2022; 25:62. [PMID: 36588806 PMCID: PMC9780511 DOI: 10.3892/etm.2022.11761] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/12/2022] [Indexed: 12/13/2022] Open
Abstract
This study aimed to investigate the clinical features of patients infected with novel coronavirus wild strains, Delta variant strains and Omicron variant strains to provide a reference for early clinical diagnosis and prognostic assessment. The demographic, clinical symptoms and ancillary examination data of 47 patients with novel coronavirus wild type strain infection, 18 with Delta variant infection and 20 with Omicron variant infection admitted to the First Hospital of Quanzhou affiliated with Fujian Medical University were collected and analyzed. The novel coronavirus wild strain and Delta strain were the predominant clinical types; patients infected with the Omicron strain were mainly asymptomatic. Fever and fatigue were the main clinical manifestations in the wild strain and Delta strain groups, whereas dry cough, nasal congestion, sore throat and fever were common clinical manifestations in the Omicron strain group. The Delta strain and Omicron variant groups had fewer comorbidities than the wild-type strain group, but no significant reduction was observed in the negative conversion time of nucleic acids. Significant differences were found in the neutrophil count/lymphocyte count ratio, lymphocyte count, eosinophil count, red blood cell count, hemoglobin level, erythrocyte sedimentation rate, C-reactive protein, prothrombin time, international normalized ratio and plasma D-dimer, PH, PaO2, lactic acid and albumin levels among the three groups. Patients infected with the Omicron strain in Quanzhou presented with mild symptoms of the upper respiratory tract as the primary clinical manifestation and had few comorbidities and a good prognosis; however, the negative conversion time of the new coronavirus nucleic acid was still considerably long.
Collapse
Affiliation(s)
- Huatang Zhang
- Department of Infection, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Wenhuang Chen
- Department of Infection, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Xiaoyi Ye
- Department of Respiratory Disease, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Yongjun Zhou
- College of Life Sciences and Chemistry, Minnan Science and Technology University, Quanzhou, Fujian 362000, P.R. China,Institute of Bioengineering and Biotechnology, Minnan Science and Technology University, Quanzhou, Fujian 362000, P.R. China
| | - Yijuan Zheng
- Department of Infection, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Zhangyan Weng
- Department of Infection, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Jianfeng Xie
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, Fujian 350001, P.R. China
| | - Kuicheng Zheng
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, Fujian 350001, P.R. China
| | - Zhijun Su
- Department of Infection, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Xibin Zhuang
- Department of Respiratory Disease, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, P.R. China,Correspondence to: Dr Xueping Yu, Department of Infection, The First Hospital of Quanzhou Affiliated to Fujian Medical University, 250 East Street, Licheng, Quanzhou, Fujian 362000, P.R. China
| | - Xueping Yu
- Department of Infection, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, P.R. China,Correspondence to: Dr Xueping Yu, Department of Infection, The First Hospital of Quanzhou Affiliated to Fujian Medical University, 250 East Street, Licheng, Quanzhou, Fujian 362000, P.R. China
| |
Collapse
|
10
|
SARS-CoV-2 Variant-Specific Infectivity and Immune Profiles Are Detectable in a Humanized Lung Mouse Model. Viruses 2022; 14:v14102272. [PMID: 36298826 PMCID: PMC9612296 DOI: 10.3390/v14102272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Small animal models that accurately model pathogenesis of SARS-CoV-2 variants are required for ongoing research efforts. We modified our human immune system mouse model to support replication of SARS-CoV-2 by implantation of human lung tissue into the mice to create TKO-BLT-Lung (L) mice and compared infection with two different variants in a humanized lung model. Infection of TKO-BLT-L mice with SARS-CoV-2 recapitulated the higher infectivity of the B.1.1.7 variant with more animals becoming infected and higher sustained viral loads compared to mice challenged with an early B lineage (614D) virus. Viral lesions were observed in lung organoids but no differences were detected between the viral variants as expected. Partially overlapping but distinct immune profiles were also observed between the variants with a greater Th1 profile in VIDO-01 and greater Th2 profile in B.1.1.7 infection. Overall, the TKO-BLT-L mouse supported SARS-CoV-2 infection, recapitulated key known similarities and differences in infectivity and pathogenesis as well as revealing previously unreported differences in immune responses between the two viral variants. Thus, the TKO-BLT-L model may serve as a useful animal model to study the immunopathobiology of newly emerging variants in the context of genuine human lung tissue and immune cells.
Collapse
|
11
|
da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
Collapse
Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| |
Collapse
|
12
|
Ikuse T, Aizawa Y, Shobukawa Y, Tomiyama N, Nakayama H, Takahashi M, Muto K, Hasegawa S, Takahashi M, Kon M, Tamura T, Matsumoto H, Saito R, Saitoh A. Household Secondary Transmission of the Severe Acute Respiratory Syndrome Coronavirus 2 Alpha Variant From a Community Cluster in a Nursery in Japan. Pediatr Infect Dis J 2022; 41:e358-e364. [PMID: 35703299 PMCID: PMC9359683 DOI: 10.1097/inf.0000000000003607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Spread of variants of concerns (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an increase in children with coronavirus disease 2019 (COVID-19). In February 2021, clusters of the Alpha variant of SARS-CoV-2 started to be reported in Niigata, Japan, including a large nursery cluster. We investigated the transmission routes and household secondary attack rates (SARs) in this cluster. METHODS Epidemiologic data related to a nursery cluster in Niigata, Japan, particularly child-origin and adult-origin SARs, were analyzed. VOCs were confirmed by whole-genome sequencing of virus from patients. RESULTS In total, 42 persons (22 children and 20 adults) in the cluster were infected with the Alpha variant. In the nursery, 13 of 81 children (16.0%) and 4 of 24 teachers (16.7%) were infected. SARS-CoV-2 later spread to 25 persons (10 children and 15 adults) outside the nursery. Child-origin and adult-origin household SARs were 27.7% (13/47) and 47.0% (8/17) ( P = 0.11), respectively, which were higher than rates attributable to non-VOCs in previous studies. CONCLUSIONS As compared with non-VOCs, the Alpha variant of SARS-CoV-2 exhibited high transmissibility among children and adults and may pose a high risk for household secondary transmission from SARS-CoV-2-infected children. Increased transmissibility of current or future VOCs could lead to greater transmission from children to adults or other children.
Collapse
Affiliation(s)
- Tatsuki Ikuse
- From the Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences
| | - Yuta Aizawa
- From the Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences
| | - Yugo Shobukawa
- Department of Active Ageing, Niigata University Graduate School of Medical and Dental Sciences
| | - Nobuko Tomiyama
- Department of Health and Welfare, Niigata Prefectural Office
| | | | | | | | - Satoshi Hasegawa
- Department of Patient Coordinate Center, Niigata Prefectural Office
| | | | - Miyako Kon
- Department of Virology, Niigata Prefectural Institute of Public Health and Environmental Science
| | - Tsutomu Tamura
- Department of Virology, Niigata Prefectural Institute of Public Health and Environmental Science
| | | | - Reiko Saito
- Department of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akihiko Saitoh
- From the Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences
| |
Collapse
|
13
|
A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma. Nat Biomed Eng 2022; 6:968-978. [PMID: 35941191 PMCID: PMC9361916 DOI: 10.1038/s41551-022-00919-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 07/01/2022] [Indexed: 12/19/2022]
Abstract
Rapid, accurate and frequent detection of the RNA of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and of serological host antibodies to the virus would facilitate the determination of the immune status of individuals who have Coronavirus disease 2019 (COVID-19), were previously infected by the virus, or were vaccinated against the disease. Here we describe the development and application of a 3D-printed lab-on-a-chip that concurrently detects, via multiplexed electrochemical outputs and within 2 h, SARS-CoV-2 RNA in saliva as well as anti-SARS-CoV-2 immunoglobulins in saliva spiked with blood plasma. The device automatedly extracts, concentrates and amplifies SARS-CoV-2 RNA from unprocessed saliva, and integrates the Cas12a-based enzymatic detection of SARS-CoV-2 RNA via isothermal nucleic acid amplification with a sandwich-based enzyme-linked immunosorbent assay on electrodes functionalized with the Spike S1, nucleocapsid and receptor-binding-domain antigens of SARS-CoV-2. Inexpensive microfluidic electrochemical sensors for performing multiplexed diagnostics at the point of care may facilitate the widespread monitoring of COVID-19 infection and immunity. A 3D-printed lab-on-a-chip allows for the concurrent rapid electrochemical detection of SARS-CoV-2 RNA in saliva and of anti-SARS-CoV-2 antibodies in saliva spiked with blood plasma.
Collapse
|
14
|
Dewald F, Detmer S, Pirkl M, Hellmich M, Heger E, Herrmann M, Zweigner J, Klein F. Viral load dynamics in SARS-CoV-2 Omicron breakthrough infections. J Infect Dis 2022; 226:1721-1725. [PMID: 35906927 PMCID: PMC9384619 DOI: 10.1093/infdis/jiac290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Indexed: 11/14/2022] Open
Abstract
In order to determine viral dynamics in Omicron breakthrough infections, we measured SARS-CoV-2 RNA in 206 double vaccinated or boostered individuals. During the first three days following the onset of symptoms, viral loads were significantly higher (Ct 21.76) in vaccinated compared to boostered (Ct 23.14) individuals (p = 0.029). However, by performing a longitudinal analysis on 32 individuals over 14 days, no difference in the viral load trajectory was observed between double vaccinated and boostered patients. Our results indicate that booster immunization results in a small reduction in detectable viral loads without significantly changing viral load dynamics over time.
Collapse
Affiliation(s)
- Felix Dewald
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Susanne Detmer
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Martin Pirkl
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Martin Hellmich
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maximilian Herrmann
- Department of Hospital Hygiene and Infection Control, University Hospital of Cologne, Cologne, Germany
| | - Janine Zweigner
- Department of Hospital Hygiene and Infection Control, University Hospital of Cologne, Cologne, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| |
Collapse
|
15
|
The importance of effect sizes when comparing cycle threshold values of SARS-CoV-2 variants. PLoS One 2022; 17:e0271808. [PMID: 35862414 PMCID: PMC9302753 DOI: 10.1371/journal.pone.0271808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/07/2022] [Indexed: 12/02/2022] Open
Abstract
Purpose We aimed to elaborate whether cycle threshold (Ct) values differ significantly between wild type SARS-CoV-2 (wtV) and certain viral variants and how strong or weak a potential significant effect might be. Methods In a retrospective study, we investigated 1873 SARS-CoV-2 positive samples for the occurrence of viral marker mutations. Age, gender, clinical setting, days after onset of symptoms, and Ct values were recorded. Statistical analysis was carried out with special consideration of effect sizes. Results During the study period wtV was detected in 1013 samples (54%), while 845 (45%) patients carried the Alpha variant of concern (VOC), and 15 (1%) the Beta VOC. For further analysis, only wtV and the Alpha VOC were included. In a multi-factor ANOVA and post-hoc test with Bonferroni-correction for the age groups we found significant main-effects for Ct values of the viral variant (wtV mean 26.4 (SD 4.27); Alpha VOC mean 25.0 (SD 3.84); F (1,1850) = 55.841; p < .001) and the clinical setting (outpatients: mean 25.7 (SD 4.1); inpatients: mean 27.0 (SD 4.2); F (1,1850) = 8.520, p = .004). However, since the effect sizes were very small (eta squared for the Alpha VOC = .029 and the clinical setting = .004), there was only a slight trend towards higher viral loads of the Alpha VOC compared to wtV. Conclusions In order to compare different variants of SARS-CoV-2 the calculation of effect sizes seems to be necessary. A combination of p-values as estimates of the existance of an effect and effect sizes as estimates of the magnitude of a potential effect may allow a better insight into transmission mechanisms of SARS-CoV-2.
Collapse
|
16
|
Chu VT, Schwartz NG, Donnelly MAP, Chuey MR, Soto R, Yousaf AR, Schmitt-Matzen EN, Sleweon S, Ruffin J, Thornburg N, Harcourt JL, Tamin A, Kim G, Folster JM, Hughes LJ, Tong S, Stringer G, Albanese BA, Totten SE, Hudziec MM, Matzinger SR, Dietrich EA, Sheldon SW, Stous S, McDonald EC, Austin B, Beatty ME, Staples JE, Killerby ME, Hsu CH, Tate JE, Kirking HL, Matanock A. Comparison of Home Antigen Testing With RT-PCR and Viral Culture During the Course of SARS-CoV-2 Infection. JAMA Intern Med 2022; 182:701-709. [PMID: 35486394 PMCID: PMC9055515 DOI: 10.1001/jamainternmed.2022.1827] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE As self-collected home antigen tests become widely available, a better understanding of their performance during the course of SARS-CoV-2 infection is needed. OBJECTIVE To evaluate the diagnostic performance of home antigen tests compared with reverse transcription-polymerase chain reaction (RT-PCR) and viral culture by days from illness onset, as well as user acceptability. DESIGN, SETTING, AND PARTICIPANTS This prospective cohort study was conducted from January to May 2021 in San Diego County, California, and metropolitan Denver, Colorado. The convenience sample included adults and children with RT-PCR-confirmed infection who used self-collected home antigen tests for 15 days and underwent at least 1 nasopharyngeal swab for RT-PCR, viral culture, and sequencing. EXPOSURES SARS-CoV-2 infection. MAIN OUTCOMES AND MEASURES The primary outcome was the daily sensitivity of home antigen tests to detect RT-PCR-confirmed cases. Secondary outcomes included the daily percentage of antigen test, RT-PCR, and viral culture results that were positive, and antigen test sensitivity compared with same-day RT-PCR and cultures. Antigen test use errors and acceptability were assessed for a subset of participants. RESULTS This study enrolled 225 persons with RT-PCR-confirmed infection (median [range] age, 29 [1-83] years; 117 female participants [52%]; 10 [4%] Asian, 6 [3%] Black or African American, 50 [22%] Hispanic or Latino, 3 [1%] Native Hawaiian or Other Pacific Islander, 145 [64%] White, and 11 [5%] multiracial individuals) who completed 3044 antigen tests and 642 nasopharyngeal swabs. Antigen test sensitivity was 50% (95% CI, 45%-55%) during the infectious period, 64% (95% CI, 56%-70%) compared with same-day RT-PCR, and 84% (95% CI, 75%-90%) compared with same-day cultures. Antigen test sensitivity peaked 4 days after illness onset at 77% (95% CI, 69%-83%). Antigen test sensitivity improved with a second antigen test 1 to 2 days later, particularly early in the infection. Six days after illness onset, antigen test result positivity was 61% (95% CI, 53%-68%). Almost all (216 [96%]) surveyed individuals reported that they would be more likely to get tested for SARS-CoV-2 infection if home antigen tests were available over the counter. CONCLUSIONS AND RELEVANCE The results of this cohort study of home antigen tests suggest that sensitivity for SARS-CoV-2 was moderate compared with RT-PCR and high compared with viral culture. The results also suggest that symptomatic individuals with an initial negative home antigen test result for SARS-CoV-2 infection should test again 1 to 2 days later because test sensitivity peaked several days after illness onset and improved with repeated testing.
Collapse
Affiliation(s)
- Victoria T Chu
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia.,Epidemic Intelligence Service, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Noah G Schwartz
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia.,Epidemic Intelligence Service, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Marisa A P Donnelly
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia.,Epidemic Intelligence Service, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Meagan R Chuey
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia.,Epidemic Intelligence Service, US Centers for Disease Control and Prevention, Atlanta, Georgia.,County of San Diego Health and Human Services Agency, San Diego, California
| | - Raymond Soto
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia.,Epidemic Intelligence Service, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anna R Yousaf
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia.,Epidemic Intelligence Service, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Emily N Schmitt-Matzen
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia.,Epidemic Intelligence Service, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sadia Sleweon
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jasmine Ruffin
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Natalie Thornburg
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jennifer L Harcourt
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Azaibi Tamin
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Gimin Kim
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jennifer M Folster
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Laura J Hughes
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Suxiang Tong
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ginger Stringer
- Colorado Department of Public Health and Environment, Denver
| | | | - Sarah E Totten
- Colorado Department of Public Health and Environment, Denver
| | | | | | - Elizabeth A Dietrich
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sarah W Sheldon
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, California
| | - Eric C McDonald
- County of San Diego Health and Human Services Agency, San Diego, California
| | - Brett Austin
- County of San Diego Health and Human Services Agency, San Diego, California
| | - Mark E Beatty
- County of San Diego Health and Human Services Agency, San Diego, California
| | - J Erin Staples
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Marie E Killerby
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Christopher H Hsu
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jacqueline E Tate
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Hannah L Kirking
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Almea Matanock
- COVID-19 Response Team, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | | |
Collapse
|
17
|
Unalan-Altintop T, Celep G, Milletli-Sezgin F, Onarer P, Gozukara M, Bilgic I, Onal E, Can ME, Demir Hİ. The Impact of Alpha Variant (B.1.1.7), Viral Load, and Age on the Clinical Course of Pediatric COVID-19 Patients. J PEDIAT INF DIS-GER 2022. [DOI: 10.1055/s-0042-1750317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Abstract
Objective The research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mainly consists of adult patients, leaving its impact on children understudied. This study aims to investigate the correlations between viral load, clinical course, age, and Alpha variant (B.1.1.7) in children.
Methods The study was conducted on children under the age of 18 years, who were admitted to Amasya University Sabuncuoglu Serefeddin Research and Training Hospital in Turkey between February and April 2021. ΔCt values, which were obtained by real-time polymerase chain reaction (PCR), were analyzed to estimate the viral loads of the patients. Alpha variant (B.1.1.7) positivity was determined by real-time PCR.
Results There was no difference between estimated viral loads of different clinical courses (p > 0.05), or between asymptomatic and symptomatic patients (p > 0.05). Viral loads were found to decrease with increasing age (p = 0.002). Also, a higher rate of symptomatic disease was found in children under the age of 4 years (p < 0.05). Alpha variant (B.1.1.7) was not found to be associated with severe disease in children (p > 0.05).
Conclusion Our results demonstrate higher viral loads and symptomatic disease in children under the age of 4 years. Alpha variant (B.1.1.7) was not found to be related to disease severity. There has not been a consensus on the vaccination of the pediatric population worldwide. More studies are needed to understand the viral kinetics of SARS-CoV-2 and its severity on children to build effective vaccination strategies in children as public health restrictions are eased.
Collapse
Affiliation(s)
- Tugce Unalan-Altintop
- Department of Medical Microbiology, Amasya University Sabuncuoglu Serefeddin Research and Training Hospital, Amasya, Turkey
| | - Gokce Celep
- Department of Pediatrics, Amasya University, Faculty of Medicine, Amasya, Turkey
| | | | - Pelin Onarer
- Department of Medical Microbiology, Amasya University Sabuncuoglu Serefeddin Research and Training Hospital, Amasya, Turkey
| | | | - Isıl Bilgic
- Department of Pediatric Respiratory Diseases, Ankara City Hospital, Ankara, Turkey
| | - Esra Onal
- Department of Pediatrics, Amasya University Sabuncuoglu Serefeddin Research and Training Hospital, Amasya, Turkey
| | - Muhammed Enis Can
- Department of Pediatrics, Amasya University Sabuncuoglu Serefeddin Research and Training Hospital, Amasya, Turkey
| | - Havva İpek Demir
- Department of Pediatrics, Evliya Celebi Research and Training Hospital, Kutahya, Turkey
| |
Collapse
|
18
|
Martin-Blondel G, Lescure FX, Assoumou L, Charpentier C, Chapplain JM, Perpoint T, Grouteau G, Cordel H, Pialoux G, Pacanowski J, Thy M, Bauvois A, Laureillard D, Hamrouni F, Algarte-Genin M, Poissy J, Descamps D, Costagliola D. Increased risk of severe COVID-19 in hospitalized patients with SARS-CoV-2 Alpha variant infection: a multicentre matched cohort study. BMC Infect Dis 2022; 22:540. [PMID: 35698029 PMCID: PMC9189443 DOI: 10.1186/s12879-022-07508-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The impact of the variant of concern (VOC) Alpha on the severity of COVID-19 has been debated. We report our analysis in France. METHODS We conducted an exposed/unexposed cohort study with retrospective data collection, comparing patients infected by VOC Alpha to contemporaneous patients infected by historical lineages. Participants were matched on age (± 2.5 years), sex and region of hospitalization. The primary endpoint was the proportion of hospitalized participants with severe COVID-19, defined as a WHO-scale > 5 or by the need of a non-rebreather mask, occurring up to day 29 after admission. We used a logistic regression model stratified on each matched pair and accounting for factors known to be associated with the severity of the disease. RESULTS We included 650 pairs of patients hospitalized between Jan 1, 2021, and Feb 28, 2021, in 47 hospitals. Median age was 70 years and 61.3% of participants were male. The proportion of participants with comorbidities was high in both groups (85.0% vs 90%, p = 0.004). Infection by VOC Alpha was associated with a higher odds of severe COVID-19 (41.7% vs 38.5%-aOR = 1.33 95% CI [1.03-1.72]). CONCLUSION Infection by the VOC Alpha was associated with a higher odds of severe COVID-19.
Collapse
Affiliation(s)
- Guillaume Martin-Blondel
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Toulouse, Toulouse, France. .,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291, CNRS UMR5051, Université Toulouse III, Toulouse, France.
| | - François-Xavier Lescure
- Service des Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude-Bernard, APHP, Paris, France
| | - Lambert Assoumou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Charlotte Charpentier
- Service de Virologie, Université de Paris, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, 75018, Paris, France
| | - Jean-Marc Chapplain
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Thomas Perpoint
- Service des Maladies Infectieuses et Tropicales, Hospices Civils de Lyon, Lyon, France
| | - Gaspard Grouteau
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Hugues Cordel
- Service des Maladies Infectieuses et Tropicales, Hôpital Avicenne, AP-HP, Bobigny, France
| | - Gilles Pialoux
- Service des Maladies Infectieuses et Tropicales, Hôpital Tenon, APHP, Paris, France
| | - Jérome Pacanowski
- Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, APHP, Paris, France
| | - Michael Thy
- Service des Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude-Bernard, APHP, Paris, France
| | - Adeline Bauvois
- Service de Médecine Interne, Hôpital Ambroise Paré, APHP, Boulogne-Billancourt, France
| | - Didier Laureillard
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
| | - Fadia Hamrouni
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Michèle Algarte-Genin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Julien Poissy
- University of Lille, Inserm U1285, CHU Lille, Pôle de Médecine Intensive Réanimation, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Diane Descamps
- Service de Virologie, Université de Paris, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, 75018, Paris, France
| | - Dominique Costagliola
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | | |
Collapse
|
19
|
Caccuri F, Messali S, Bortolotti D, Di Silvestre D, De Palma A, Cattaneo C, Bertelli A, Zani A, Milanesi M, Giovanetti M, Campisi G, Gentili V, Bugatti A, Filippini F, Scaltriti E, Pongolini S, Tucci A, Fiorentini S, d’Ursi P, Ciccozzi M, Mauri P, Rizzo R, Caruso A. Competition for Dominance Within Replicating Quasispecies During Prolonged SARS-CoV-2 Infection in an Immunocompromised Host. Virus Evol 2022; 8:veac042. [PMID: 35706980 PMCID: PMC9129230 DOI: 10.1093/ve/veac042] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/10/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) emerge for their capability to better adapt to the human host aimed and enhance human-to-human transmission. Mutations in spike largely contributed to adaptation. Viral persistence is a prerequisite for intra-host virus evolution, and this likely occurred in immunocompromised patients who allow intra-host long-term viral replication. The underlying mechanism leading to the emergence of variants during viral persistence in the immunocompromised host is still unknown. Here, we show the existence of an ensemble of minor mutants in the early biological samples obtained from an immunocompromised patient and their dynamic interplay with the master mutant during a persistent and productive long-term infection. In particular, after 222 days of active viral replication, the original master mutant, named MB610, was replaced by a minor quasispecies (MB61222) expressing two critical mutations in spike, namely Q493K and N501T. Isolation of the two viruses allowed us to show that MB61222 entry into target cells occurred mainly by the fusion at the plasma membrane (PM), whereas endocytosis characterized the entry mechanism used by MB610. Interestingly, coinfection of two human cell lines of different origin with the SARS-CoV-2 isolates highlighted the early and dramatic predominance of MB61222 over MB610 replication. This finding may be explained by a faster replicative activity of MB61222 as compared to MB610 as well as by the capability of MB61222 to induce peculiar viral RNA-sensing mechanisms leading to an increased production of interferons (IFNs) and, in particular, of IFN-induced transmembrane protein 1 (IFITM1) and IFITM2. Indeed, it has been recently shown that IFITM2 is able to restrict SARS-CoV-2 entry occurring by endocytosis. In this regard, MB61222 may escape the antiviral activity of IFITMs by using the PM fusion pathway for entry into the target cell, whereas MB610 cannot escape this host antiviral response during MB61222 coinfection, since it has endocytosis as the main pathway of entry. Altogether, our data support the evidence of quasispecies fighting for host dominance by taking benefit from the cell machinery to restrict the productive infection of competitors in the viral ensemble. This finding may explain, at least in part, the extraordinary rapid worldwide turnover of VOCs that use the PM fusion pathway to enter into target cells over the original pandemic strain.
Collapse
Affiliation(s)
- Francesca Caccuri
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Serena Messali
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Daria Bortolotti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Dario Di Silvestre
- Proteomic and Metabolomic Laboratory, Institute of Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
| | - Antonella De Palma
- Proteomic and Metabolomic Laboratory, Institute of Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
| | - Chiara Cattaneo
- Department of Hematology, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Anna Bertelli
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Alberto Zani
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Maria Milanesi
- Section of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Giovanni Campisi
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Valentina Gentili
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Antonella Bugatti
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Federica Filippini
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 43126 Parma, Italy
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 43126 Parma, Italy
| | - Alessandra Tucci
- Department of Hematology, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Simona Fiorentini
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Pasqualina d’Ursi
- Institute of Technologies in Biomedicine, National Research Council, 20090 Segrate, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Pierluigi Mauri
- Proteomic and Metabolomic Laboratory, Institute of Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Arnaldo Caruso
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| |
Collapse
|
20
|
Michaelsen TY, Bennedbæk M, Christiansen LE, Jørgensen MSF, Møller CH, Sørensen EA, Knutsson S, Brandt J, Jensen TBN, Chiche-Lapierre C, Collados EF, Sørensen T, Petersen C, Le-Quy V, Sereika M, Hansen FT, Rasmussen M, Fonager J, Karst SM, Marvig RL, Stegger M, Sieber RN, Skov R, Legarth R, Krause TG, Fomsgaard A, Albertsen M. Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark. Genome Med 2022; 14:47. [PMID: 35505393 PMCID: PMC9064402 DOI: 10.1186/s13073-022-01045-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Background In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the transmissibility, introduction, and onward transmission of B.1.1.7 in Denmark. Methods We analyzed a comprehensive set of 60,178 SARS-CoV-2 genomes generated from high-throughput sequencing by the Danish COVID-19 Genome Consortium, representing 34% of all positive cases in the period 14 November 2020 to 7 February 2021. We calculated the transmissibility of B.1.1.7 relative to other lineages using Poisson regression. Including all 1976 high-quality B.1.1.7 genomes collected in the study period, we constructed a time-scaled phylogeny, which was coupled with detailed travel history and register data to outline the introduction and onward transmission of B.1.1.7 in Denmark. Results In a period with unchanged restrictions, we estimated an increased B.1.1.7 transmissibility of 58% (95% CI: [56%, 60%]) relative to other lineages. Epidemiological and phylogenetic analyses revealed that 37% of B.1.1.7 cases were related to the initial introduction in November 2020. The relative number of cases directly linked to introductions varied between 10 and 50% throughout the study period. Conclusions Our findings corroborate early estimates of increased transmissibility of B.1.1.7. Both substantial early expansion when B.1.1.7 was still unmonitored and continuous foreign introductions contributed considerably to case numbers. Finally, our study highlights the benefit of balanced travel restrictions and self-isolation procedures coupled with comprehensive surveillance efforts, to sustain epidemic control in the face of emerging variants. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01045-7.
Collapse
Affiliation(s)
- Thomas Y Michaelsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marc Bennedbæk
- Centre of Excellence for Health, Immunity and Infection (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lasse E Christiansen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | - Mia S F Jørgensen
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Camilla H Møller
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Emil A Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Knutsson
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Jakob Brandt
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Thomas B N Jensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Emilio F Collados
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Celine Petersen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Vang Le-Quy
- Unit for Research Data Services (CLAAUDIA), Aalborg University, Aalborg, Denmark
| | - Mantas Sereika
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Frederik T Hansen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Søren M Karst
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert Skov
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Rebecca Legarth
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Tyra G Krause
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| |
Collapse
|
21
|
Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant. Epidemics 2022; 39:100578. [PMID: 35636310 PMCID: PMC9098518 DOI: 10.1016/j.epidem.2022.100578] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 04/14/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
From 24 December 2020 to 8 February 2021, 163 cases of SARS-CoV-2 Alpha variant of concern (VOC) were identified in Chieti province, Abruzzo region. Epidemiological data allowed the identification of 14 epi-clusters. With one exception, all the epi-clusters were linked to the town of Guardiagrele: 149 contacts formed the network, two-thirds of which were referred to the family/friends context. Real data were then used to estimate transmission parameters. According to our method, the calculated Re(t) was higher than 2 before the 12 December 2020. Similar values were obtained from other studies considering Alpha VOC. Italian sequence data were combined with a random subset of sequences obtained from the GISAID database. Genomic analysis showed close identity between the sequences from Guardiagrele, forming one distinct clade. This would suggest one or limited unspecified viral introductions from outside to Abruzzo region in early December 2020, which led to the diffusion of Alpha VOC in Guardiagrele and in neighbouring municipalities, with very limited inter-regional mixing. SARS-CoV-2 Alpha VOC has been identified in Guardiagrele (Abruzzo, Italy) starting from late December 2020. Epidemiological investigations led to the identification of epi-clusters comprising 163 Alpha VOC cases. A reconstructed transmission chain can be used to estimate transmission parameters including Re(t). A comparison between sequences in the GISAID database supports limited virus introduction scenario in the area.
Collapse
|
22
|
Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Zhou R, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Nat Microbiol 2022; 7:640-652. [PMID: 35484231 PMCID: PMC9084242 DOI: 10.1038/s41564-022-01105-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 03/15/2022] [Indexed: 02/07/2023]
Abstract
The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to 'superspreading'. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant-of-concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be explained simply by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
Collapse
Affiliation(s)
- Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Pamela P Martinez
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Laura L Gibson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Junko Jarrett
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tongyu Liu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kimberly K O Walden
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Darci C Edmonson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karen K Chiu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hannah Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kevin R Scardina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shannon Bradley
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stacy L Gloss
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Crystal Reinhart
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jagadeesh Yedetore
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jessica Quicksall
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alyssa N Owens
- Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - John Broach
- UMass Memorial Medical Center, Worcester, MA, USA
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruce Barton
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, USA
| | - Peter Lazar
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - William J Heetderks
- National Institute for Biomedical Imaging and Bioengineering, Bethesda, MD, USA
| | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David D McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
23
|
Cojocaru C, Cojocaru E, Turcanu A, Zaharia D. Clinical challenges of SARS‑CoV‑2 variants (Review). Exp Ther Med 2022; 23:416. [PMID: 35601074 PMCID: PMC9117961 DOI: 10.3892/etm.2022.11343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/08/2022] [Indexed: 11/06/2022] Open
Abstract
Since the first cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, there have been challenges recognizing the clinical features of SARS-CoV-2 and identifying therapeutic options. This has been compounded by viral mutations that affect clinical response and primary epidemiological indicators. Multiple variants of SARS-CoV-2 have been identified and classified on the basis of nomenclature implemented by scientific organizations and the World Health Organisation (WHO). A total of five variants of concern (VOCs) have been identified to date. The present study aimed to analyse clinical and epidemiological features of each variant. Based on these characteristics, predictions were made about potential future evolution. Considering the time and location of SARS-CoV-2 VOC emergence, it was hypothesised that mutations were not due to pressure caused by the vaccines introduced in December 2020 but were dependent on natural characteristics of the virus. In the process of adapting to the human body, SARS-CoV-2 is expected to undergo evolution to become more contagious but less deadly. SARS-CoV-2 was hypothesized to continue spread through isolated epidemic outbreaks due to the unimmunized population, mostly unvaccinated children and adults, and for coronaviruses to continue to present a public health problem.
Collapse
Affiliation(s)
- Cristian Cojocaru
- Medical III Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Elena Cojocaru
- Morpho‑Functional Sciences II Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adina Turcanu
- Medical III Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Dragos Zaharia
- Department 4 Cardio‑thoracic Pathology, Faculty of Medicine, University of Medicine and Pharmacy ‘Carol Davila’, 050471 Bucharest, Romania
| |
Collapse
|
24
|
de Souza AS, de Freitas Amorim VM, Guardia GDA, dos Santos FF, Ulrich H, Galante PAF, de Souza RF, Guzzo CR. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. Viruses 2022; 14:827. [PMID: 35458557 PMCID: PMC9029021 DOI: 10.3390/v14040827] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host's immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) the increase in Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with the increase in RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment in Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
Collapse
Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Vitor Martins de Freitas Amorim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Filipe F. dos Santos
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| |
Collapse
|
25
|
Yang Z, Zhang S, Tang YP, Zhang S, Xu DQ, Yue SJ, Liu QL. Clinical Characteristics, Transmissibility, Pathogenicity, Susceptible Populations, and Re-infectivity of Prominent COVID-19 Variants. Aging Dis 2022; 13:402-422. [PMID: 35371608 PMCID: PMC8947836 DOI: 10.14336/ad.2021.1210] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/10/2021] [Indexed: 12/11/2022] Open
Abstract
In addition to the rapid, global spread of SARS-CoV-2, new and comparatively more contagious variants are of considerable concern. These emerging mutations have become a threat to the global public health, creating COVID-19 surges in different countries. However, information on these emerging variants is limited and scattered. In this review, we discuss new variants that have emerged worldwide and identify several variants of concern, such as B.1.1.7, B.1.351, P.1, B.1.617.2 and B.1.1.529, and their basic characteristics. Other significant variants such as C.37, B.1.621, B.1.525, B.1.526, AZ.5, C.1.2, and B.1.617.1 are also discussed. This review highlights the clinical characteristics of these variants, including transmissibility, pathogenicity, susceptible population, and re-infectivity. It provides the latest information on the recent variants of SARS-CoV-2. The summary of this information will help researchers formulate reasonable strategies to curb the ongoing COVID-19 pandemic.
Collapse
Affiliation(s)
- Zhen Yang
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China.,2School of Public Health, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Shuo Zhang
- 3School of Clinical Medicine (Guang'anmen Hospital), Beijing University of Chinese Medicine, Beijing, China
| | - Yu-Ping Tang
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Sai Zhang
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Ding-Qiao Xu
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Shi-Jun Yue
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Qi-Ling Liu
- 2School of Public Health, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| |
Collapse
|
26
|
Arora P, Sidarovich A, Graichen L, Hörnich B, Hahn A, Hoffmann M, Pöhlmann S. Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. PLoS One 2022; 17:e0265453. [PMID: 35333910 PMCID: PMC8956166 DOI: 10.1371/journal.pone.0265453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/01/2022] [Indexed: 01/12/2023] Open
Abstract
Several SARS-CoV-2 variants emerged that harbor mutations in the surface unit of the viral spike (S) protein that enhance infectivity and transmissibility. Here, we analyzed whether ten naturally-occurring mutations found within the extended loop harboring the S1/S2 cleavage site of the S protein, a determinant of SARS-CoV-2 cell tropism and pathogenicity, impact S protein processing and function. None of the mutations increased but several decreased S protein cleavage at the S1/S2 site, including S686G and P681H, the latter of which is found in variants of concern B.1.1.7 (Alpha variant) and B.1.1.529 (Omicron variant). None of the mutations reduced ACE2 binding and cell-cell fusion although several modulated the efficiency of host cell entry. The effects of mutation S686G on viral entry were cell-type dependent and could be linked to the availability of cathepsin L for S protein activation. These results show that polymorphisms at the S1/S2 site can modulate S protein processing and host cell entry.
Collapse
Affiliation(s)
- Prerna Arora
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Anzhalika Sidarovich
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Bojan Hörnich
- Junior Research Group Herpesviruses - Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Alexander Hahn
- Junior Research Group Herpesviruses - Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail: (MH); (SP)
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail: (MH); (SP)
| |
Collapse
|
27
|
Xiao C, Mao L, Wang Z, Gao L, Zhu G, Su J, Chen X, Yuan J, Hu Y, Yin Z, Xie J, Ji W, Niu H, Gao F, Luo OJ, Xiao L, Wang P, Chen G. SARS-CoV-2 variant B.1.1.7 caused HLA-A2 + CD8 + T cell epitope mutations for impaired cellular immune response. iScience 2022; 25:103934. [PMID: 35194575 PMCID: PMC8851741 DOI: 10.1016/j.isci.2022.103934] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/29/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Here, we evaluated the immune properties of the HLA-A2 restricted CD8+ T cell epitopes containing mutations from B.1.1.7, and furthermore performed a comprehensive analysis of the SARS-CoV-2 specific CD8+ T cell responses from COVID-19 convalescent patients and SARS-CoV-2 vaccinees recognizing the ancestral Wuhan strain compared to B.1.1.7. First, most of the predicted CD8+ T cell epitopes showed proper binding with HLA-A2, whereas epitopes from B.1.1.7 had lower binding capability than those from the ancestral strain. In addition, these peptides could effectively induce the activation and cytotoxicity of CD8+ T cells. Our results further showed that at least two site mutations in B.1.1.7 resulted in a decrease in CD8+ T cell activation and a possible immune evasion, namely A1708D mutation in ORF1ab1707-1716 and I2230T mutation in ORF1ab2230-2238. Our current analysis provides information that contributes to the understanding of SARS-CoV-2-specific CD8+ T cell responses elicited by infection of mutated strains or vaccination.
Collapse
Affiliation(s)
- Chanchan Xiao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
| | - Lipeng Mao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
| | - Zhigang Wang
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou 510000, China
| | - Lijuan Gao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
| | - Guodong Zhu
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
- Department of Geriatrics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510000, China
| | - Jun Su
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou 510000, China
| | - Xiongfei Chen
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510000, China
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510000, China
| | - Yutian Hu
- Meng Yi Center Limited, Macau 999078, China
| | - Zhinan Yin
- Biomedical Translational Research Institute, Jinan University, Guangzhou 510000, China
| | - Jun Xie
- ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 200052, China
- Arthritis Institute of Integrated Traditional Chinese and Western Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai University of Chinese Traditional Medicine, Shanghai 200052, China
| | - Weiqing Ji
- ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 200052, China
- Arthritis Institute of Integrated Traditional Chinese and Western Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai University of Chinese Traditional Medicine, Shanghai 200052, China
| | - Haitao Niu
- School of Medicine & Institute of Laboratory Animal Sciences, Jinan University, Guangzhou 510000, China
| | - Feng Gao
- School of Medicine, Jinan University, Guangzhou 510000, China
| | - Oscar Junhong Luo
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou 510000, China
| | - Lianbo Xiao
- ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 200052, China
- Arthritis Institute of Integrated Traditional Chinese and Western Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai University of Chinese Traditional Medicine, Shanghai 200052, China
| | - Pengcheng Wang
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
| | - Guobing Chen
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou 510000, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou 510000, China
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou 510000, China
| |
Collapse
|
28
|
Jajou R, Mutsaers- van Oudheusden AJG, Verweij JJ, Rietveld A, Murk JL. SARS-CoV-2 transmitters have more than three times higher viral loads than non-transmitters – practical use of viral load for disease control. J Clin Virol 2022; 150-151:105131. [PMID: 35395500 PMCID: PMC8920080 DOI: 10.1016/j.jcv.2022.105131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 01/19/2023]
|
29
|
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature 2022; 602:487-495. [PMID: 34942634 PMCID: PMC8850198 DOI: 10.1038/s41586-021-04352-y] [Citation(s) in RCA: 191] [Impact Index Per Article: 95.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
The emergence of SARS-CoV-2 variants of concern suggests viral adaptation to enhance human-to-human transmission1,2. Although much effort has focused on the characterization of changes in the spike protein in variants of concern, mutations outside of spike are likely to contribute to adaptation. Here, using unbiased abundance proteomics, phosphoproteomics, RNA sequencing and viral replication assays, we show that isolates of the Alpha (B.1.1.7) variant3 suppress innate immune responses in airway epithelial cells more effectively than first-wave isolates. We found that the Alpha variant has markedly increased subgenomic RNA and protein levels of the nucleocapsid protein (N), Orf9b and Orf6-all known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein that is required for activation of the RNA-sensing adaptor MAVS. Moreover, the activity of Orf9b and its association with TOM70 was regulated by phosphorylation. We propose that more effective innate immune suppression, through enhanced expression of specific viral antagonist proteins, increases the likelihood of successful transmission of the Alpha variant, and may increase in vivo replication and duration of infection4. The importance of mutations outside the spike coding region in the adaptation of SARS-CoV-2 to humans is underscored by the observation that similar mutations exist in the N and Orf9b regulatory regions of the Delta and Omicron variants.
Collapse
Affiliation(s)
- Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - Mehdi Bouhaddou
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | | | - Lorena Zuliani-Alvarez
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Ben Polacco
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Adrian Pelin
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Andrea Fossati
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manisha Ummadi
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Ajda Rojc
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jane Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Marie L Bischof
- Division of Infection and Immunity, University College London, London, UK
| | - Kirsten Obernier
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia Richards
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kuei-Ho Chen
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bhavya Harjai
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Joseph Hiatt
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aminu Jahun
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Jacqueline M Fabius
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Yasu Takeuchi
- Division of Infection and Immunity, University College London, London, UK
| | - Paola Bonfanti
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Kevan Shokat
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Natalia Jura
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Division of Advanced Therapies, National Institute for Biological Standards and Control, South Mimms, UK
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Klim Verba
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Pedro Beltrao
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle L Swaney
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London, UK.
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK.
| | - Nevan J Krogan
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
30
|
da Silva SJR, de Lima SC, da Silva RC, Kohl A, Pena L. Viral Load in COVID-19 Patients: Implications for Prognosis and Vaccine Efficacy in the Context of Emerging SARS-CoV-2 Variants. Front Med (Lausanne) 2022; 8:836826. [PMID: 35174189 PMCID: PMC8841511 DOI: 10.3389/fmed.2021.836826] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022] Open
Abstract
The worldwide spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an unprecedented public health crisis in the 21st century. As the pandemic evolves, the emergence of SARS-CoV-2 has been characterized by the emergence of new variants of concern (VOCs), which resulted in a catastrophic impact on SARS-CoV-2 infection. In light of this, research groups around the world are unraveling key aspects of the associated illness, coronavirus disease 2019 (COVID-19). A cumulative body of data has indicated that the SARS-CoV-2 viral load may be a determinant of the COVID-19 severity. Here we summarize the main characteristics of the emerging variants of SARS-CoV-2, discussing their impact on viral transmissibility, viral load, disease severity, vaccine breakthrough, and lethality among COVID-19 patients. We also provide a rundown of the rapidly expanding scientific evidence from clinical studies and animal models that indicate how viral load could be linked to COVID-19 prognosis and vaccine efficacy among vaccinated individuals, highlighting the differences compared to unvaccinated individuals.
Collapse
Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Suelen Cristina de Lima
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
| | - Ronaldo Celerino da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Brazil
| |
Collapse
|
31
|
Is the Alpha Variant of SARS-CoV-2 Associated with a Higher Viral Load Than the Historical Strain in Saliva Samples in Patients with Mild to Moderate Symptoms? Life (Basel) 2022; 12:life12020163. [PMID: 35207451 PMCID: PMC8879902 DOI: 10.3390/life12020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 11/17/2022] Open
Abstract
During the COVID-19 pandemic, several generic variants emerged, including the Alpha variant, with increased transmissibility compared to historical strains. We aimed to compare the evolution of the viral load between patients infected with the Alpha variant and those infected with the historical SARS-CoV-2 strains, while taking into account the time interval between the onset of symptoms and samples. We used data collected from patients with an acute respiratory infection (mild to moderate symptoms) and seen in consultation in primary care, included in a prospective longitudinal study, COVID-A. Patients performed four salivary samples during the follow-up. All patients who had at least one of the saliva samples test positive for SARS-CoV-2 were included in the analysis. Overall, 118 patients were included: 89 infected by the historical strain and 29 infected by the Alpha variant. Even though we tended to observe a higher viral load in the Alpha variant group, we found no significant difference in the evolution of the viral load in saliva samples between patients infected with the Alpha variant of the SARS-CoV-2 and those infected by historical strains when controlling for the time interval between the onset of symptoms and sampling.
Collapse
|
32
|
Lee JY, Wing PAC, Gala DS, Noerenberg M, Järvelin AI, Titlow J, Zhuang X, Palmalux N, Iselin L, Thompson MK, Parton RM, Prange-Barczynska M, Wainman A, Salguero FJ, Bishop T, Agranoff D, James W, Castello A, McKeating JA, Davis I. Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences. eLife 2022; 11:74153. [PMID: 35049501 PMCID: PMC8776252 DOI: 10.7554/elife.74153] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/21/2021] [Indexed: 12/11/2022] Open
Abstract
Despite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is an urgent need to understand the early stages of viral replication and transcription. We used single-molecule fluorescence in situ hybridisation (smFISH) to quantify positive sense RNA genomes with 95% detection efficiency, while simultaneously visualising negative sense genomes, subgenomic RNAs, and viral proteins. Our absolute quantification of viral RNAs and replication factories revealed that SARS-CoV-2 genomic RNA is long-lived after entry, suggesting that it avoids degradation by cellular nucleases. Moreover, we observed that SARS-CoV-2 replication is highly variable between cells, with only a small cell population displaying high burden of viral RNA. Unexpectedly, the B.1.1.7 variant, first identified in the UK, exhibits significantly slower replication kinetics than the Victoria strain, suggesting a novel mechanism contributing to its higher transmissibility with important clinical implications.
Collapse
Affiliation(s)
- Jeffrey Y Lee
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Peter AC Wing
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), The University of OxfordOxfordUnited Kingdom
| | - Dalia S Gala
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Marko Noerenberg
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom,MRC-University of Glasgow Centre for Virus Research, The University of GlasgowGlasgowUnited Kingdom
| | - Aino I Järvelin
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Joshua Titlow
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, The University of GlasgowGlasgowUnited Kingdom
| | - Louisa Iselin
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Mary Kay Thompson
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Richard M Parton
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Maria Prange-Barczynska
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Ludwig Institute for Cancer Research, The University of OxfordOxfordUnited Kingdom
| | - Alan Wainman
- Sir William Dunn School of Pathology, The University of OxfordOxfordUnited Kingdom
| | | | - Tammie Bishop
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Ludwig Institute for Cancer Research, The University of OxfordOxfordUnited Kingdom
| | - Daniel Agranoff
- Department of Infectious Diseases, University Hospitals Sussex NHS Foundation TrustBrightonUnited Kingdom
| | - William James
- Sir William Dunn School of Pathology, The University of OxfordOxfordUnited Kingdom,James & Lillian Martin Centre, Sir William Dunn School of Pathology, The University of OxfordOxfordUnited Kingdom
| | - Alfredo Castello
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom,MRC-University of Glasgow Centre for Virus Research, The University of GlasgowGlasgowUnited Kingdom
| | - Jane A McKeating
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), The University of OxfordOxfordUnited Kingdom
| | - Ilan Davis
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| |
Collapse
|
33
|
A Review on Evolution of Emerging SARS-CoV-2 Variants based on Spike Glycoprotein. Int Immunopharmacol 2022; 105:108565. [PMID: 35123183 PMCID: PMC8799522 DOI: 10.1016/j.intimp.2022.108565] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/30/2022]
Abstract
Since the inception of SARS-CoV-2 in December 2019, many variants have emerged over time. Some of these variants have resulted in transmissibility changes of the virus and may also have impact on diagnosis, therapeutics and even vaccines, thereby raising particular concerns in the scientific community. The variants which have mutations in Spike glycoprotein are the primary focus as it is the main target for neutralising antibodies. SARS-CoV-2 is known to infect human through Spike glycoprotein and uses receptor-binding domain (RBD) to bind to the ACE2 receptor in human. Thus, it is of utmost importance to study these variants and their corresponding mutations. Such 12 different important variants identified so far are B.1.1.7 (Alpha), B.1.351 (Beta), B.1.525 (Eta), B.1.427/B.1.429 (Epsilon), B.1.526 (Iota), B.1.617.1 (Kappa), B.1.617.2 (Delta), C.37 (Lambda), P.1 (Gamma), P.2 (Zeta), P.3 (Theta) and the recently discovered B.1.1.529 (Omicron). These variants have 84 unique mutations in Spike glycoprotein. To analyse such mutations, multiple sequence alignment of 77681 SARS-CoV-2 genomes of 98 countries over the period from January 2020 to July 2021 is performed followed by phylogenetic analysis. Also, characteristics of new emerging variants are elaborately discussed. The individual evolution of these mutation points and the respective variants are visualised and their characteristics are also reported. Moreover, to judge the characteristics of the non-synonymous mutation points (substitutions), their biological functions are evaluated by PolyPhen-2 while protein structural stability is evaluated using I-Mutant 2.0.
Collapse
|
34
|
Lyngse FP, Mølbak K, Skov RL, Christiansen LE, Mortensen LH, Albertsen M, Møller CH, Krause TG, Rasmussen M, Michaelsen TY, Voldstedlund M, Fonager J, Steenhard N, Kirkeby CT. Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load. Nat Commun 2021; 12:7251. [PMID: 34903718 PMCID: PMC8669007 DOI: 10.1038/s41467-021-27202-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/08/2021] [Indexed: 01/03/2023] Open
Abstract
New lineages of SARS-CoV-2 are of potential concern due to higher transmissibility, risk of severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and risk factors, such as age of primary case and viral load remains poorly understood. Here, we used comprehensive administrative data from Denmark, comprising the full population (January 11 to February 7, 2021), to estimate household transmissibility. This study included 5,241 households with primary cases; 808 were infected with lineage B.1.1.7 and 4,433 with other lineages. Here, we report an attack rate of 38% in households with a primary case infected with B.1.1.7 and 27% in households with other lineages. Primary cases infected with B.1.1.7 had an increased transmissibility of 1.5-1.7 times that of primary cases infected with other lineages. The increased transmissibility of B.1.1.7 was multiplicative across age and viral load.
Collapse
Affiliation(s)
- Frederik Plesner Lyngse
- Department of Economics & Center for Economic Behaviour and Inequality, University of Copenhagen, Copenhagen, Denmark.
- Danish Ministry of Health, Copenhagen, Denmark.
- Statens Serum Institut, Copenhagen, Denmark.
| | - Kåre Mølbak
- Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Laust Hvas Mortensen
- Statistics Denmark, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | | | | | | | | | | | | | - Carsten Thure Kirkeby
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
35
|
Domingo P, de Benito N. Alpha variant SARS-CoV-2 infection: How it all starts. EBioMedicine 2021; 74:103703. [PMID: 34800902 PMCID: PMC8598133 DOI: 10.1016/j.ebiom.2021.103703] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/08/2023] Open
Affiliation(s)
- Pere Domingo
- Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, Institut de Recerca del Hospital de la Santa Creu i Sant Pau, Sant Quintí, 89, Barcelona 08041, Spain.
| | - Natividad de Benito
- Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, Institut de Recerca del Hospital de la Santa Creu i Sant Pau, Sant Quintí, 89, Barcelona 08041, Spain
| |
Collapse
|
36
|
Amato L, Jurisic L, Puglia I, Di Lollo V, Curini V, Torzi G, Di Girolamo A, Mangone I, Mancinelli A, Decaro N, Calistri P, Di Giallonardo F, Lorusso A, D’Alterio N. Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Emerg Microbes Infect 2021; 10:1148-1155. [PMID: 34019466 PMCID: PMC8205086 DOI: 10.1080/22221751.2021.1933609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 01/24/2023]
Abstract
Several lineages of SARS-CoV-2 are currently circulating worldwide. During SARS-CoV-2 diagnostic activities performed in Abruzzo region (central Italy) several strains belonging to the B.1.177.75 lineage tested negative for the N gene but positive for the ORF1ab and S genes (+/+/- pattern) by the TaqPath COVID-19 CE-IVD RT-PCR Kit manufactured by Thermofisher. By sequencing, a unique mutation, synonymous 28948C > T, was found in the N-negative B.1.177.75 strains. Although we do not have any knowledge upon the nucleotide sequences of the primers and probe adopted by this kit, it is likely that N gene dropout only occurs when 28948C > T is coupled with 28932C > T, this latter present, in turn, in all B.1.177.75 sequences available on public databases. Furthermore, epidemiological analysis was also performed. The majority of the N-negative B.1.177.75 cases belonged to two clusters apparently unrelated to each other and both clusters involved young people. However, the phylogeny for sequences containing the +/+/- pattern strongly supports a genetic connection and one common source for both clusters. Though, genetic comparison suggests a connection rather than indicating the independent emergence of the same mutation in two apparently unrelated clusters. This study highlights once more the importance of sharing genomic data to link apparently unrelated epidemiological clusters and to, remarkably, update molecular tests.
Collapse
Affiliation(s)
- Laura Amato
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Lucija Jurisic
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Ilaria Puglia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Valeria Di Lollo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Giuseppe Torzi
- Azienda Sanitaria Locale, Lanciano-Vasto-Chieti, Chieti, Italy
| | | | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | | | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano (Bari), Italy
| | - Paolo Calistri
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | | | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| | - Nicola D’Alterio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM), Teramo, Italy
| |
Collapse
|
37
|
Boogaerts HLF, Smits P, Hans G, Bouly L, Coeck E, Vandamme S, Jansens H, Goossens H, Matheeussen V. Laboratory analysis of two Delta SARS-CoV-2 variant outbreaks in the Port of Antwerp. Acta Clin Belg 2021; 77:925-932. [PMID: 34851231 DOI: 10.1080/17843286.2021.2010966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION The B.1.617.2 SARS-CoV-2 or Delta variant, first detected in India, has shown a rapid global spread due to its high transmissibility and now represents more than 99% of the currently circulating variants in Europe. METHODS AND RESULT In May 2021, two ships that had recently arrived in the Port of Antwerp reported crew members with COVID-like symptoms. SARS-CoV-2 RNA was detected in nasopharyngeal swabs in 30 out of 45 skippers and the B.1.617.2 variant was identified via whole genome sequencing. Crew members were isolated or quarantined and repeatedly tested to assess the evolution of their SARS-CoV-2 viral load based on the cycle threshold (CT) values of the PCR reaction. Viral cultures were also taken at day 7 to detect viable virus and were compared with the subjects CT value at that moment. The shipper's clinical condition was closely observed using a digital home monitoring tool. Eleven crew members (37%) required hospitalization, with CT values of SARS-CoV-2 RNA being a good predictive factor for the hospitalization need. Furthermore, a clear correlation between CT values and positive viral culture was observed, hinting infectiousness even longer than 10 days after the intitial positive PCR test. CONCLUSION Our study of 2 Delta variant clusters shows that the initial CT value is a good predictor for hospitalization need and suggests that patients infected with this variant may remain infectious for a longer time period.
Collapse
Affiliation(s)
- Hélène L. F. Boogaerts
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Patrick Smits
- Department of Infection Prevention, Flemish Agency for Care and Health, Antwerp, Belgium
| | - Guy Hans
- Multidisciplinary Pain Center (PCT), Antwerp University Hospital (UZA), Edegem, Belgium
| | - Liza Bouly
- Department of Infection Prevention, Flemish Agency for Care and Health, Antwerp, Belgium
| | - Eline Coeck
- Department of Infection Prevention, Flemish Agency for Care and Health, Antwerp, Belgium
| | - Sarah Vandamme
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Hilde Jansens
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, Antwerp University Hospital (UZA), Edegem, Belgium
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
- Department of Infection Prevention, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Herman Goossens
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, Antwerp University Hospital (UZA), Edegem, Belgium
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Veerle Matheeussen
- Department of Microbiology and National Reference Centre for Respiratory Pathogens, Antwerp University Hospital (UZA), Edegem, Belgium
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
- Department of Medical Biochemistry, University of Antwerp, Wilrijk, Belgium
| |
Collapse
|
38
|
Rosenke K, Feldmann F, Okumura A, Hansen F, Tang-Huau TL, Meade-White K, Kaza B, Callison J, Lewis MC, Smith BJ, Hanley PW, Lovaglio J, Jarvis MA, Shaia C, Feldmann H. UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Emerg Microbes Infect 2021; 10:2173-2182. [PMID: 34724885 PMCID: PMC8635622 DOI: 10.1080/22221751.2021.1997074] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The continuing emergence of SARS-CoV-2 variants calls for regular assessment to identify differences in viral replication, shedding and associated disease. In this study, we compared African green monkeys infected intranasally with either the UK B.1.1.7 (Alpha) variant or its contemporary D614G progenitor. Both variants caused mild respiratory disease with no significant differences in clinical presentation. Significantly higher levels of viral RNA and infectious virus were found in upper and lower respiratory tract samples and tissues from B.1.1.7 infected animals. Interestingly, D614G infected animals showed significantly higher levels of viral RNA and infectious virus in rectal swabs and gastrointestinal tissues. Our results indicate that B.1.1.7 infection in African green monkeys is associated with increased respiratory replication and shedding but no disease enhancement similar to human B.1.1.7 cases.
Collapse
Affiliation(s)
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | | | | | | | | | | | | | | | - Brian J Smith
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Patrick W Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jamie Lovaglio
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Michael A Jarvis
- Laboratory of Virology, Hamilton, MT, USA.,University of Plymouth, Plymouth, UK.,The Vaccine Group Ltd, Plymouth, UK
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | | |
Collapse
|
39
|
Monel B, Planas D, Grzelak L, Smith N, Robillard N, Staropoli I, Goncalves P, Porrot F, Guivel-Benhassine F, Guinet ND, Rodary J, Puech J, Euzen V, Bélec L, Orvoen G, Nunes L, Moulin V, Fourgeaud J, Wack M, Imbeaud S, Campagne P, Duffy D, Santo JPD, Bruel T, Péré H, Veyer D, Schwartz O. Release of infectious virus and cytokines in nasopharyngeal swabs from individuals infected with non-alpha or alpha SARS-CoV-2 variants: an observational retrospective study. EBioMedicine 2021; 73:103637. [PMID: 34678613 PMCID: PMC8526063 DOI: 10.1016/j.ebiom.2021.103637] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The dynamics of SARS-CoV-2 alpha variant shedding and immune responses at the nasal mucosa remain poorly characterised. METHODS We measured infectious viral release, antibodies and cytokines in 426 PCR+ nasopharyngeal swabs from individuals harboring non-alpha or alpha variants. FINDINGS With both lineages, viral titers were variable, ranging from 0 to >106 infectious units. Rapid antigenic diagnostic tests were positive in 94% of samples with infectious virus. 68 % of individuals carried infectious virus within two days after onset of symptoms. This proportion decreased overtime. Viable virus was detected up to 14 days. Samples containing anti-spike IgG or IgA did not generally harbor infectious virus. Ct values were slightly but not significantly lower with alpha. This variant was characterized by a fast decrease of infectivity overtime and a marked release of 13 cytokines (including IFN-b, IP-10 and IL-10). INTERPRETATION The alpha variant displays modified viral decay and cytokine profiles at the nasopharyngeal mucosae during symptomatic infection. FUNDING This retrospective study has been funded by Institut Pasteur, ANRS, Vaccine Research Institute, Labex IBEID, ANR/FRM and IDISCOVR, Fondation pour la Recherche Médicale.
Collapse
Affiliation(s)
- Blandine Monel
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France
| | - Delphine Planas
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France; Vaccine Research Institute, Creteil, France
| | - Ludivine Grzelak
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France; Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Nikaïa Smith
- Translational Immunology Lab, Department of Immunology, Inserm U1223, Institut Pasteur, Paris
| | - Nicolas Robillard
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France
| | - Isabelle Staropoli
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France
| | - Pedro Goncalves
- Innate Immunity Unit, Department of Immunology, Department of Immunology, Inserm U1223, Institut Pasteur, Paris; Inserm U1223, Paris, France
| | - Françoise Porrot
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France
| | - Florence Guivel-Benhassine
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France
| | | | - Julien Rodary
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France
| | - Julien Puech
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France
| | - Victor Euzen
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France
| | - Laurent Bélec
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France; Hôpital européen Georges Pompidou INSERM U970, PARCC, Faculté de Médecine, Université de Paris, Paris, France
| | - Galdric Orvoen
- Hôpital Vaugirard, Service de gériatrie, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Léa Nunes
- Hôpital Corentin Celton, Service de gériatrie, Assistance Publique-Hôpitaux de Paris, Issy-les-Moulineaux, France
| | - Véronique Moulin
- Hôpital Corentin Celton, Service de gériatrie, Assistance Publique-Hôpitaux de Paris, Issy-les-Moulineaux, France
| | - Jacques Fourgeaud
- Université de Paris, EHU 7328 PACT, Institut Imagine, Paris, France; Virology Department, AP-HP, Necker Enfants Malades Hospital, Paris, France
| | - Maxime Wack
- Hôpital Européen Georges Pompidou, Département d'Informatique Médicale, Biostatistiques et Santé Publique
| | - Sandrine Imbeaud
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France
| | | | - Darragh Duffy
- Translational Immunology Lab, Department of Immunology, Inserm U1223, Institut Pasteur, Paris
| | - James P Di Santo
- Innate Immunity Unit, Department of Immunology, Department of Immunology, Inserm U1223, Institut Pasteur, Paris; Inserm U1223, Paris, France
| | - Timothée Bruel
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France; Vaccine Research Institute, Creteil, France
| | - Hélène Péré
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France
| | - David Veyer
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France; INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France; Vaccine Research Institute, Creteil, France.
| |
Collapse
|
40
|
Corchis-Scott R, Geng Q, Seth R, Ray R, Beg M, Biswas N, Charron L, Drouillard KD, D'Souza R, Heath DD, Houser C, Lawal F, McGinlay J, Menard SL, Porter LA, Rawlings D, Scholl ML, Siu KWM, Tong Y, Weisener CG, Wilhelm SW, McKay RML. Averting an Outbreak of SARS-CoV-2 in a University Residence Hall through Wastewater Surveillance. Microbiol Spectr 2021; 9:e0079221. [PMID: 34612693 DOI: 10.1101/2021.06.23.21259176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by reverse transcriptase quantitative PCR (RT-qPCR) in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore swab approach, SARS-CoV-2 was detected in wastewater samples just 2 days after passive samplers were deployed. These samples also tested positive for the B.1.1.7 (Alpha) variant of concern (VOC) using RT-qPCR. The positive result triggered a public health case-finding response, including a mobile testing unit deployed to the residence hall the following day, with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of Alpha variant COVID-19. These individuals were relocated to a separate quarantine facility, averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the Alpha VOC of SARS-CoV-2 in individuals from a nonclinical setting. IMPORTANCE Among early adopters of wastewater monitoring for SARS-CoV-2 have been colleges and universities throughout North America, many of whom are using this approach to monitor congregate living facilities for early evidence of COVID-19 infection as an integral component of campus screening programs. Yet, while there have been numerous examples where wastewater monitoring on a university campus has detected evidence for infection among community members, there are few examples where this monitoring triggered a public health response that may have averted an actual outbreak. This report details a wastewater-testing program targeting a residence hall on a university campus during spring 2021, when there was mounting concern globally over the emergence of SARS-CoV-2 variants of concern, reported to be more transmissible than the wild-type Wuhan strain. In this communication, we present a clear example of how wastewater monitoring resulted in actionable responses by university administration and public health, which averted an outbreak of COVID-19 on a university campus.
Collapse
Affiliation(s)
- Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Rajesh Seth
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- Civil and Environmental Engineering, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Rajan Ray
- Civil and Environmental Engineering, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Mohsan Beg
- Student Counselling Centre, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Nihar Biswas
- Civil and Environmental Engineering, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Lynn Charron
- Residence Services, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Kenneth D Drouillard
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- School of the Environment, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Ramsey D'Souza
- Windsor-Essex County Health Unit, Windsor, Ontario, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- Department of Integrative Biology, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Chris Houser
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- School of the Environment, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Felicia Lawal
- Windsor-Essex County Health Unit, Windsor, Ontario, Canada
| | - James McGinlay
- Residence Services, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Sherri Lynne Menard
- Environmental Health and Safety, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Lisa A Porter
- Department of Biomedical Sciences, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Diane Rawlings
- Residence Services, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Matthew L Scholl
- Student Health Services, University of Windsorgrid.267455.7University of Windsor, grid.267455.7, Windsor, Ontario, Canada
| | - K W Michael Siu
- Department of Chemistry and Biochemistry, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- School of the Environment, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee, USA
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - R Michael L McKay
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- School of the Environment, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| |
Collapse
|
41
|
Corchis-Scott R, Geng Q, Seth R, Ray R, Beg M, Biswas N, Charron L, Drouillard KD, D’Souza R, Heath DD, Houser C, Lawal F, McGinlay J, Menard SL, Porter LA, Rawlings D, Scholl ML, Siu KWM, Tong Y, Weisener CG, Wilhelm SW, McKay RML. Averting an Outbreak of SARS-CoV-2 in a University Residence Hall through Wastewater Surveillance. Microbiol Spectr 2021; 9:e0079221. [PMID: 34612693 PMCID: PMC8510253 DOI: 10.1128/spectrum.00792-21] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/06/2021] [Indexed: 12/23/2022] Open
Abstract
A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by reverse transcriptase quantitative PCR (RT-qPCR) in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore swab approach, SARS-CoV-2 was detected in wastewater samples just 2 days after passive samplers were deployed. These samples also tested positive for the B.1.1.7 (Alpha) variant of concern (VOC) using RT-qPCR. The positive result triggered a public health case-finding response, including a mobile testing unit deployed to the residence hall the following day, with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of Alpha variant COVID-19. These individuals were relocated to a separate quarantine facility, averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the Alpha VOC of SARS-CoV-2 in individuals from a nonclinical setting. IMPORTANCE Among early adopters of wastewater monitoring for SARS-CoV-2 have been colleges and universities throughout North America, many of whom are using this approach to monitor congregate living facilities for early evidence of COVID-19 infection as an integral component of campus screening programs. Yet, while there have been numerous examples where wastewater monitoring on a university campus has detected evidence for infection among community members, there are few examples where this monitoring triggered a public health response that may have averted an actual outbreak. This report details a wastewater-testing program targeting a residence hall on a university campus during spring 2021, when there was mounting concern globally over the emergence of SARS-CoV-2 variants of concern, reported to be more transmissible than the wild-type Wuhan strain. In this communication, we present a clear example of how wastewater monitoring resulted in actionable responses by university administration and public health, which averted an outbreak of COVID-19 on a university campus.
Collapse
Affiliation(s)
- Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Rajesh Seth
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Civil and Environmental Engineering, University of Windsor, Windsor, Ontario, Canada
| | - Rajan Ray
- Civil and Environmental Engineering, University of Windsor, Windsor, Ontario, Canada
| | - Mohsan Beg
- Student Counselling Centre, University of Windsor, Windsor, Ontario, Canada
| | - Nihar Biswas
- Civil and Environmental Engineering, University of Windsor, Windsor, Ontario, Canada
| | - Lynn Charron
- Residence Services, University of Windsor, Windsor, Ontario, Canada
| | - Kenneth D. Drouillard
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- School of the Environment, University of Windsor, Windsor, Ontario, Canada
| | - Ramsey D’Souza
- Windsor-Essex County Health Unit, Windsor, Ontario, Canada
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - Chris Houser
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- School of the Environment, University of Windsor, Windsor, Ontario, Canada
| | - Felicia Lawal
- Windsor-Essex County Health Unit, Windsor, Ontario, Canada
| | - James McGinlay
- Residence Services, University of Windsor, Windsor, Ontario, Canada
| | - Sherri Lynne Menard
- Environmental Health and Safety, University of Windsor, Windsor, Ontario, Canada
| | - Lisa A. Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
| | - Diane Rawlings
- Residence Services, University of Windsor, Windsor, Ontario, Canada
| | - Matthew L. Scholl
- Student Health Services, University of Windsor, Windsor, Ontario, Canada
| | - K. W. Michael Siu
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Christopher G. Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- School of the Environment, University of Windsor, Windsor, Ontario, Canada
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee, USA
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - R. Michael L. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- School of the Environment, University of Windsor, Windsor, Ontario, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| |
Collapse
|
42
|
Mallach G, Kasloff SB, Kovesi T, Kumar A, Kulka R, Krishnan J, Robert B, McGuinty M, den Otter-Moore S, Yazji B, Cutts T. Aerosol SARS-CoV-2 in hospitals and long-term care homes during the COVID-19 pandemic. PLoS One 2021; 16:e0258151. [PMID: 34591919 PMCID: PMC8483369 DOI: 10.1371/journal.pone.0258151] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/19/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Few studies have quantified aerosol concentrations of SARS-CoV-2 in hospitals and long-term care homes, and fewer still have examined samples for viability. This information is needed to clarify transmission risks beyond close contact. METHODS We deployed particulate air samplers in rooms with COVID-19 positive patients in hospital ward and ICU rooms, rooms in long-term care homes experiencing outbreaks, and a correctional facility experiencing an outbreak. Samplers were placed between 2 and 3 meters from the patient. Aerosol (small liquid particles suspended in air) samples were collected onto gelatin filters by Ultrasonic Personal Air Samplers (UPAS) fitted with <2.5μm (micrometer) and <10 μm size-selective inlets operated for 16 hours (total 1.92m3), and with a Coriolis Biosampler over 10 minutes (total 1.5m3). Samples were assayed for viable SARS-CoV-2 virus and for the viral genome by multiplex PCR using the E and N protein target sequences. We validated the sampling methods by inoculating gelatin filters with viable vesicular stomatitis virus (VSV), and with three concentrations of viable SARS-CoV-2, operating personal samplers for 16hrs, and quantifying viable virus recovery by TCID50 assay. RESULTS In total, 138 samples were collected from 99 rooms. RNA samples were positive in 9.1% (6/66) of samples obtained with the UPAS 2.5μm samplers, 13.5% (7/52) with the UPAS 10μm samplers, and 10.0% (2/20) samples obtained with the Coriolis samplers. Culturable virus was not recovered in any samples. Viral RNA was detected in 15.1% of the rooms sampled. There was no significant difference in viral RNA recovery between the different room locations or samplers. Method development experiments indicated minimal loss of SARS-CoV-2 viability via the personal air sampler operation.
Collapse
Affiliation(s)
- Gary Mallach
- Water and Air Quality Bureau, Health Canada, Ottawa, Canada
| | - Samantha B. Kasloff
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Tom Kovesi
- Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, Canada
| | - Anand Kumar
- Sections of Critical Care Medicine and Infectious Diseases, Departments of Medicine, Medical Microbiology and Pharmacology, University of Manitoba, Winnipeg, Canada
| | - Ryan Kulka
- Water and Air Quality Bureau, Health Canada, Ottawa, Canada
| | - Jay Krishnan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Benoit Robert
- Department of Family Medicine, University of Ottawa, Ottawa, Canada
| | - Michaeline McGuinty
- Department of Medicine, Ottawa Hospital, University of Ottawa, Ottawa, Canada
| | | | - Bashour Yazji
- Department of Medicine, Ottawa Hospital, University of Ottawa, Ottawa, Canada
| | - Todd Cutts
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| |
Collapse
|
43
|
Thye AYK, Law JWF, Pusparajah P, Letchumanan V, Chan KG, Lee LH. Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis. Biomedicines 2021; 9:1303. [PMID: 34680420 PMCID: PMC8533361 DOI: 10.3390/biomedicines9101303] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 09/18/2021] [Indexed: 12/12/2022] Open
Abstract
The worldwide battle against the SARS-CoV-2 virus rages on, with millions infected and many innocent lives lost. The causative organism, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a beta coronavirus that belongs to the Coronaviridae family. Many clinically significant variants have emerged, as the virus's genome is prone to various mutations, leading to antigenic drift and resulting in evasion of host immune recognition. The current variants of concern (VOCs) include B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), and P.1 (Gamma). The emerging variants contain various important mutations on the spike protein, leading to deleterious consequences, such as immune invasion and vaccine escape. These adverse effects result in increased transmissibility, morbidity, and mortality and the evasion of detection by existing or currently available diagnostic tests, potentially delaying diagnosis and treatment. This review discusses the key mutations present in the VOC strains and provides insights into how these mutations allow for greater transmissibility and immune evasion than the progenitor strain. Continuous monitoring and surveillance of VOC strains play a vital role in preventing and controlling the virus's spread.
Collapse
Affiliation(s)
- Angel Yun-Kuan Thye
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
| | - Jodi Woan-Fei Law
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
| | - Priyia Pusparajah
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
| | - Vengadesh Letchumanan
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang 212013, China
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Malaysia; (A.Y.-K.T.); (J.W.-F.L.); (P.P.)
| |
Collapse
|
44
|
Messali S, Campisi G, Giovanetti M, Ciccozzi M, Caruso A, Caccuri F. The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. J Med Virol 2021; 94:413-416. [PMID: 34515998 PMCID: PMC8661962 DOI: 10.1002/jmv.27333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 11/12/2022]
Abstract
In December 2020, Italy experienced the first case of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) B.1.1.7 lineage. In January 2021, we identified 21 cases of this variant in Corzano, defining the first outbreak of SARS-CoV-2 B.1.1.7 lineage in Italy. The high transmissibility of the B.1.1.7 variant represented an important benefit for the virus, which became rapidly dominant on the territory. Containment measures induced the epidemic curve onto a decreasing trajectory underlining the importance of appropriate control and surveillance for restraint of virus spread. Highlights The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage occurred in Lombardy in January 2021. The outbreak originated by a single introduction of the B.1.1.7 lineage. The genomic sequencing revealed, for the first time, the presence of the V551F mutation in the B.1.1.7 lineage in Italy. Surveillance, prompt sequencing and tracing efforts were fundamental to identify and to quickly contain the outbreak.
Collapse
Affiliation(s)
- Serena Messali
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giovanni Campisi
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo, Cruz, Brazil.,Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| |
Collapse
|
45
|
Zhang H, Deng S, Ren L, Zheng P, Hu X, Jin T, Tan X. Profiling CD8 + T cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants. Cell Rep 2021; 36:109708. [PMID: 34506741 PMCID: PMC8390359 DOI: 10.1016/j.celrep.2021.109708] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/28/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Cellular immunity is important in determining the disease severity of COVID-19 patients. However, current understanding of SARS-CoV-2 epitopes mediating cellular immunity is limited. Here we apply T-Scan, a recently developed method, to identify CD8+ T cell epitopes from COVID-19 patients of four major HLA-A alleles. Several identified epitopes are conserved across human coronaviruses, which might mediate pre-existing cellular immunity to SARS-CoV-2. In addition, we identify and validate four epitopes that were mutated in the newly circulating variants, including the Delta variant. The mutations significantly reduce T cell responses to the epitope peptides in convalescent and vaccinated samples. We further determine the crystal structure of HLA-A∗02:01/HLA-A∗24:02 in complex with the epitope KIA_S/NYN_S, respectively, which reveals the importance of K417 and L452 of the spike protein for binding to HLA. Our data suggest that evading cellular immunity might contribute to the increased transmissibility and disease severity associated with the new SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Hang Zhang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shasha Deng
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Liting Ren
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Peiyi Zheng
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiaowen Hu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xu Tan
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| |
Collapse
|
46
|
Migueres M, Lhomme S, Trémeaux P, Dimeglio C, Ranger N, Latour J, Dubois M, Nicot F, Miedouge M, Mansuy JM, Izopet J. Evaluation of two RT-PCR screening assays for identifying SARS-CoV-2 variants. J Clin Virol 2021; 143:104969. [PMID: 34509927 PMCID: PMC8411575 DOI: 10.1016/j.jcv.2021.104969] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 01/26/2023]
Abstract
Background The recent emergence of new SARS CoV-2 variants (variants of concern, VOC) that spread rapidly and may lead to immune escape has emphasized the urgent need to monitor and control their spread. Methods We analyzed 2018 SARS-CoV-2 positive specimens collected between February 9 and March 22, 2021 using the Thermofisher® TaqPath™ COVID-19 CE-IVD RT-PCR kit (TaqPath) and the ID solutions® ID™ SARS-CoV-2/UK/SA Variant Triplex RT-PCR (ID triplex) assay to screen for VOCs. Results The ID triplex assay identified 62.8% of them as VOCs: 61.8% B.1.1.7 and 0.9% B.1.351/P.1. The agreement between the ID triplex results for B.1.1.7 and the TaqPath S gene target failure (SGTF)/ S gene target late detection (SGTL) profile for this variant agreed very well (k = 0.86). A low virus load was the main cause of discrepancies. Sequencing discordant results with both assays indicated that the TaqPath assay detected the B.1.1.7 lineage slightly better. Both assays suggested that the virus loads of B.1.1.7 variants were significantly higher than those of non-B.1.1.7 strains. Only 10/20 B1.351/P.1 strains detected with the ID triplex assay were confirmed by sequencing. Conclusions We conclude that the SGTF/SGTL profiles identified using the TaqPath assay and ID triplex results are suitable for detecting the B.1.1.7 lineage. The ID triplex assay, which rapidly determines all three current VOCs simultaneously, could be a valuable tool for limiting virus spread by supporting contact-tracing and isolation.
Collapse
Affiliation(s)
- M Migueres
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse 31300, France; Université Toulouse III Paul-Sabatier, Toulouse, France.
| | - S Lhomme
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse 31300, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - P Trémeaux
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - C Dimeglio
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - N Ranger
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - J Latour
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - M Dubois
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - F Nicot
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - M Miedouge
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - J M Mansuy
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - J Izopet
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse 31300, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| |
Collapse
|
47
|
Rotondo JC, Martini F, Maritati M, Mazziotta C, Di Mauro G, Lanzillotti C, Barp N, Gallerani A, Tognon M, Contini C. SARS-CoV-2 Infection: New Molecular, Phylogenetic, and Pathogenetic Insights. Efficacy of Current Vaccines and the Potential Risk of Variants. Viruses 2021; 13:1687. [PMID: 34578269 PMCID: PMC8473168 DOI: 10.3390/v13091687] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly discovered coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic. COVID-19 has rapidly become a public health emergency of international concern. Although remarkable scientific achievements have been reached since the beginning of the pandemic, the knowledge behind this novel coronavirus, in terms of molecular and pathogenic characteristics and zoonotic potential, is still relatively limited. Today, there is a vaccine, or rather several vaccines, which, for the first time in the history of highly contagious infectious diseases that have plagued mankind, has been manufactured in just one year. Currently, four vaccines are licensed by regulatory agencies, and they use RNA or viral vector technologies. The positive effects of the vaccination campaign are being felt in many parts of the world, but the disappearance of this new infection is still far from being a reality, as it is also threatened by the presence of novel SARS-CoV-2 variants that could undermine the effectiveness of the vaccine, hampering the immunization control efforts. Indeed, the current findings indicate that SARS-CoV-2 is adapting to transmission in humans more efficiently, while further divergence from the initial archetype should be considered. In this review, we aimed to provide a collection of the current knowledge regarding the molecular, phylogenetic, and pathogenetic insights into SARS-CoV-2. The most recent findings obtained with respect to the impact of novel emerging SARS-CoV-2 variants as well as the development and implementation of vaccines are highlighted.
Collapse
Affiliation(s)
- John Charles Rotondo
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Martina Maritati
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Chiara Mazziotta
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Giulia Di Mauro
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Carmen Lanzillotti
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Nicole Barp
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Altea Gallerani
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Carlo Contini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| |
Collapse
|
48
|
Ong SWX, Chiew CJ, Ang LW, Mak TM, Cui L, Toh MPHS, Lim YD, Lee PH, Lee TH, Chia PY, Maurer-Stroh S, Lin RTP, Leo YS, Lee VJ, Lye DC, Young BE. Clinical and Virological Features of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern: A Retrospective Cohort Study Comparing B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta). Clin Infect Dis 2021; 75:e1128-e1136. [PMID: 34423834 PMCID: PMC8522361 DOI: 10.1093/cid/ciab721] [Citation(s) in RCA: 234] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The impact of SARS-CoV-2 variants of concern (VOCs) on disease severity is unclear. In this retrospective study, we compared the outcomes of patients infected with B.1.1.7, B.1.351, and B.1.617.2 with wild-type strains from early 2020. METHODS National surveillance data from January to May 2021 were obtained and outcomes in relation to VOCs were explored. Detailed patient-level data from all patients with VOC infection admitted to our center between December 2020 and May 2021 were analyzed. Clinical outcomes were compared with a cohort of 846 patients admitted from January to April 2020. RESULTS A total of 829 patients in Singapore in the study period were infected with these 3 VOCs. After adjusting for age and sex, B.1.617.2 was associated with higher odds of oxygen requirement, intensive care unit admission, or death (adjusted odds ratio [aOR], 4.90; 95% confidence interval [CI]: 1.43-30.78). Of these patients, 157 were admitted to our center. After adjusting for age, sex, comorbidities, and vaccination, the aOR for pneumonia with B.1.617.2 was 1.88 (95% CI: .95-3.76) compared with wild-type. These differences were not seen with B.1.1.7 and B.1.351. Vaccination status was associated with decreased severity. B.1.617.2 was associated with significantly lower polymerase chain reaction cycle threshold (Ct) values and longer duration of Ct value ≤30 (median duration 18 days for B.1.617.2, 13 days for wild-type). CONCLUSIONS B.1.617.2 was associated with increased severity of illness, and with lower Ct values and longer viral shedding. These findings provide impetus for the rapid implementation of vaccination programs.
Collapse
Affiliation(s)
- Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Calvin J Chiew
- National Centre for Infectious Diseases, Singapore, Singapore,Ministry of Health, Singapore, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Matthias Paul H S Toh
- National Centre for Infectious Diseases, Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | | | - Pei Hua Lee
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tau Hong Lee
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore,A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore,Department of Biological Sciences, National University of Singapore, Singapore
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vernon J Lee
- Ministry of Health, Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- Correspondence: Barnaby Young, National Centre for Infectious Diseases, 16 Jln Tan Tock Seng, Singapore 308442 ()
| |
Collapse
|
49
|
Osterman A, Iglhaut M, Lehner A, Späth P, Stern M, Autenrieth H, Muenchhoff M, Graf A, Krebs S, Blum H, Baiker A, Grzimek-Koschewa N, Protzer U, Kaderali L, Baldauf HM, Keppler OT. Comparison of four commercial, automated antigen tests to detect SARS-CoV-2 variants of concern. Med Microbiol Immunol 2021; 210:263-275. [PMID: 34415422 PMCID: PMC8377707 DOI: 10.1007/s00430-021-00719-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 08/13/2021] [Indexed: 12/23/2022]
Abstract
A versatile portfolio of diagnostic tests is essential for the containment of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Besides nucleic acid-based test systems and point-of-care (POCT) antigen (Ag) tests, quantitative, laboratory-based nucleocapsid Ag tests for SARS-CoV-2 have recently been launched. Here, we evaluated four commercial Ag tests on automated platforms and one POCT to detect SARS-CoV-2. We evaluated PCR-positive (n = 107) and PCR-negative (n = 303) respiratory swabs from asymptomatic and symptomatic patients at the end of the second pandemic wave in Germany (February–March 2021) as well as clinical isolates EU1 (B.1.117), variant of concern (VOC) Alpha (B.1.1.7) or Beta (B.1.351), which had been expanded in a biosafety level 3 laboratory. The specificities of automated SARS-CoV-2 Ag tests ranged between 97.0 and 99.7% (Lumipulse G SARS-CoV-2 Ag (Fujirebio): 97.03%, Elecsys SARS-CoV-2 Ag (Roche Diagnostics): 97.69%; LIAISON® SARS-CoV-2 Ag (Diasorin) and SARS-CoV-2 Ag ELISA (Euroimmun): 99.67%). In this study cohort of hospitalized patients, the clinical sensitivities of tests were low, ranging from 17.76 to 52.34%, and analytical sensitivities ranged from 420,000 to 25,000,000 Geq/ml. In comparison, the detection limit of the Roche Rapid Ag Test (RAT) was 9,300,000 Geq/ml, detecting 23.58% of respiratory samples. Receiver-operating-characteristics (ROCs) and Youden’s index analyses were performed to further characterize the assays’ overall performance and determine optimal assay cutoffs for sensitivity and specificity. VOCs carrying up to four amino acid mutations in nucleocapsid were detected by all five assays with characteristics comparable to non-VOCs. In summary, automated, quantitative SARS-CoV-2 Ag tests show variable performance and are not necessarily superior to a standard POCT. The efficacy of any alternative testing strategies to complement nucleic acid-based assays must be carefully evaluated by independent laboratories prior to widespread implementation.
Collapse
Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Iglhaut
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Lehner
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Armin Baiker
- Public Health Microbiology Unit, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Natascha Grzimek-Koschewa
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- Max Von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
- Max Von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.
| |
Collapse
|
50
|
Meyer M, Holfter A, Ruebsteck E, Gruell H, Dewald F, Koerner RW, Klein F, Lehmann C, Huenseler C, Weber LT. The Alpha Variant (B.1.1.7) of SARS-CoV-2 in Children: First Experience from 3544 Nucleic Acid Amplification Tests in a Cohort of Children in Germany. Viruses 2021; 13:v13081600. [PMID: 34452464 PMCID: PMC8402740 DOI: 10.3390/v13081600] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
In May 2021, the Alpha variant (B.1.1.7) of SARS-CoV-2 was found in 91% of the SARS-CoV-2 cases in Germany. Not much is known about the symptoms, courses of disease, and infectiousness in pediatric patients with the Alpha variant. Objective: The aim of this retrospective analysis was to gain information on the infection with the Alpha variant in children and adolescents. Methods: Between 12 January 2021 and 3 June 2021, all nucleic acid amplification tests (NAATs) of children who received a swab for SARS-CoV-2 were included. Data were collected on standardized questionnaires. The analysis of data was anonymized and retrospective. Results: We investigated 3544 NAATs; 95 children were tested positive (2.7%) for SARS-CoV-2. For the sub-analysis, 65 children were analyzed. In 59 children, the Alpha variant was found (90.8%), and 54.2% (n = 32/59) were symptomatic. The most common symptoms were fever, cough, and rhinitis. The median Ct value was 24.0 (min 17.0; max 32.7). Conclusions: We can underline early findings that children are still less effected by SARS-CoV-2 infection with the spread of the Alpha variant. We found no evidence that children infected with the Alpha variant showed more severe symptoms or suffered from a more severe clinical course than those infected with the wild type.
Collapse
Affiliation(s)
- Meike Meyer
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (E.R.); (R.W.K.); (C.H.); (L.T.W.)
- Correspondence: ; Tel.: +49-221-478-42128
| | - Anna Holfter
- Departement of Pediatrics, Elisabeth-Krankenhaus Rheydt, 41239 Moenchengladbach, Germany;
| | - Esra Ruebsteck
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (E.R.); (R.W.K.); (C.H.); (L.T.W.)
| | - Henning Gruell
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (H.G.); (F.D.); (F.K.)
| | - Felix Dewald
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (H.G.); (F.D.); (F.K.)
| | - Robert Walter Koerner
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (E.R.); (R.W.K.); (C.H.); (L.T.W.)
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (H.G.); (F.D.); (F.K.)
| | - Clara Lehmann
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany;
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
| | - Christoph Huenseler
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (E.R.); (R.W.K.); (C.H.); (L.T.W.)
| | - Lutz Thorsten Weber
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (E.R.); (R.W.K.); (C.H.); (L.T.W.)
| |
Collapse
|