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Bremner L, Vitola J, Cerci R, Campisi R, Araujo Ríos R, Massardo T, Gutierrez-Villamil C, Solis F, Peix A, Speckter H, Sanchez Velez M, Flores AC, Madu E, Alexánderson-Rosas E, Ortellado J, Morales R, Mut F, Vera L, Hirschfeld CB, Shaw LJ, Williams MC, Villines TC, Better N, Dorbala S, Karthikeyan G, Malkovskiy E, Cohen YA, Randazzo M, Pascual TN, Pynda Y, Dondi M, Paez D, Einstein AJ. Cardiovascular testing recovery in Latin America one year into the COVID-19 pandemic: An analysis of data from an international longitudinal survey. IJC HEART & VASCULATURE 2024; 52:101404. [PMID: 38590383 PMCID: PMC11000160 DOI: 10.1016/j.ijcha.2024.101404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/10/2024]
Abstract
Background The COVID-19 pandemic disproportionately impacted Latin America (LATAM), significantly disrupting cardiovascular testing. This study evaluated cardiac procedure recovery in LATAM one year after the outbreak. Methods The International Atomic Energy Agency (IAEA) surveyed 669 centers in 107 countries worldwide, including 135 facilities in 19 LATAM countries, to assess cardiovascular procedure volumes in March 2019, April 2020, and April 2021, and changes in center practices and staffing conditions one year into the COVID-19 pandemic. Findings LATAM centers reported a 21 % decrease in procedure volumes in April 2021 from pre-pandemic-baseline, vs. a 0 % change in the rest of the world (RoW), and greater volume reductions for almost all procedure types. Centers in Central America and Mexico reported the largest procedure reductions (47 % reduction) compared to the Caribbean (15 %), and South America (14 %, p = 0.01), and this LATAM region was a significant predictor of lower procedure recovery in multivariable regression. More LATAM centers reported reduced salaries and increased layoffs of clinical staff compared to RoW, and LATAM respondents estimated that half of physician and non-physician staff experienced excess psychological stress related to the pandemic, compared to 25 % and 30 % in RoW (p < 0.001). Conclusions Cardiovascular testing recovery in LATAM trailed behind RoW for most procedure types, with centers in Central America and Mexico reporting the greatest volume reductions. This study found lasting impacts of COVID-19 on cardiovascular care in LATAM and the need for mental health support for LATAM healthcare workers in current and future pandemics.
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Affiliation(s)
- Luca Bremner
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | | | | | - Roxana Campisi
- Diagnóstico Maipú and Instituto Argentino de Diagnóstico Y Tratamiento S.A., Buenos Aires, Argentina
| | | | | | | | - Felix Solis
- Hospital Escalante Pradilla, Perez Zeledon, Costa Rica
| | - Amalia Peix
- Institute of Cardiology and Cardiovascular Surgery, La Habana, Cuba
| | | | - Mayra Sanchez Velez
- Sociedad Ecuatoriana de Cardiología Y a La Sociedad Española de Imagen Cardíaca, Ecuador
| | | | - Ernest Madu
- Heart Institute of the Caribbean and HIC Heart Hospital, Kingston, Jamaica
| | | | | | - Rosanna Morales
- Departamento de Medicina Nuclear, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | | | | | - Cole B. Hirschfeld
- Division of Cardiology, Weill Cornell Medicine and NewYork-Presbyterian Hospital, New York, NY, USA
| | - Leslee J. Shaw
- Blavatnik Family Women’s Health Research Institute, Mount Sinai Medical Center, New York, NY, USA
| | | | - Todd C. Villines
- Division of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Nathan Better
- Cabrini Health, Royal Melbourne Hospital, Monash University and University of Melbourne, Melbourne, Australia, Melbourne, Australia
| | - Sharmila Dorbala
- Departments of Medicine and Radiology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ganesan Karthikeyan
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, India
| | - Eli Malkovskiy
- Seymour, Paul and Gloria Milstein Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center and NewYork-Presbyterian Hospital, New York, NY, USA
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Yosef A. Cohen
- Seymour, Paul and Gloria Milstein Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center and NewYork-Presbyterian Hospital, New York, NY, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
- Children's Hospital at Montefiore, New York, NY, USA
| | - Michael Randazzo
- Section of Cardiology, University of Chicago Medical Center, Chicago, IL, USA
| | | | - Yaroslav Pynda
- Division of Human Health, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Maurizio Dondi
- Division of Human Health, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Diana Paez
- Division of Human Health, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Andrew J. Einstein
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Seymour, Paul and Gloria Milstein Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center and NewYork-Presbyterian Hospital, New York, NY, USA
- Department of Radiology, Columbia University Irving Medical Center and New York-Presbyterian Hospital, New York, NY, USA
| | - INCAPS COVID
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Quanta Diagnostico, Curitiba, Brazil
- Diagnóstico Maipú and Instituto Argentino de Diagnóstico Y Tratamiento S.A., Buenos Aires, Argentina
- Instituto de Medicina Nuclear, Sucre, Bolivia
- Hospital Clinico Universidad de Chile, Santiago, Chile
- Fundacion Cardioinfantil, Instituto de Cardiologia, Bogota, Colombia
- Hospital Escalante Pradilla, Perez Zeledon, Costa Rica
- Institute of Cardiology and Cardiovascular Surgery, La Habana, Cuba
- Cedimat, Santo Domingo, Dominican Republic
- Sociedad Ecuatoriana de Cardiología Y a La Sociedad Española de Imagen Cardíaca, Ecuador
- Clinica de Radiologia Brito Mejia Peña, San Salvador, El Salvador
- Heart Institute of the Caribbean and HIC Heart Hospital, Kingston, Jamaica
- Instituto Nacional de Cardiologia Ignacio Chavez, Ciudad de Mexico, Mexico
- Central Hospital, Social Institute, Asunción, Paraguay
- Departamento de Medicina Nuclear, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
- Italian Hospital, Montevideo, Uruguay
- Urologico San Roman, Caracas, Venezuela
- Division of Cardiology, Weill Cornell Medicine and NewYork-Presbyterian Hospital, New York, NY, USA
- Blavatnik Family Women’s Health Research Institute, Mount Sinai Medical Center, New York, NY, USA
- BHF Centre for Cardiovascular Science, University of Edinburgh, United Kingdom
- Division of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Cabrini Health, Royal Melbourne Hospital, Monash University and University of Melbourne, Melbourne, Australia, Melbourne, Australia
- Departments of Medicine and Radiology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, India
- Seymour, Paul and Gloria Milstein Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center and NewYork-Presbyterian Hospital, New York, NY, USA
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
- Children's Hospital at Montefiore, New York, NY, USA
- Section of Cardiology, University of Chicago Medical Center, Chicago, IL, USA
- Philippine Nuclear Research Institute, Quezon City, Philippines
- Division of Human Health, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
- Department of Radiology, Columbia University Irving Medical Center and New York-Presbyterian Hospital, New York, NY, USA
| | - 2
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Quanta Diagnostico, Curitiba, Brazil
- Diagnóstico Maipú and Instituto Argentino de Diagnóstico Y Tratamiento S.A., Buenos Aires, Argentina
- Instituto de Medicina Nuclear, Sucre, Bolivia
- Hospital Clinico Universidad de Chile, Santiago, Chile
- Fundacion Cardioinfantil, Instituto de Cardiologia, Bogota, Colombia
- Hospital Escalante Pradilla, Perez Zeledon, Costa Rica
- Institute of Cardiology and Cardiovascular Surgery, La Habana, Cuba
- Cedimat, Santo Domingo, Dominican Republic
- Sociedad Ecuatoriana de Cardiología Y a La Sociedad Española de Imagen Cardíaca, Ecuador
- Clinica de Radiologia Brito Mejia Peña, San Salvador, El Salvador
- Heart Institute of the Caribbean and HIC Heart Hospital, Kingston, Jamaica
- Instituto Nacional de Cardiologia Ignacio Chavez, Ciudad de Mexico, Mexico
- Central Hospital, Social Institute, Asunción, Paraguay
- Departamento de Medicina Nuclear, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
- Italian Hospital, Montevideo, Uruguay
- Urologico San Roman, Caracas, Venezuela
- Division of Cardiology, Weill Cornell Medicine and NewYork-Presbyterian Hospital, New York, NY, USA
- Blavatnik Family Women’s Health Research Institute, Mount Sinai Medical Center, New York, NY, USA
- BHF Centre for Cardiovascular Science, University of Edinburgh, United Kingdom
- Division of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Cabrini Health, Royal Melbourne Hospital, Monash University and University of Melbourne, Melbourne, Australia, Melbourne, Australia
- Departments of Medicine and Radiology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, India
- Seymour, Paul and Gloria Milstein Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center and NewYork-Presbyterian Hospital, New York, NY, USA
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
- Children's Hospital at Montefiore, New York, NY, USA
- Section of Cardiology, University of Chicago Medical Center, Chicago, IL, USA
- Philippine Nuclear Research Institute, Quezon City, Philippines
- Division of Human Health, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
- Department of Radiology, Columbia University Irving Medical Center and New York-Presbyterian Hospital, New York, NY, USA
| | - Investigators Group
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Quanta Diagnostico, Curitiba, Brazil
- Diagnóstico Maipú and Instituto Argentino de Diagnóstico Y Tratamiento S.A., Buenos Aires, Argentina
- Instituto de Medicina Nuclear, Sucre, Bolivia
- Hospital Clinico Universidad de Chile, Santiago, Chile
- Fundacion Cardioinfantil, Instituto de Cardiologia, Bogota, Colombia
- Hospital Escalante Pradilla, Perez Zeledon, Costa Rica
- Institute of Cardiology and Cardiovascular Surgery, La Habana, Cuba
- Cedimat, Santo Domingo, Dominican Republic
- Sociedad Ecuatoriana de Cardiología Y a La Sociedad Española de Imagen Cardíaca, Ecuador
- Clinica de Radiologia Brito Mejia Peña, San Salvador, El Salvador
- Heart Institute of the Caribbean and HIC Heart Hospital, Kingston, Jamaica
- Instituto Nacional de Cardiologia Ignacio Chavez, Ciudad de Mexico, Mexico
- Central Hospital, Social Institute, Asunción, Paraguay
- Departamento de Medicina Nuclear, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
- Italian Hospital, Montevideo, Uruguay
- Urologico San Roman, Caracas, Venezuela
- Division of Cardiology, Weill Cornell Medicine and NewYork-Presbyterian Hospital, New York, NY, USA
- Blavatnik Family Women’s Health Research Institute, Mount Sinai Medical Center, New York, NY, USA
- BHF Centre for Cardiovascular Science, University of Edinburgh, United Kingdom
- Division of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Cabrini Health, Royal Melbourne Hospital, Monash University and University of Melbourne, Melbourne, Australia, Melbourne, Australia
- Departments of Medicine and Radiology, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, India
- Seymour, Paul and Gloria Milstein Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center and NewYork-Presbyterian Hospital, New York, NY, USA
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
- Children's Hospital at Montefiore, New York, NY, USA
- Section of Cardiology, University of Chicago Medical Center, Chicago, IL, USA
- Philippine Nuclear Research Institute, Quezon City, Philippines
- Division of Human Health, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
- Department of Radiology, Columbia University Irving Medical Center and New York-Presbyterian Hospital, New York, NY, USA
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Khalil AM, Martinez-Sobrido L, Mostafa A. Zoonosis and zooanthroponosis of emerging respiratory viruses. Front Cell Infect Microbiol 2024; 13:1232772. [PMID: 38249300 PMCID: PMC10796657 DOI: 10.3389/fcimb.2023.1232772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Lung infections in Influenza-Like Illness (ILI) are triggered by a variety of respiratory viruses. All human pandemics have been caused by the members of two major virus families, namely Orthomyxoviridae (influenza A viruses (IAVs); subtypes H1N1, H2N2, and H3N2) and Coronaviridae (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). These viruses acquired some adaptive changes in a known intermediate host including domestic birds (IAVs) or unknown intermediate host (SARS-CoV-2) following transmission from their natural reservoirs (e.g. migratory birds or bats, respectively). Verily, these acquired adaptive substitutions facilitated crossing species barriers by these viruses to infect humans in a phenomenon that is known as zoonosis. Besides, these adaptive substitutions aided the variant strain to transmit horizontally to other contact non-human animal species including pets and wild animals (zooanthroponosis). Herein we discuss the main zoonotic and reverse-zoonosis events that occurred during the last two pandemics of influenza A/H1N1 and SARS-CoV-2. We also highlight the impact of interspecies transmission of these pandemic viruses on virus evolution and possible prophylactic and therapeutic interventions. Based on information available and presented in this review article, it is important to close monitoring viral zoonosis and viral reverse zoonosis of pandemic strains within a One-Health and One-World approach to mitigate their unforeseen risks, such as virus evolution and resistance to limited prophylactic and therapeutic interventions.
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Affiliation(s)
- Ahmed Magdy Khalil
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Luis Martinez-Sobrido
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ahmed Mostafa
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, Giza, Egypt
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Baboo S, Diedrich JK, Torres JL, Copps J, Singh B, Garrett PT, Ward AB, Paulson JC, Yates JR. Evolving spike-protein N-glycosylation in SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539897. [PMID: 37214937 PMCID: PMC10197516 DOI: 10.1101/2023.05.08.539897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bhavya Singh
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Patrick T. Garrett
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - James C. Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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4
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Rodriguez-Nuñez M, Cepeda MDV, Bello C, Lopez MA, Sulbaran Y, Loureiro CL, Liprandi F, Jaspe RC, Pujol FH, Rangel HR. Neutralization of Different Variants of SARS-CoV-2 by a F(ab')2 Preparation from Sera of Horses Immunized with the Viral Receptor Binding Domain. Antibodies (Basel) 2023; 12:80. [PMID: 38131802 PMCID: PMC10740526 DOI: 10.3390/antib12040080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The Receptor Binding Domain (RBD) of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is the functional region of the viral Spike protein (S), which is involved in cell attachment to target cells. The virus has accumulated progressively mutations in its genome, particularly in the RBD region, many of them associated with immune evasion of the host neutralizing antibodies. Some of the viral lineages derived from this evolution have been classified as Variant of Interest (VOI) or Concern (VOC). The neutralizing capacity of a F(ab')2 preparation from sera of horses immunized with viral RBD was evaluated by lytic plaque reduction assay against different SARS-CoV-2 variants. A F(ab')2 preparation of a hyperimmune serum after nine immunizations with RBD exhibited a high titer of neutralizing antibodies against the ancestral-like strain (1/18,528). A reduction in the titer of the F(ab')2 preparation was observed against the different variants tested compared to the neutralizing activity against the ancestral-like strain. The highest reduction in the neutralization titer was observed for the Omicron VOC (4.7-fold), followed by the Mu VOI (2.6), Delta VOC (1.8-fold), and Gamma VOC (1.5). Even if a progressive reduction in the neutralizing antibodies titer against the different variants evaluated was observed, the serum still exhibited a neutralizing titer against the Mu VOI and the Omicron VOC (1/7113 and 1/3918, respectively), the evaluated strains most resistant to neutralization. Therefore, the preparation retained neutralizing activity against all the strains tested.
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Affiliation(s)
- Mariajosé Rodriguez-Nuñez
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Mariana del Valle Cepeda
- Biotecfar S.A., Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1050, Venezuela; (M.d.V.C.); (C.B.); (M.A.L.)
| | - Carlos Bello
- Biotecfar S.A., Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1050, Venezuela; (M.d.V.C.); (C.B.); (M.A.L.)
| | - Miguel Angel Lopez
- Biotecfar S.A., Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1050, Venezuela; (M.d.V.C.); (C.B.); (M.A.L.)
| | - Yoneira Sulbaran
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Carmen Luisa Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela;
| | - Rossana Celeste Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Héctor Rafael Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
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5
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Toyama M, Vargas L, Ticliahuanca S, Quispe AM. Regional clustering and waves patterns due to COVID-19 by the index virus and the lambda/gamma, and delta/omicron SARS-CoV-2 variants in Peru. Gates Open Res 2023; 6:74. [PMID: 38045771 PMCID: PMC10692151 DOI: 10.12688/gatesopenres.13644.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2023] [Indexed: 12/05/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) impact varies substantially due to various factors, so it is critical to characterize its main differences to inform decision-makers about where to focus their interventions and differentiate mitigation strategies. Up to this date, little is known about the patterns and regional clustering of COVID-19 waves worldwide. Methods We assessed the patterns and regional clustering of COVID-19 waves in Peru by using the weekly mortality rates for each of the 25 regions as an outcome of interest. We obtained the death counts from the National Informatics System of Deaths and population estimates from the National Registry of Identification and Civil Status. In addition, we characterized each wave according to its duration, peak, and mortality rates by age group and gender. Additionally, we used polynomial regression models to compare them graphically and performed a cluster analysis to identify regional patterns. Results We estimated the average mortality rate at the first, second, and third waves at 13.01, 14.12, and 9.82 per 100,000 inhabitants, respectively, with higher mortality rates among elders and men. The patterns of each wave varied substantially in terms of duration, peak, impact, and wave shapes. Based on our clustering analysis, during the first wave caused by the index virus, the 25 regions of Peru presented six different wave patterns. However, the regions were clustered in two different wave patterns during the second and third, caused by alpha/lambda/delta and omicron. Conclusions The propagation of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants behaved in Peru with varying wave patterns and regional clustering. During the COVID-19 pandemic, the weekly mortality rates followed different spatiotemporal patterns with solid clustering, which might help project the impact of future waves of COVID-19.
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Affiliation(s)
- Melissa Toyama
- Facultad de Medicina Humana, Universidad Nacional Mayor de San Marcos, Lima, Lima, 15001, Peru
| | - Lucía Vargas
- Facultad de Derecho y Ciencia Política, Universidad Nacional Mayor de San Marcos, Lima, Lima, Peru
| | - Sofía Ticliahuanca
- Facultad de Derecho y Ciencia Política, Universidad Nacional Mayor de San Marcos, Lima, Lima, Peru
| | - Antonio M Quispe
- Facultad de Medicina Humana, Universidad Continental, Huancayo, Junin, 12000, Peru
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Campos CJ, Pajuelo-Reyes C, Rojas LM, De La Cruz-Vargas JA, Tejedo JR, Tapia-Limonchi R, Tsukayama P, Chenet SM. Prevalence of SARS-CoV-2 Variants and Disease Outcome of COVID-19 Patients in the Amazonas Region of Peru. Am J Trop Med Hyg 2023; 109:523-526. [PMID: 37524331 PMCID: PMC10484257 DOI: 10.4269/ajtmh.22-0739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/13/2023] [Indexed: 08/02/2023] Open
Abstract
Peru was severely affected by COVID-19 with a fatality rate that reached up to 6%. In this study, the relationship between SARS-CoV-2 variants and COVID-19 disease outcome in Amazonas, a region of northeastern Peru, was evaluated. The variants were determined by genomic sequencing, and clinical-epidemiological data were collected from 590 patients between April 2021 and February 2022. There was no association between mortality and hospitalization with any of the variants, but we did find that Omicron is more likely to infect vaccinated and nonvaccinated people. A significant association was also found between unvaccinated patients and hospitalization. Interestingly, in the indigenous population, there were fewer hospitalizations than in the general population. In conclusion, SARS-CoV-2 variants were not associated with the disease outcome in the Amazonas region, and indigenous population were found to be less vulnerable to severe COVID-19 illness.
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Affiliation(s)
- Christian J. Campos
- Laboratorio Referencial de Salud de Chachapoyas, Dirección Regional de Salud Amazonas, Chachapoyas, Perú
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Perú
| | - Cecilia Pajuelo-Reyes
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Perú
| | - Luis M. Rojas
- Laboratorio Referencial de Salud de Chachapoyas, Dirección Regional de Salud Amazonas, Chachapoyas, Perú
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Perú
| | | | - Juan R. Tejedo
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Perú
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
- Diabetes and Associated Metabolic Diseases Networking Biomedical Research Centre, Madrid, Spain
| | - Rafael Tapia-Limonchi
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Perú
- Instituto de Investigaciones en Ciencias Biomédicas, Universidad Ricardo Palma, Lima, Perú
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Stella M. Chenet
- Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Perú
- Instituto de Investigaciones en Ciencias Biomédicas, Universidad Ricardo Palma, Lima, Perú
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7
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Bou-Hamad I, Hoteit R. Factors motivating lebanese youth to adopt COVID-19 good practices: a cross-sectional study. Front Public Health 2023; 11:987187. [PMID: 37457278 PMCID: PMC10340084 DOI: 10.3389/fpubh.2023.987187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Background It is now widely acknowledged that young people can be asymptomatic carriers of the COVID-19 virus. While vaccines are successful, COVID-19 good practices continue to be useful in controlling the virus transmission. This study aimed to investigate the associated risk factors impacting the youths' adoption of COVID-19 good practices in Lebanon. Methods Data were collected through an online survey. The analyzed sample included 602 young people. Results Our results indicate that around half the youth sample in our study adhere to COVID-19 good practices. COVID-19 good practices are more likely to be adopted by individuals who are more worried about their health and those who live with their partners. Furthermore, media trust was a significant predictor of COVID-19 good practices. Conclusion Media can play a larger role in promoting good practices through youth-targeted programs. By identifying community influencers and encouraging peer-to-peer communication, it is possible to engage youth who distrust the media and persuade them to adopt COVID-19 good practices.
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Affiliation(s)
- Imad Bou-Hamad
- Department of Business Information and Decision Systems, Suliman S. Olayan School of Business, American University of Beirut, Beirut, Lebanon
| | - Reem Hoteit
- Clinical Research Institute, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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8
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Justo Arevalo S, Uribe Calampa CS, Jimenez Silva C, Quiñones Aguilar M, Bouckaert R, Rebello Pinho JR. Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru. Nat Commun 2023; 14:3557. [PMID: 37322028 PMCID: PMC10272135 DOI: 10.1038/s41467-023-39216-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
At over 0.6% of the population, Peru has one of the highest SARS-CoV-2 mortality rate in the world. Much effort to sequence genomes has been done in this country since mid-2020. However, an adequate analysis of the dynamics of the variants of concern and interest (VOCIs) is missing. We investigated the dynamics of the COVID-19 pandemic in Peru with a focus on the second wave, which had the greatest case fatality rate. The second wave in Peru was dominated by Lambda and Gamma. Analysis of the origin of Lambda shows that it most likely emerged in Peru before the second wave (June-November, 2020). After its emergence it reached Argentina and Chile from Peru where it was locally transmitted. During the second wave in Peru, we identify the coexistence of two Lambda and three Gamma sublineages. Lambda sublineages emerged in the center of Peru whereas the Gamma sublineages more likely originated in the north-east and mid-east. Importantly, it is observed that the center of Peru played a prominent role in transmitting SARS-CoV-2 to other regions within Peru.
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Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru.
- Laboratório Clínico do Hospital Israelita Albert Einstein, São Paulo, Brasil.
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil.
| | | | | | | | - Remco Bouckaert
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Joao Renato Rebello Pinho
- Laboratório Clínico do Hospital Israelita Albert Einstein, São Paulo, Brasil
- LIM03/07, Department of Gastroenterology and Pathology, University of São Paulo School of Medicine, São Paulo, Brazil
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9
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Pandit R, Matthews QL. A SARS-CoV-2: Companion Animal Transmission and Variants Classification. Pathogens 2023; 12:775. [PMID: 37375465 DOI: 10.3390/pathogens12060775] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The continuous emergence of novel viruses and their diseases are a threat to global public health as there have been three outbreaks of coronaviruses that are highly pathogenic to humans in the span of the last two decades, severe acute respiratory syndrome (SARS)-CoV in 2002, Middle East respiratory syndrome (MERS)-CoV in 2012, and novel SARS-CoV-2 which emerged in 2019. The unprecedented spread of SARS-CoV-2 worldwide has given rise to multiple SARS-CoV-2 variants that have either altered transmissibility, infectivity, or immune escaping ability, causing diseases in a broad range of animals including human and non-human hosts such as companion, farm, zoo, or wild animals. In this review, we have discussed the recent SARS-CoV-2 outbreak, potential animal reservoirs, and natural infections in companion and farm animals, with a particular focus on SARS-CoV-2 variants. The expeditious development of COVID-19 vaccines and the advancements in antiviral therapeutics have contained the COVID-19 pandemic to some extent; however, extensive research and surveillance concerning viral epidemiology, animal transmission, variants, or seroprevalence in diverse hosts are essential for the future eradication of COVID-19.
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Affiliation(s)
- Rachana Pandit
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Qiana L Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
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10
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Bills C, Xie X, Shi PY. The multiple roles of nsp6 in the molecular pathogenesis of SARS-CoV-2. Antiviral Res 2023; 213:105590. [PMID: 37003304 PMCID: PMC10063458 DOI: 10.1016/j.antiviral.2023.105590] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/19/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve and adapt after its emergence in late 2019. As the causative agent of the coronavirus disease 2019 (COVID-19), the replication and pathogenesis of SARS-CoV-2 have been extensively studied by the research community for vaccine and therapeutics development. Given the importance of viral spike protein in viral infection/transmission and vaccine development, the scientific community has thus far primarily focused on studying the structure, function, and evolution of the spike protein. Other viral proteins are understudied. To fill in this knowledge gap, a few recent studies have identified nonstructural protein 6 (nsp6) as a major contributor to SARS-CoV-2 replication through the formation of replication organelles, antagonism of interferon type I (IFN-I) responses, and NLRP3 inflammasome activation (a major factor of severe disease in COVID-19 patients). Here, we review the most recent progress on the multiple roles of nsp6 in modulating SARS-CoV-2 replication and pathogenesis.
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Affiliation(s)
- Cody Bills
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, USA; World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA; Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, Texas, USA.
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11
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Zabidi NZ, Liew HL, Farouk IA, Puniyamurti A, Yip AJW, Wijesinghe VN, Low ZY, Tang JW, Chow VTK, Lal SK. Evolution of SARS-CoV-2 Variants: Implications on Immune Escape, Vaccination, Therapeutic and Diagnostic Strategies. Viruses 2023; 15:v15040944. [PMID: 37112923 PMCID: PMC10145020 DOI: 10.3390/v15040944] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. Individuals with advanced age or underlying comorbidities, including hypertension, diabetes and cardiovascular diseases, are at a higher risk of increased disease severity. Hence, this has resulted in an urgent need for the development of better therapeutic and preventive approaches. This review describes the origin and evolution of human coronaviruses, particularly SARS-CoV-2 and its variants as well as sub-variants. Risk factors that contribute to disease severity and the implications of co-infections are also considered. In addition, various antiviral strategies against COVID-19, including novel and repurposed antiviral drugs targeting viral and host proteins, as well as immunotherapeutic strategies, are discussed. We critically evaluate strategies of current and emerging vaccines against SARS-CoV-2 and their efficacy, including immune evasion by new variants and sub-variants. The impact of SARS-CoV-2 evolution on COVID-19 diagnostic testing is also examined. Collectively, global research and public health authorities, along with all sectors of society, need to better prepare against upcoming variants and future coronavirus outbreaks.
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Affiliation(s)
- Nur Zawanah Zabidi
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Hern Liang Liew
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Isra Ahmad Farouk
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashwini Puniyamurti
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | | | - Zheng Yao Low
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Julian W Tang
- Department of Respiratory Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Vincent T K Chow
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Sunil K Lal
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Selangor, Malaysia
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12
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Liu W, Li H. COVID-19: Attacks Immune Cells and Interferences With Antigen Presentation Through MHC-Like Decoy System. J Immunother 2023; 46:75-88. [PMID: 36799912 PMCID: PMC9987643 DOI: 10.1097/cji.0000000000000455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/24/2023] [Indexed: 02/18/2023]
Abstract
The high mortality of coronavirus disease 2019 is related to poor antigen presentation and lymphopenia. Cytomegalovirus and the herpes family encode a series of major histocompatibility complex (MHC)-like molecules required for targeted immune responses to achieve immune escape. In this present study, domain search results showed that many proteins of the severe acute respiratory syndrome coronavirus 2 virus had MHC-like domains, which were similar to decoys for the human immune system. MHC-like structures could bind to MHC receptors of immune cells (such as CD4 + T-cell, CD8 + T-cell, and natural killer-cell), interfering with antigen presentation. Then the oxygen free radicals generated by E protein destroyed immune cells after MHC-like of S protein could bind to them. Mutations in the MHC-like region of the viral proteins such as S promoted weaker immune resistance and more robust transmission. S 127-194 were the primary reason for the robust transmission of delta variants. The S 144-162 regulated the formation of S trimer. The mutations of RdRP: G671S and N: D63G of delta variant caused high viral load. S 62-80 of alpha, beta, lambda variants were the important factor for fast-spreading. S 616-676 and 1014-1114 were causes of high mortality for gamma variants infections. These sites were in the MHC-like structure regions.
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Affiliation(s)
- Wenzhong Liu
- School of Computer Science and Engineering, Sichuan University of Science and Engineering, Zigong, China
- School of Life Science and Food Engineering, Yibin University, Yibin, China
| | - Hualan Li
- School of Life Science and Food Engineering, Yibin University, Yibin, China
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13
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Quispe-Ricalde MA, Castelán-Sánchez HG, Meza-Rodríguez PM, Dávila-Ramos S, Sierra JL, Batista-Garcia R, Concha-Velasco F, Lucana SF, De Santa Cruz J, Zea V, Galarza M, Caceres-Rey O, Tsukayama P, Foronda P, Soto-Chambi BJ, Abreu N. Evidence of natural selection and dominance of SARS-CoV-2 variant Lambda (C.37) over variants of concern in Cusco, Peru. Arch Virol 2023; 168:88. [PMID: 36786950 PMCID: PMC9926449 DOI: 10.1007/s00705-022-05645-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/13/2022] [Indexed: 02/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage C.37 (Lambda) has spread rapidly in Peru and other Latin American countries. However, most studies in Peru have focused on Lima, the capital city, without knowing the dynamics of the spread of the variant in other departments. Cusco, Peru, is one of the most popular departments in the country for tourists, so the introduction of new variants of SARS-CoV-2 might occur despite closure of the borders. Therefore, in this work, we analyzed the variants circulating in Cusco. The aim of this work was to better understand the distribution of SARS-CoV-2 lineages circulating in Cusco and to characterize the genomes of these strains. To this end, 46 SARS-CoV-2 genomes from vaccinated and unvaccinated patients were sequenced in the first half of 2021. The genomes were analyzed using phylogenetic and natural selection methods. Phylogenetic trees from Cusco showed dominance of the Lambda lineage over the variants of concern (VOCs), and there was no clustering of variants by district. Natural selection analysis revealed mutations, mainly in the spike protein, at positions 75, 246, 247, 707, 769, and 1020. In addition, we found that unvaccinated patients accumulated more new mutations than did vaccinated patients, and these included the F101Y mutation in ORF7a, E419A in NSP3, a deletion in S (21,618-22,501), and a deletion in ORF3a (25,437-26,122).
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Affiliation(s)
- Maria Antonieta Quispe-Ricalde
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de San Antonio Abad del Cusco, Av. de La Cultura 733, C.P. 0800, Cusco, Perú.
| | - Hugo G Castelán-Sánchez
- Programa de Investigadoras e Investigadores por México. Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Crédito Constructo, Benito Juárez, Ciudad de México, C.P. 03940, México.
| | - Pablo M Meza-Rodríguez
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa, Cuernavaca, Morelos, C.P. 62209, México
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa, Cuernavaca, Morelos, C.P. 62209, México
| | - José Luis Sierra
- Escuela de Postgrado, Universidad Nacional de San Antonio Abad del Cusco, Av. de La Cultura 733, Cusco, C.P. 0800, Perú
| | - Ramón Batista-Garcia
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa, Cuernavaca, Morelos, C.P. 62209, México
| | - Fátima Concha-Velasco
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
- Dirección de epidemiología e investigación. Gerencia regional de salud, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - Sonia Flores Lucana
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - José De Santa Cruz
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - Víctor Zea
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - Marco Galarza
- Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Perú
| | - Omar Caceres-Rey
- Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Perú
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porres 15102, Lima, C.P. 15102, Perú
- Instituto de Medicina Tropical Alexander von Humboldt, Av. Honorio Delgado 430, San Martín de Porres, Lima, Peru
- Wellcome Sanger Institute, Saffron Walden, Cambridge, Reino Unido. Z.P. CB10 1SA, Hinxton, UK
| | - Pilar Foronda
- University Institute of Tropical Diseases and Public Health of the Canary Islands, Av. Astrofísico FranciscoSánchez, s/n, San Cristóbal de La Laguna, Tenerife, C.P.38200, Spain
| | - Brandon Jason Soto-Chambi
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de San Antonio Abad del Cusco, Av. de La Cultura 733, C.P. 0800, Cusco, Perú
| | - Nestor Abreu
- University Institute of Tropical Diseases and Public Health of the Canary Islands, Av. Astrofísico FranciscoSánchez, s/n, San Cristóbal de La Laguna, Tenerife, C.P.38200, Spain.
- NERTALAB, SL., C, /José Rodríguez Mouré, 4, Santa Cruz de Tenerife, Tenerife, C.P. 38008, España.
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14
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Han T, Luo Z, Ji L, Wu P, Li G, Liu X, Lai Y. Identification of natural compounds as SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation. Front Microbiol 2023; 13:1095068. [PMID: 36817101 PMCID: PMC9930647 DOI: 10.3389/fmicb.2022.1095068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/29/2022] [Indexed: 02/05/2023] Open
Abstract
Background Base mutations increase the contagiousness and transmissibility of the Delta and Lambda strains and lead to the severity of the COVID-19 pandemic. Molecular docking and molecular dynamics (MD) simulations are frequently used for drug discovery and relocation. Small molecular compounds from Chinese herbs have an inhibitory effect on the virus. Therefore, this study used computational simulations to investigate the effects of small molecular compounds on the spike (S) protein and the binding between them and angiotensin-converting enzyme 2 (ACE2) receptors. Methods In this study, molecular docking, MD simulation, and protein-protein analysis were used to explore the medicinal target inhibition of Chinese herbal medicinal plant chemicals on SARS-CoV-2. 12,978 phytochemicals were screened against S proteins of SARS-CoV-2 Lambda and Delta mutants. Results Molecular docking showed that 65.61% and 65.28% of the compounds had the relatively stable binding ability to the S protein of Lambda and Delta mutants (docking score ≤ -6). The top five compounds with binding energy with Lambda and Delta mutants were clematichinenoside AR2 (-9.7), atratoglaucoside,b (-9.5), physalin b (-9.5), atratoglaucoside, a (-9.4), Ochnaflavone (-9.3) and neo-przewaquinone a (-10), Wikstrosin (-9.7), xilingsaponin A (-9.6), ardisianoside G (-9.6), and 23-epi-26-deoxyactein (-9.6), respectively. Four compounds (Casuarictin, Heterophylliin D, Protohypericin, and Glansrin B) could interact with S protein mutation sites of Lambda and Delta mutants, respectively, and MD simulation results showed that four plant chemicals and spike protein have good energy stable complex formation ability. In addition, protein-protein docking was carried out to evaluate the changes in ACE2 binding ability caused by the formation of four plant chemicals and S protein complexes. The analysis showed that the binding of four plant chemicals to the S protein could reduce the stability of the binding to ACE2, thereby reducing the replication ability of the virus. Conclusion To sum up, the study concluded that four phytochemicals (Casuarictin, Heterophylliin D, Protohypericin, and Glansrin B) had significant effects on the binding sites of the SARS-CoV-2 S protein. This study needs further in vitro and in vivo experimental validation of these major phytochemicals to assess their potential anti-SARS-CoV-2. Graphical abstract.
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Affiliation(s)
- Tiantian Han
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ziqing Luo
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lichun Ji
- The Third Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peng Wu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Geng Li
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Geng Li, ✉
| | - Xiaohong Liu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China,Xiaohong Liu, ✉
| | - Yanni Lai
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China,Yanni Lai, ✉
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15
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Fano-Sizgorich D, Vásquez-Velásquez C, Orellana LR, Ponce-Torres C, Gamboa-Serpa H, Alvarez-Huambachano K, Gonzales GF. Risk of death, hospitalization and intensive care unit admission by SARS-CoV-2 variants in Peru: a retrospective study. Int J Infect Dis 2023; 127:144-149. [PMID: 36563957 PMCID: PMC9763211 DOI: 10.1016/j.ijid.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Peru has had the highest death toll from the pandemic worldwide; however, it is not clear what the effects of the different variants on these outcomes are. The study aimed to evaluate the risk of death, hospitalization, and intensive care unit (ICU) admission rates of COVID-19 according to the SARS-CoV-2 variants detected in Peru from March 2020-February 2022. METHODS Retrospective study using open-access databases were published by the Peruvian Ministry of Health. Databases of genomic sequencing, death, COVID-19 cases, hospitalization and ICU, and vaccination were used. Crude and adjusted Cox proportional hazards regressions with clustered variances were modeled to calculate the hazard ratio (HR) of outcomes by variant. RESULTS Lambda variant had the highest risk of death (HR 1.92, 95% CI 1.37-2.68), whereas the Delta variant had the lowest risk (HR 0.50, 95% CI 0.31-0.82). Mu variant had the highest risk of hospitalization (HR: 2.39, 95% CI 1.56-3.67), Omicron the lowest (HR 0.45, 95%CI 0.23-0.90), and Gamma had the highest ICU admission rate (HR 1.95, 95%CI 1.40-2.71). CONCLUSION SARS-CoV-2 variants showed distinctive risks of clinical outcomes, which could have implications for the management of infected persons during the pandemic.
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Affiliation(s)
- Diego Fano-Sizgorich
- Laboratorio de Endocrinología y Reproducción, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Latin American Center of Excellence for Climate Change and Health, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Cinthya Vásquez-Velásquez
- Laboratorio de Endocrinología y Reproducción, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Dirección de Laboratorio de Salud Pública, Dirección Regional de Salud del Callao, Callao, Peru
| | - Laura R Orellana
- EMERGE, Emerging Diseases and Climate Change Research Unit, Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Christian Ponce-Torres
- Latin American Center of Excellence for Climate Change and Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Gustavo F Gonzales
- Laboratorio de Endocrinología y Reproducción, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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16
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Zsichla L, Müller V. Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors. Viruses 2023; 15:175. [PMID: 36680215 PMCID: PMC9863423 DOI: 10.3390/v15010175] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.
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Affiliation(s)
- Levente Zsichla
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
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Zambrana Montaño R, Culasso ACA, Fernández F, Marquez N, Debat H, Salmerón M, Zamora AM, Ruíz de Huidobro G, Costas D, Alabarse G, Charre MA, Fridman AD, Mamani C, Vaca F, Maza Diaz C, Raskovsky V, Lavaque E, Lesser V, Cajal P, Agüero F, Calvente C, Torres C, Viegas M. Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina. Virus Res 2023; 323:198936. [PMID: 36181975 PMCID: PMC9599208 DOI: 10.1016/j.virusres.2022.198936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/10/2022] [Accepted: 09/24/2022] [Indexed: 01/25/2023]
Abstract
Studies about the evolution of SARS-CoV-2 lineages in different backgrounds such as naive populations are still scarce, especially from South America. This work aimed to study the introduction and diversification pattern of SARS-CoV-2 during the first year of the COVID-19 pandemic in the Northwestern Argentina (NWA) region and to analyze the evolutionary dynamics of the main lineages found. In this study, we analyzed a total of 260 SARS-CoV-2 whole-genome sequences from Argentina, belonging to the Provinces of Jujuy, Salta, and Tucumán, from March 31st, 2020, to May 22nd, 2021, which covered the full first wave and the early second wave of the COVID-19 pandemic in Argentina. In the first wave, eight lineages were identified: B.1.499 (76.9%), followed by N.5 (10.2%), B.1.1.274 (3.7%), B.1.1.348 (3.7%), B.1 (2.8%), B.1.600 (0.9%), B.1.1.33 (0.9%) and N.3 (0.9%). During the early second wave, the first-wave lineages were displaced by the introduction of variants of concern (VOC) (Alpha, Gamma), or variants of interest (VOI) (Lambda, Zeta, Epsilon) and other lineages with more limited distribution. Phylodynamic analyses of the B.1.499 and N.5, the two most prevalent lineages in the NWA, revealed that the rate of evolution of lineage N.5 (7.9 × 10-4 substitutions per site per year, s/s/y) was a ∼40% faster than that of lineage B.1.499 (5.6 × 10-4 s/s/y), although both are in the same order of magnitude than other non-VOC lineages. No mutations associated with a biological characteristic of importance were observed as signatures markers of the phylogenetic groups established in Northwestern Argentina, however, single sequences in non-VOC lineages did present mutations of biological importance or associated with VOCs as sporadic events, showing that many of these mutations could emerge from circulation in the general population. This study contributed to the knowledge about the evolution of SARS-CoV-2 in a pre-vaccination and without post-exposure immunization period.
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Affiliation(s)
- Romina Zambrana Montaño
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrés Carlos Alberto Culasso
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Franco Fernández
- Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Nathalie Marquez
- Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Mariana Salmerón
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | - Ana María Zamora
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | | | - Dardo Costas
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | - Graciela Alabarse
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | | | - Ariel David Fridman
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Claudia Mamani
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Fabiana Vaca
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Claudia Maza Diaz
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Viviana Raskovsky
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Esteban Lavaque
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Veronica Lesser
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Pamela Cajal
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Fernanda Agüero
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Cintia Calvente
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Carolina Torres
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Mariana Viegas
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Gallo 1330, 2do piso, C1425EFD, Argentina.
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Molina-Mora JA, Reales-González J, Camacho E, Duarte-Martínez F, Tsukayama P, Soto-Garita C, Brenes H, Cordero-Laurent E, Ribeiro dos Santos A, Guedes Salgado C, Santos Silva C, Santana de Souza J, Nunes G, Negri T, Vidal A, Oliveira R, Oliveira G, Muñoz-Medina JE, Salas-Lais AG, Mireles-Rivera G, Sosa E, Turjanski A, Monzani MC, Carobene MG, Remes Lenicov F, Schottlender G, Fernández Do Porto DA, Kreuze JF, Sacristán L, Guevara-Suarez M, Cristancho M, Campos-Sánchez R, Herrera-Estrella A. Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021. Front Public Health 2023; 11:1095202. [PMID: 36935725 PMCID: PMC10018007 DOI: 10.3389/fpubh.2023.1095202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- *Correspondence: Jose Arturo Molina-Mora
| | | | - Erwin Camacho
- Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, Colombia
| | - Francisco Duarte-Martínez
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Pablo Tsukayama
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Claudio Soto-Garita
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Hebleen Brenes
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Estela Cordero-Laurent
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | | | | | - Caio Santos Silva
- Instituto de Ciências Biológica, Universidade Federal do Pará, Belém, Brazil
| | | | - Gisele Nunes
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Tatianne Negri
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Amanda Vidal
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Renato Oliveira
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Guilherme Oliveira
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Guadalupe Mireles-Rivera
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Ezequiel Sosa
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Adrián Turjanski
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Cecilia Monzani
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauricio G. Carobene
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Remes Lenicov
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gustavo Schottlender
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Luisa Sacristán
- Vicerrectoria de Investigación y Creación, Universidad de Los Andes, Bogotá, Colombia
| | | | - Marco Cristancho
- Vicerrectoria de Investigación y Creación, Universidad de Los Andes, Bogotá, Colombia
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
- Alfredo Herrera-Estrella
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19
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Delshad M, Sanaei MJ, Pourbagheri-Sigaroodi A, Bashash D. Host genetic diversity and genetic variations of SARS-CoV-2 in COVID-19 pathogenesis and the effectiveness of vaccination. Int Immunopharmacol 2022; 111:109128. [PMID: 35963158 PMCID: PMC9359488 DOI: 10.1016/j.intimp.2022.109128] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/15/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the outbreak of coronavirus disease 2019 (COVID-19), has shown a vast range of clinical manifestations from asymptomatic to life-threatening symptoms. To figure out the cause of this heterogeneity, studies demonstrated the trace of genetic diversities whether in the hosts or the virus itself. With this regard, this review provides a comprehensive overview of how host genetic such as those related to the entry of the virus, the immune-related genes, gender-related genes, disease-related genes, and also host epigenetic could influence the severity of COVID-19. Besides, the mutations in the genome of SARS-CoV-2 __leading to emerging of new variants__ per se affect the affinity of the virus to the host cells and enhance the immune escape capacity. The current review discusses these variants and also the latest data about vaccination effectiveness facing the most important variants.
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Affiliation(s)
- Mahda Delshad
- Department of Laboratory Sciences, School of Allied Medical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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20
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The Receptor Binding Domain of SARS-CoV-2 Lambda Variant Has a Better Chance Than the Delta Variant in Evading BNT162b2 COVID-19 mRNA Vaccine-Induced Humoral Immunity. Int J Mol Sci 2022; 23:ijms231911325. [PMID: 36232627 PMCID: PMC9569855 DOI: 10.3390/ijms231911325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/07/2022] [Accepted: 09/20/2022] [Indexed: 12/04/2022] Open
Abstract
The SARS-CoV-2 Delta and Lambda variants had been named variants of concern (VOC) and variants of interest (VOI), respectively, by the World Health Organization (WHO). Both variants have two mutations in the spike receptor binding domain (RBD) region, with L452R and T478K mutations in the Delta variant, and L452Q and F490S mutations in the Lambda variant. We used surface plasmon resonance (SPR)-based technology to evaluate the effect of these mutations on human angiotensin-converting enzyme 2 (ACE2) and Bamlanivimab binding. The affinity for the RBD ligand, ACE2, of the Delta RBD is approximately twice as strong as that of the wild type RBD, an increase that accounts for the increased infectivity of the Delta variant. On the other hand, in spite of its amino acid changes, the Lambda RBD has similar affinity to ACE2 as the wild type RBD. The protective anti-wild type RBD antibody Bamlanivimab binds very poorly to the Delta RBD and not at all to the Lambda RBD. Nevertheless, serum antibodies from individuals immunized with the BNT162b2 vaccine were found to bind well to the Delta RBD, but less efficiently to the Lambda RBD in contrast. As a result, the blocking ability of ACE2 binding by serum antibodies was decreased more by the Lambda than the Delta RBD. Titers of sera from BNT162b2 mRNA vaccinated individuals dropped 3-fold within six months of vaccination regardless of whether the target RBD was wild type, Delta or Lambda. This may account partially for the fall off with time in the protective effect of vaccines against any variant.
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21
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Schwalb A, Armyra E, Méndez-Aranda M, Ugarte-Gil C. COVID-19 in Latin America and the Caribbean: Two years of the pandemic. J Intern Med 2022; 292:409-427. [PMID: 35411985 PMCID: PMC9115176 DOI: 10.1111/joim.13499] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Worldwide, nations have struggled during the coronavirus disease 2019 (COVID-19) pandemic. However, Latin America and the Caribbean faced an unmatched catastrophic toll. As of March 2022, the region has reported approximately 15% of cases and 28% of deaths worldwide. Considering the relatively late arrival of SARS-CoV-2, several factors in the region were determinants of the humanitarian crisis that ensued. Pandemic unpreparedness, fragile healthcare systems, forthright inequalities, and poor governmental support facilitated the spread of the virus throughout the region. Moreover, reliance on repurposed and ineffective drugs such as hydroxychloroquine and ivermectin-to treat or prevent COVID-19-was publicised through misinformation and created a false sense of security and poor adherence to social distancing measures. While there were hopes that herd immunity could be achieved after the region's disastrous first peak, the emergence of the Gamma, Lambda, and Mu variants made this unattainable. This review explores how Latin America and the Caribbean fared during the first 2 years of the pandemic, and how, despite all the challenges, the region became a global leader in COVID-19 vaccination, with 63% of its population fully vaccinated.
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Affiliation(s)
- Alvaro Schwalb
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.,London School of Hygiene and Tropical Medicine, London, UK
| | - Eleonora Armyra
- Health Innovation Lab, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Melissa Méndez-Aranda
- Facultad de Ciencias y Filosofía, Laboratorio de Investigación en Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - César Ugarte-Gil
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.,London School of Hygiene and Tropical Medicine, London, UK.,School of Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
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22
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Jiang W, Zhang Z, Zhu Y, Chen B, Gu C, Liu Z, Zhang X, Xiong H, Zhang Y, Zheng B, Wang R, Jiao S, Wang A, Zhang T, Zhang J, Wang S, Zhang B, Li G, Gui X. Pre-Clinical Development of a Potent Neutralizing Antibody MW3321 With Extensive SARS-CoV-2 Variants Coverage. Front Pharmacol 2022; 13:926750. [PMID: 35873586 PMCID: PMC9304585 DOI: 10.3389/fphar.2022.926750] [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: 04/23/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, several variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged and have consistently replaced the previous dominant variant. Therapeutics against variants of SARS-CoV-2 are urgently needed. Ideal SARS-CoV-2 therapeutic antibodies would have high potency in viral neutralization against several emerging variants. Neutralization antibodies targeting SARS-CoV-2 could provide immediate protection after SARS-CoV-2 infection, especially for the most vulnerable populations. In this work, we comprehensively characterize the breadth and efficacy of SARS-CoV-2 RBD-targeting fully human monoclonal antibody (mAb) MW3321. MW3321 retains full neutralization activity to all tested 12 variants that have arisen in the human population, which are assigned as VOC (Variants of Concern) and VOI (Variants of Interest) due to their impacts on public health. Escape mutation experiments using replicating SARS-CoV-2 pseudovirus show that escape mutants were not generated until passage 6 for MW3321, which is much more resistant to escape mutation compared with another clinical staged SARS-CoV-2 neutralizing mAb MW3311. MW3321 could effectively reduce viral burden in hACE2-transgenic mice challenged with either wild-type or Delta SARS-CoV-2 strains through viral neutralization and Fc-mediated effector functions. Moreover, MW3321 exhibits a typical hIgG1 pharmacokinetic and safety profile in cynomolgus monkeys. These data support the development of MW3321 as a monotherapy or cocktail against SARS-CoV-2-related diseases.
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Affiliation(s)
- Wen Jiang
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
| | - Zherui Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yuhe Zhu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China
| | - Ben Chen
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
| | - Chunying Gu
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
| | - Zhiyan Liu
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
| | - Xukai Zhang
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
| | - Hualong Xiong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China
| | - Yanan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bin Zheng
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
| | - Rongjuan Wang
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
- Beijing Kohnoor Science and Technology Co., Ltd., Beijing, China
| | - Shasha Jiao
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
- Beijing Kohnoor Science and Technology Co., Ltd., Beijing, China
| | - An Wang
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
| | - Tianying Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China
| | - Jinchao Zhang
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
| | - Shuang Wang
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
- Beijing Kohnoor Science and Technology Co., Ltd., Beijing, China
- *Correspondence: Shuang Wang, ; Bo Zhang, ; Gang Li, ; Xun Gui,
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Shuang Wang, ; Bo Zhang, ; Gang Li, ; Xun Gui,
| | - Gang Li
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
- *Correspondence: Shuang Wang, ; Bo Zhang, ; Gang Li, ; Xun Gui,
| | - Xun Gui
- Mabwell (Shanghai) Bioscience Co., Ltd., Shanghai, China
- *Correspondence: Shuang Wang, ; Bo Zhang, ; Gang Li, ; Xun Gui,
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23
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Toyama M, Vargas L, Ticliahuanca S, Quispe AM. Regional clustering and waves patterns due to COVID-19 by the index virus and the lambda/gamma, and delta/omicron SARS-CoV-2 variants in Peru. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13644.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Coronavirus disease 2019 (COVID-19) impact varies substantially due to various factors, so it is critical to characterize its main differences to inform decision-makers about where to focus their interventions and differentiate mitigation strategies. Up to this date, little is known about the patterns and regional clustering of COVID-19 waves worldwide. Methods: We assessed the patterns and regional clustering of COVID-19 waves in Peru by using the weekly mortality rates for each of the 25 regions as an outcome of interest. We obtained the death counts from the National Informatics System of Deaths and population estimates from the National Registry of Identification and Civil Status. In addition, we characterized each wave according to its duration, peak, and mortality rates by age group and gender. Additionally, we used polynomial regression models to compare them graphically and performed a cluster analysis to identify regional patterns. Results: We estimated the average mortality rate at the first, second, and third wave at 13.01, 14.12, and 9.82 per 100,000 inhabitants, respectively, with higher mortality rates among elders and men. The patterns of each wave varied substantially in terms of duration, peak, impact, and wave shapes. Based on our clustering analysis, during the first wave caused by the index virus, the 25 regions of Peru presented six different wave patterns. However, the regions were clustered in two different wave patterns during the second and third, caused by alpha/lambda/delta and omicron. Conclusions: The propagation of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants behaved in Peru with varying wave patterns and regional clustering. During the COVID-19 pandemic, the weekly mortality rates followed different spatiotemporal patterns with solid clustering, which might help project the impact of future waves of COVID-19.
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Chavda VP, Patel AB, Vaghasiya DD. SARS-CoV-2 variants and vulnerability at the global level. J Med Virol 2022; 94:2986-3005. [PMID: 35277864 PMCID: PMC9088647 DOI: 10.1002/jmv.27717] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/24/2022]
Abstract
Numerous variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have evolved. Viral variants may evolve with harmful susceptibility to the immunity established with the existing COVID-19 vaccination. These variants are more transmissible, induce relatively extreme illness, have evasive immunological features, decrease neutralization using antibodies from vaccinated persons, and are more susceptible to re-infection. The Centers for Disease Control and Prevention (CDC) has categorized SARS-CoV-2 mutations as variants of interest (VOI), variants of concern (VOC), and variants of high consequence (VOHC). At the moment, four VOC and many variants of interest have been defined and require constant observation. This review article summarizes various variants of SARS-CoV-2 surfaced with special emphasis on VOCs that are spreading across the world, as well as several viral mutational impacts and how these modifications alter the properties of the virus.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical TechnologyL.M. College of PharmacyAhmedabadGujaratIndia
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25
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Description of a One-Year Succession of Variants of Interest and Concern of SARS-CoV-2 in Venezuela. Viruses 2022; 14:v14071378. [PMID: 35891359 PMCID: PMC9317613 DOI: 10.3390/v14071378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
Some of the lineages of SARS-CoV-2, the new coronavirus responsible for COVID-19, exhibit higher transmissibility or partial resistance to antibody-mediated neutralization and were designated by WHO as Variants of Interests (VOIs) or Concern (VOCs). The aim of this study was to monitor the dissemination of VOIs and VOCs in Venezuela from March 2021 to February 2022. A 614 nt genomic fragment was sequenced for the detection of some relevant mutations of these variants. Their presence was confirmed by complete genome sequencing, with a correlation higher than 99% between both methodologies. After the introduction of the Gamma VOC since the beginning of the year 2021, the variants Alpha VOC and Lambda VOI were detected as early as March 2021, at a very low frequency. In contrast, the Mu VOI, detected in May 2021, was able to circulate throughout the country. After the detection of the Delta VOC in June 2021, it became the predominant circulating variant. With the arrival of the Omicron VOC in December, this variant was able to displace the Delta one in less than one month.
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26
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Dutta D, Naiyer S, Mansuri S, Soni N, Singh V, Bhat KH, Singh N, Arora G, Mansuri MS. COVID-19 Diagnosis: A Comprehensive Review of the RT-qPCR Method for Detection of SARS-CoV-2. Diagnostics (Basel) 2022; 12:diagnostics12061503. [PMID: 35741313 PMCID: PMC9221722 DOI: 10.3390/diagnostics12061503] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/15/2022] Open
Abstract
The world is grappling with the coronavirus disease 2019 (COVID-19) pandemic, the causative agent of which is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 symptoms are similar to the common cold, including fever, sore throat, cough, muscle and chest pain, brain fog, dyspnoea, anosmia, ageusia, and headache. The manifestation of the disease can vary from being asymptomatic to severe life-threatening conditions warranting hospitalization and ventilation support. Furthermore, the emergence of mutecated variants of concern (VOCs) is paramount to the devastating effect of the pandemic. This highly contagious virus and its emergent variants challenge the available advanced viral diagnostic methods for high-accuracy testing with faster result yields. This review is to shed light on the natural history, pathology, molecular biology, and efficient diagnostic methods of COVID-19, detecting SARS-CoV-2 in collected samples. We reviewed the gold standard RT-qPCR method for COVID-19 diagnosis to confer a better understanding and application to combat the COVID-19 pandemic. This comprehensive review may further develop awareness about the management of the COVID-19 pandemic.
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Affiliation(s)
- Debashis Dutta
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence: (D.D.); (M.S.M.)
| | - Sarah Naiyer
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60616, USA;
| | | | - Neeraj Soni
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Vandana Singh
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Khalid Hussain Bhat
- SKUAST Kashmir, Division of Basic Science and Humanities, Faculty of Agriculture, Wadura Sopore 193201, JK, India;
| | - Nishant Singh
- Cell and Gene Therapy Absorption System, Exton, PA 19335, USA;
| | - Gunjan Arora
- Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - M. Shahid Mansuri
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Correspondence: (D.D.); (M.S.M.)
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27
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Naman ZT, Kadhim S, Al-Isawi ZJK, Butch CJ, Muhseen ZT. Computational Investigations of Traditional Chinese Medicinal Compounds against the Omicron Variant of SARS-CoV-2 to Rescue the Host Immune System. Pharmaceuticals (Basel) 2022; 15:ph15060741. [PMID: 35745660 PMCID: PMC9227372 DOI: 10.3390/ph15060741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
Macrodomain-I of the NSP3 (non-structural protein 3) is responsible for immune response hijacking in the SARS-CoV-2 infection known as COVID-19. In the omicron variant (B.1.1.529), this domain harbors a new mutation, V1069I, which may increase the binding of ADPr and consequently the infection severity. This macrodomain-I, due to its significant role in infection, is deemed to be an important drug target. Hence, using structural bioinformatics and molecular simulation approaches, we performed a virtual screening of the traditional Chinese medicines (TCM) database for potential anti-viral drugs. The screening of 57,000 compounds yielded the 10 best compounds with docking scores better than the control ADPr. Among the top ten, the best three hits—TCM42798, with a docking score of −13.70 kcal/mol, TCM47007 of −13.25 kcal/mol, and TCM30675 of −12.49 kcal/mol—were chosen as the best hits. Structural dynamic features were explored including stability, compactness, flexibility, and hydrogen bonding, further demonstrating the anti-viral potential of these hits. Using the MM/GBSA approach, the total binding free energy for each complex was reported to be −69.78 kcal/mol, −50.11 kcal/mol, and −47.64 kcal/mol, respectively, which consequently reflect the stronger binding and inhibitory potential of these compounds. These agents might suppress NSP3 directly, allowing the host immune system to recuperate. The current study lays the groundwork for the development of new drugs to combat SARS-CoV-2 and its variants.
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Affiliation(s)
- Ziad Tareq Naman
- Department of Medical Laboratory Techniques, Al-Ma’Moon University College, Aladhamia, Baghdad 72029, Iraq;
| | - Salim Kadhim
- College of Pharmacy, University of Alkafeel, Najaf 61001, Iraq;
| | - Zahraa J. K. Al-Isawi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Kufa, Najaf 61001, Iraq;
| | - Christopher J. Butch
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210093, China
- Correspondence: (C.J.B.); (Z.T.M.)
| | - Ziyad Tariq Muhseen
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
- Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon 51001, Iraq
- Correspondence: (C.J.B.); (Z.T.M.)
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28
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Ricciardi S, Guarino AM, Giaquinto L, Polishchuk EV, Santoro M, Di Tullio G, Wilson C, Panariello F, Soares VC, Dias SSG, Santos JC, Souza TML, Fusco G, Viscardi M, Brandi S, Bozza PT, Polishchuk RS, Venditti R, De Matteis MA. The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle. Nature 2022; 606:761-768. [PMID: 35551511 DOI: 10.1038/s41586-022-04835-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022]
Abstract
SARS-CoV-2, like other coronaviruses, builds a membrane-bound replication organelle (RO) to enable RNA replication1. The SARS-CoV-2 RO is composed of double membrane vesicles (DMVs) tethered to the endoplasmic reticulum (ER) by thin membrane connectors2, but the viral proteins and the host factors involved are currently unknown. Here we identify the viral non-structural proteins (NSPs) that generate the SARS-CoV-2 RO. NSP3 and NSP4 generate the DMVs while NSP6, through oligomerization and an amphipathic helix, zippers ER membranes and establishes the connectors. The NSP6ΔSGF mutant, which arose independently in the α, β, γ, η, ι, and λ variants of SARS-CoV-2, behaves as a gain-of-function mutant with a higher ER-zippering activity. We identified three main roles for NSP6: to act as a filter in RO-ER communication allowing lipid flow but restricting access of ER luminal proteins to the DMVs, to position and organize DMV clusters, and to mediate contact with lipid droplets (LDs) via the LD-tethering complex DFCP1-Rab18. NSP6 thus acts as an organizer of DMV clusters and can provide a selective track to refurbish them with LD-derived lipids. Importantly, both properly formed NSP6 connectors and LDs are required for SARS-CoV-2 replication. Our findings, uncovering the biological activity of NSP6 of SARS-CoV-2 and of other coronaviruses, have the potential to fuel the search for broad antiviral agents.
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Affiliation(s)
- Simona Ricciardi
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy.,Dept. Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Laura Giaquinto
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Elena V Polishchuk
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Michele Santoro
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Giuseppe Di Tullio
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | - Cathal Wilson
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy
| | | | - Vinicius C Soares
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Programa de Imunologia e Inflamação, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Suelen S G Dias
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Julia C Santos
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Thiago M L Souza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde (CDTS) and National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), FIOCRUZ, Rio de Janeiro, Brazil
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, (Naples), Italy
| | - Maurizio Viscardi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, (Naples), Italy
| | - Sergio Brandi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, (Naples), Italy
| | - Patrícia T Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Roman S Polishchuk
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy.
| | - Rossella Venditti
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy. .,Dept. Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, (Naples), Italy. .,Dept. Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.
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29
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Zhou H, Ni WJ, Huang W, Wang Z, Cai M, Sun YC. Advances in Pathogenesis, Progression, Potential Targets and Targeted Therapeutic Strategies in SARS-CoV-2-Induced COVID-19. Front Immunol 2022; 13:834942. [PMID: 35450063 PMCID: PMC9016159 DOI: 10.3389/fimmu.2022.834942] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
As the new year of 2020 approaches, an acute respiratory disease quietly caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as coronavirus disease 2019 (COVID-19) was reported in Wuhan, China. Subsequently, COVID-19 broke out on a global scale and formed a global public health emergency. To date, the destruction that has lasted for more than two years has not stopped and has caused the virus to continuously evolve new mutant strains. SARS-CoV-2 infection has been shown to cause multiple complications and lead to severe disability and death, which has dealt a heavy blow to global development, not only in the medical field but also in social security, economic development, global cooperation and communication. To date, studies on the epidemiology, pathogenic mechanism and pathological characteristics of SARS-CoV-2-induced COVID-19, as well as target confirmation, drug screening, and clinical intervention have achieved remarkable effects. With the continuous efforts of the WHO, governments of various countries, and scientific research and medical personnel, the public’s awareness of COVID-19 is gradually deepening, a variety of prevention methods and detection methods have been implemented, and multiple vaccines and drugs have been developed and urgently marketed. However, these do not appear to have completely stopped the pandemic and ravages of this virus. Meanwhile, research on SARS-CoV-2-induced COVID-19 has also seen some twists and controversies, such as potential drugs and the role of vaccines. In view of the fact that research on SARS-CoV-2 and COVID-19 has been extensive and in depth, this review will systematically update the current understanding of the epidemiology, transmission mechanism, pathological features, potential targets, promising drugs and ongoing clinical trials, which will provide important references and new directions for SARS-CoV-2 and COVID-19 research.
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Affiliation(s)
- Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei-Jian Ni
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei Huang
- The Third People's Hospital of Hefei, The Third Clinical College of Anhui Medical University, Hefei, China
| | - Zhen Wang
- Anhui Provincial Children's Hospital, Children's Hospital of Fudan University-Anhui Campus, Hefei, China
| | - Ming Cai
- Department of Pharmacy, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yan-Cai Sun
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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30
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A potent human monoclonal antibody with pan-neutralizing activities directly dislocates S trimer of SARS-CoV-2 through binding both up and down forms of RBD. Signal Transduct Target Ther 2022; 7:114. [PMID: 35383141 PMCID: PMC8980211 DOI: 10.1038/s41392-022-00954-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of novel coronavirus disease (COVID-19). The neutralizing monoclonal antibodies (mAbs) targeting the receptor-binding domain (RBD) of SARS-CoV-2 are among the most promising strategies to prevent and treat COVID-19. However, SARS-CoV-2 variants of concern (VOCs) profoundly reduced the efficacies of most of mAbs and vaccines approved for clinical use. Herein, we demonstrated mAb 35B5 efficiently neutralizes both wild-type (WT) SARS-CoV-2 and VOCs, including B.1.617.2 (delta) variant, in vitro and in vivo. Cryo-electron microscopy (cryo-EM) revealed that 35B5 neutralizes SARS-CoV-2 by targeting a unique epitope that avoids the prevailing mutation sites on RBD identified in circulating VOCs, providing the molecular basis for its pan-neutralizing efficacy. The 35B5-binding epitope could also be exploited for the rational design of a universal SARS-CoV-2 vaccine.
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31
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Thakur V, Bhola S, Thakur P, Patel SKS, Kulshrestha S, Ratho RK, Kumar P. Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe. Infection 2022; 50:309-325. [PMID: 34914036 PMCID: PMC8675301 DOI: 10.1007/s15010-021-01734-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/16/2021] [Indexed: 02/06/2023]
Abstract
The coronavirus disease-19 has left a permanent mark on the history of the human race. Severe acute respiratory syndrome coronavirus-2 is a positive-sense single-stranded RNA virus, first reported in Wuhan, China, in December 2019 and from there took over the world. Being highly susceptible to mutations, the virus's numerous variants started to appear, and some were more lethal and infectious than the parent. The effectiveness of the vaccine is also affected severely against the new variant. In this study, the infectious mechanism of the coronavirus is explained with a focus on different variants and their respective mutations, which play a critical role in the increased transmissibility, infectivity, and immune escape of the virus. As India has already faced the second wave of the pandemic, the future outlook on the likeliness of a third wave with respect to the Indian variants such as kappa, delta, and Delta Plus is also discussed. This review article aims to reflect the catastrophe of the variants of SARS-CoV-2 and the possibility of developing even more severe variants in the near future.
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Affiliation(s)
- Vikram Thakur
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
- Viral Regional Diagnostic Laboratory (VRDL), Government Medical College, Patiala, 147001, India
| | - Shivam Bhola
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Pryanka Thakur
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | | | - Saurabh Kulshrestha
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Radha Kanta Ratho
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India.
| | - Pradeep Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India.
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32
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Barletta WA. The Influence of SARS-CoV-2 Variants on National Case-Fatality Rates: Correlation and Validation Study. JMIRX MED 2022; 3:e32935. [PMID: 35969709 PMCID: PMC9364421 DOI: 10.2196/32935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/07/2022] [Accepted: 02/08/2022] [Indexed: 01/19/2023]
Abstract
Background In 2021, new variants of the SARS-CoV-2 virus appeared with increased transmissibility and virulence as compared with the original wild variant. The first variants of concern (VoCs), Alpha (B1.1.7) and Gamma (P.1), first appeared in the United Kingdom and Brazil, respectively. The Delta (B.1.617.2) variant, seen in India in October 2020, dominated COVID-19 infections across all regions through the second half of 2021. Objective This research explores the degree to which SARS-CoV-2 VoCs generate waves of fluctuations in case-fatality rates (CFRs) across countries in several regions, increase the risk of mortality to persons with certain comorbidities, and decrease the risk of mortality as the percentage of fully vaccinated populations increases. Methods This analysis introduces a measure of the temporal dynamics of COVID-19 infections in the form of a proxy CFR (pCFR), which can be compared among countries. It uses economic and demographic data reported by the World Bank and International Monetary Fund, plus publicly available epidemiological and medical statistics reported to the relevant national and international public health authorities. From these ecological data, pandemic average and daily COVID-19 CFRs and their correlations with potential cofactors were computed for 2021, a year dominated by the spread of World Health Organization-designated VoCs. The study does not investigate disease pathology; rather, it compares the daily case rates and pCFRs to reveal underlying contributing factors that vary from country to country and region to region. Results The in-depth global regression analysis of cofactors found that the strongest single correlation with COVID-19 fatality was 0.36 (SD 0.02) with P<.001 for chronic kidney disease. No other single physiological cofactors display positive correlations exceeding 0.26 (SD 0.26), with P=.008 (asthma) and P=.01 (coronary disease). The study confirms that the pCFR is a valuable metric for tracking waves of infection due to different VoCs within countries. Conclusions The influence of social, economic, and medical cofactors on the CFR due to VoCs remains qualitatively similar, albeit strengthened, to the levels found for the wild strain. The strong regional variations of the influence of all cofactors observed for the wild strain persists in infections for all VoCs with very strong correlation coefficients seen in the Middle East for asthma (0.76), coronary heart disease (0.60), lung disease (0.70), and chronic kidney disease (0.52). Strong regional variations emphasize the influence on COVID-19 mortality due to regional differences in national economics, patterns of health care policies, and variations in cultural practices and environment. The pCFR-based analysis reveals clear patterns of the spread of VoCs across regions, but there is little evidence for the spread of the Lambda and Mu (B.1.621) variants of interest outside of South America.
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Affiliation(s)
- William A Barletta
- Department of Physics Massachusetts Institute of Technology Cambridge, MA United States
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33
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Acevedo ML, Gaete-Argel A, Alonso-Palomares L, de Oca MM, Bustamante A, Gaggero A, Paredes F, Cortes CP, Pantano S, Martínez-Valdebenito C, Angulo J, Le Corre N, Ferrés M, Navarrete MA, Valiente-Echeverría F, Soto-Rifo R. Differential neutralizing antibody responses elicited by CoronaVac and BNT162b2 against SARS-CoV-2 Lambda in Chile. Nat Microbiol 2022; 7:524-529. [PMID: 35365787 DOI: 10.1038/s41564-022-01092-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/23/2022] [Indexed: 01/21/2023]
Abstract
SARS-CoV-2 variant Lambda was dominant in several South American countries, including Chile. To ascertain the efficacy of local vaccination efforts, we used pseudotyped viruses to characterize the neutralization capacity of antibodies elicited by CoronaVac (n = 53) and BNT162b2 (n = 56) in healthcare workers from Clínica Santa María and the Faculty of Medicine at Universidad de Chile, as well as in convalescent plasma from individuals infected during the first wave visiting the Hospital Clínico at Pontificia Universidad Católica (n = 30). We observed that BNT162b2 elicits higher neutralizing antibody titres than CoronaVac, with differences ranging from 7.4-fold for the ancestral spike (Wuhan-Hu-1) to 8.2-fold for the Lambda spike and 13-fold for the Delta spike. Compared with the ancestral virus, neutralization against D614G, Alpha, Gamma, Lambda and Delta variants was reduced by between 0.93- and 4.22-fold for CoronaVac, 1.04- and 2.38-fold for BNT162b2, and 1.26- and 2.67-fold for convalescent plasma. Comparative analyses among the spike structures of the different variants suggest that mutations in the spike protein from the Lambda variant, including the 246-252 deletion in an antigenic supersite at the N-terminal domain loop and L452Q/F490S within the receptor-binding domain, may account for immune escape. Interestingly, analyses using pseudotyped and whole viruses showed increased entry rates into HEK293T-ACE2 cells, but reduced replication rates in Vero-E6 cells for the Lambda variant when compared with the Alpha, Gamma and Delta variants. Our data show that inactivated virus and messenger RNA vaccines elicit different levels of neutralizing antibodies with different potency to neutralize SARS-CoV-2 variants, including the variant of interest Lambda.
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Affiliation(s)
- Mónica L Acevedo
- Laboratorio de Virología Molecular y Celular, Programa de Virología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Aracelly Gaete-Argel
- Laboratorio de Virología Molecular y Celular, Programa de Virología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Luis Alonso-Palomares
- Laboratorio de Virología Molecular y Celular, Programa de Virología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | | | - Andrés Bustamante
- Laboratorio de Virología Molecular y Celular, Programa de Virología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Aldo Gaggero
- Laboratorio de Virología Ambiental, Programa de Virología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Fabio Paredes
- Departamento de Epidemiología, Ministerio de Salud de Chile, Santiago, Chile
| | - Claudia P Cortes
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile.,Clínica Santa María, Santiago, Chile.,Departamento de Medicina Centro, Universidad de Chile, Santiago, Chile
| | - Sergio Pantano
- Biomolecular Simulations Group, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Constanza Martínez-Valdebenito
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Laboratorio de Infectología y Virología Molecular, Laboratorio de Bioseguridad Nivel 3, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jenniffer Angulo
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Laboratorio de Infectología y Virología Molecular, Laboratorio de Bioseguridad Nivel 3, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Le Corre
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Laboratorio de Infectología y Virología Molecular, Laboratorio de Bioseguridad Nivel 3, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela Ferrés
- Departamento de Enfermedades Infecciosas e Inmunología Pediátricas, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Laboratorio de Infectología y Virología Molecular, Laboratorio de Bioseguridad Nivel 3, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Fernando Valiente-Echeverría
- Laboratorio de Virología Molecular y Celular, Programa de Virología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile. .,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile.
| | - Ricardo Soto-Rifo
- Laboratorio de Virología Molecular y Celular, Programa de Virología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile. .,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile.
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34
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Biswas B, Chattopadhyay S, Hazra S, Hansda AK, Goswami R. COVID-19 pandemic: the delta variant, T-cell responses, and the efficacy of developing vaccines. Inflamm Res 2022; 71:377-396. [PMID: 35292834 PMCID: PMC8923340 DOI: 10.1007/s00011-022-01555-5] [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: 10/14/2021] [Revised: 02/07/2022] [Accepted: 02/16/2022] [Indexed: 12/15/2022] Open
Abstract
Background The mayhem COVID-19 that was ushered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) was declared pandemic by the World Health Organization in March 2020. Since its initial outbreak in late 2019, the virus has affected hundreds of million adults in the world and killing millions in the process. After the approval of newly developed vaccines, severe challenges remain to manufacture and administer them to the adult population globally in quick time. However, we have witnessed several mutations of the virus leading to ‘waves’ of viral spread and mortality. WHO has categorized these mutations as variants of concern (VOCs) and variants of interest (VOIs). The mortality due to COVID-19 has also been associated with various comorbidities and improper immune response. This has created further complications in understanding the nature of the SARS-CoV2–host interaction that has fuelled doubts in the efficacy of the approved vaccines. Whether there is requirement of booster dose and whether the impending wave could affect the children are some of the hotly debated topics. Materials and Methods A systematic literature review of PubMed, Medline, Scopus, Google Scholar was utilized to understand the nature of Delta variant and how it alters our T-cell responses and cytokine production and neutralizes vaccine-generated antibodies.
Conclusion In this review, we discuss the variants of SARS-CoV2 with specific focus on the Delta variant. We also specifically review the T-cell response against the virus and bring a narrative of various factors that may hold the key to fight against this marauding virus.
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Affiliation(s)
- Biswajit Biswas
- School of Bioscience, IIT Kharagpur, Kharagpur, 721302, West Bengal, India
| | | | - Sayantee Hazra
- School of Bioscience, IIT Kharagpur, Kharagpur, 721302, West Bengal, India
| | | | - Ritobrata Goswami
- School of Bioscience, IIT Kharagpur, Kharagpur, 721302, West Bengal, India.
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35
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Vo GV, Bagyinszky E, An SSA. COVID-19 Genetic Variants and Their Potential Impact in Vaccine Development. Microorganisms 2022; 10:microorganisms10030598. [PMID: 35336173 PMCID: PMC8954257 DOI: 10.3390/microorganisms10030598] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
In the two years since the SARS-CoV-2 pandemic started, it has caused over 5 million deaths and 400 million infected cases, and the world continues to be on high alert for COVID-19. Among the variants of interest and concern of SARS-CoV-2, the current Omicron (B.1.1.529) and stealth Omicron (BA.2) raised serious concerns due to rapid rates of infection caused by numerous mutations in the spike protein, which could escape from the antibody-mediated neutralization and increase the risk of reinfections. Hence, this work aims to describe the most relevant mutations in the SARS-CoV-2 spike protein, discuss vaccine against variant of concerns, describe rare adverse events after COVID-19 vaccination, introduce the most available promising COVID-19 vaccine candidates, and provide few perspectives of the future variants.
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Affiliation(s)
- Giau Van Vo
- Department of Biomedical Engineering, School of Medicine, Vietnam National University Ho Chi Minh City (VNU-HCM), Ho Chi Minh City 70000, Vietnam;
- Research Center for Genetics and Reproductive Health (CGRH), School of Medicine, Vietnam National University, Ho Chi Minh City (VNU-HCM), Ho Chi Minh City 70000, Vietnam
- Vietnam National University Ho Chi Minh City (VNU-HCM), Ho Chi Minh City 70000, Vietnam
| | - Eva Bagyinszky
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam 13120, Korea
- Correspondence: (E.B.); (S.S.A.A.)
| | - Seong Soo A. An
- Department of Bionano Technology, Gachon University, Seongnam 13120, Korea
- Correspondence: (E.B.); (S.S.A.A.)
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36
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Rayati Damavandi A, Dowran R, Al Sharif S, Kashanchi F, Jafari R. Molecular variants of SARS-CoV-2: antigenic properties and current vaccine efficacy. Med Microbiol Immunol 2022; 211:79-103. [PMID: 35235048 PMCID: PMC8889515 DOI: 10.1007/s00430-022-00729-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/09/2022] [Indexed: 12/30/2022]
Abstract
An ongoing pandemic of newly emerged SARS-CoV-2 has puzzled many scientists and health care policymakers around the globe. The appearance of the virus was accompanied by several distinct antigenic changes, specifically spike protein which is a key element for host cell entry of virus and major target of currently developing vaccines. Some of these mutations enable the virus to attach to receptors more firmly and easily. Moreover, a growing number of trials are demonstrating higher transmissibility and, in some of them, potentially more serious forms of illness related to novel variants. Some of these lineages, especially the Beta variant of concern, were reported to diminish the neutralizing activity of monoclonal and polyclonal antibodies present in both convalescent and vaccine sera. This could imply that these independently emerged variants could make antiviral strategies prone to serious threats. The rapid changes in the mutational profile of new clades, especially escape mutations, suggest the convergent evolution of the virus due to immune pressure. Nevertheless, great international efforts have been dedicated to producing efficacious vaccines with cutting-edge technologies. Despite the partial decrease in vaccines efficacy against worrisome clades, most current vaccines are still effective at preventing mild to severe forms of disease and hospital admission or death due to coronavirus disease 2019 (COVID-19). Here, we summarize existing evidence about newly emerged variants of SARS-CoV-2 and, notably, how well vaccines work against targeting new variants and modifications of highly flexible mRNA vaccines that might be required in the future.
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Affiliation(s)
- Amirmasoud Rayati Damavandi
- Students' Scientific Research Center, Exceptional Talents Development Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Razieh Dowran
- Students' Scientific Research Center, Exceptional Talents Development Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sarah Al Sharif
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Reza Jafari
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran. .,Hematology, Immune Cell Therapy, and Stem Cell Transplantation Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran.
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37
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Khan A, Randhawa AW, Balouch AR, Mukhtar N, Sayaf AM, Suleman M, Khan T, Ali S, Ali SS, Wang Y, Mohammad A, Wei DQ. Blocking key mutated hotspot residues in the RBD of the omicron variant (B.1.1.529) with medicinal compounds to disrupt the RBD-hACE2 complex using molecular screening and simulation approaches. RSC Adv 2022; 12:7318-7327. [PMID: 35424688 PMCID: PMC8982251 DOI: 10.1039/d2ra00277a] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/14/2022] [Indexed: 12/30/2022] Open
Abstract
A new variant of SARS-CoV-2 known as the omicron variant (B.1.1.529) reported in South Africa with 30 mutations in the whole spike protein, among which 15 mutations are in the receptor-binding domain, is continuously spreading exponentially around the world. The omicron variant is reported to be highly contagious with antibody-escaping activity. The emergence of antibody-escaping variants is alarming, and thus the quick discovery of small molecule inhibitors is needed. Hence, the current study uses computational drug screening and molecular dynamics simulation approaches (replicated) to identify novel drugs that can inhibit the binding of the receptor-binding domain (RBD) with hACE2. Screening of the North African, East African and North-East African medicinal compound databases by employing a multi-step screening approach revealed four compounds, namely (-)-pipoxide (C1), 2-(p-hydroxybenzyl) benzofuran-6-ol (C2), 1-(4-hydroxy-3-methoxyphenyl)-2-{4-[(E)-3-hydroxy-1-propenyl]-2-methoxyphenoxy}-1,3-propanediol (C3), and Rhein (C4), with excellent anti-viral properties against the RBD of the omicron variant. Investigation of the dynamics demonstrates stable behavior, good residue flexibility profiles, and structural compactness. Validation of the top hits using computational bioactivity analysis, binding free energy calculations and dissociation constant (K D) analysis also indicated the anti-viral properties of these compounds. In conclusion, this study will help in the design and discovery of novel drug therapeutics, which may be used against the emerging omicron variant of SARS-CoV-2.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | | | | | - Naila Mukhtar
- Department of Botany, University of Okara Punjab Pakistan
| | - Abrar Mohammad Sayaf
- School of Chemical Sciences, Universiti Sains Malaysia Pulau Pinang 11800 Malaysia
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat Kanju Khyber Pakhtunkhwa Pakistan
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | - Shahid Ali
- Centre for Biotechnology and Microbiology, University of Swat Kanju Khyber Pakhtunkhwa Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat Kanju Khyber Pakhtunkhwa Pakistan
| | - Yanjing Wang
- Engineering Research Center of Cell and Therapeutics Antibody, School of Pharmacy, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute Dasman Kuwait
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200030 P.R. China
- Peng Cheng Laboratory Vanke Cloud City Phase I Building 8, Xili Street, Nashan District Shenzhen Guangdong 518055 P.R China
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38
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Tsai TI, Khalili JS, Gilchrist M, Waight AB, Cohen D, Zhuo S, Zhang Y, Ding M, Zhu H, Mak ANS, Zhu Y, Goulet DR. ACE2-Fc fusion protein overcomes viral escape by potently neutralizing SARS-CoV-2 variants of concern. Antiviral Res 2022; 199:105271. [PMID: 35240221 PMCID: PMC8882475 DOI: 10.1016/j.antiviral.2022.105271] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/06/2022] [Accepted: 02/23/2022] [Indexed: 01/01/2023]
Abstract
COVID-19, an infectious disease caused by the SARS-CoV-2 virus, emerged globally in early 2020 and has remained a serious public health issue. To date, although several preventative vaccines have been approved by FDA and EMA, vaccinated individuals increasingly suffer from breakthrough infections. Therapeutic antibodies may provide an alternative strategy to neutralize viral infection and treat serious cases; however, the clinical data and our experiments show that some FDA-approved monoclonal antibodies lose function against COVID-19 variants such as Omicron. Therefore, in this study, we present a novel therapeutic agent, SI-F019, an ACE2-Fc fusion protein whose neutralization efficiency is not compromised, but actually strengthened, by the mutations of dominant variants including Omicron. Comprehensive biophysical analyses revealed the mechanism of increased inhibition to be enhanced interaction of SI-F019 with all the tested spike variants, in contrast to monoclonal antibodies which tended to show weaker binding to some variants. The results imply that SI-F019 may be a broadly useful agent for treatment of COVID-19.
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Affiliation(s)
- Tsung-I Tsai
- SystImmune Inc., 15318 NE 95th St., Redmond, WA, 98052, USA
| | | | - Mark Gilchrist
- SystImmune Inc., 15318 NE 95th St., Redmond, WA, 98052, USA
| | | | - Daniella Cohen
- SystImmune Inc., 15318 NE 95th St., Redmond, WA, 98052, USA
| | - Shi Zhuo
- Chengdu Strait Technology Industry Development Park, Wenjiang Dist., Chengdu, Sichuan, 611130, China
| | - Yong Zhang
- Chengdu Strait Technology Industry Development Park, Wenjiang Dist., Chengdu, Sichuan, 611130, China
| | - Muran Ding
- Chengdu Strait Technology Industry Development Park, Wenjiang Dist., Chengdu, Sichuan, 611130, China
| | - Hai Zhu
- SystImmune Inc., 15318 NE 95th St., Redmond, WA, 98052, USA
| | | | - Yi Zhu
- SystImmune Inc., 15318 NE 95th St., Redmond, WA, 98052, USA
| | - Dennis R Goulet
- SystImmune Inc., 15318 NE 95th St., Redmond, WA, 98052, USA.
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39
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Torres C, Mojsiejczuk L, Acuña D, Alexay S, Amadio A, Aulicino P, Debat H, Fay F, Fernández F, Giri AA, Goya S, König G, Lucero H, Nabaes Jodar M, Pianciola L, Sfalcin JA, Acevedo RM, Bengoa Luoni S, Bolatti EM, Brusés B, Cacciabue M, Casal PE, Cerri A, Chouhy D, Dus Santos MJ, Eberhardt MF, Fernandez A, Fernández PDC, Fernández Do Porto D, Formichelli L, Gismondi MI, Irazoqui M, Campos ML, Lusso S, Marquez N, Muñoz M, Mussin J, Natale M, Oria G, Pisano MB, Posner V, Puebla A, Re V, Sosa E, Villanova GV, Zaiat J, Zunino S, Acevedo ME, Acosta J, Alvarez Lopez C, Álvarez ML, Angeleri P, Angelletti A, Arca M, Ayala NA, Barbas G, Bertone A, Bonnet A, Bourlot I, Cabassi V, Castello A, Castro G, Cavatorta AL, Ceriani C, Cimmino C, Cipelli J, Colmeiro M, Cordero A, Cristina C, Di Bella S, Dolcini G, Ercole R, Espasandin Y, Espul C, Falaschi A, Fernandez Moll F, Foussal MD, Gatelli A, Goñi S, Jofré ME, Jaramillo J, Labarta N, Lacaze MA, Larreche R, Leiva V, Levin G, Luczak E, Mandile M, Marino G, Massone C, Mazzeo M, Medina C, Monaco B, Montoto L, Mugna V, Musto A, Nadalich V, Nieto MV, Ojeda G, Piedrabuena AC, Pintos C, Pozzati M, Rahhal M, Rechimont C, Remes Lenicov F, Rompato G, Seery V, Siri L, Spina J, Streitenberger C, Suárez A, Suárez J, Sujansky P, Talia JM, Theaux C, Thomas G, Ticeira M, Tittarelli E, Toro R, Uez O, Zaffanella MB, Ziehm C, Zubieta M. Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina. Front Med (Lausanne) 2021; 8:755463. [PMID: 34957143 PMCID: PMC8703000 DOI: 10.3389/fmed.2021.755463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 11/02/2021] [Indexed: 11/23/2022] Open
Abstract
SARS-CoV-2 variants with concerning characteristics have emerged since the end of 2020. Surveillance of SARS-CoV-2 variants was performed on a total of 4,851 samples from the capital city and 10 provinces of Argentina, during 51 epidemiological weeks (EWs) that covered the end of the first wave and the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 41/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the identification of signature mutations associated with variants. In addition, whole-genome sequences were obtained from 637 samples. The main variants found were Gamma and Lambda, and to a lesser extent, Alpha, Zeta, and Epsilon, and more recently, Delta. Whereas, Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires. The lineages that circulated on the first wave were replaced by emergent variants in a term of a few weeks. At the end of the ongoing second wave, Delta began to be detected, replacing Gamma and Lambda. This scenario is consistent with the Latin American variant landscape, so far characterized by a concurrent increase in Delta circulation and a stabilization in the number of cases. The cost-effective surveillance protocol presented here allowed for a rapid response in a resource-limited setting, added information on the expansion of Lambda in South America, and contributed to the implementation of public health measures to control the disease spread in Argentina.
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Affiliation(s)
- Carolina Torres
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Laura Mojsiejczuk
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Dolores Acuña
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Sofía Alexay
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Ariel Amadio
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Investigación de la Cadena Láctea (IDICAL) INTA-CONICET, Rafaela, Argentina
| | - Paula Aulicino
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Juan P. Garrahan”, Buenos Aires, Argentina
| | - Humberto Debat
- Instituto de Patología Vegetal – Centro de Investigaciones Agropecuarias – Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | | | - Franco Fernández
- Instituto de Patología Vegetal – Centro de Investigaciones Agropecuarias – Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Adriana A. Giri
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario CONICET, Rosario, Argentina
| | - Stephanie Goya
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Guido König
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular INTA-CONICET, Hurlingham, Argentina
| | - Horacio Lucero
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Resistencia, Argentina
| | - Mercedes Nabaes Jodar
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Luis Pianciola
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | | | - Raúl M. Acevedo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Botánica del Nordeste, Universidad Nacional del Nordeste-CONICET, Resistencia, Argentina
| | - Sofía Bengoa Luoni
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular INTA-CONICET, Hurlingham, Argentina
| | - Elisa M. Bolatti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario CONICET, Rosario, Argentina
| | - Bettina Brusés
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Resistencia, Argentina
| | - Marco Cacciabue
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular INTA-CONICET, Hurlingham, Argentina
| | - Pablo E. Casal
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario CONICET, Rosario, Argentina
| | - Agustina Cerri
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario CONICET, Rosario, Argentina
| | - Diego Chouhy
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario CONICET, Rosario, Argentina
| | - María José Dus Santos
- Instituto de Virología e Innovaciones Tecnológicas INTA-CONICET, Hurlingham, Argentina
- Laboratorio de Diagnóstico-UNIDAD COVID- Universidad Nacional de Hurlingham, Hurlingham, Argentina
| | - María Florencia Eberhardt
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Investigación de la Cadena Láctea (IDICAL) INTA-CONICET, Rafaela, Argentina
| | - Ailen Fernandez
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | - Paula del Carmen Fernández
- Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular INTA-CONICET, Hurlingham, Argentina
| | - Darío Fernández Do Porto
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Laura Formichelli
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Resistencia, Argentina
| | - María Inés Gismondi
- CIBIC Laboratorio, Rosario, Argentina
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Matías Irazoqui
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Investigación de la Cadena Láctea (IDICAL) INTA-CONICET, Rafaela, Argentina
| | - Melina Lorenzini Campos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Resistencia, Argentina
| | - Silvina Lusso
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Nathalie Marquez
- Instituto de Patología Vegetal – Centro de Investigaciones Agropecuarias – Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Marianne Muñoz
- Unidad de Genómica del Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Hurlingham, Argentina
| | - Javier Mussin
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Resistencia, Argentina
| | - Mónica Natale
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Griselda Oria
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Resistencia, Argentina
| | - María Belén Pisano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Victoria Posner
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio Mixto de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Andrea Puebla
- Unidad de Genómica del Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Hurlingham, Argentina
| | - Viviana Re
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ezequiel Sosa
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Gabriela V. Villanova
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio Mixto de Biotecnología Acuática, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jonathan Zaiat
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Sebastián Zunino
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
- Laboratorio de Virología Molecular, Hospital Blas L. Dubarry, Mercedes, Argentina
| | - María Elina Acevedo
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Julián Acosta
- Centro de Tecnología en Salud Pública, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Cristina Alvarez Lopez
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - María Laura Álvarez
- Laboratorio del Hospital Zonal Dr. Ramón Carrillo, San Carlos de Bariloche, Argentina
| | - Patricia Angeleri
- Comité Operativo de Emergencia COVID, Ministerio de Salud de la Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Andrés Angelletti
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- Laboratorio de Virología, HIEAyC “San Juan de Dios”, La Plata, Argentina
| | - Manuel Arca
- Laboratorio de Virología del Hospital JJ Urquiza, Concepción del Uruguay, Argentina
| | - Natalia A. Ayala
- Laboratorio Central de Salud Pública del Chaco, Resistencia, Argentina
| | - Gabriela Barbas
- Secretaria de Prevención y Promoción, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Ana Bertone
- Laboratorio de la Dirección de Epidemiología, Santa Rosa, Argentina
| | - Agustina Bonnet
- Laboratorio de Virología del Hospital JJ Urquiza, Concepción del Uruguay, Argentina
| | - Ignacio Bourlot
- Laboratorio de Biología Molecular del Hospital Centenario, Gualeguaychú, Argentina
| | - Victoria Cabassi
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Alejandro Castello
- Unidad de Emergencia COVID-19, Plataforma de Servicios Biotecnológicos, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Gonzalo Castro
- Laboratorio Central de la Provincia de Córdoba, Ministerio de Salud la Provincia de Córdoba, Córdoba, Argentina
| | - Ana Laura Cavatorta
- Centro de Tecnología en Salud Pública, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carolina Ceriani
- Laboratorio de Virología, Facultad de Veterinaria, Universidad Nacional del Centro de la Provincia de Buenos Aires, Buenos Aires, Argentina
| | - Carlos Cimmino
- Instituto Nacional de Epidemiología “Dr. Jara”, Mar del Plata, Argentina
| | - Julián Cipelli
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - María Colmeiro
- Laboratorio de Virología, HIEAyC “San Juan de Dios”, La Plata, Argentina
| | - Andrés Cordero
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Carolina Cristina
- Centro de Investigaciones Básicas y Aplicadas, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Junín, Argentina
| | - Sofia Di Bella
- Laboratorio de Virología, HIEAyC “San Juan de Dios”, La Plata, Argentina
| | - Guillermina Dolcini
- Laboratorio de Virología, Facultad de Veterinaria, Universidad Nacional del Centro de la Provincia de Buenos Aires, Buenos Aires, Argentina
| | - Regina Ercole
- Laboratorio de Virología, HIEAyC “San Juan de Dios”, La Plata, Argentina
| | - Yesica Espasandin
- Laboratorio del Hospital Zonal Dr. Ramón Carrillo, San Carlos de Bariloche, Argentina
| | - Carlos Espul
- Dirección de Epidemiología y Red de Laboratorios del Ministerio de Salud de la Provincia de Mendoza, Mendoza, Argentina
| | - Andrea Falaschi
- Dirección de Epidemiología y Red de Laboratorios del Ministerio de Salud de la Provincia de Mendoza, Mendoza, Argentina
| | - Facundo Fernandez Moll
- Centro de Investigaciones Básicas y Aplicadas, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Junín, Argentina
| | - María Delia Foussal
- Servicio de Inmunología, Hospital Dr. Julio C Perrando, Resistencia, Argentina
| | - Andrea Gatelli
- Laboratorio de Virología, HIEAyC “San Juan de Dios”, La Plata, Argentina
| | - Sandra Goñi
- Unidad de Emergencia COVID-19, Plataforma de Servicios Biotecnológicos, Universidad Nacional de Quilmes, Bernal, Argentina
| | | | - José Jaramillo
- Laboratorio de Virología Molecular, Hospital Blas L. Dubarry, Mercedes, Argentina
| | - Natalia Labarta
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - María Agustina Lacaze
- Programa Laboratorio de Salud Pública “Dr Dalmiro Pérez Laborda”, Ministerio de Salud de la Provincia de San Luis, San Luis, Argentina
| | - Rocio Larreche
- Laboratorio de Biología Molecular Bolívar, LABBO, Bolívar, Argentina
| | | | - Gustavo Levin
- Laboratorio de Biología Molecular del Hospital Centenario, Gualeguaychú, Argentina
| | - Erica Luczak
- Laboratorio del Hospital Interzonal General de Agudos “Evita”, Lanús, Argentina
| | - Marcelo Mandile
- Unidad de Emergencia COVID-19, Plataforma de Servicios Biotecnológicos, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Gioia Marino
- Laboratorio Pediátrico Avelino Castelán, Resistencia, Argentina
| | - Carla Massone
- Laboratorio de Virología Molecular, Hospital Blas L. Dubarry, Mercedes, Argentina
| | - Melina Mazzeo
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | - Carla Medina
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Belén Monaco
- Laboratorio de Virología Molecular, Hospital Blas L. Dubarry, Mercedes, Argentina
| | - Luciana Montoto
- Laboratorio de Biología Molecular Hospital Pedro de Elizalde, Buenos Aires, Argentina
| | | | | | - Victoria Nadalich
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Victoria Nieto
- Laboratorio de Virología, Facultad de Veterinaria, Universidad Nacional del Centro de la Provincia de Buenos Aires, Buenos Aires, Argentina
| | | | - Andrea C. Piedrabuena
- Servicio de Microbiología, Hospital 4 de Junio, Presidencia Roque Saenz Peña, Argentina
| | - Carolina Pintos
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | - Marcia Pozzati
- Laboratorio de Biología Molecular, Hospital Cosme Argerich, Buenos Aires, Argentina
| | - Marilina Rahhal
- Laboratorio de Hospital El Cruce Dr. Néstor C. Kirchner, Florencio Varela, Argentina
| | | | - Federico Remes Lenicov
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida, CONICET-UBA, Buenos Aires, Argentina
| | | | - Vanesa Seery
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida, CONICET-UBA, Buenos Aires, Argentina
| | - Leticia Siri
- Laboratorio de Biología Molecular del Hospital Centenario, Gualeguaychú, Argentina
| | - Julieta Spina
- Laboratorio de Biología Molecular, Hospital Dr. Héctor Cura, Olavarría, Argentina
| | - Cintia Streitenberger
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Ariel Suárez
- Departamento de Biología y Genética Molecular; IACA Laboratorios, Bahía Blanca, Argentina
| | - Jorgelina Suárez
- Centro de Investigaciones Básicas y Aplicadas, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Junín, Argentina
| | - Paula Sujansky
- Comité Operativo de Emergencia COVID, Ministerio de Salud de la Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Juan Manuel Talia
- Programa Laboratorio de Salud Pública “Dr Dalmiro Pérez Laborda”, Ministerio de Salud de la Provincia de San Luis, San Luis, Argentina
| | - Clara Theaux
- Laboratorio de Biología Molecular del Hospital General de Agudos Dr. Carlos G. Durand, Buenos Aires, Argentina
| | - Guillermo Thomas
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Marina Ticeira
- Laboratorio de Biología Molecular Bolívar, LABBO, Bolívar, Argentina
| | - Estefanía Tittarelli
- Departamento de Biología y Genética Molecular; IACA Laboratorios, Bahía Blanca, Argentina
| | - Rosana Toro
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Osvaldo Uez
- Instituto Nacional de Epidemiología “Dr. Jara”, Mar del Plata, Argentina
| | | | - Cecilia Ziehm
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Neuquén, Argentina
| | - Martin Zubieta
- Laboratorio de Hospital El Cruce Dr. Néstor C. Kirchner, Florencio Varela, Argentina
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Machado BAS, Hodel KVS, Fonseca LMDS, Mascarenhas LAB, Andrade LPCDS, Rocha VPC, Soares MBP, Berglund P, Duthie MS, Reed SG, Badaró R. The Importance of RNA-Based Vaccines in the Fight against COVID-19: An Overview. Vaccines (Basel) 2021; 9:1345. [PMID: 34835276 PMCID: PMC8623509 DOI: 10.3390/vaccines9111345] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 12/23/2022] Open
Abstract
In recent years, vaccine development using ribonucleic acid (RNA) has become the most promising and studied approach to produce safe and effective new vaccines, not only for prophylaxis but also as a treatment. The use of messenger RNA (mRNA) as an immunogenic has several advantages to vaccine development compared to other platforms, such as lower coast, the absence of cell cultures, and the possibility to combine different targets. During the COVID-19 pandemic, the use of mRNA as a vaccine became more relevant; two out of the four most widely applied vaccines against COVID-19 in the world are based on this platform. However, even though it presents advantages for vaccine application, mRNA technology faces several pivotal challenges to improve mRNA stability, delivery, and the potential to generate the related protein needed to induce a humoral- and T-cell-mediated immune response. The application of mRNA to vaccine development emerged as a powerful tool to fight against cancer and non-infectious and infectious diseases, for example, and represents a relevant research field for future decades. Based on these advantages, this review emphasizes mRNA and self-amplifying RNA (saRNA) for vaccine development, mainly to fight against COVID-19, together with the challenges related to this approach.
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Affiliation(s)
- Bruna Aparecida Souza Machado
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (L.A.B.M.); (L.P.C.d.S.A.); (V.P.C.R.); (M.B.P.S.); (R.B.)
| | - Katharine Valéria Saraiva Hodel
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (L.A.B.M.); (L.P.C.d.S.A.); (V.P.C.R.); (M.B.P.S.); (R.B.)
| | - Larissa Moraes dos Santos Fonseca
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (L.A.B.M.); (L.P.C.d.S.A.); (V.P.C.R.); (M.B.P.S.); (R.B.)
| | - Luís Alberto Brêda Mascarenhas
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (L.A.B.M.); (L.P.C.d.S.A.); (V.P.C.R.); (M.B.P.S.); (R.B.)
| | - Leone Peter Correia da Silva Andrade
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (L.A.B.M.); (L.P.C.d.S.A.); (V.P.C.R.); (M.B.P.S.); (R.B.)
| | - Vinícius Pinto Costa Rocha
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (L.A.B.M.); (L.P.C.d.S.A.); (V.P.C.R.); (M.B.P.S.); (R.B.)
| | - Milena Botelho Pereira Soares
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (L.A.B.M.); (L.P.C.d.S.A.); (V.P.C.R.); (M.B.P.S.); (R.B.)
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador 40296-710, Brazil
| | - Peter Berglund
- HDT Bio, 1616 Eastlake Ave E, Seattle, WA 98102, USA; (P.B.); (M.S.D.); (S.G.R.)
| | - Malcolm S. Duthie
- HDT Bio, 1616 Eastlake Ave E, Seattle, WA 98102, USA; (P.B.); (M.S.D.); (S.G.R.)
| | - Steven G. Reed
- HDT Bio, 1616 Eastlake Ave E, Seattle, WA 98102, USA; (P.B.); (M.S.D.); (S.G.R.)
| | - Roberto Badaró
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (K.V.S.H.); (L.M.d.S.F.); (L.A.B.M.); (L.P.C.d.S.A.); (V.P.C.R.); (M.B.P.S.); (R.B.)
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41
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Zuckerman N, Nemet I, Kliker L, Atari N, Lustig Y, Bucris E, Bar Ilan D, Geva M, Sorek-Abramovich R, Weiner C, Rainy N, Bar-Chaim A, Benveniste-Levkovitz P, Abu Hamed R, Regev-Yochay G, Hevkin O, Mor O, Alroy-Preis S, Mendelson E, Mandelboim M. The SARS-CoV-2 Lambda variant and its neutralisation efficiency following vaccination with Comirnaty, Israel, April to June 2021. Euro Surveill 2021; 26:2100974. [PMID: 34763751 PMCID: PMC8646983 DOI: 10.2807/1560-7917.es.2021.26.45.2100974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023] Open
Abstract
The SARS-CoV-2 Lambda (Pango lineage designation C.37) variant of interest, initially identified in Peru, has spread to additional countries. First detected in Israel in April 2021 following importations from Argentina and several European countries, the Lambda variant infected 18 individuals belonging to two main transmission chains without further spread. Micro-neutralisation assays following Comirnaty (BNT162b2 mRNA, BioNTech-Pfizer) vaccination demonstrated a significant 1.6-fold reduction in neutralising titres compared with the wild type virus, suggesting increased susceptibility of vaccinated individuals to infection.
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Affiliation(s)
- Neta Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Ital Nemet
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Limor Kliker
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Nofar Atari
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Dana Bar Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | - Miranda Geva
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Chen Weiner
- Shamir Medical Center, Be'er Ya'akov, Israel
| | - Nir Rainy
- Shamir Medical Center, Be'er Ya'akov, Israel
| | | | | | | | - Gili Regev-Yochay
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Sheba Medical Center, Tel-Hashomer, Israel
| | - Ofra Hevkin
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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