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Kodsi IA, Rayes DE, Koweyes J, Khoury CA, Rahy K, Thoumi S, Chamoun M, Haddad H, Mokhbat J, Tokajian S. Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon. Virus Res 2024; 339:199289. [PMID: 38036064 PMCID: PMC10704499 DOI: 10.1016/j.virusres.2023.199289] [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: 10/18/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country. METHODS A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology. RESULTS Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42). CONCLUSIONS The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.
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Affiliation(s)
- Ibrahim Al Kodsi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Douaa El Rayes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Kelven Rahy
- School of Medicine, Lebanese American University, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University, Lebanon
| | | | - Hoda Haddad
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Jacques Mokhbat
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon.
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2
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Vieira DFB, Bandeira DM, da Silva MAN, de Almeida ALT, Araújo M, Machado AB, Tort LFL, Nacife VP, Siqueira MM, Motta FC, Pauvolid-Corrêa A, Barth OM. Comparative analysis of SARS-CoV-2 variants Alpha (B.1.1.7), Gamma (P.1), Zeta (P.2) and Delta (B.1.617.2) in Vero-E6 cells: ultrastructural characterization of cytopathology and replication kinetics. Braz J Infect Dis 2024; 28:103706. [PMID: 38081327 PMCID: PMC10776915 DOI: 10.1016/j.bjid.2023.103706] [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: 09/04/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
This study compares the effects of virus-cell interactions among SARS-CoV-2 variants of concern (VOCs) isolated in Brazil in 2021, hypothesizing a correlation between cellular alterations and mortality and between viral load and transmissibility. For this purpose, reference isolates of Alpha, Gamma, Zeta, and Delta variants were inoculated into monolayers of Vero-E6 cells. Viral RNA was quantified in cell supernatants by RT‒PCR, and infected cells were analyzed by Transmission Electron Microscopy (TEM) for qualitative and quantitative evaluation of cellular changes 24, 48, and 72 hours postinfection (hpi). Ultrastructural analyses showed that all variants of SARS-CoV-2 altered the structure and function of mitochondria, nucleus, and rough endoplasmic reticulum of cells. Monolayers infected with the Delta variant showed the highest number of modified cells and the greatest statistically significant differences compared to those of other variants. Viral particles were observed in the cytosol and the cell membrane in 100 % of the cells at 48 hpi. Alpha showed the highest mean particle diameter (79 nm), and Gamma and Delta were the smallest (75 nm). Alpha and Gamma had the highest particle frequency per field at 48 hpi, while the same was observed for Zeta and Delta at 72 hpi and 24 hpi, respectively. The cycle threshold of viral RNA varied among the target protein, VOC, and time of infection. The findings presented here demonstrate that all four VOCs evaluated caused ultrastructural changes in Vero-E6 cells, which were more prominent when infection occured with the Delta variant.
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Affiliation(s)
- Debora Ferreira Barreto Vieira
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil.
| | - Derick Mendes Bandeira
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil
| | - Marcos Alexandre Nunes da Silva
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil
| | - Ana Luisa Teixeira de Almeida
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil
| | - Mia Araújo
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Ana Beatriz Machado
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Luis Fernando Lopez Tort
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil; Universidad de la República, Centro Universitario Regional - Litoral Norte, Laboratório de Virologia Molecular, Departamento de Ciências Biológicas, Salto, Uruguai
| | - Valéria Pereira Nacife
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Marilda M Siqueira
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Fernando Couto Motta
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil
| | - Alex Pauvolid-Corrêa
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brazil; Universidade Federal de Viçosa, Departamento de Veterinária, Laboratório de Virologia Veterinária de Viçosa, Viçosa, MG, Brazil
| | - Ortrud Monika Barth
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Laboratório de Morfologia e Morfogênese Viral, Rio de Janeiro, RJ, Brazil
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3
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Penetra SLS, Santos HFP, Resende PC, Bastos LS, da Silva MFB, Pina-Costa A, Lopes RS, Saboia-Vahia L, de Oliveira ACA, Pereira EC, Filho FM, Wakimoto MD, Calvet GA, Fuller TL, Whitworth J, Smith C, Nielsen-Saines K, Carvalho MS, Espíndola OM, Guaraldo L, Siqueira MM, Brasil P. SARS-CoV-2 Reinfection Cases in a Household-Based Prospective Cohort in Rio de Janeiro. J Infect Dis 2023; 228:1680-1689. [PMID: 37571849 PMCID: PMC11032242 DOI: 10.1093/infdis/jiad336] [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: 03/23/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/13/2023] Open
Abstract
This was a household-based prospective cohort study conducted in Rio de Janeiro, in which people with laboratory-confirmed coronavirus disease 2019 (COVID-19) and their household contacts were followed from April 2020 through June 2022. Ninety-eight reinfections were identified, with 71 (72.5%) confirmed by genomic analyses and lineage definition in both infections. During the pre-Omicron period, 1 dose of any COVID-19 vaccine was associated with a reduced risk of reinfection, but during the Omicron period not even booster vaccines had this effect. Most reinfections were asymptomatic or milder in comparison with primary infections, a justification for continuing active surveillance to detect infections in vaccinated individuals. Our findings demonstrated that vaccination may not prevent infection or reinfection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). Therefore we highlight the need to continuously update the antigenic target of SARS CoV-2 vaccines and administer booster doses to the population regularly, a strategy well established in the development of vaccines for influenza immunization programs.
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Affiliation(s)
- Stephanie L S Penetra
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heloisa F P Santos
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Soares Bastos
- Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michele F B da Silva
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anielle Pina-Costa
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata Serrano Lopes
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Saboia-Vahia
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Any Caroline Alves de Oliveira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elisa Cavalcante Pereira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando Medeiros Filho
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mayumi D Wakimoto
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Guilherme A Calvet
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Trevon L Fuller
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
- University of California, Los Angeles, Los Angeles, California, USA
| | - Jimmy Whitworth
- International Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher Smith
- International Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | | | - Marilia Sá Carvalho
- Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Otávio M Espíndola
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lusiele Guaraldo
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marilda M Siqueira
- Laboratory of Respiratory Viruses and Measles National Influenza Centre, Americas Regional Reference Lab for Measles and Rubella, Reference Laboratory for COVID-19 World Health Organization, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia Brasil
- Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
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4
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Freitas MTDS, Sena LOC, Fukutani KF, dos Santos CA, Neto FDCB, Ribeiro JS, dos Reis ES, Balbino VDQ, de Sá Paiva Leitão S, de Aragão Batista MV, Lipscomb MW, de Moura TR. The increase in SARS-CoV-2 lineages during 2020-2022 in a state in the Brazilian Northeast is associated with a number of cases. Front Public Health 2023; 11:1222152. [PMID: 38186707 PMCID: PMC10771345 DOI: 10.3389/fpubh.2023.1222152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 11/15/2023] [Indexed: 01/09/2024] Open
Abstract
SARS-CoV-2 has caused a high number of deaths in several countries. In Brazil, there were 37 million confirmed cases of COVID-19 and 700,000 deaths caused by the disease. The population size and heterogeneity of the Brazilian population should be considered in epidemiological surveillance due to the varied tropism of the virus. As such, municipalities and states must be factored in for their unique specificities, such as socioeconomic conditions and population distribution. Here, we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and their dynamics in each microregion from Sergipe state, northeastern Brazil, in the first 3 years of the pandemic. We analyzed 586 genomes sequenced between March 2020 and November 2022 extracted from the GISAID database. Phylogenetic analyses were carried out for each data set to reconstruct evolutionary history. Finally, the existence of a correlation between the number of lineages and infection cases by SARS-CoV-2 was evaluated. Aracaju, the largest city in northeastern Brazil, had the highest number of samples sequenced. This represented 54.6% (320) of the genomes, and consequently, the largest number of lineages identified. Studies also analyzed the relationship between mean lineage distributions and mean monthly infections, daily cases, daily deaths, and hospitalizations of vaccinated and unvaccinated patients. For this, a correlation matrix was created. Results revealed that the increase in the average number of SARS-CoV-2 variants was related to the average number of SARS-CoV-2 cases in both unvaccinated and vaccinated individuals. Thus, our data indicate that it is necessary to maintain epidemiological surveillance, especially in capital cities, since they have a high rate of circulation of resident and non-resident inhabitants, which contributes to the dynamics of the virus.
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Affiliation(s)
- Moises Thiago de Souza Freitas
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Brazil
- Parasitic Biology Graduate Program, Federal University of Sergipe, São Cristóvão, Brazil
| | - Ludmila Oliveira Carvalho Sena
- Health Foundation Parreiras Horta, Central Laboratory of Public Health (LACEN/SE), Sergipe State Health Secretariat, Aracaju, Brazil
| | - Kiyoshi Ferreira Fukutani
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Cliomar Alves dos Santos
- Health Foundation Parreiras Horta, Central Laboratory of Public Health (LACEN/SE), Sergipe State Health Secretariat, Aracaju, Brazil
| | | | - Julienne Sousa Ribeiro
- Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
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5
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Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun 2023; 14:6030. [PMID: 37758692 PMCID: PMC10533562 DOI: 10.1038/s41467-023-41442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT.
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Affiliation(s)
- Kelsey M Haas
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Michael J McGregor
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Thong T Nguyen
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Heejin Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Michael A P Williams
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Veronica V Rezelj
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Alexandra Hardy
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Andrea Fossati
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Erica J Stevenson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Ellie Sukerman
- Division of Infectious Diseases, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Tiffany Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sudhir Penugonda
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal and IRYCIS, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Yuan Zhou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Giorgi Metreveli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bhavya Harjai
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Tia A Tummino
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - James E Melnyk
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Jyoti Batra
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Laura Martin-Sancho
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Infectious Disease, Imperial College London, London, SW7 2BX, UK
| | - Jared Carlson-Stevermer
- Synthego Corporation, Redwood City, CA, 94063, USA
- Serotiny Inc., South San Francisco, CA, 94080, USA
| | - Alexander S Jureka
- Molecular Virology and Vaccine Team, Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization & Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, 30333, USA
- General Dynamics Information Technology, Federal Civilian Division, Atlanta, GA, 30329, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Brian K Shoichet
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63105, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Jeffrey R Johnson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medical Biosciences, University of the Western Cape, Bellville, 7535, Western Cape, South Africa
| | - Sumit K Chanda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Tonia C Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Maureen E Smith
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, 53706, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marco Vignuzzi
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Lorena Zuliani-Alvarez
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kris M White
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Judd F Hultquist
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
| | - Robyn M Kaake
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
| | - Adolfo García-Sastre
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
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La Torre G, Paglione G, Barone LC, Cammalleri V, Faticoni A, Marte M, Pocino RN, Previte CM, Bongiovanni A, Colaprico C, Ricci E, Imeshtari V, Manai MV, Shaholli D, Barletta VI, Carluccio G, Moretti L, Vezza F, Volpicelli L, Massetti AP, Cinti L, Roberto P, Napoli A, Antonelli G, Mastroianni CM, Sernia S. Evaluation of the Factors Associated with Reinfections towards SARS-CoV-2 Using a Case Control Design. J Clin Med 2023; 12:jcm12113861. [PMID: 37298055 DOI: 10.3390/jcm12113861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
OBJECTIVE The risk of reinfection with SARS-CoV-2 has been rapidly increased with the circulation of concerns about variants. So, the aim of our study was to evaluate the factors that increase the risk of this reinfection in healthcare workers compared to those who have never been positive and those who have had only one positivity. METHODS A case-control study was carried out at the Teaching Hospital Policlinico Umberto I in Rome, Sapienza University of Rome, in the period between 6 March 2020 and 3 June 2022. Cases are healthcare workers who have developed a reinfection with the SARS-CoV-2 virus, while controls were either healthcare workers who tested positive once or those who have never tested positive for SARS-CoV-2. RESULTS 134 cases and 267 controls were recruited. Female gender is associated with a higher odds of developing reinfection (OR: 2.42; 95% CI: 1.38-4.25). Moreover, moderate or high alcohol consumption is associated with higher odds of reinfection (OR: 1.49; 95% CI: 1.19-1.87). Diabetes is also associated with higher odds of reinfection (OR: 3.45; 95% CI: 1.41-8.46). Finally, subjects with increased red blood cell counts have higher odds of reinfection (OR: 1.69; 95% CI: 1.21-2.25). CONCLUSION From the prevention point of view, these findings indicate that particular attention should be paid to subjects with diabetes mellitus, women and alcoholic drinkers. These results could also suggest that contact tracing represents a fundamental approach model against the SARS-CoV-2 pandemic, together with the health information of participants.
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Affiliation(s)
- Giuseppe La Torre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Gianluca Paglione
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Lavinia Camilla Barone
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Vittoria Cammalleri
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Augusto Faticoni
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Mattia Marte
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Roberta Noemi Pocino
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Carlo Maria Previte
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Andrea Bongiovanni
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Corrado Colaprico
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Eleonora Ricci
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Valentin Imeshtari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Maria Vittoria Manai
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - David Shaholli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Vanessa India Barletta
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Giovanna Carluccio
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Luca Moretti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesca Vezza
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Lorenzo Volpicelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Anna Paola Massetti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Lilia Cinti
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Piergiorgio Roberto
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Anna Napoli
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Sabina Sernia
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
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SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19. Diagnostics (Basel) 2023; 13:diagnostics13030559. [PMID: 36766664 PMCID: PMC9913917 DOI: 10.3390/diagnostics13030559] [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: 01/06/2023] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.
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8
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Refocus on Immunogenic Characteristics of Convalescent COVID-19 Challenged by Prototype SARS-CoV-2. Vaccines (Basel) 2023; 11:vaccines11010123. [PMID: 36679968 PMCID: PMC9866260 DOI: 10.3390/vaccines11010123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023] Open
Abstract
Background: Mass basic and booster immunization programs effectively contained the spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus, also known as COVID-19. However, the emerging Variants of Concern (VOCs) of COVID-19 evade the immune protection of the vaccine and increase the risk of reinfection. Methods: Serum antibodies of 384 COVID-19 cases recovered from SARS-CoV-2 infection were examined. Correlations between clinical symptoms and antibodies against VOCs were analyzed. Result: All 384 cases (aged 43, range 1−90) were from 15 cities of Guangdong, China. The specific IgA, IgG, and IgM antibodies could be detected within 4−6 weeks after infection. A broad cross-reaction between SARS-CoV-2 and Severe Acute Respiratory Syndrome Coronavirus, but not with Middle East Respiratory Syndrome Coronavirus was found. The titers of neutralization antibodies (NAbs) were significantly correlated with IgG (r = 0.667, p < 0.001), but showed poor neutralizing effects against VOCs. Age, fever, and hormone therapy were independent risk factors for NAbs titers reduction against VOCs. Conclusion: Humoral immunity antibodies from the original strain of COVID-19 showed weak neutralization effects against VOCs, and decreased neutralizing ability was associated with initial age, fever, and hormone therapy, which hindered the effects of the COVID-19 vaccine developed from the SARS-CoV-2 prototype virus.
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9
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SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis. Viruses 2022; 14:v14122715. [PMID: 36560720 PMCID: PMC9784312 DOI: 10.3390/v14122715] [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: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/09/2022] Open
Abstract
Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 were included. Ninety-six different strains were reported, with variant of concern (VOC) gamma (n = 35,398), VOC delta (n = 15,780), and the variant of interest zeta (n = 1983) being the most common. The top three states with the most samples in the published articles were São Paulo, Rio de Janeiro, and Minas Gerais. Whereas the first year of the pandemic presented primary circulation of B.1.1.28 and B.1.1.33 variants, consecutive replacements were observed between them and VOI zeta, VOC gamma, VOC delta, and VOC omicron. VOI mu, VOI lambda, VOC alpha, and VOC beta were also detected but failed to reach significant circulation. Co-infection, re-infection, and vaccine breakthrough reports were found. Article co-citation differed from the co-authorship structure. Despite the limitations, we expect to give an overview of Brazil's genomic surveillance studies and contribute to future research execution.
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10
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Freire-Neto FP, Teixeira DG, da Cunha DCS, Morais IC, Tavares CPM, Gurgel GP, Medeiros SDN, dos Santos DC, Sales ADO, Jeronimo SMB. SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in northeastern Brazil. PLoS Negl Trop Dis 2022; 16:e0010337. [PMID: 36191040 PMCID: PMC9560550 DOI: 10.1371/journal.pntd.0010337] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/13/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in Rio Grande do Norte, northeastern Brazil, was diagnosed on March 12, 2020; thereafter, multiple surges of infection occurred, similar to what was seen elsewhere. These surges were mostly due to SARS-CoV-2 mutations leading to emergence of variants of concern (VoC). The introduction of new VoCs in a population previously exposed to SARS-CoV-2 or after vaccination has been a challenge to understanding the kinetics of the protective immune response against this virus. The aim of this study was to investigate the outbreak of SARS-CoV-2 reinfections observed in mid-January 2022 in Rio Grande do Norte state, Brazil. It describes the clinical and genomic characteristics of nine cases of reinfection that occurred coincident with the introduction of the omicron variant. METHODOLOGY/PRINCIPAL FINDINGS Of a total of 172,965 individuals with upper respiratory symptoms tested for SARS-CoV-2, between March 2020 through mid-February 2022, 58,097 tested positive. Of those, 444 had documented a second SARS-CoV-2 infection and nine reinfection cases were selected for sequencing. Genomic analysis revealed that virus lineages diverged between primary infections and the reinfections, with the latter caused by the Omicron (BA.1) variant among individuals fully vaccinated against SARS-CoV-2. CONCLUSIONS/SIGNIFICANCE Our findings suggest that the Omicron variant is able to evade both natural and vaccine-induced immunity, since all nine cases had prior natural infection and, in addition, were fully vaccinated, emphasizing the need to develop effective blocking vaccines.
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Affiliation(s)
- Francisco P. Freire-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Departmento de Bioquímica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- Getúlio Sales Diagnósticos, Natal, Rio Grande do Norte, Brazil
| | - Diego G. Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Dayse C. S. da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Ingryd C. Morais
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Celisa P. M. Tavares
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | | | - David C. dos Santos
- Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Selma M. B. Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Departmento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil
- Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais, Natal, Rio Grande do Norte, Brazil
- * E-mail:
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11
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Freire-Neto FP, Teixeira DG, da Cunha DCS, Morais IC, Tavares CPM, Gurgel GP, Medeiros SDN, Santos DCD, Sales ADO, Jeronimo SMB. SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in northeastern Brazil. PLoS Negl Trop Dis 2022; 16:e0010337. [PMID: 36191040 DOI: 10.1101/2022.04.08.22272726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/13/2022] [Accepted: 08/31/2022] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND The first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in Rio Grande do Norte, northeastern Brazil, was diagnosed on March 12, 2020; thereafter, multiple surges of infection occurred, similar to what was seen elsewhere. These surges were mostly due to SARS-CoV-2 mutations leading to emergence of variants of concern (VoC). The introduction of new VoCs in a population previously exposed to SARS-CoV-2 or after vaccination has been a challenge to understanding the kinetics of the protective immune response against this virus. The aim of this study was to investigate the outbreak of SARS-CoV-2 reinfections observed in mid-January 2022 in Rio Grande do Norte state, Brazil. It describes the clinical and genomic characteristics of nine cases of reinfection that occurred coincident with the introduction of the omicron variant. METHODOLOGY/PRINCIPAL FINDINGS Of a total of 172,965 individuals with upper respiratory symptoms tested for SARS-CoV-2, between March 2020 through mid-February 2022, 58,097 tested positive. Of those, 444 had documented a second SARS-CoV-2 infection and nine reinfection cases were selected for sequencing. Genomic analysis revealed that virus lineages diverged between primary infections and the reinfections, with the latter caused by the Omicron (BA.1) variant among individuals fully vaccinated against SARS-CoV-2. CONCLUSIONS/SIGNIFICANCE Our findings suggest that the Omicron variant is able to evade both natural and vaccine-induced immunity, since all nine cases had prior natural infection and, in addition, were fully vaccinated, emphasizing the need to develop effective blocking vaccines.
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Affiliation(s)
- Francisco P Freire-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Departmento de Bioquímica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- Getúlio Sales Diagnósticos, Natal, Rio Grande do Norte, Brazil
| | - Diego G Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Dayse C S da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Ingryd C Morais
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Celisa P M Tavares
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | | | - David C Dos Santos
- Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Selma M B Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Departmento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil
- Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais, Natal, Rio Grande do Norte, Brazil
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12
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Marinov GK, Mladenov M, Rangachev A, Alexiev I. SARS-CoV-2 reinfections during the first three major COVID-19 waves in Bulgaria. PLoS One 2022; 17:e0274509. [PMID: 36084070 PMCID: PMC9462809 DOI: 10.1371/journal.pone.0274509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic has had a devastating impact on the world over the past two years (2020-2021). One of the key questions about its future trajectory is the protection from subsequent infections and disease conferred by a previous infection, as the SARS-CoV-2 virus belongs to the coronaviruses, a group of viruses the members of which are known for their ability to reinfect convalescent individuals. Bulgaria, with high rates of previous infections combined with low vaccination rates and an elderly population, presents a somewhat unique context to study this question. METHODS We use detailed governmental data on registered COVID-19 cases to evaluate the incidence and outcomes of COVID-19 reinfections in Bulgaria in the period between March 2020 and early December 2021. RESULTS For the period analyzed, a total of 4,106 cases of individuals infected more than once were observed, including 31 cases of three infections and one of four infections. The number of reinfections increased dramatically during the Delta variant-driven wave of the pandemic towards the end of 2021. We observe a moderate reduction of severe outcomes (hospitalization and death) in reinfections relative to primary infections, and a more substantial reduction of severe outcomes in breakthrough infections in vaccinated individuals. CONCLUSIONS In the available datasets from Bulgaria, prior infection appears to provide some protection from severe outcomes, but to a lower degree than the reduction in severity of breakthrough infections in the vaccinated compared to primary infections in the unvaccinated.
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Affiliation(s)
- Georgi K. Marinov
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | | | - Antoni Rangachev
- Institute of Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia, Bulgaria
- International Center for Mathematical Sciences-Sofia, Sofia, Bulgaria
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
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Cer RZ, Voegtly LJ, Adhikari BN, Pike BL, Lueder MR, Glang LA, Malagon F, Ana ES, Regeimbal JM, Potts-Szoke MF, Schully KL, Smith DR, Bishop-Lilly KA. Genomic and virologic characterization of samples from a shipboard outbreak of COVID-19 reveals distinct variants within limited temporospatial parameters. Front Microbiol 2022; 13:960932. [PMID: 36033872 PMCID: PMC9399806 DOI: 10.3389/fmicb.2022.960932] [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: 06/03/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Early in the pandemic, in March of 2020, an outbreak of COVID-19 occurred aboard the aircraft carrier USS Theodore Roosevelt (CVN-71), during deployment in the Western Pacific. Out of the crew of 4,779 personnel, 1,331 service members were suspected or confirmed to be infected with SARS-CoV-2. The demographic, epidemiologic, and laboratory findings of service members from subsequent investigations have characterized the outbreak as widespread transmission of virus with relatively mild symptoms and asymptomatic infection among mostly young healthy adults. At the time, there was no available vaccination against COVID-19 and there was very limited knowledge regarding SARS-CoV-2 mutation, dispersal, and transmission patterns among service members in a shipboard environment. Since that time, other shipboard outbreaks from which data can be extracted have occurred, but these later shipboard outbreaks have occurred largely in settings where the majority of the crew were vaccinated, thereby limiting spread of the virus, shortening duration of the outbreaks, and minimizing evolution of the virus within those close quarters settings. On the other hand, since the outbreak on the CVN-71 occurred prior to widespread vaccination, it continued over the course of roughly two months, infecting more than 25% of the crew. In order to better understand genetic variability and potential transmission dynamics of COVID-19 in a shipboard environment of immunologically naïve, healthy individuals, we performed whole-genome sequencing and virus culture from eighteen COVID-19-positive swabs collected over the course of one week. Using the unique variants identified in those genomes, we detected seven discrete groups of individuals within the population aboard CVN-71 infected with viruses of distinct genomic signature. This is in stark contrast to a recent outbreak aboard another U.S. Navy ship with >98% vaccinated crew after a port visit in Reykjavik, Iceland, where the outbreak lasted only approximately 2 weeks and the virus was clonal. Taken together, these results demonstrate the utility of sequencing from complex clinical samples for molecular epidemiology and they also suggest that a high rate of vaccination among a population in close communities may greatly reduce spread, thereby restricting evolution of the virus.
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Affiliation(s)
- Regina Z. Cer
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Logan J. Voegtly
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Bishwo N. Adhikari
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Defense Threat Reduction Agency, Ft. Belvoir, VA, United States
| | - Brian L. Pike
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Matthew R. Lueder
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Lindsay A. Glang
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Francisco Malagon
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Ernesto Santa Ana
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - James M. Regeimbal
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Maria F. Potts-Szoke
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Kevin L. Schully
- The Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Darci R. Smith
- Department of Microbiology and Immunology, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Kimberly A. Bishop-Lilly
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- *Correspondence: Kimberly A. Bishop-Lilly,
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14
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De Marco C, Veneziano C, Massacci A, Pallocca M, Marascio N, Quirino A, Barreca GS, Giancotti A, Gallo L, Lamberti AG, Quaresima B, Santamaria G, Biamonte F, Scicchitano S, Trecarichi EM, Russo A, Torella D, Quattrone A, Torti C, Matera G, De Filippo C, Costanzo FS, Viglietto G. Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy. Front Microbiol 2022; 13:934993. [PMID: 35966675 PMCID: PMC9366435 DOI: 10.3389/fmicb.2022.934993] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, we report on the results of SARS-CoV-2 surveillance performed in an area of Southern Italy for 12 months (from March 2021 to February 2022). To this study, we have sequenced RNA from 609 isolates. We have identified circulating VOCs by Sanger sequencing of the S gene and defined their genotypes by whole-genome NGS sequencing of 157 representative isolates. Our results indicated that B.1 and Alpha were the only circulating lineages in Calabria in March 2021; while Alpha remained the most common variant between April 2021 and May 2021 (90 and 73%, respectively), we observed a concomitant decrease in B.1 cases and appearance of Gamma cases (6 and 21%, respectively); C.36.3 and Delta appeared in June 2021 (6 and 3%, respectively); Delta became dominant in July 2021 while Alpha continued to reduce (46 and 48%, respectively). In August 2021, Delta became the only circulating variant until the end of December 2021. As of January 2022, Omicron emerged and took over Delta (72 and 28%, respectively). No patient carrying Beta, Iota, Mu, or Eta variants was identified in this survey. Among the genomes identified in this study, some were distributed all over Europe (B1_S477N, Alpha_L5F, Delta_T95, Delta_G181V, and Delta_A222V), some were distributed in the majority of Italian regions (B1_S477N, B1_Q675H, Delta_T95I and Delta_A222V), and some were present mainly in Calabria (B1_S477N_T29I, B1_S477N_T29I_E484Q, Alpha_A67S, Alpha_A701S, and Alpha_T724I). Prediction analysis of the effects of mutations on the immune response (i.e., binding to class I MHC and/or recognition of T cells) indicated that T29I in B.1 variant; A701S in Alpha variant; and T19R in Delta variant were predicted to impair binding to class I MHC whereas the mutations A67S identified in Alpha; E484K identified in Gamma; and E156G and ΔF157/R158 identified in Delta were predicted to impair recognition by T cells. In conclusion, we report on the results of SARS-CoV-2 surveillance in Regione Calabria in the period between March 2021 and February 2022, identified variants that were enriched mainly in Calabria, and predicted the effects of identified mutations on host immune response.
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Affiliation(s)
- Carmela De Marco
- Department of Experimental and Clinical Medicine, “Magna Graecia” University, Catanzaro, Italy
- Interdepartmental Center of Services, Molecular Genomics and Pathology, “Magna Graecia” University, Catanzaro, Italy
- Carmela De Marco
| | - Claudia Veneziano
- Department of Experimental and Clinical Medicine, “Magna Graecia” University, Catanzaro, Italy
- Interdepartmental Center of Services, Molecular Genomics and Pathology, “Magna Graecia” University, Catanzaro, Italy
| | - Alice Massacci
- UOSD Biostatistics, Bioinformatics, and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Matteo Pallocca
- UOSD Biostatistics, Bioinformatics, and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Nadia Marascio
- Department of Health Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Angela Quirino
- Department of Health Sciences, “Magna Graecia” University, Catanzaro, Italy
- “Mater Domini” University Hospital, Catanzaro, Italy
| | | | | | - Luigia Gallo
- “Mater Domini” University Hospital, Catanzaro, Italy
| | | | - Barbara Quaresima
- Department of Experimental and Clinical Medicine, “Magna Graecia” University, Catanzaro, Italy
- Interdepartmental Center of Services, Molecular Genomics and Pathology, “Magna Graecia” University, Catanzaro, Italy
| | - Gianluca Santamaria
- Department of Experimental and Clinical Medicine, “Magna Graecia” University, Catanzaro, Italy
| | - Flavia Biamonte
- Department of Experimental and Clinical Medicine, “Magna Graecia” University, Catanzaro, Italy
- Interdepartmental Center of Services, Molecular Genomics and Pathology, “Magna Graecia” University, Catanzaro, Italy
| | - Stefania Scicchitano
- Department of Experimental and Clinical Medicine, “Magna Graecia” University, Catanzaro, Italy
| | - Enrico Maria Trecarichi
- “Mater Domini” University Hospital, Catanzaro, Italy
- Department of Medical and Surgical Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Alessandro Russo
- “Mater Domini” University Hospital, Catanzaro, Italy
- Department of Medical and Surgical Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Daniele Torella
- Department of Experimental and Clinical Medicine, “Magna Graecia” University, Catanzaro, Italy
- “Mater Domini” University Hospital, Catanzaro, Italy
| | - Aldo Quattrone
- Neuroscience Research Center, “Magna Graecia” University, Catanzaro, Italy
| | - Carlo Torti
- “Mater Domini” University Hospital, Catanzaro, Italy
- Department of Medical and Surgical Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Giovanni Matera
- Department of Health Sciences, “Magna Graecia” University, Catanzaro, Italy
- “Mater Domini” University Hospital, Catanzaro, Italy
| | | | - Francesco Saverio Costanzo
- Department of Experimental and Clinical Medicine, “Magna Graecia” University, Catanzaro, Italy
- Interdepartmental Center of Services, Molecular Genomics and Pathology, “Magna Graecia” University, Catanzaro, Italy
- “Mater Domini” University Hospital, Catanzaro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, “Magna Graecia” University, Catanzaro, Italy
- “Mater Domini” University Hospital, Catanzaro, Italy
- *Correspondence: Giuseppe Viglietto
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15
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Bonura F, Genovese D, Amodio E, Calamusa G, Sanfilippo GL, Cacioppo F, Giammanco GM, De Grazia S, Ferraro D. Neutralizing Antibodies Response against SARS-CoV-2 Variants of Concern Elicited by Prior Infection or mRNA BNT162b2 Vaccination. Vaccines (Basel) 2022; 10:vaccines10060874. [PMID: 35746482 PMCID: PMC9229788 DOI: 10.3390/vaccines10060874] [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: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 12/21/2022] Open
Abstract
In order to determine the humoral protective response against SARS-CoV-2, the vaccine-induced and naturally induced neutralizing antibodies (NtAbs) responses against SARS-CoV-2 variants circulating in Italy through in vitro live virus neutralization assay were evaluated. A total of 39 SARS-CoV-2 recovered subjects (COVID-19+) and 63 subjects with a two-dose cycle of the BNT16262 vaccine were enrolled. A single serum sample was tested for COVID-19+ at 35–52 days post-positive swab, while vaccinees blood samples were taken at one (V1) and at three months (V3) after administration of the second vaccine dose. Significantly higher NtAb titers were found against B.1 and Alpha in both COVID-19+ and vaccinees, while lower NtAb titers were detected against Delta, Gamma, and Omicron variants. A comparison between groups showed that NtAb titers were significantly higher in both V1 and V3 than in COVID-19+, except against the Omicron variant where no significant difference was found. COVID-19+ showed lower neutralizing titers against all viral variants when compared to the vaccinees. Two-dose vaccination induced a sustained antibody response against each analyzed variant, except for Omicron. The evolution process of SARS-CoV-2, through variants originating from an accumulation of mutations, can erode the neutralizing effectiveness of natural and vaccine-elicited immunity. Therefore, a need for new vaccines should be evaluated to contain the ongoing pandemic.
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16
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Yu M, Zhu Y, Li Y, Chen Z, Li Z, Wang J, Li Z, Zhang F, Ding J. Design of a Recombinant Multivalent Epitope Vaccine Based on SARS-CoV-2 and Its Variants in Immunoinformatics Approaches. Front Immunol 2022; 13:884433. [PMID: 35603198 PMCID: PMC9120605 DOI: 10.3389/fimmu.2022.884433] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 01/08/2023] Open
Abstract
The development of an effective multivalent vaccine against SARS-CoV-2 variants is an important means to improve the global public health situation caused by COVID-19. In this study, we identified the antigen epitopes of the main global epidemic SARS-CoV-2 and mutated virus strains using immunoinformatics approach, and screened out 8 cytotoxic T lymphocyte epitopes (CTLEs), 17 helper T lymphocyte epitopes (HTLEs), 9 linear B-cell epitopes (LBEs) and 4 conformational B-cell epitopes (CBEs). The global population coverage of CTLEs and HTLEs was 93.16% and 99.9% respectively. These epitopes were spliced together by corresponding linkers and recombined into multivalent vaccine. In silico tests, the vaccine protein was a non-allergen and the docking with TLR-3 molecule showed a strong interaction. The results of immune simulation showed that the vaccine may be helpful to initiate both cellular and humoral immunity against all VOC. The optimistic immunogenicity of the vaccine was confirmed in vivo and in vitro finally. Therefore, our vaccine may have potential protection against SARS-CoV-2 and its variants.
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Affiliation(s)
- Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Yuejie Zhu
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yujiao Li
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Chen
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Zhiwei Li
- Clinical Laboratory Center, Xinjiang Uygur Autonomous Region People’s Hospital, Urumqi, China
| | - Jing Wang
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Zheng Li
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
| | - Jianbing Ding
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
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17
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Cojocaru C, Cojocaru E, Turcanu A, Zaharia D. Clinical challenges of SARS‑CoV‑2 variants (Review). Exp Ther Med 2022; 23:416. [PMID: 35601074 PMCID: PMC9117961 DOI: 10.3892/etm.2022.11343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/08/2022] [Indexed: 11/06/2022] Open
Abstract
Since the first cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, there have been challenges recognizing the clinical features of SARS-CoV-2 and identifying therapeutic options. This has been compounded by viral mutations that affect clinical response and primary epidemiological indicators. Multiple variants of SARS-CoV-2 have been identified and classified on the basis of nomenclature implemented by scientific organizations and the World Health Organisation (WHO). A total of five variants of concern (VOCs) have been identified to date. The present study aimed to analyse clinical and epidemiological features of each variant. Based on these characteristics, predictions were made about potential future evolution. Considering the time and location of SARS-CoV-2 VOC emergence, it was hypothesised that mutations were not due to pressure caused by the vaccines introduced in December 2020 but were dependent on natural characteristics of the virus. In the process of adapting to the human body, SARS-CoV-2 is expected to undergo evolution to become more contagious but less deadly. SARS-CoV-2 was hypothesized to continue spread through isolated epidemic outbreaks due to the unimmunized population, mostly unvaccinated children and adults, and for coronaviruses to continue to present a public health problem.
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Affiliation(s)
- Cristian Cojocaru
- Medical III Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Elena Cojocaru
- Morpho‑Functional Sciences II Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adina Turcanu
- Medical III Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Dragos Zaharia
- Department 4 Cardio‑thoracic Pathology, Faculty of Medicine, University of Medicine and Pharmacy ‘Carol Davila’, 050471 Bucharest, Romania
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18
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Gräf T, Bello G, Naveca FG, Gomes M, Cardoso VLO, da Silva AF, Dezordi FZ, Dos Santos MC, Santos KCDO, Batista ÉLR, Magalhães ALÁ, Vinhal F, Miyajima F, Faoro H, Khouri R, Wallau GL, Delatorre E, Siqueira MM, Resende PC. Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil. iScience 2022; 25:104156. [PMID: 35368908 PMCID: PMC8957357 DOI: 10.1016/j.isci.2022.104156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/23/2022] [Accepted: 03/21/2022] [Indexed: 11/03/2022] Open
Abstract
The COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56-3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59-3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil.
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Affiliation(s)
- Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Leônidas e Maria Deane Institute, Fiocruz, Manaus, Brazil
| | - Marcelo Gomes
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Programa de Computação Científica (PROCC), Fiocruz, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | | | - Fábio Miyajima
- Fundação Oswaldo Cruz - Fiocruz Ceará, Fortaleza, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas (ICC), Fiocruz-PR, Curitiba, Parana, Brazil
| | - Ricardo Khouri
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Gabriel Luz Wallau
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Edson Delatorre
- Departamento de Biologia. Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
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19
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Kang CK, Kim M, Hong J, Kim G, Lee S, Chang E, Choe PG, Kim NJ, Kim IS, Seo JY, Song D, Lee DS, Shin HM, Kim YW, Lee CH, Park WB, Kim HR, Oh MD. Distinct Immune Response at 1 Year Post-COVID-19 According to Disease Severity. Front Immunol 2022; 13:830433. [PMID: 35392102 PMCID: PMC8980227 DOI: 10.3389/fimmu.2022.830433] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/23/2022] [Indexed: 01/10/2023] Open
Abstract
Background Despite the fact of ongoing worldwide vaccination programs for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding longevity, breadth, and type of immune response to coronavirus disease-19 (COVID-19) is still important to optimize the vaccination strategy and estimate the risk of reinfection. Therefore, we performed thorough immunological assessments 1 year post-COVID-19 with different severity. Methods We analyzed peripheral blood mononuclear cells and plasma samples at 1 year post-COVID-19 in patients who experienced asymptomatic, mild, and severe illness to assess titers of various isotypes of antibodies (Abs) against SARS-CoV-2 antigens, phagocytic capability, and memory B- and T-cell responses. Findings A total of 24 patients (7, 9, and 8 asymptomatic, mild, and severe patients, respectively) and eight healthy volunteers were included in this study. We firstly showed that disease severity is correlated with parameters of immune responses at 1 year post-COVID-19 that play an important role in protecting against reinfection with SARS-CoV-2, namely, the phagocytic capacity of Abs and memory B-cell responses. Interpretation Various immune responses at 1 year post-COVID-19, particularly the phagocytic capacity and memory B-cell responses, were dependent on the severity of the prior COVID-19. Our data could provide a clue for a tailored vaccination strategy after natural infection according to the severity of COVID-19.
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Affiliation(s)
- Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Minji Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, South Korea
- BrainKorea21 (BK21) FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
| | - Jisu Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- BrainKorea21 (BK21) FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, South Korea
| | - Gwanghun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, South Korea
- BrainKorea21 (BK21) FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
| | - Soojin Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, South Korea
- BrainKorea21 (BK21) FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
| | - Euijin Chang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Ik Soo Kim
- Department of Microbiology, School of Medicine, Gachon University, Incheon, South Korea
| | - Jun-Young Seo
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea
- BrainKorea21 (BK21) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Daesub Song
- College of Pharmacy, Korea University, Sejong, South Korea
| | - Dong-Sup Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, South Korea
- BrainKorea21 (BK21) FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
| | - Hyun Mu Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- BrainKorea21 (BK21) FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
| | - Yong-Woo Kim
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
| | - Chang-Han Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- BrainKorea21 (BK21) FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, South Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
- *Correspondence: Hang-Rae Kim, ; Wan Beom Park, ; Chang-Han Lee,
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
- *Correspondence: Hang-Rae Kim, ; Wan Beom Park, ; Chang-Han Lee,
| | - Hang-Rae Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, South Korea
- BrainKorea21 (BK21) FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Medical Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
- *Correspondence: Hang-Rae Kim, ; Wan Beom Park, ; Chang-Han Lee,
| | - Myoung-don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
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20
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Henriques-Santos BM, Farjun B, Corrêa IA, Figueiredo JDB, Fidalgo-Neto AA, Kuriyama SN. SARS-CoV-2 Variant Determination Through SNP Assays in Samples From Industry Workers From Rio de Janeiro, Brazil. Front Microbiol 2022; 12:757783. [PMID: 35222292 PMCID: PMC8863740 DOI: 10.3389/fmicb.2021.757783] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/23/2021] [Indexed: 12/20/2022] Open
Abstract
Since the first reported case in December 2019, SARS-CoV-2 infections have become a major public health worldwide. Even with the increasing vaccination in several countries and relaxing of social distancing measures, the pandemic remains a threat especially due to the emergence of new SARS-CoV-2 variants. Despite the presence of an enzyme capable of proofreading its genome, high rates of replication provide a source of accumulation of mutations within the viral genome. In this retrospective study, samples from a cohort of industry workers tested by the SESI’s COVID-19 mass testing program from September 2020 to May 2021 were analyzed using a mutation panel in order to describe the circulation of currently identified SARS-CoV-2 variants within the samples obtained in Rio de Janeiro State. Our results demonstrated that the variant of interest (VOI) Zeta has been in circulation since October 2020 and reached 87% of prevalence in February 2021 followed by a decrease due to the emergence of Gamma variant of concern (VOC). Gamma was detected in January 2021 in our studied population, and its prevalence increased during the following months, reaching absolute prevalence within positive samples in May. The Alpha variant was detected only in 4–7% of samples during March and April while Beta VOC was not detected in our study. Our data agree with sequencing genomic surveillance databases and highlight the importance of continuous mass testing programs and variant detection in order to control viral spread and guide public health measures.
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Affiliation(s)
| | - Bruna Farjun
- SESI Innovation Center for Occupational Health, Industry Federation of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isadora Alonso Corrêa
- Department of Virology, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Janaina de Barros Figueiredo
- SESI Innovation Center for Occupational Health, Industry Federation of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Antonio Augusto Fidalgo-Neto
- SENAI Innovation Institute for Green Chemistry, Industry Federation of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sergio Noboru Kuriyama
- SESI Innovation Center for Occupational Health, Industry Federation of the State of Rio de Janeiro, Rio de Janeiro, Brazil
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21
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Tian D, Sun Y, Zhou J, Ye Q. The global epidemic of SARS-CoV-2 variants and their mutational immune escape. J Med Virol 2022; 94:847-857. [PMID: 34609003 PMCID: PMC8661756 DOI: 10.1002/jmv.27376] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/23/2021] [Accepted: 10/01/2021] [Indexed: 12/16/2022]
Abstract
During the COVID-19 pandemic, genetic variants of SARS-CoV-2 have been emerging and spreading around the world. Several SARS-CoV-2 endemic variants were found in United Kingdom, South Africa, Japan, and India between 2020 and April 2021. Studies have shown that many SARS-CoV-2 variants are more infectious than early wild strain and produce immune escape. These SARS-CoV-2 variants have brought new challenges to the prevention and control of COVID-19. This review summarizes and analyzes the biological characteristics of different amino acid mutations and the epidemic characteristics and immune escape of different SARS-CoV-2 variants. We hope to provide scientific reference for the monitoring, prevention, and control measures of new SARS-CoV-2 variants and the development strategy of the second-generation vaccine.
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Affiliation(s)
- Dandan Tian
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - YanHong Sun
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - JianMing Zhou
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - Qing Ye
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
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22
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de Lima Gianfelice PR, Sovek Oyarzabal R, Cunha A, Vicensi Grzybowski JM, da Conceição Batista F, E N Macau E. The starting dates of COVID-19 multiple waves. CHAOS (WOODBURY, N.Y.) 2022; 32:031101. [PMID: 35364850 DOI: 10.1063/5.0079904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
The severe acute respiratory syndrome of coronavirus 2 spread globally very quickly, causing great concern at the international level due to the severity of the associated respiratory disease, the so-called COVID-19. Considering Rio de Janeiro city (Brazil) as an example, the first diagnosis of this disease occurred in March 2020, but the exact moment when the local spread of the virus started is uncertain as the Brazilian epidemiological surveillance system was not widely prepared to detect suspected cases of COVID-19 at that time. Improvements in this surveillance system occurred over the pandemic, but due to the complex nature of the disease transmission process, specifying the exact moment of emergence of new community contagion outbreaks is a complicated task. This work aims to propose a general methodology to determine possible start dates for the multiple community outbreaks of COVID-19, using for this purpose a parametric statistical approach that combines surveillance data, nonlinear regression, and information criteria to obtain a statistical model capable of describing the multiple waves of contagion observed. The dynamics of COVID-19 in the city of Rio de Janeiro is taken as a case study, and the results suggest that the original strain of the virus was already circulating in Rio de Janeiro city as early as late February 2020, probably being massively disseminated in the population during the carnival festivities.
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Affiliation(s)
| | - Ricardo Sovek Oyarzabal
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos 12247-014, Brazil
| | - Americo Cunha
- Department of Applied Mathematics, Rio de Janeiro State University, Rio de Janeiro 20550-900, Brazil
| | - Jose Mario Vicensi Grzybowski
- Environmental Science and Technology Postgraduate Program, Federal University of Fronteira Sul, Erechim 99700-970, Brazil
| | | | - Elbert E N Macau
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos 12247-014, Brazil
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23
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Fajardo Á, Perbolianachis P, Ferreiro I, Moreno P, Moratorio G. Molecular accuracy vs antigenic speed: SARS-CoV-2 testing strategies. Curr Opin Pharmacol 2022; 62:152-158. [PMID: 35042168 PMCID: PMC8687762 DOI: 10.1016/j.coph.2021.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023]
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has hit every corner of the world faster than any infectious disease ever known. In this context, rapid and accurate testing of positive cases are essential to follow the test-trace-isolate strategy (TETRIS), which has proven to be a key approach to constrain viral spread. Here, we discuss how to interpret and combine molecular or/and antigen-based detection methods for SARS-CoV-2 as well as when they should be used. Their application can be cleverly designed as an algorithm to prevent viral dissemination according to distinct epidemiological contexts within surveillance programs.
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Affiliation(s)
- Álvaro Fajardo
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur, Montevideo, Uruguay; Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Paula Perbolianachis
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur, Montevideo, Uruguay; Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Irene Ferreiro
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur, Montevideo, Uruguay; Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pilar Moreno
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur, Montevideo, Uruguay; Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
| | - Gonzalo Moratorio
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur, Montevideo, Uruguay; Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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24
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Ngwe Tun MM, Sakura T, Sakurai Y, Kurosaki Y, Inaoka DK, Shioda N, Yasuda J, Kita K, Morita K. Antiviral activity of 5-aminolevulinic acid against variants of severe acute respiratory syndrome coronavirus 2. Trop Med Health 2022; 50:6. [PMID: 34991723 PMCID: PMC8739347 DOI: 10.1186/s41182-021-00397-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began to emerge in 2020 and have been spreading globally during the coronavirus disease 2019 (COVID-19) pandemic. Despite the presence of different COVID-19 vaccines, the discovery of effective antiviral therapeutics for the treatment of patients infected with SARS-CoV-2 are still urgently needed. A natural amino acid, 5-aminolevulinic acid (5-ALA), has exhibited both antiviral and anti-inflammatory activities. In a previous study, we demonstrated an in vitro antiviral effect of 5-ALA against SARS-CoV-2 infection without significant cytotoxicity. In the present study, we sought to investigate whether 5-ALA with or without sodium ferrous citrate (SFC) can inhibit in vitro both the original SARS-CoV-2 Wuhan strain and its variants, including the Alpha, Beta, Gamma and Delta strains. METHODS The antiviral activity of ALA with or without SFC was determined in Vero-E6 cell. The virus inhibition was quantified by real time RT-PCR. RESULTS Co-administration of 5-ALA and SFC inhibited the Wuhan, Alpha and Delta variants of SARS-CoV-2 with IC50 values of 235, 173 and 397 µM, respectively, and the Beta and Gamma variants with IC50 values of 1311 and 1516 µM. CONCLUSION Our study suggests that 5-ALA with SFC warrants accelerated clinical evaluation as an antiviral drug candidate for treating patients infected with SARS-CoV-2 variants.
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Affiliation(s)
- Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Takaya Sakura
- Shionogi Global Infectious Diseases Division, Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Yasuteru Sakurai
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Yohei Kurosaki
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Daniel Ken Inaoka
- Shionogi Global Infectious Diseases Division, Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan.
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, 852-8523, Japan.
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, 852-8523, Japan.
- Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan.
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
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25
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Alves PA, de Oliveira EG, Franco-Luiz APM, Almeida LT, Gonçalves AB, Borges IA, Rocha FDS, Rocha RP, Bezerra MF, Miranda P, Capanema FD, Martins HR, Weber G, Teixeira SMR, Wallau GL, do Monte-Neto RL. Optimization and Clinical Validation of Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification, a Fast, Highly Sensitive and Specific COVID-19 Molecular Diagnostic Tool That Is Robust to Detect SARS-CoV-2 Variants of Concern. Front Microbiol 2021; 12:713713. [PMID: 34867841 PMCID: PMC8637279 DOI: 10.3389/fmicb.2021.713713] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/28/2021] [Indexed: 12/23/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic unfolded due to the widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission reinforced the urgent need for affordable molecular diagnostic alternative methods for massive testing screening. We present the clinical validation of a pH-dependent colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) for SARS-CoV-2 detection. The method revealed a limit of detection of 19.3 ± 2.7 viral genomic copies/μL when using RNA extracted samples obtained from nasopharyngeal swabs collected in guanidine-containing viral transport medium. Typical RT-LAMP reactions were performed at 65°C for 30 min. When compared to reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), up to cycle-threshold (Ct) value 32, RT-LAMP presented 98% [95% confidence interval (CI) = 95.3-99.5%] sensitivity and 100% (95% CI = 94.5-100%) specificity for SARS-CoV-2 RNA detection targeting E and N genes. No cross-reactivity was detected when testing other non-SARS-CoV virus, confirming high specificity. The test is compatible with primary RNA extraction-free samples. We also demonstrated that colorimetric RT-LAMP can detect SARS-CoV-2 variants of concern and variants of interest, such as variants occurring in Brazil named gamma (P.1), zeta (P.2), delta (B.1.617.2), B.1.1.374, and B.1.1.371. The method meets point-of-care requirements and can be deployed in the field for high-throughput COVID-19 testing campaigns, especially in countries where COVID-19 testing efforts are far from ideal to tackle the pandemics. Although RT-qPCR is considered the gold standard for SARS-CoV-2 RNA detection, it requires expensive equipment, infrastructure, and highly trained personnel. In contrast, RT-LAMP emerges as an affordable, inexpensive, and simple alternative for SARS-CoV-2 molecular detection that can be applied to massive COVID-19 testing campaigns and save lives.
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Affiliation(s)
- Pedro A. Alves
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
- Centro de Tecnologia em Vacinas, UFMG/Fiocruz, Belo Horizonte, Brazil
| | | | | | | | | | - Iara A. Borges
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | | | - Raissa P. Rocha
- Centro de Tecnologia em Vacinas, UFMG/Fiocruz, Belo Horizonte, Brazil
| | - Matheus F. Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
| | - Pâmella Miranda
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávio D. Capanema
- Núcleo de Inovação Tecnológica, Fundação Hospitalar do Estado de Minas Gerais, Belo Horizonte, Brazil
| | - Henrique R. Martins
- Visuri Equipamentos e Serviços, Belo Horizonte, Brazil
- Departamento de Engenharia Elétrica, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Gabriel Luz Wallau
- Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
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26
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Cedro-Tanda A, Gómez-Romero L, Alcaraz N, de Anda-Jauregui G, Peñaloza F, Moreno B, Escobar-Arrazola MA, Ramirez-Vega OA, Munguia-Garza P, Garcia-Cardenas F, Cisneros-Villanueva M, Moreno-Camacho JL, Rodriguez-Gallegos J, Luna-Ruiz Esparza MA, Fernández Rojas MA, Mendoza-Vargas A, Reyes-Grajeda JP, Campos-Romero A, Angulo O, Ruiz R, Sheinbaum-Pardo C, Sifuentes-Osornio J, Kershenobich D, Hidalgo-Miranda A, Herrera LA. The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. Viruses 2021; 13:2182. [PMID: 34834987 PMCID: PMC8617872 DOI: 10.3390/v13112182] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We reported the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. We reported the effective reproduction number (Rt) of B.1.1.519 and presented evidence of its geographical origin based on phylogenetic analysis. We also studied its evolution via haplotype analysis and identified the most recurrent haplotypes. Finally, we studied the clinical impact of B.1.1.519. The B.1.1.519 variant was predominant between November 2020 and May 2021, reaching 90% of all cases sequenced in February 2021. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. Its Rt varies between 0.5 and 2.9. Its geographical origin remain to be investigated. Patients infected with variant B.1.1.519 showed a highly significant adjusted odds ratio (aOR) increase of 1.85 over non-B.1.1.519 patients for developing a severe/critical outcome (p = 0.000296, 1.33-2.6 95% CI) and a 2.35-fold increase for hospitalization (p = 0.005, 1.32-4.34 95% CI). The continuous monitoring of this and other variants will be required to control the ongoing pandemic as it evolves.
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Affiliation(s)
- Alberto Cedro-Tanda
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Nicolás Alcaraz
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Guillermo de Anda-Jauregui
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
- Cátedras CONACYT para Jóvenes Investigadores, CONACYT, Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Mexico City 03940, Mexico
| | - Fernando Peñaloza
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Bernardo Moreno
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Marco A. Escobar-Arrazola
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (M.A.E.-A.); (O.A.R.-V.); (P.M.-G.)
| | - Oscar A. Ramirez-Vega
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (M.A.E.-A.); (O.A.R.-V.); (P.M.-G.)
| | - Paulina Munguia-Garza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (M.A.E.-A.); (O.A.R.-V.); (P.M.-G.)
| | - Francisco Garcia-Cardenas
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Mireya Cisneros-Villanueva
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Jose L. Moreno-Camacho
- Clinical Laboratory Division, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (J.L.M.-C.); (J.R.-G.)
| | - Jorge Rodriguez-Gallegos
- Clinical Laboratory Division, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (J.L.M.-C.); (J.R.-G.)
- Molecular Biology Laboratory, National Reference Center, Salud Digna, Tlalnepantla de Baz, Estado de Mexico 54075, Mexico
| | - Marco A. Luna-Ruiz Esparza
- Innovation and Research Department, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (M.A.L.-R.E.); (M.A.F.R.); (A.C.-R.)
| | - Miguel A. Fernández Rojas
- Innovation and Research Department, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (M.A.L.-R.E.); (M.A.F.R.); (A.C.-R.)
| | - Alfredo Mendoza-Vargas
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Juan Pablo Reyes-Grajeda
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, Culiacan, Sinaloa 80000, Mexico; (M.A.L.-R.E.); (M.A.F.R.); (A.C.-R.)
| | - Ofelia Angulo
- Secretaría de Educación, Ciencia, Tecnología e Innovacion, Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Rosaura Ruiz
- Secretaría de Educación, Ciencia, Tecnología e Innovacion, Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Claudia Sheinbaum-Pardo
- Gobierno de la Ciudad de México, Antiguo Palacio del Ayuntamiento, Avenida Plaza de la Constitución 2, Colonia Centro, Mexico City 06010, Mexico;
| | - José Sifuentes-Osornio
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (J.S.-O.); (D.K.)
| | - David Kershenobich
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (J.S.-O.); (D.K.)
| | - Alfredo Hidalgo-Miranda
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
| | - Luis A. Herrera
- Instituto Nacional de Medicina Genómica, INMEGEN, Periferico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (N.A.); (G.d.A.-J.); (F.P.); (B.M.); (F.G.-C.); (M.C.-V.); (A.M.-V.); (J.P.R.-G.)
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico; (M.A.E.-A.); (O.A.R.-V.); (P.M.-G.)
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27
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Lo Muzio L, Ambosino M, Lo Muzio E, Quadri MFA. SARS-CoV-2 Reinfection Is a New Challenge for the Effectiveness of Global Vaccination Campaign: A Systematic Review of Cases Reported in Literature. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:11001. [PMID: 34682746 PMCID: PMC8535385 DOI: 10.3390/ijerph182011001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/03/2021] [Accepted: 10/09/2021] [Indexed: 12/28/2022]
Abstract
Reinfection with SARS-CoV-2 seems to be a rare phenomenon. The objective of this study is to carry out a systematic search of literature on the SARS-CoV-2 reinfection in order to understand the success of the global vaccine campaigns. A systematic search was performed. Inclusion criteria included a positive RT-PCR test of more than 90 days after the initial test and the confirmed recovery or a positive RT-PCR test of more than 45 days after the initial test that is accompanied by compatible symptoms or epidemiological exposure, naturally after the confirmed recovery. Only 117 articles were included in the final review with 260 confirmed cases. The severity of the reinfection episode was more severe in 92/260 (35.3%) with death only in 14 cases. The observation that many reinfection cases were less severe than initial cases is interesting because it may suggest partial protection from disease. Another interesting line of data is the detection of different clades or lineages by genome sequencing between initial infection and reinfection in 52/260 cases (20%). The findings are useful and contribute towards the role of vaccination in response to the COVID-19 infections. Due to the reinfection cases with SARS-CoV-2, it is evident that the level of immunity is not 100% for all individuals. These data highlight how it is necessary to continue to observe all the prescriptions recently indicated in the literature in order to avoid new contagion for all people after healing from COVID-19 or becoming asymptomatic positive.
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Affiliation(s)
- Lorenzo Lo Muzio
- Department of Clinical and Experimental Medicine, University of Foggia, 70122 Foggia, Italy;
- Consorzio Interuniversitario Nazionale per la Bio-Oncologia (C.I.N.B.O.), 66100 Chieti, Italy
| | - Mariateresa Ambosino
- Department of Clinical and Experimental Medicine, University of Foggia, 70122 Foggia, Italy;
| | - Eleonora Lo Muzio
- Department of Translational Medicine and for Romagna, University of Ferrara, 44121 Ferrara, Italy;
| | - Mir Faeq Ali Quadri
- Department of Preventive Dental Sciences, Jazan University, Jazan 82511, Saudi Arabia;
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28
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Wolf JM, Kipper D, Borges GR, Streck AF, Lunge VR. Temporal spread and evolution of SARS-CoV-2 in the second pandemic wave in Brazil. J Med Virol 2021; 94:926-936. [PMID: 34596904 PMCID: PMC8661965 DOI: 10.1002/jmv.27371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil that presented more than 21 million coronavirus disease 2019 cases and 590 000 deaths. The recent emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide. The present study describes the temporal spreading and evolution of SARS‐CoV2 in the beginning of the second pandemic wave in Brazil, highlighting the fast dissemination of the two major concerning variants (P.1 and P.2). A total of 2507 SARS‐CoV‐2 whole‐genome sequences (WGSs) with available information from the country (Brazil) and sampling date (July 2020–February 2021), were obtained and the frequencies of the lineages were evaluated in the period of the growing second pandemic wave. The results demonstrated the increasing prevalence of P.1 and P.2 lineages in the period evaluated. P.2 lineage was first detected in the middle of 2020, but a high increase occurred only in the last trimester of this same year and the spreading to all Brazilian regions. P.1 lineage emerged even later, first in the North region in December 2020 and really fast dissemination to all other Brazilian regions in January and February 2021. All SARS‐CoV‐2 WGSs of P.1 and P.2 were further separately evaluated with a Bayesian approach. The rates of nucleotide and amino acid substitutions were statistically higher in P.1 than P.2 (p < 0.01). The phylodynamic analysis demonstrated that P.2 gradually spread in all the country from September 2020 to January 2021, while P.1 disseminated even faster from December 2020 to February 2021. Skyline plots of both lineages demonstrated a slight rise in the spreading for P.2 and exponential growth for P.1. In conclusion, these data demonstrated that the P.1 (recently renamed as Gamma) and P.2 lineages have predominated in the second pandemic wave due to the very high spreading across all geographic regions in Brazil at the end of 2020 and beginning of 2021. In Brazil, P.1 (Gamma) and P.2 lineages have predominated in the second pandemic wave. The Bayesian approach showed very high spreading for both lineages across all geographic regions at the end of 2020 and the beginning of 2021. P.2 increased only in the last trimester of 2020 and the spreading to all Brazilian regions. P.1 (Gamma) emerged even later with fast dissemination to all Brazilian regions in January and February 2021.
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Affiliation(s)
- Jonas M Wolf
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - Diéssy Kipper
- Laboratório de Diagnóstico em Medicina Veterinária, Universidade de Caxias do Sul, UCS, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Gabriela R Borges
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - André F Streck
- Laboratório de Diagnóstico em Medicina Veterinária, Universidade de Caxias do Sul, UCS, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Vagner R Lunge
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil.,Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
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29
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Yang J, Yan Y, Zhong W. Application of omics technology to combat the COVID-19 pandemic. MedComm (Beijing) 2021; 2:381-401. [PMID: 34766152 PMCID: PMC8554664 DOI: 10.1002/mco2.90] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
As of August 27, 2021, the ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to over 220 countries, areas, and territories. Thus far, 214,468,601 confirmed cases, including 4,470,969 deaths, have been reported to the World Health Organization. To combat the COVID-19 pandemic, multiomics-based strategies, including genomics, transcriptomics, proteomics, and metabolomics, have been used to study the diagnosis methods, pathogenesis, prognosis, and potential drug targets of COVID-19. In order to help researchers and clinicians to keep up with the knowledge of COVID-19, we summarized the most recent progresses reported in omics-based research papers. This review discusses omics-based approaches for studying COVID-19, summarizing newly emerged SARS-CoV-2 variants as well as potential diagnostic methods, risk factors, and pathological features of COVID-19. This review can help researchers and clinicians gain insight into COVID-19 features, providing direction for future drug development and guidance for clinical treatment, so that patients can receive appropriate treatment as soon as possible to reduce the risk of disease progression.
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Affiliation(s)
- Jingjing Yang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
- School of Pharmaceutical SciencesHainan UniversityHaikouHainanChina
| | - Yunzheng Yan
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Wu Zhong
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
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30
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Deng X, Evdokimova M, O’Brien A, Rowe CL, Clark NM, Harrington A, Reid GE, Uprichard SL, Baker SC. Breakthrough Infections with Multiple Lineages of SARS-CoV-2 Variants Reveals Continued Risk of Severe Disease in Immunosuppressed Patients. Viruses 2021; 13:1743. [PMID: 34578324 PMCID: PMC8472867 DOI: 10.3390/v13091743] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 12/13/2022] Open
Abstract
The pandemic of COVID-19 caused by SARS-CoV-2 infection continues to spread around the world. Vaccines that elicit protective immunity have reduced infection and mortality, however new viral variants are arising that may evade vaccine-induced immunity or cause disease in individuals who are unable to develop robust vaccine-induced responses. Investigating the role of viral variants in causing severe disease, evading vaccine-elicited immunity, and infecting vulnerable individuals is important for developing strategies to control the pandemic. Here, we report fourteen breakthrough infections of SARS-CoV-2 in vaccinated individuals with symptoms ranging from asymptomatic/mild (6/14) to severe disease (8/14). High viral loads with a median Ct value of 19.6 were detected in the nasopharyngeal specimens from subjects regardless of disease severity. Sequence analysis revealed four distinct virus lineages, including alpha and gamma variants of concern. Immunosuppressed individuals were more likely to be hospitalized after infection (p = 0.047), however no specific variant was associated with severe disease. Our results highlight the high viral load that can occur in asymptomatic breakthrough infections and the vulnerability of immunosuppressed individuals to post-vaccination infections by diverse variants of SARS-CoV-2.
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Affiliation(s)
- Xufang Deng
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA; (X.D.); (M.E.); (A.O.); (C.L.R.); (S.L.U.)
| | - Monika Evdokimova
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA; (X.D.); (M.E.); (A.O.); (C.L.R.); (S.L.U.)
| | - Amornrat O’Brien
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA; (X.D.); (M.E.); (A.O.); (C.L.R.); (S.L.U.)
| | - Cynthia L. Rowe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA; (X.D.); (M.E.); (A.O.); (C.L.R.); (S.L.U.)
| | - Nina M. Clark
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA; (N.M.C.); (G.E.R.)
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA;
| | - Amanda Harrington
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA;
- Department of Pathology and Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA
| | - Gail E. Reid
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA; (N.M.C.); (G.E.R.)
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA;
| | - Susan L. Uprichard
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA; (X.D.); (M.E.); (A.O.); (C.L.R.); (S.L.U.)
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA; (N.M.C.); (G.E.R.)
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA;
| | - Susan C. Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA; (X.D.); (M.E.); (A.O.); (C.L.R.); (S.L.U.)
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA;
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31
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Fernández J, Bruneau N, Fasce R, Martín HS, Balanda M, Bustos P, Ulloa S, Mora J, Ramírez E. Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. J Med Virol 2021; 94:399-403. [PMID: 34460119 PMCID: PMC8662277 DOI: 10.1002/jmv.27310] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/27/2021] [Indexed: 01/12/2023]
Abstract
Vaccination generates a neutralizing immune response against SARS‐CoV‐2. The genomic surveillance is showing the emergence of variants with mutations in spike, the main target of neutralizing antibodies. To understand the impact of these variants, we report the neutralization potency against alpha, gamma, and D614G SARS‐CoV‐2 variants in 44 individuals that received two doses of CoronaVac vaccine, an inactivated SARS‐CoV‐2 vaccine. Plasma samples collected at 60 days after the second dose of CoronaVac were analyzed by the reduction of cytopathic effect in Vero E6 cells with the three infectious variants of SARS‐CoV‐2. Plasma showed lower neutralization with alpha (geometric mean titer [GMT] = 18.5) and gamma (GMT = 10.0) variants than with D614G (GMT = 75.1) variant. Efficient neutralization against the alpha and gamma variants was not detected in 31.8% and 59.1% of plasma, respectively. These findings suggest the alpha and gamma variants could escape from neutralization by antibodies elicited by vaccination. Robust genomic and biological surveillance of viral variants could help to develop effective strategies for the control of SARS‐CoV‐2.
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Affiliation(s)
- Jorge Fernández
- Subdepartment of Molecular Genetics, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Nicole Bruneau
- Section of Oncogenic Viruses, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Rodrigo Fasce
- Subdepartment of Viral Diseases, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Héctor San Martín
- Section of Oncogenic Viruses, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Monserrat Balanda
- Section of Oncogenic Viruses, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Patricia Bustos
- Section of Respiratory Viruses, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Soledad Ulloa
- Subdepartment of Molecular Genetics, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Judith Mora
- Department of National and Reference Biomedical Laboratory, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Eugenio Ramírez
- Section of Oncogenic Viruses, Instituto de Salud Pública de Chile, Santiago, Chile
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32
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Peghin M, Bouza E, Fabris M, De Martino M, Palese A, Bontempo G, Graziano E, Gerussi V, Bressan V, Sartor A, Isola M, Tascini C, Curcio F. Low risk of reinfections and relation with serological response after recovery from the first wave of COVID-19. Eur J Clin Microbiol Infect Dis 2021; 40:2597-2604. [PMID: 34378086 PMCID: PMC8354681 DOI: 10.1007/s10096-021-04335-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/05/2021] [Indexed: 12/17/2022]
Abstract
The aim of the study was to assess reinfection rates in relation to long-term antibody dynamics against SARS-CoV-2 after the first wave. A prospective longitudinal study with monthly serological follow-up during the first 4 months, and then at 6, 8, and 10 months after the disease onset of all recovered adult in- and outpatients with COVID-19 attending Udine Hospital (Italy) from March to May 2020. During the follow-up, reinfections were collected. A total of 546 unselected individuals with COVID-19 acquired from March to May 2020 were included (292 female, mean age 53 years). After a median follow-up of 10 months (IQR 6.2–10.4), reinfection occurred in 6 (1.1%) patients, median age of 44.5 years (IQR 33‒49). All had a previous history of mild COVID-19 (all were healthcare workers) and reinfection occurred a median of 9 months (IQR 8.2‒10.2) after the onset of the first episode. Patients with reinfection were either seronegative (2/56, n = 3.6%), seroreverted (2/137, 1.5%), or seropositive (2/353, 0.6%) (p = 0.085). All reinfections were mild (n = 5) or asymptomatic (n = 1). After reinfection, none of patients developed IgM response and only two had a transitory boosted IgG immunization response. In an unselected population after the first wave of COVID-19, after a prolonged observation period (mean 10 months), reinfection was very uncommon; occurred in patients with a previous history of mild infection, mostly with weak or absent serological response; and manifested with mild or asymptomatic clinical presentation.
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Affiliation(s)
- Maddalena Peghin
- Infectious Diseases Division, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Presidio Ospedaliero Universitario Santa Maria della Misericordia Piazzale Santa Maria della Misericordia 15 33010, Udine, Italy.
| | - Emilio Bouza
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
- Gregorio Marañón Health Research Institute, Madrid, Spain
- CIBER of Respiratory Diseases (CIBERES CB06/06/0058), Madrid, Spain
| | - Martina Fabris
- Institute of Clinical Pathology, Department of Laboratory Medicine, University of Udine, ASUFC, Udine, Italy
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Maria De Martino
- Division of Medical Statistics, Department of Medicine (DAME), University of Udine 33100, Udine, Italy
| | - Alvisa Palese
- Department of Medical Sciences, School of Nursing, University of Udine 33100, Udine, Italy
| | - Giulia Bontempo
- Infectious Diseases Division, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Presidio Ospedaliero Universitario Santa Maria della Misericordia Piazzale Santa Maria della Misericordia 15 33010, Udine, Italy
| | - Elena Graziano
- Infectious Diseases Division, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Presidio Ospedaliero Universitario Santa Maria della Misericordia Piazzale Santa Maria della Misericordia 15 33010, Udine, Italy
| | - Valentina Gerussi
- Infectious Diseases Division, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Presidio Ospedaliero Universitario Santa Maria della Misericordia Piazzale Santa Maria della Misericordia 15 33010, Udine, Italy
| | - Valentina Bressan
- Department of Medical Sciences, School of Nursing, University of Udine 33100, Udine, Italy
| | - Assunta Sartor
- Institute of Clinical Pathology, Department of Laboratory Medicine, University of Udine, ASUFC, Udine, Italy
| | - Miriam Isola
- Division of Medical Statistics, Department of Medicine (DAME), University of Udine 33100, Udine, Italy
| | - Carlo Tascini
- Infectious Diseases Division, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Presidio Ospedaliero Universitario Santa Maria della Misericordia Piazzale Santa Maria della Misericordia 15 33010, Udine, Italy
| | - Francesco Curcio
- Institute of Clinical Pathology, Department of Laboratory Medicine, University of Udine, ASUFC, Udine, Italy
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33
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Massachi J, Donohue KC, Kelly JD. Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection Cases Corroborated by Sequencing. Am J Trop Med Hyg 2021; 105:884-889. [PMID: 34370705 PMCID: PMC8592142 DOI: 10.4269/ajtmh.21-0365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
Evaluating cases of reinfection may offer some insight into areas for further investigation regarding durability of immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sixty cases of reinfection with viral sequencing were identified in PubMed, Embase, Web of Science, and medRxiv before May 1, 2021.Episodes of infection were separated by a median of 116 days. Severity of illness was greater among individuals reinfected within 90 days of initial infection, no asymptomatic initial cases developed severe reinfection, nearly half of cases had suspected escape variants, and nearly all individuals tested following reinfection were found to have detectable levels of anti-SARS-CoV-2 antibodies. This analysis is limited by the heterogeneous methods used among reports. Reinfection continues to be relatively rare. As the case rate presumably increases over time, this review will inform measurements to determine the natural history and causal determinants of reinfection in more rigorous observational cohort studies and other standardized surveillance approaches.
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Affiliation(s)
- Jonathan Massachi
- School of Medicine, University of California, San Francisco, California
| | | | - John Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
- Institute of Global Health Sciences, University of California, San Francisco, California
- F. I. Proctor Foundation, University of California, San Francisco, California
- San Francisco VA Medical Center, San Francisco, California
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34
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Escandón K, Rasmussen AL, Bogoch II, Murray EJ, Escandón K, Popescu SV, Kindrachuk J. COVID-19 false dichotomies and a comprehensive review of the evidence regarding public health, COVID-19 symptomatology, SARS-CoV-2 transmission, mask wearing, and reinfection. BMC Infect Dis 2021; 21:710. [PMID: 34315427 PMCID: PMC8314268 DOI: 10.1186/s12879-021-06357-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Scientists across disciplines, policymakers, and journalists have voiced frustration at the unprecedented polarization and misinformation around coronavirus disease 2019 (COVID-19) pandemic. Several false dichotomies have been used to polarize debates while oversimplifying complex issues. In this comprehensive narrative review, we deconstruct six common COVID-19 false dichotomies, address the evidence on these topics, identify insights relevant to effective pandemic responses, and highlight knowledge gaps and uncertainties. The topics of this review are: 1) Health and lives vs. economy and livelihoods, 2) Indefinite lockdown vs. unlimited reopening, 3) Symptomatic vs. asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, 4) Droplet vs. aerosol transmission of SARS-CoV-2, 5) Masks for all vs. no masking, and 6) SARS-CoV-2 reinfection vs. no reinfection. We discuss the importance of multidisciplinary integration (health, social, and physical sciences), multilayered approaches to reducing risk ("Emmentaler cheese model"), harm reduction, smart masking, relaxation of interventions, and context-sensitive policymaking for COVID-19 response plans. We also address the challenges in understanding the broad clinical presentation of COVID-19, SARS-CoV-2 transmission, and SARS-CoV-2 reinfection. These key issues of science and public health policy have been presented as false dichotomies during the pandemic. However, they are hardly binary, simple, or uniform, and therefore should not be framed as polar extremes. We urge a nuanced understanding of the science and caution against black-or-white messaging, all-or-nothing guidance, and one-size-fits-all approaches. There is a need for meaningful public health communication and science-informed policies that recognize shades of gray, uncertainties, local context, and social determinants of health.
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Affiliation(s)
- Kevin Escandón
- School of Medicine, Universidad del Valle, Cali, Colombia.
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Georgetown Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
| | - Isaac I Bogoch
- Division of Infectious Diseases, University of Toronto, Toronto General Hospital, Toronto, Canada
| | - Eleanor J Murray
- Department of Epidemiology, Boston University School of Public Health, Boston, USA
| | - Karina Escandón
- Department of Anthropology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Saskia V Popescu
- Georgetown Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
- Schar School of Policy and Government, George Mason University, Fairfax, VA, USA
| | - Jason Kindrachuk
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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35
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Yu ALF, Liphaus BL, Ferreira PM, Tanamachi AT, Masuda ET, Trevisan CM, Lucas PCDC, Bugno A, Carvalhanas TRMP. SARS-CoV-2 reinfection: report of two cases in Southeast Brazil. Rev Inst Med Trop Sao Paulo 2021; 63:e50. [PMID: 34161556 PMCID: PMC8216690 DOI: 10.1590/s1678-9946202163050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/25/2021] [Indexed: 11/21/2022] Open
Abstract
From February 26, 2020 to March 11, 2021, coronavirus disease 2019 (COVID-19) pandemic resulted in 11,439,558 cases and 277,102 deaths in Brazil. Among them, 2,195,130 cases and 63,965 deaths occurred in Sao Paulo State, Southeast Brazil. The recent emergence and rise of new variants of SARS-CoV-2 is of concern because of their higher transmissibility and possible association with more severe disease. Cases of SARS-CoV-2 reinfections have been described since December 2020 in Brazil. This report describes two cases of COVID-19 reinfection, that occurred five and six months after the first infection, during the second wave of the pandemic in Sao Paulo State. Both patients presented mild symptoms in the two COVID-19 episodes and different lineages of SARS-CoV-2 were identified: B.1.1.33 and B.1.1.28 lineages in case 1 and B1.1.128 and P. 2 lineages in case 2.
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Affiliation(s)
- Ana Lucia Frugis Yu
- Secretaria de Estado da Saúde de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac", Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Bernadete L Liphaus
- Secretaria de Estado da Saúde de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac", Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Patrícia Marques Ferreira
- Secretaria de Estado da Saúde de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac", Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Angela Tiemi Tanamachi
- Secretaria de Estado da Saúde de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac", Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Eliana Tiemi Masuda
- Secretaria de Estado da Saúde de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac", Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Camila Martins Trevisan
- Secretaria de Estado da Saúde de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac", Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Pamella Cristina de Carvalho Lucas
- Secretaria de Estado da Saúde de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac", Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Adriana Bugno
- Secretaria de Estado da Saúde de São Paulo, Coordenadoria de Controle de Doenças, Instituto Adolfo Lutz, São Paulo, São Paulo, Brazil
| | - Telma Regina Marques Pinto Carvalhanas
- Secretaria de Estado da Saúde de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac", Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
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36
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Inagaki H, Saito A, Kaneko C, Sugiyama H, Okabayashi T, Fujimoto S. Rapid Inactivation of SARS-CoV-2 Variants by Continuous and Intermittent Irradiation with a Deep-Ultraviolet Light-Emitting Diode (DUV-LED) Device. Pathogens 2021; 10:754. [PMID: 34203643 PMCID: PMC8232135 DOI: 10.3390/pathogens10060754] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/16/2022] Open
Abstract
More than 1 year has passed since social activities have been restricted due to the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More recently, novel SARS-CoV-2 variants have been spreading around the world, and there is growing concern that they may have higher transmissibility and that the protective efficacy of vaccines may be weaker against them. Immediate measures are needed to reduce human exposure to the virus. In this study, the antiviral efficacy of deep-ultraviolet light-emitting diode (DUV-LED) irradiation (280 ± 5 nm, 3.75 mW/cm2) against three SARS-CoV-2 variants was evaluated. For the B.1.1.7, B.1.351, and P.1 variant strains, irradiation of the virus stocks for 1 s resulted in infectious titer reduction rates of 96.3%, 94.6%, and 91.9%, respectively, and with irradiation for 5 s, the rates increased to 99.9%, 99.9%, and 99.8%, respectively. We also tested the effect of pulsed DUV-LED irradiation (7.5 mW/cm2, duty rate: 50%, frequency: 1 kHz) under the same output conditions as for continuous irradiation and found that the antiviral efficacy of pulsed and continuous irradiation was the same. These findings suggest that by further developing and optimizing the DUV-LED device to increase its output, it may be possible to instantly inactivate SARS-CoV-2 with DUV-LED irradiation.
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Affiliation(s)
- Hiroko Inagaki
- M&N Collaboration Research Laboratory, Department of Medical Environment Innovation, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan; (H.I.); (H.S.)
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan; (A.S.); (T.O.)
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-2192, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki 889-2192, Japan;
| | - Chiho Kaneko
- Center for Animal Disease Control, University of Miyazaki, Miyazaki 889-2192, Japan;
| | - Hironobu Sugiyama
- M&N Collaboration Research Laboratory, Department of Medical Environment Innovation, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan; (H.I.); (H.S.)
- Nikkiso Co., Ltd., Tokyo 150-6022, Japan
| | - Tamaki Okabayashi
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan; (A.S.); (T.O.)
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-2192, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki 889-2192, Japan;
| | - Shouichi Fujimoto
- Department of Hemovascular Medicine and Artificial Organs, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
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