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Wu J, Yang H, Yu D, Yang X. Blood-derived product therapies for SARS-CoV-2 infection and long COVID. MedComm (Beijing) 2023; 4:e426. [PMID: 38020714 PMCID: PMC10651828 DOI: 10.1002/mco2.426] [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: 06/28/2023] [Revised: 10/15/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is capable of large-scale transmission and has caused the coronavirus disease 2019 (COVID-19) pandemic. Patients with COVID-19 may experience persistent long-term health issues, known as long COVID. Both acute SARS-CoV-2 infection and long COVID have resulted in persistent negative impacts on global public health. The effective application and development of blood-derived products are important strategies to combat the serious damage caused by COVID-19. Since the emergence of COVID-19, various blood-derived products that target or do not target SARS-CoV-2 have been investigated for therapeutic applications. SARS-CoV-2-targeting blood-derived products, including COVID-19 convalescent plasma, COVID-19 hyperimmune globulin, and recombinant anti-SARS-CoV-2 neutralizing immunoglobulin G, are virus-targeting and can provide immediate control of viral infection in the short term. Non-SARS-CoV-2-targeting blood-derived products, including intravenous immunoglobulin and human serum albumin exhibit anti-inflammatory, immunomodulatory, antioxidant, and anticoagulatory properties. Rational use of these products can be beneficial to patients with SARS-CoV-2 infection or long COVID. With evidence accumulated since the pandemic began, we here summarize the progress of blood-derived product therapies for COVID-19, discuss the effective methods and scenarios regarding these therapies, and provide guidance and suggestions for clinical treatment.
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Affiliation(s)
- Junzheng Wu
- Chengdu Rongsheng Pharmaceuticals Co., Ltd.ChengduChina
| | | | - Ding Yu
- Chengdu Rongsheng Pharmaceuticals Co., Ltd.ChengduChina
- Beijing Tiantan Biological Products Co., Ltd.BeijingChina
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Nabaes Jodar MS, Torres C, Mojsiejczuk L, Acuña D, Valinotto LE, Goya S, Natale M, Lusso S, Alexay S, Amadio A, Irazoqui M, Fernandez F, Acevedo ME, Alvarez Lopez C, Angelletti A, Aulicino P, Bolatti E, Brusés B, Cacciahue M, Cavatorta A, Cerri A, Cordero A, Debat H, Dus Santos MJ, Eberhardt MF, Ercole R, Espul C, Farber M, Fay F, Fernandez A, Ferrini F, Formichelli L, Ceballos S, Gallego F, Giri A, Gismondi M, Acevedo RM, Gramundi I, Ibañez ME, Konig G, Leiva V, Lorenzini Campos M, Lucero H, Marquez N, Mazzeo M, Mistchenko AS, Montoto L, Muñoz M, Nadalich V, Nardi C, Ortiz B, Pianciola L, Pintos C, Puebla A, Rastellini C, Rojas AE, Sfalcin J, Suarez A, Theaux C, Thomas G, Tittarelli E, Toro R, Villanova V, Wenk G, Ziehm C, Zimmermann MC, Zunino S, Pais P, Viegas M. The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37. Viruses 2023; 15:1382. [PMID: 37376681 DOI: 10.3390/v15061382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial--temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern.
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Affiliation(s)
- Mercedes Soledad Nabaes Jodar
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
| | - Carolina Torres
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Investigaciones En Bacteriologia y Virologia Molecular (IbaViM), Junín 956, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Laura Mojsiejczuk
- Instituto de Investigaciones En Bacteriologia y Virologia Molecular (IbaViM), Junín 956, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Dolores Acuña
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
| | - Laura Elena Valinotto
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
| | - Stephanie Goya
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Monica Natale
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Silvina Lusso
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Sofia Alexay
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Ariel Amadio
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Investigación de La Cadena Lactea (IDICAL) INTA-CONICET, Ruta 34 Km 227, Rafaela 2300, Argentina
| | - Matias Irazoqui
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Investigación de La Cadena Lactea (IDICAL) INTA-CONICET, Ruta 34 Km 227, Rafaela 2300, Argentina
| | - Franco Fernandez
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, Córdoba 5020, Argentina
| | - Maria Elina Acevedo
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Cristina Alvarez Lopez
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Andres Angelletti
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
| | - Paula Aulicino
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría Prof. Juan P. Garrahan, Avenida Brasil 1175, Ciudad Autónoma de Buenos Aires 1260, Argentina
| | - Elisa Bolatti
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina
| | - Bettina Brusés
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Av. Las Heras 727, Resistencia 3500, Argentina
| | - Marco Cacciahue
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Ana Cavatorta
- Centro de Tecnología En Salud Pública, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario 2000, Argentina
| | - Agustina Cerri
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina
| | - Andres Cordero
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
| | - Humberto Debat
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, Córdoba 5020, Argentina
| | - Maria Jose Dus Santos
- Instituto de Virología e Innovaciones Tecnológicas (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
- Laboratorio de Diagnostico-UNIDAD COVID, Universidad Nacional de Hurlingham, Hurlingham 1686, Argentina
| | - Maria Florencia Eberhardt
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Investigación de La Cadena Lactea (IDICAL) INTA-CONICET, Ruta 34 Km 227, Rafaela 2300, Argentina
| | - Regina Ercole
- Laboratorio de Virología, HIEAyC San Juan de Dios, Calles 27 y 70, La Plata 1900, Argentina
| | - Carlos Espul
- Dirección de Epidemiologia y Red de Laboratorios Del Ministerio de Salud de La Provincia de Mendoza, Mendoza 5500, Argentina
| | - Marisa Farber
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Fabián Fay
- CIBIC Laboratorio, Pte. Roca 746, Rosario 2000, Argentina
| | - Ailen Fernandez
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Florencia Ferrini
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Laboratorio de Medicina Genómica, Facultad de Medicina, Universidad Nacional Del Nordeste, Córdoba 1430, Argentina
| | - Laura Formichelli
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Av. Las Heras 727, Resistencia 3500, Argentina
| | - Santiago Ceballos
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Cadic-Conicet, Universidad Nacional de Tierra del Fuego, Houssay 200, Ushuaia 9410, Argentina
| | - Fernando Gallego
- Hospital Regional Ushuaia, Av. 12 de Octubre y Maipú, Ushuaia 9410, Argentina
| | - Adriana Giri
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina
| | - Maria Gismondi
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Raul Maximiliano Acevedo
- Instituto de Botánica Del Nordeste-UNNE, Sargento Juan Bautista Cabral 2131, Corrientes 3400, Argentina
| | - Ivan Gramundi
- Hospital Regional Ushuaia, Av. 12 de Octubre y Maipú, Ushuaia 9410, Argentina
| | - María Eugenia Ibañez
- Biología Molecular-Laboratorio Central, Hospital Alemán, Av. Pueyrredón 1640, Cuidad Autónoma de Buenos Aires 1118, Argentina
| | - Guido Konig
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Viviana Leiva
- Laboratorio de Salud Pública, Talcahuano 2194, Godoy Cruz 5501, Argentina
| | - Melina Lorenzini Campos
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Av. Las Heras 727, Resistencia 3500, Argentina
| | - Horacio Lucero
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Av. Las Heras 727, Resistencia 3500, Argentina
| | - Nathalie Marquez
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, Córdoba 5020, Argentina
| | - Melina Mazzeo
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Alicia Susana Mistchenko
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
- Comisión Investigaciones Científicas de La Provincia de Buenos Aires, Camino General Belgrano y 526, La Plata 1900, Argentina
| | - Luciana Montoto
- Laboratorio de Biología Molecular Hospital Pedro de Elizalde, Avenida Manuel A Montes de Oca 1402, Cuidad Autónoma de Buenos Aires 1270, Argentina
| | - Marianne Muñoz
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Victoria Nadalich
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
| | - Cristina Nardi
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA) de La Universidad Nacional de Tierra Del Fuego (UNTDF), Houssay 200, Ushuaia 9410, Argentina
| | - Belén Ortiz
- Laboratorio de Salud Pública, Talcahuano 2194, Godoy Cruz 5501, Argentina
| | - Luis Pianciola
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Carolina Pintos
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Andrea Puebla
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Carolina Rastellini
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Alejandro Ezequiel Rojas
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA) de La Universidad Nacional de Tierra Del Fuego (UNTDF), Houssay 200, Ushuaia 9410, Argentina
| | - Javier Sfalcin
- CIBIC Laboratorio, Pte. Roca 746, Rosario 2000, Argentina
| | - Ariel Suarez
- Departamento de Biología y Genética Molecular, IACA Laboratorios, San Martín 68, Bahía Blanca 8000, Argentina
| | - Clara Theaux
- Laboratorio de Biología Molecular Del Hospital General de Agudos, Carlos G. Durand, Diaz Vélez 5044, Cuidad Autónoma de Buenos Aires 1405, Argentina
| | - Guillermo Thomas
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Estefania Tittarelli
- Departamento de Biología y Genética Molecular, IACA Laboratorios, San Martín 68, Bahía Blanca 8000, Argentina
| | - Rosana Toro
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
| | - Vanina Villanova
- Laboratorio Mixto de Biotecnología Acuática, Av. Eduardo Carrasco y Cordiviola, Rosario 2000, Argentina
| | - Gretel Wenk
- Laboratorio de Biología Molecular Hospital Pedro de Elizalde, Avenida Manuel A Montes de Oca 1402, Cuidad Autónoma de Buenos Aires 1270, Argentina
| | - Cecilia Ziehm
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Maria Carla Zimmermann
- Laboratorio de Medicina Genómica, Facultad de Medicina, Universidad Nacional Del Nordeste, Córdoba 1430, Argentina
| | - Sebastian Zunino
- Laboratorio de Virología Molecular, Hospital Blas L. Dubarry, Calle 12 825, Mercedes 6600, Argentina
| | - Proyecto Pais
- Consorcio Argentino de Genómica de SARS-CoV-2, Proyecto Argentino Interinstitucional de Genómica de SARS-CoV-2, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Mariana Viegas
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
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LaRotta J, Escobar O, Ávila-Aguero ML, Torres JP, Sini de Almeida R, Morales GDC, Srivastava A. COVID-19 in Latin America: A Snapshot in Time and the Road Ahead. Infect Dis Ther 2023; 12:389-410. [PMID: 36633818 PMCID: PMC9835740 DOI: 10.1007/s40121-022-00748-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023] Open
Abstract
Since its initial detection in Brazil in February 2020, SARS-CoV-2 and the associated COVID-19 pandemic have continued to devastate Latin America. Specific comorbidities, as well as sociodemographic and lifestyle factors that may be more prevalent in underserved areas, have been identified as risk factors for COVID-19 infection or associated adverse outcomes. Dynamics of infections and deaths in Latin America have varied by country and temporally, as has SARS-CoV-2 variant prevalence; however, more recently, the Delta and subsequent Omicron variants have become ubiquitous. Successful pandemic responses have involved robust infection mitigation measures, testing, and smart deployment of healthcare resourcing. While in some Latin American countries up to 90% of the population is fully vaccinated (i.e., 2 doses) against COVID-19, other countries have failed to reach the World Health Organization's 70% target. Continued focus on comprehensive surveillance, strategies to maximize vaccine availability and uptake, and mitigation of collateral damage on other aspects of public health and social services are critical for managing the COVID-19 pandemic. This review summarizes the COVID-19 experience in Latin America, including epidemiology and vaccination. Key learnings and future considerations for the ongoing pandemic response are also discussed.
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Affiliation(s)
- Jorge LaRotta
- Vaccines Medical and Scientific Affairs, Pfizer SAS, AV Suba 95-66, Bogotá, Colombia.
| | - Omar Escobar
- Vaccines Medical and Scientific Affairs, Pfizer SAS, AV Suba 95-66, Bogotá, Colombia
| | - María L Ávila-Aguero
- Pediatric Infectious Diseases, Hospital Nacional de Niños, San José, Costa Rica
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, CT, USA
| | - Juan Pablo Torres
- Departamento de Pediatría y Cirugía Infantil Oriente, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | | | - Amit Srivastava
- Vaccines, Medical Development, Scientific and Clinical Affairs, Pfizer Inc, Cambridge, MA, USA
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Omicron Waves in Argentina: Dynamics of SARS-CoV-2 Lineages BA.1, BA.2 and the Emerging BA.2.12.1 and BA.4/BA.5. Viruses 2023; 15:v15020312. [PMID: 36851525 PMCID: PMC9965068 DOI: 10.3390/v15020312] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.
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Zambrana Montaño R, Culasso ACA, Fernández F, Marquez N, Debat H, Salmerón M, Zamora AM, Ruíz de Huidobro G, Costas D, Alabarse G, Charre MA, Fridman AD, Mamani C, Vaca F, Maza Diaz C, Raskovsky V, Lavaque E, Lesser V, Cajal P, Agüero F, Calvente C, Torres C, Viegas M. Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina. Virus Res 2023; 323:198936. [PMID: 36181975 PMCID: PMC9599208 DOI: 10.1016/j.virusres.2022.198936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/10/2022] [Accepted: 09/24/2022] [Indexed: 01/25/2023]
Abstract
Studies about the evolution of SARS-CoV-2 lineages in different backgrounds such as naive populations are still scarce, especially from South America. This work aimed to study the introduction and diversification pattern of SARS-CoV-2 during the first year of the COVID-19 pandemic in the Northwestern Argentina (NWA) region and to analyze the evolutionary dynamics of the main lineages found. In this study, we analyzed a total of 260 SARS-CoV-2 whole-genome sequences from Argentina, belonging to the Provinces of Jujuy, Salta, and Tucumán, from March 31st, 2020, to May 22nd, 2021, which covered the full first wave and the early second wave of the COVID-19 pandemic in Argentina. In the first wave, eight lineages were identified: B.1.499 (76.9%), followed by N.5 (10.2%), B.1.1.274 (3.7%), B.1.1.348 (3.7%), B.1 (2.8%), B.1.600 (0.9%), B.1.1.33 (0.9%) and N.3 (0.9%). During the early second wave, the first-wave lineages were displaced by the introduction of variants of concern (VOC) (Alpha, Gamma), or variants of interest (VOI) (Lambda, Zeta, Epsilon) and other lineages with more limited distribution. Phylodynamic analyses of the B.1.499 and N.5, the two most prevalent lineages in the NWA, revealed that the rate of evolution of lineage N.5 (7.9 × 10-4 substitutions per site per year, s/s/y) was a ∼40% faster than that of lineage B.1.499 (5.6 × 10-4 s/s/y), although both are in the same order of magnitude than other non-VOC lineages. No mutations associated with a biological characteristic of importance were observed as signatures markers of the phylogenetic groups established in Northwestern Argentina, however, single sequences in non-VOC lineages did present mutations of biological importance or associated with VOCs as sporadic events, showing that many of these mutations could emerge from circulation in the general population. This study contributed to the knowledge about the evolution of SARS-CoV-2 in a pre-vaccination and without post-exposure immunization period.
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Affiliation(s)
- Romina Zambrana Montaño
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrés Carlos Alberto Culasso
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Franco Fernández
- Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Nathalie Marquez
- Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Mariana Salmerón
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | - Ana María Zamora
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | | | - Dardo Costas
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | - Graciela Alabarse
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | | | - Ariel David Fridman
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Claudia Mamani
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Fabiana Vaca
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Claudia Maza Diaz
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Viviana Raskovsky
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Esteban Lavaque
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Veronica Lesser
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Pamela Cajal
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Fernanda Agüero
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Cintia Calvente
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Carolina Torres
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Mariana Viegas
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Gallo 1330, 2do piso, C1425EFD, Argentina.
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Alves HJ, de Araújo JLF, Fonseca PLC, Moreira FRR, Bonfim DM, Queiroz DC, Miguita L, de Souza RM, Geddes VEV, Costa WC, de Oliveira JS, Medeiros ELA, de Souza CSA, Saliba JW, Menezes AL, de Oliveira ES, Adelino TER, Guimaraes NR, Ribeiro AA, Moreira RG, Zauli DAG, Silva JDP, Malta FSV, Ferreira ACDS, Silva AVFG, Alfenas-Zerbini P, de Souza FO, Sabino ADP, Xavier LDA, Carobin NV, de Carvalho AF, Lourenço KL, Teixeira SMR, Fernandes APSM, da Fonseca FG, Abrahão JS, Iani FCDM, Rodrigues RAL, de Souza RP, Aguiar RS. Monitoring the Establishment of VOC Gamma in Minas Gerais, Brazil: A Retrospective Epidemiological and Genomic Surveillance Study. Viruses 2022; 14:v14122747. [PMID: 36560750 PMCID: PMC9781153 DOI: 10.3390/v14122747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Since its first identification in Brazil, the variant of concern (VOC) Gamma has been associated with increased infection and transmission rates, hospitalizations, and deaths. Minas Gerais (MG), the second-largest populated Brazilian state with more than 20 million inhabitants, observed a peak of cases and deaths in March-April 2021. We conducted a surveillance study in 1240 COVID-19-positive samples from 305 municipalities distributed across MG's 28 Regional Health Units (RHU) between 1 March to 27 April 2021. The most common variant was the VOC Gamma (71.2%), followed by the variant of interest (VOI) zeta (12.4%) and VOC alpha (9.6%). Although the predominance of Gamma was found in most of the RHUs, clusters of Zeta and Alpha variants were observed. One Alpha-clustered RHU has a history of high human mobility from countries with Alpha predominance. Other less frequent lineages, such as P.4, P.5, and P.7, were also identified. With our genomic characterization approach, we estimated the introduction of Gamma on 7 January 2021, at RHU Belo Horizonte. Differences in mortality between the Zeta, Gamma and Alpha variants were not observed. We reinforce the importance of vaccination programs to prevent severe cases and deaths during transmission peaks.
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Affiliation(s)
- Hugo José Alves
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - João Locke Ferreira de Araújo
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Paula Luize Camargos Fonseca
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Diego Menezes Bonfim
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Daniel Costa Queiroz
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Lucyene Miguita
- Departamento de Patologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Rafael Marques de Souza
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Victor Emmanuel Viana Geddes
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Walyson Coelho Costa
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Jaqueline Silva de Oliveira
- Subsecretaria de Vigilância em Saúde, Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte 31585-200, Brazil
| | - Eva Lídia Arcoverde Medeiros
- Subsecretaria de Vigilância em Saúde, Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte 31585-200, Brazil
| | | | | | - André Luiz Menezes
- Secretaria Municipal de Saúde, Prefeitura de Belo Horizonte, Belo Horizonte 30130-040, Brazil
| | | | | | | | | | - Rennan Garcias Moreira
- Centro de Laboratórios Multiusuários, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | | | | | - Alessandro Clayton de Souza Ferreira
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Poliane Alfenas-Zerbini
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Flavia Oliveira de Souza
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Adriano de Paula Sabino
- Laboratório de Institucional de Pesquisa em Biomarcadores, LINBIO, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Laura do Amaral Xavier
- Laboratório de Institucional de Pesquisa em Biomarcadores, LINBIO, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Natália Virtude Carobin
- Laboratório de Institucional de Pesquisa em Biomarcadores, LINBIO, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Alex Fiorini de Carvalho
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil
| | - Karine Lima Lourenço
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte 31310-260, Brazil
| | | | | | | | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31279-901, Brazil
| | | | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31279-901, Brazil
| | - Renan Pedra de Souza
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Correspondence: (R.P.d.S.); (R.S.A.)
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro 22281-100, Brazil
- Correspondence: (R.P.d.S.); (R.S.A.)
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7
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Castro GM, Sicilia P, Bolzon ML, Lopez L, Barbás MG, Pisano MB, Ré VE. Tracking SARS-CoV-2 Variants Using a Rapid Typification Strategy: A Key Tool for Early Detection and Spread Investigation of Omicron in Argentina. Front Med (Lausanne) 2022; 9:851861. [PMID: 35665324 PMCID: PMC9157384 DOI: 10.3389/fmed.2022.851861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 variants of concern (VOC) and interest (VOI) present mutations in reference to the original virus, being more transmissible. We implemented a rapid strategy for the screening of SARS-CoV-2 VOC/VOIs using real time RT-PCR and performed monitoring and surveillance of the variants in our region. Consecutive real-time RT-PCRs for detection of the relevant mutations/deletions present in the Spike protein in VOC/VOIs (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems) were implemented. A total of 6,640 SARS-CoV-2 RNA samples (Cts < 30) from infected individuals in Central Argentina during 2021 were analyzed using different algorithms that were gradually adapted to the changing scenarios of local variant circulation. The strategy developed allowed the early detection and the identification of VOC/VOIs that circulated through the year, with a 100% of concordance with the WGS. The analyses of the samples showed introductions of VOCs Alpha and Gamma in February and March 2021, respectively. Gamma showed an exponential increase, with a peak of detection in July (72%), being responsible of the second wave of COVID19 in Argentina. Since VOC Delta entered into the region, it increased gradually, together with VOI Lambda, replacing VOC Gamma, until being the main variant (84.9%) on November. By December, these variants were replaced by the emergent VOC Omicron in a term of 2 weeks, producing the third wave. We report a useful tool for VOC/VOI detection, capable to quickly and cost-effectively monitor currently recognized variants in resource-limited settings, which allowed to track the recent expansion of Omicron in our region, and contributed to the implementation of public health measures to control the disease spread.
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Affiliation(s)
- Gonzalo M Castro
- Laboratorio Central de la Provincia de Córdoba, Ministerio de Salud, Gobierno de la Provincia de Córdoba, Córdoba, Argentina
| | - Paola Sicilia
- Laboratorio Central de la Provincia de Córdoba, Ministerio de Salud, Gobierno de la Provincia de Córdoba, Córdoba, Argentina
| | - María Laura Bolzon
- Laboratorio Central de la Provincia de Córdoba, Ministerio de Salud, Gobierno de la Provincia de Córdoba, Córdoba, Argentina
| | - Laura Lopez
- Área de Epidemiología, Ministerio de Salud, Gobierno de la Provincia de Córdoba, Córdoba, Argentina
| | - María Gabriela Barbás
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud, Gobierno de la Provincia de Córdoba, Córdoba, Argentina
| | - María Belén Pisano
- Instituto de Virología "Dr. J. M. Vanella", CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Viviana E Ré
- Instituto de Virología "Dr. J. M. Vanella", CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
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Fiori M, Bello G, Wschebor N, Lecumberry F, Ferragut A, Mordecki E. Decoupling between SARS-CoV-2 transmissibility and population mobility associated with increasing immunity from vaccination and infection in South America. Sci Rep 2022; 12:6874. [PMID: 35478213 PMCID: PMC9044384 DOI: 10.1038/s41598-022-10896-4] [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: 09/29/2021] [Accepted: 04/14/2022] [Indexed: 12/12/2022] Open
Abstract
All South American countries from the Southern cone (Argentina, Brazil, Chile, Paraguay and Uruguay) experienced severe COVID-19 epidemic waves during early 2021 driven by the expansion of variants Gamma and Lambda, however, there was an improvement in different epidemic indicators since June 2021. To investigate the impact of national vaccination programs and natural infection on viral transmission in those South American countries, we analyzed the coupling between population mobility and the viral effective reproduction number [Formula: see text]. Our analyses reveal that population mobility was highly correlated with viral [Formula: see text] from January to May 2021 in all countries analyzed; but a clear decoupling occurred since May-June 2021, when the rate of viral spread started to be lower than expected from the levels of social interactions. These findings support that populations from the South American Southern cone probably achieved the conditional herd immunity threshold to contain the spread of regional SARS-CoV-2 variants circulating at that time.
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Affiliation(s)
- Marcelo Fiori
- Instituto de Matemática y Estadística "Rafael Laguardia", Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay.
| | - Gonzalo Bello
- Laboratorio de AIDS e Imunologia Molecular. Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Nicolás Wschebor
- Instituto de Física, Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay
| | - Federico Lecumberry
- Instituto de Ingeniería Eléctrica, Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay
| | - Andrés Ferragut
- Facultad de Ingeniería, Universidad ORT, Montevideo, Uruguay
| | - Ernesto Mordecki
- Centro de Matemática, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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