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Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina

2021; Frontiers Media; Volume: 8; Linguagem: Inglês

10.3389/fmed.2021.755463

2296-858X

Carolina Torres, Laura Mojsiejczuk, Dolores Acuña, Sofía Alexay, Ariel Amadío, Paula Aulicino, Humberto Debat, Fabián Fay, Franco Daniel Fernández, Adriana A. Giri, Stephanie Goya, G König, Horacio Lucero, Mercedes Nabaes Jodar, Luis Pianciola, Javier Sfalcin, Raúl M. Acevedo, Sofía Bengoa Luoni, Elisa M. Bolatti, Bettina Brusés, Marco Cacciabue, Pablo E. Casal, Agustina Cerri, Diego Chouhy, María José Dus Santos, María Florencia Eberhardt, A. Fernández, Paula Fernández, Darío Fernández Do Porto, Laura Formichelli, María Inés Gismondi, José Matías Irazoqui, Melina Lorenzini Campos, Silvina Lusso, Nathalie Marquez, Marianne Muñoz, Javier Mussin, Mónica Natale, Griselda Inés Oria, María Belén Pisano, Victoria Posner, Andrea Puebla, Viviana Ré, Ezequiel Sosa, Gabriela Vanina Villanova, Jonathan Zaiat, Sebastián Zunino, María Elina Acevedo, Julián Acosta, Cristina Álvarez López, María Laura Vergara Álvarez, Patricia Angeleri, Andrés Angelletti, Manuel Arca, Natalia A. Ayala, Gabriela Barbás, Ana Maria Amarillo Bertone, Agustina Bonnet, Ignacio Bourlot, Victoria Cabassi, Alejandro A. Castello, Gonzalo Castro, Ana Laura Cavatorta, Carolina Ceriani, Carlos Cimmino, Julián Cipelli, María Colmeiro, Andrés I. Cordero, Carolina Cristina, Sofia Di Bella, Guillermina Laura Dolcini, Regina Ercole, Yesica Espasandin, Carlos Espul, Andrea Falaschi, Facundo Fernandez Moll, María Delia Foussal, Andrea Gatelli, Sandra Elizabeth Goñi, Maria Jofre, José Luis González Jaramillo, Natalia Labarta, María Agustina Lacaze, Rocio Larreche, Viviana Leiva, Gustavo Levin, Erica Luczak, Marcelo G. Mandile, Gioia Marino, Carla Massone, M Mazzeo, Carla Mishell León Medina, B. Monaco, Luciana Montoto, Viviana Mugna, Alejandra Musto, Victoria Nadalich, María Victoria Nieto, Guillermo Ojeda, Andrea C. Piedrabuena, Carolina Pintos, Marcia Pozzati, Marilina Rahhal, Claudia Rechimont, Federico Remes Lenicov, G. Rompato, Vanesa Seery, Leticia Siri, Julieta Spina, Cintia Streitenberger, Ariel Suárez, Jorgelina Suárez, Paula Sujansky, Juan Manuel Talia, Clara Theaux, Guillermo Thomas, Marina Ticeira, Estefanía Tittarelli, Rosana Toro, Osvaldo Uez, María Belén Zaffanella, Cecilia Ziehm, Martín Zubieta,

CRISPR and Genetic Engineering

SARS-CoV-2 variants with concerning characteristics have emerged since the end of 2020. Surveillance of SARS-CoV-2 variants was performed on a total of 4,851 samples from the capital city and 10 provinces of Argentina, during 51 epidemiological weeks (EWs) that covered the end of the first wave and the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 41/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the identification of signature mutations associated with variants. In addition, whole-genome sequences were obtained from 637 samples. The main variants found were Gamma and Lambda, and to a lesser extent, Alpha, Zeta, and Epsilon, and more recently, Delta. Whereas, Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires. The lineages that circulated on the first wave were replaced by emergent variants in a term of a few weeks. At the end of the ongoing second wave, Delta began to be detected, replacing Gamma and Lambda. This scenario is consistent with the Latin American variant landscape, so far characterized by a concurrent increase in Delta circulation and a stabilization in the number of cases. The cost-effective surveillance protocol presented here allowed for a rapid response in a resource-limited setting, added information on the expansion of Lambda in South America, and contributed to the implementation of public health measures to control the disease spread in Argentina.