Cost-effective method to perform SARS-CoV-2 variant surveillance: detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina

Torres, Carolina; Mojsiejczuk, Laura Noelia; Acuña, Dolores; Alexay, Sofía; Amadio, Ariel Fernando; Aulicino, Paula; Debat, Humberto Julio; Fay, Fabian; Fernández, Franco; Giri, Adriana Angelica; Goya, Stephanie; König, Guido Alberto; Lucero, Horacio; Nabaes Jodar, Mercedes Soledad; Pianciola, Luis; Sfalcin, Javier A.; Acevedo, Raúl Maximiliano; Bengoa Luoni, Sofia Ailin; Bolatti, Elisa Maria; Brusés, Bettina Laura; Cacciabue, Marco Polo Domingo; Casal, Pablo Ezequiel; Cerri, Agustina; Chouhy, Diego; Dus Santos, María José; Eberhardt, Maria Florencia; Fernández, Ailén; Fernández, Paula del Carmen; Fernández Do Porto, Darío Augusto; Formichelli, Laura Belén; Gismondi, María Inés; Irazoqui, José Matías; Lorenzini Campos, Melina Noelia; Lusso, Silvina; Marquez, Nathalie; Muñoz, Marianne; Mussin, Javier Esteban; Natale, Mónica Inés; Oria, Griselda Ines; Pisano, María Belén; Posner, Victoria Maria; Puebla, Andrea; Ré, Viviana Elizabeth; Sosa, Ezequiel; Villanova, Gabriela Vanina; Zaiat, Jonathan Javier; Zunino, Sebastián; Acevedo, María Elina; Acosta, Julián; Alvarez Lopez, Cristina; Álvarez, María Laura; Angeleri, Patricia; Angelletti, Andrés; Arca, Manuel; Ayala, Natalia A.; Barbas, Maria Gabriela; Bertone, Ana; Bonnet, Maria Agustina; Bourlot, Ignacio; Cabassi, María Victoria; Castello, Alejandro; Castro, Gonzalo; Cavatorta, Ana Laura; Ceriani, Maria Carolina; Cimmino, Carlos José; Cipelli, Julián; Colmeiro, María; Cordero, Andrés; Cristina, Silvia Carolina; Di Bella, Sofia; Dolcini, Guillermina Laura; Ercole, Regina; Espasandin, Yesica Romina; Espul, Carlos; Falaschi, Andrea; Fernández Moll, Facundo Lucio; Foussal, María Delia; Gatelli, Andrea; Goñi, Sandra Elizabeth; Jofré, María Estela; Jaramillo Ortiz, José Manuel; Labarta, Natalia; Lacaze, María Agustina; Larreche Calahorrano, María Rocío; Leiva, Viviana; Levin, Gustavo Javier; Luczak, Erica Natalia; Mandile, Marcelo Gastón; Marino, Gioia; Massone, Carla Antonella; Mazzeo, Melina; Medina, Carla; Monaco, Belén; Montoto, Luciana; Mugna, Viviana; Musto, Alejandra Beatriz; Nadalich, Victoria; Nieto Farías, María Victoria; Ojeda, Guillermo; Piedrabuena, Andrea C.; Pintos, Carolina; Pozzati, Marcia; Rahhal, Marilina; Rechimont, Claudia; Remes Lenicov, Federico; Rompato, Gabriela; Seery, Vanesa; Siri, Leticia; Spina, Maria Julieta; Streitenberger, Cintia; Suárez, Ariel; Suárez, Jorgelina; Sujansky, Paula; Talia, Juan Manuel; Theaux, Clara; Thomas, Guillermo; Ticeira, Marina; Tittarelli, Estefanía; Toro, Rosana; Uez, Osvaldo; Zaffanella, María Belén; Ziehm, Cecilia; Zubieta, Martin; Mistchenko, Alicia Susana; Valinotto, Laura Elena; Viegas, Mariana

Cost-effective method to perform SARS-CoV-2 variant surveillance: detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina

2021

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

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Cost-effective method to perform SARS-CoV-2 variant surveillance: detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina

2021

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