Frontiers in Medicine (Dec 2021)

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

  • Carolina Torres,
  • Carolina Torres,
  • Laura Mojsiejczuk,
  • Laura Mojsiejczuk,
  • Dolores Acuña,
  • Dolores Acuña,
  • Sofía Alexay,
  • Ariel Amadio,
  • Ariel Amadio,
  • Paula Aulicino,
  • Paula Aulicino,
  • Humberto Debat,
  • Fabián Fay,
  • Franco Fernández,
  • Adriana A. Giri,
  • Adriana A. Giri,
  • Stephanie Goya,
  • Guido König,
  • Horacio Lucero,
  • Mercedes Nabaes Jodar,
  • Mercedes Nabaes Jodar,
  • Luis Pianciola,
  • Javier A. Sfalcin,
  • Raúl M. Acevedo,
  • Raúl M. Acevedo,
  • Sofía Bengoa Luoni,
  • Elisa M. Bolatti,
  • Elisa M. Bolatti,
  • Bettina Brusés,
  • Marco Cacciabue,
  • Pablo E. Casal,
  • Agustina Cerri,
  • Agustina Cerri,
  • Diego Chouhy,
  • Diego Chouhy,
  • María José Dus Santos,
  • María José Dus Santos,
  • María Florencia Eberhardt,
  • María Florencia Eberhardt,
  • Ailen Fernandez,
  • Paula del Carmen Fernández,
  • Darío Fernández Do Porto,
  • Darío Fernández Do Porto,
  • Laura Formichelli,
  • María Inés Gismondi,
  • María Inés Gismondi,
  • Matías Irazoqui,
  • Matías Irazoqui,
  • Melina Lorenzini Campos,
  • Melina Lorenzini Campos,
  • Silvina Lusso,
  • Nathalie Marquez,
  • Marianne Muñoz,
  • Javier Mussin,
  • Javier Mussin,
  • Mónica Natale,
  • Griselda Oria,
  • María Belén Pisano,
  • María Belén Pisano,
  • Victoria Posner,
  • Victoria Posner,
  • Andrea Puebla,
  • Viviana Re,
  • Viviana Re,
  • Ezequiel Sosa,
  • Gabriela V. Villanova,
  • Gabriela V. Villanova,
  • Jonathan Zaiat,
  • Sebastián Zunino,
  • Sebastián Zunino,
  • María Elina Acevedo,
  • Julián Acosta,
  • Cristina Alvarez Lopez,
  • María Laura Álvarez,
  • Patricia Angeleri,
  • Andrés Angelletti,
  • Andrés Angelletti,
  • Manuel Arca,
  • Natalia A. Ayala,
  • Gabriela Barbas,
  • Ana Bertone,
  • Agustina Bonnet,
  • Ignacio Bourlot,
  • Victoria Cabassi,
  • Alejandro Castello,
  • Gonzalo Castro,
  • Ana Laura Cavatorta,
  • Carolina Ceriani,
  • Carlos Cimmino,
  • Julián Cipelli,
  • María Colmeiro,
  • Andrés Cordero,
  • Carolina Cristina,
  • Sofia Di Bella,
  • Guillermina Dolcini,
  • Regina Ercole,
  • Yesica Espasandin,
  • Carlos Espul,
  • Andrea Falaschi,
  • Facundo Fernandez Moll,
  • María Delia Foussal,
  • Andrea Gatelli,
  • Sandra Goñi,
  • María Estela Jofré,
  • José Jaramillo,
  • Natalia Labarta,
  • María Agustina Lacaze,
  • Rocio Larreche,
  • Viviana Leiva,
  • Gustavo Levin,
  • Erica Luczak,
  • Marcelo Mandile,
  • Gioia Marino,
  • Carla Massone,
  • Melina Mazzeo,
  • Carla Medina,
  • Belén 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,
  • Gabriela 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,
  • Martin Zubieta

DOI
https://doi.org/10.3389/fmed.2021.755463
Journal volume & issue
Vol. 8

Abstract

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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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