Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina
Authors: Torres Carolina , Mojsiejczuk Laura , Acuña Dolores , Alexay Sofía , Amadio Ariel , Aulicino Paula , Debat Humberto , Fay Fabián , Fernández Franco , Giri Adriana A. , Goya Stephanie , König Guido , Lucero Horacio , Nabaes Jodar Mercedes , Pianciola Luis , Sfalcin Javier A. , Acevedo Raúl M. , Bengoa Luoni Sofía , Bolatti Elisa M. , Brusés Bettina , Cacciabue Marco , Casal Pablo E. , Cerri Agustina , Chouhy Diego , Dus Santos María José , Eberhardt María Florencia , Fernandez Ailen , Fernández Paula del Carmen , Fernández Do Porto Darío , Formichelli Laura , Gismondi María Inés , Irazoqui Matías , Campos Melina Lorenzini , Lusso Silvina , Marquez Nathalie , Muñoz Marianne , Mussin Javier , Natale Mónica , Oria Griselda , Pisano María Belén , Posner Victoria , Puebla Andrea , Re Viviana , Sosa Ezequiel , Villanova Gabriela V. , Zaiat Jonathan , Zunino Sebastián , Acevedo María Elina , Acosta Julián , Alvarez Lopez Cristina , Álvarez María Laura , Angeleri Patricia , Angelletti Andrés , Arca Manuel , Ayala Natalia A. , Barbas Gabriela , Bertone Ana , Bonnet Agustina , Bourlot Ignacio , Cabassi Victoria , Castello Alejandro , Castro Gonzalo , Cavatorta Ana Laura , Ceriani Carolina , Cimmino Carlos , Cipelli Julián , Colmeiro María , Cordero Andrés , Cristina Carolina , Di Bella Sofia , Dolcini Guillermina , Ercole Regina , Espasandin Yesica , Espul Carlos , Falaschi Andrea , Fernandez Moll Facundo , Foussal María Delia , Gatelli Andrea , Goñi Sandra , Jofré María Estela , Jaramillo José , Labarta Natalia , Lacaze María Agustina , Larreche Rocio , Leiva Viviana , Levin Gustavo , Luczak Erica , Mandile Marcelo , Marino Gioia , Massone Carla , Mazzeo Melina , Medina Carla , Monaco Belén , Montoto Luciana , Mugna Viviana , Musto Alejandra , Nadalich Victoria , Nieto 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 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 
Published: December 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.