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. 2021 Dec 10:8:755463.
doi: 10.3389/fmed.2021.755463. eCollection 2021.

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

Carolina Torres  1   2 , Laura Mojsiejczuk  1   2 , Dolores Acuña  2   3 , Sofía Alexay  3 , Ariel Amadio  2   4 , Paula Aulicino  2   5 , Humberto Debat  6 , Fabián Fay  7 , Franco Fernández  6 , Adriana A Giri  2   8 , Stephanie Goya  3 , Guido König  9 , Horacio Lucero  10 , Mercedes Nabaes Jodar  2   3 , Luis Pianciola  11 , Javier A Sfalcin  7 , Raúl M Acevedo  2   12 , Sofía Bengoa Luoni  9 , Elisa M Bolatti  2   8 , Bettina Brusés  10 , Marco Cacciabue  9 , Pablo E Casal  8 , Agustina Cerri  2   8 , Diego Chouhy  2   8 , María José Dus Santos  13   14 , María Florencia Eberhardt  2   4 , Ailen Fernandez  11 , Paula Del Carmen Fernández  9 , Darío Fernández Do Porto  2   15 , Laura Formichelli  10 , María Inés Gismondi  7   16 , Matías Irazoqui  2   4 , Melina Lorenzini Campos  2   10 , Silvina Lusso  3 , Nathalie Marquez  6 , Marianne Muñoz  17 , Javier Mussin  2   10 , Mónica Natale  3 , Griselda Oria  10 , María Belén Pisano  2   18 , Victoria Posner  2   19 , Andrea Puebla  17 , Viviana Re  2   18 , Ezequiel Sosa  20 , Gabriela V Villanova  2   19 , Jonathan Zaiat  20 , Sebastián Zunino  11   21 , María Elina Acevedo  3 , Julián Acosta  22 , Cristina Alvarez Lopez  3 , María Laura Álvarez  23 , Patricia Angeleri  24 , Andrés Angelletti  25   26 , Manuel Arca  27 , Natalia A Ayala  28 , Gabriela Barbas  29 , Ana Bertone  30 , Agustina Bonnet  27 , Ignacio Bourlot  31 , Victoria Cabassi  25 , Alejandro Castello  32 , Gonzalo Castro  33 , Ana Laura Cavatorta  22 , Carolina Ceriani  34 , Carlos Cimmino  35 , Julián Cipelli  3 , María Colmeiro  26 , Andrés Cordero  25 , Carolina Cristina  36 , Sofia Di Bella  26 , Guillermina Dolcini  34 , Regina Ercole  26 , Yesica Espasandin  23 , Carlos Espul  37 , Andrea Falaschi  37 , Facundo Fernandez Moll  36 , María Delia Foussal  38 , Andrea Gatelli  26 , Sandra Goñi  32 , María Estela Jofré  39 , José Jaramillo  21 , Natalia Labarta  3 , María Agustina Lacaze  40 , Rocio Larreche  39 , Viviana Leiva  41 , Gustavo Levin  31 , Erica Luczak  42 , Marcelo Mandile  32 , Gioia Marino  43 , Carla Massone  21 , Melina Mazzeo  11 , Carla Medina  3 , Belén Monaco  21 , Luciana Montoto  44 , Viviana Mugna  45 , Alejandra Musto  41 , Victoria Nadalich  25 , María Victoria Nieto  34 , Guillermo Ojeda  45 , Andrea C Piedrabuena  46 , Carolina Pintos  11 , Marcia Pozzati  47 , Marilina Rahhal  48 , Claudia Rechimont  30 , Federico Remes Lenicov  49 , Gabriela Rompato  45 , Vanesa Seery  49 , Leticia Siri  31 , Julieta Spina  50 , Cintia Streitenberger  3 , Ariel Suárez  51 , Jorgelina Suárez  36 , Paula Sujansky  24 , Juan Manuel Talia  40 , Clara Theaux  52 , Guillermo Thomas  3 , Marina Ticeira  39 , Estefanía Tittarelli  51 , Rosana Toro  25 , Osvaldo Uez  35 , María Belén Zaffanella  50 , Cecilia Ziehm  11 , Martin Zubieta  48 , Alicia S Mistchenko  3   53 , Laura Valinotto  2   3 , Mariana Viegas  2   3
Affiliations

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

Carolina Torres et al. Front Med (Lausanne). .

Abstract

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.

Keywords: Delta; Gamma; Lambda; SARS-CoV-2; South America; spike sequences; surveillance; variants.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Location of cases analyzed in this work and pie charts representing the frequency of each variant detected in every region between EW44/2020 and EW41/2021. 1. Buenos Aires city, 2. Great Buenos Aires (North, West, South), 3. Province of Buenos Aires, 4. Province of Entre Ríos, 5. Province of Santa Fe, 6. Province of Chaco, 7. Province of Córdoba, 8. Province of San Luis, 9. Province of Mendoza, 10. Province of La Pampa, 11. Province of Neuquén, and 12. Province of Río Negro. *cases associated with an outbreak (n = 15) (Supplementary Table 1). **cases (n = 9) mainly associated with the first part of the period analyzed (Supplementary Table 1).
Figure 2
Figure 2
(A) Confirmed cases in Argentina, the city of Buenos Aires (CABA) and the province of Buenos Aires in the year 2021. (B) Frequency of SARS-CoV-2 variants and sequences with or without mutations of interest by epidemiological week (n = 2,625). Only cases from the metropolitan area of Buenos Aires (MABA) that did not present a history of travel or close contact with travelers are included; in cases with registered epidemiological links, only one case was considered representative. (C) The cumulative number of cases between EW 17/2021 and EW 40/2021 of SARS-CoV-2 variants and sequences with or without mutations of interest within the different regions of the MABA: CABA, Great Buenos Aires (GBA), and Great La Plata (GLP). Only cases that did not present a history of travel or close contact with travelers are included; in cases sharing an epidemiological link, only one was included. (A,B) are on the same time scale.
Figure 3
Figure 3
Phylogenetic tree of SARS-CoV-2 whole-genome sequences of Alpha (lineage B.1.1.7). B.1.1.1 sequences were used as outgroup. Only the largest group with Argentinean sequences is shown. The SH-like/UFB values for the relevant groups are indicated for some groups. UFB, ultrafast bootstrap. The right panel (a) represents an inset of the largest B.1.1.7 group from the tree.
Figure 4
Figure 4
Phylogenetic tree of SARS-CoV-2 whole-genome sequences of Gamma (lineage P.1). B.1.1.28 sequences were used as outgroup. Only selected groups with Argentinean sequences are shown. The SH-like/UFB values for the relevant groups are indicated for some groups. *P.1-like-I and **P.1-like-II described by Gräf et al. (15). UFB, ultrafast bootstrap. The panels (a–d) represent insets of some groups from the tree.
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References

    1. World Health Organization. Tracking SARS-CoV-2 Variants. (2021). Available online at: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
    1. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. . Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. (2021) 26:1–10. 10.2807/1560-7917.ES.2021.26.16.2100348 - DOI - PMC - PubMed
    1. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. Lancet. (2021) 397:2461–2. 10.1016/S0140-6736(21)01358-1 - DOI - PMC - PubMed
    1. Garcia-Beltran WF, Lam EC, St., Denis K, Nitido AD, Garcia ZH, Hauser BM, et al. . Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell. (2021) 184:2372–83.e9. 10.1016/j.cell.2021.03.013 - DOI - PMC - PubMed
    1. Wang P, Casner RG, Nair MS, Wang M, Yu J, Cerutti G, et al. . Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. Cell Host & Microbe. (2021) 29:747–51. 10.1016/j.chom.2021.04.007 - DOI - PMC - PubMed