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. 2023 Jan 22;15(2):312.
doi: 10.3390/v15020312.

Omicron Waves in Argentina: Dynamics of SARS-CoV-2 Lineages BA.1, BA.2 and the Emerging BA.2.12.1 and BA.4/BA.5

Carolina Torres  1   2 , Mercedes Nabaes Jodar  2   3 , Dolores Acuña  2   3 , Romina Micaela Zambrana Montaño  1   2 , Andrés Carlos Alberto Culasso  1   2 , Ariel Fernando Amadio  2   4 , Paula Aulicino  2   5 , Santiago Ceballos  6 , Marco Cacciabue  7 , Humberto Debat  8 , María José Dus Santos  9   10 , María Florencia Eberhardt  2   4 , Carlos Espul  11 , Fabián Fay  12 , María Ailén Fernández  13 , Franco Fernández  8 , Juan Manuel Fernandez Muñoz  14 , Florencia Ferrini  15 , Fernando Gallego  6 , Adriana Angélica Giri  16 , Agustina Cerri  16 , Elisa Bolatti  16 , María Ines Gismondi  7   17 , Stephanie Goya  3 , Iván Gramundi  6 , José Matías Irazoqui  2   4 , Guido Alberto König  7 , Viviana Leiva  11 , Horacio Lucero  18 , Nathalie Marquez  8 , Cristina Nardi  6 , Belén Ortiz  11 , Luis Pianciola  13 , Carolina Beatriz Pintos  13 , Andrea Fabiana Puebla  7 , Carolina Victoria Rastellini  13 , Alejandro Ezequiel Rojas  6 , Javier Sfalcin  12 , Ariel Suárez  19 , Estefanía Tittarelli  19 , Rosana Toro  20 , Gabriela Vanina Villanova  2   21 , María Cecilia Ziehm  13 , María Carla Zimmermann  15 , Sebastián Zunino  17   22 , Proyecto Pais Working Group  23 , Laura Valinotto  2   3 , Mariana Viegas  2   3
Affiliations

Omicron Waves in Argentina: Dynamics of SARS-CoV-2 Lineages BA.1, BA.2 and the Emerging BA.2.12.1 and BA.4/BA.5

Carolina Torres et al. Viruses. .

Abstract

The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.

Keywords: BA.1; BA.2; BA.4; BA.5; Omicron; SARS-CoV-2; South America; dynamics; evolution; variants.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Sampling points for genomic surveillance of SARS-CoV-2 variants in Argentina.
Figure 2
Figure 2
(a) Number of cases reported in Argentina from EW44/2021 to EW31/2022. Note that in EW15/2022 (between the third and the fourth waves), Argentina modified the COVID-19 massive testing criterion and since then, testing in public hospitals is only performed in populations under a higher risk for severe disease (>50 years or comorbidities). Data from https://ourworldindata.org/coronavirus#explore-the-global-situation, accessed on 1 December 2023. The arrows are colored according to the variant present at each moment of the wave. (b) Frequency of variant detection analyzed by epidemiological week, 2021–2022. Data from Spike and complete genome sequencing of samples from cases that did not present epidemiological link with travel (n = 3431).
Figure 3
Figure 3
Phylogenetic tree of SARS-CoV-2 sequences focused on Omicron BA.1 and its sublineages. SH-aLRT support values are indicated at nodes for some groups. The branches and tips of the tree are colored according to the City or Provinces indicated in the legend. Black-colored tips represent sequences from other countries or sequences included as references for other lineages.
Figure 4
Figure 4
Phylogenetic tree of SARS-CoV-2 sequences, focused on Omicron BA.2 and its sublineages. SH-aLRT and UFB support values are indicated at nodes for some groups. The branches and tips of the tree are colored according to the City or Provinces indicated in the legend. Black-colored tips represent sequences from other countries or sequences included as references for other lineages.
Figure 5
Figure 5
Phylogenetic tree of SARS-CoV-2 sequences, focused on Omicron BA.4/BA.5 and their sublineages. SH-aLRT and UFB support values are indicated at nodes for some groups. The branches and tips of the tree are colored according to the City or Provinces indicated in the legend. Black-colored tips represent sequences from other countries or sequences included as references for other lineages.
See this image and copyright information in PMC

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