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

Torres, Carolina; Jodar, Mercedes Nabaes; Acuña, Dolores; Montaño, Romina Micaela Zambrana; Culasso, Andrés Carlos Alberto; Amadío, Ariel Fernando; Aulicino, Paula; Ceballos, Santiago; Cacciabue, Marco; Debat, Humberto Julio; Santos, María José Dus; Eberhardt, María Florencia; Espul, Carlos; Fay, Fabián; Fernández, María Ailén; Fernández, Franco Daniel; Fernandez-Muñoz, Juan Manuel; Ferrini, Florencia; Gallego, Fernando Martín; Giri, Adriana A.; Cerri, Agustina; Bolatti, Elisa Maria; Gismondi, María Inés; Goya, Stephanie; Gramundi, Ivan; Irazoqui, José Matías; König, Guido; Leiva, Viviana; Lucero, Horacio; Marquez, Nathalie; Nardi, Cristina Fernanda; Ortiz, Belén; Pianciola, Luis; Pintos, Carolina; Puebla, Andrea Fabiana; Rastellini, Carolina Victoria; Rojas, Alejandro Ezequiel; Sfalcin, Javier; Suarez, Ariel; Tittarelli, Estefanía; Toro, Rosana; Villanova, Gabriela Vanina; Ziehm, María Cecilia; Zimmermann, Maria; Zunino, Sebastián; Valinotto, Laura; Viegas, Mariana

doi:10.3390/v15020312

Cited by 11 publications

(10 citation statements)

References 27 publications

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“…Compared to the reference sequence hCoV-19/Wuhan/WIV04/2019 (GISAID accession number EPI_ISL_402124), the 1263 genome sequences displayed a total of 1631 amino acid changes in different viral genes (912 in ORF1a/1b, 268 in S, 121 in N, 114 in ORF3a, 94 in ORF7a, 47 in ORF8, 28 in M, 18 in ORF6, 17 in ORF7b, and 12 in E). In the Argentine sequences, all the C.37 lineage defining amino acid changes [ 41 ], shown in grey in Figure 4 A, were found at a frequency higher than 95.9%.…”

Section: Resultsmentioning

confidence: 99%

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The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37

Jodar

Torres

Mojsiejczuk³

et al. 2023

Viruses

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The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial–-temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern.

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Section: Resultsmentioning

confidence: 99%

“…The Lambda variant is characterized by multiple lineage-specific deletions and amino acid substitutions in its viral genome, as shown in Figure 4 A [ 41 ]. Specifically, the spike protein of the Lambda variant has a unique pattern of eight mutations (G75V, T76I, R246N, Δ247-253, L452Q, F490S, D614G, and T859N).…”

Section: Discussionmentioning

confidence: 99%

The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37

Jodar

Torres

Mojsiejczuk³

et al. 2023

Viruses

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“…In winter 2021, the BA.1 variant and its subvariants started a new epidemiological surge worldwide. Afterward, BA.2 superseded them as the predominant variant in the world [8,9], allowing the epidemic wave of BA.1 to continue in some countries [10,11], or causing a separate wave in other countries [12,13], or leading to a small number of cases without an associated epidemic wave in others [14,15]. The genomic sequences of BA.1 and BA.2 variants (and their subvariants) differ by 23 amino acids [6], resulting in enhanced replication capacity and transmissibility of BA.2 [9,16,17].…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico

Taboada,

Zárate,

García-López

et al. 2023

Microbial Genomics

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In Mexico, the BA.4 and BA.5 Omicron variants dominated the fifth epidemic wave (summer 2022), superseding BA.2, which had circulated during the inter-wave period. The present study uses genome sequencing and statistical and phylogenetic analyses to examine these variants' abundance, distribution, and genetic diversity in Mexico from April to August 2022. Over 35 % of the sequenced genomes in this period corresponded to the BA.2 variant, 8 % to the BA.4 and 56 % to the BA.5 variant. Multiple subvariants were identified, but the most abundant, BA.2.9, BA.2.12.1, BA.5.1, BA.5.2, BA.5.2.1 and BA.4.1, circulated across the entire country, not forming geographical clusters. Contrastingly, other subvariants exhibited a geographically restricted distribution, most notably in the Southeast region, which showed a distinct subvariant dynamic. This study supports previous results showing that this region may be a significant entry point and contributed to introducing and evolving novel variants in Mexico. Furthermore, a differential distribution was observed for certain subvariants among specific States through time, which may have contributed to the overall increased diversity observed during this wave compared to the previous ones. This study highlights the importance of sustaining genomic surveillance to identify novel variants that may impact public health.

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“…A study conducted in the United States showed that breakthrough infections with Omicron variant were more likely, even in subjects with a booster dose, probably due to immune escape [ 46 ]. Overall, variants found in our study were coincident to the most frequently circulating variants in the community at each time, regardless of the type of vaccine and vaccination status [ 4 , 34 ].…”

Section: Discussionmentioning

confidence: 98%

“…As determined by viral sequencing, the most prevalent variant detected in our study was Delta, followed by Omicron, Gamma and Lambda. Each variant was prevalent in the period of highest circulation in Buenos Aires city and surroundings, according to data from Argentina [ 3 , 4 , 34 ].…”

Section: Discussionmentioning

confidence: 99%

Persistence of SARS-CoV-2 RNA shedding and infectivity in immunized population: Prospective study along different epidemiological periods in Argentina

Theaux,

Martin,

Montoto Piazza

et al. 2023

PLoS ONE

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During the pandemic of COVID-19, numerous waves of infections affected the two hemispheres with different impacts on each country. Throughout these waves, and with the emergence of new variants, health systems and scientists have tried to provide real-time responses to the complex biology of SARS-CoV-2, dealing with different clinical presentations, biological characteristics, and clinical impact of these variants. In this context, knowing the extent period in which an infected individual releases infectious viral particles has important implications for public health. This work aimed to investigate viral RNA shedding and infectivity of SARS-CoV-2 beyond 10 days after symptom onset (SO). A prospective multicenter study was performed between July/2021 and February/2022 on 116 immunized strategic personnel with COVID-19 diagnosed by RT-qPCR, with asymptomatic (7%), mild (91%) or moderate disease (2%). At the time of diagnosis, 70% had 2 doses of vaccines, 26% had 2 plus a booster, and 4% had one dose. After day 10 from SO, sequential nasopharyngeal swabs were taken to perform RT-qPCR, viral isolation, and S gene sequencing when possible. Viral sequences were obtained in 98 samples: 43% were Delta, 16% Lambda, 15% Gamma, 25% Omicron (BA.1) and 1% Non-VOC/VOI, in accordance with the main circulating variants at each moment. SARS-CoV-2 RNA was detected 10 days post SO in 57% of the subjects. Omicron was significantly less persistent. Noteworthy, infective viruses could not be isolated in any of the samples. In conclusion, a 10-days isolation period was useful to prevent further infections, and proved valid for the variants studied. Recently, even shorter periods have been applied, as the Omicron variant is prevalent, and worldwide population is largely vaccinated. In the future, facing the possible emergence of new variants and considering immunological status, a return to 10 days may be necessary.

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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

Cited by 11 publications

References 27 publications

The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37

The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico

Persistence of SARS-CoV-2 RNA shedding and infectivity in immunized population: Prospective study along different epidemiological periods in Argentina

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