Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries
Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage’s genomic and epidemiological characteristics. However, in South America, thi...
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| Format: | Article |
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MDPI AG
2022-06-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/6/1234 |
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| author | Nicolas Luna Marina Muñoz Angie L. Ramírez Luz H. Patiño Sergio Andres Castañeda Nathalia Ballesteros Juan David Ramírez |
| author_facet | Nicolas Luna Marina Muñoz Angie L. Ramírez Luz H. Patiño Sergio Andres Castañeda Nathalia Ballesteros Juan David Ramírez |
| author_sort | Nicolas Luna |
| collection | DOAJ |
| description | Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage’s genomic and epidemiological characteristics. However, in South America, this variant’s arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health. |
| first_indexed | 2024-03-09T22:14:41Z |
| format | Article |
| id | doaj.art-cdda96a6458b450c82f7fe9606de13f2 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T22:14:41Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-cdda96a6458b450c82f7fe9606de13f22023-11-23T19:25:57ZengMDPI AGViruses1999-49152022-06-01146123410.3390/v14061234Genomic Diversity of SARS-CoV-2 Omicron Variant in South American CountriesNicolas Luna0Marina Muñoz1Angie L. Ramírez2Luz H. Patiño3Sergio Andres Castañeda4Nathalia Ballesteros5Juan David Ramírez6Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, ColombiaCentro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, ColombiaCentro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, ColombiaCentro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, ColombiaCentro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, ColombiaCentro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, ColombiaCentro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, ColombiaGenomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage’s genomic and epidemiological characteristics. However, in South America, this variant’s arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health.https://www.mdpi.com/1999-4915/14/6/1234SARS-CoV-2Omicron sublineagesSouth Americanucleotide diversityphylogenomic analysis |
| spellingShingle | Nicolas Luna Marina Muñoz Angie L. Ramírez Luz H. Patiño Sergio Andres Castañeda Nathalia Ballesteros Juan David Ramírez Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries Viruses SARS-CoV-2 Omicron sublineages South America nucleotide diversity phylogenomic analysis |
| title | Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries |
| title_full | Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries |
| title_fullStr | Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries |
| title_full_unstemmed | Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries |
| title_short | Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries |
| title_sort | genomic diversity of sars cov 2 omicron variant in south american countries |
| topic | SARS-CoV-2 Omicron sublineages South America nucleotide diversity phylogenomic analysis |
| url | https://www.mdpi.com/1999-4915/14/6/1234 |
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