Characterizing SARS-CoV-2 genome diversity circulating in South American countries: Signatures of potentially emergent lineages?

Marina Muñoz, Luz H. Patiño, Nathalia Ballesteros, Alberto Paniz-Mondolfi, Juan David Ramírez

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


Objectives: To evaluate the genomic diversity and geographic distribution of SARS-CoV-2 lineages in South America. Methods: SARS-CoV-2 lineages from a public dataset of 5583 South American genome assemblies were analyzed. Polymorphisms in the main open reading frames were identified and compared to those in the main lineages of epidemiological concern: B.1.1.7 (UK) and B.1.351 (South Africa). Results: Across 16 South American countries, 169 lineages were identified; major lineage B had the greatest diversity and broadest geographic distribution. Seventeen predominant lineages were analyzed revealing 2 dominant lineages of concern: P.1 (Brazilian variant) and B.1.1.7 with 94 and 28 genomes, respectively, both with 33 polymorphisms (other lineages displayed ≤24 polymorphisms). A high number of polymorphisms were detected with a limited number of common variable positions, in common with the profile of the main lineages of epidemiological concern. Conclusions: The ever-increasing genetic diversity of SARS-CoV-2 continues to lead to novel lineage emergence. Various variants and lineages are now present across South America, dominated by major lineage B. The circulation of P.1 and B.1.1.7 and the high number of polymorphisms highlight the importance of genomic surveillance to determine introduction events, identify transmission chains, trace emergence, and implement prevention, vaccination and control strategies.

Original languageEnglish (US)
Pages (from-to)329-332
Number of pages4
JournalInternational Journal of Infectious Diseases
StatePublished - Apr 2021

All Science Journal Classification (ASJC) codes

  • Microbiology (medical)
  • Infectious Diseases


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