Phylogenomic evidence of reinfection and persistence of sars-cov-2: First report from Colombia

Juan David Ramírez, Marina Muñoz, Nathalia Ballesteros, Luz H. Patiño, Sergio Castañeda, Carlos A. Rincón, Claudia Mendez, Carolina Oliveros, Julie Perez, Elizabeth K. Márquez, Frank de los Santos Ortiz, Camilo A. Correa-Cárdenas, Maria Clara Duque, Alberto Paniz-Mondolfi

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics. Utilizing Oxford Nanopore technologies, we sequenced paired samples of three patients with positive RT-PCR results in a 1–2-month window period, and subsequent phylogenetics and genetic polymorphism analysis of these genomes was performed. Herein, we report, for the first time, genomic evidence of one case of reinfection in Colombia, exhibiting different SARS-CoV-2 lineage classifications between samples (B.1 and B.1.1.269). Furthermore, we report two cases of possible viral persistence, highlighting the importance of deepening our understanding on the evolutionary intra-host traits of this virus throughout different timeframes of disease progression. These results emphasize the relevance of genomic surveillance as a tool for understanding SARS-CoV-2 infection dynamics, and how this may translate effectively to future control and mitigations efforts, such as the national vaccination program.

Original languageEnglish (US)
Article number282
Issue number3
StatePublished - Mar 2021

All Science Journal Classification (ASJC) codes

  • Immunology
  • Pharmacology
  • Drug Discovery
  • Infectious Diseases
  • Pharmacology (medical)


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