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. 2021 Mar 19;9(3):282.
doi: 10.3390/vaccines9030282.

Phylogenomic Evidence of Reinfection and Persistence of SARS-CoV-2: First Report from Colombia

Juan David Ramírez  1 , Marina Muñoz  1 , Nathalia Ballesteros  1 , Luz H Patiño  1 , Sergio Castañeda  1 , Carlos A Rincón  2 , Claudia Mendez  2 , Carolina Oliveros  2 , Julie Perez  2 , Elizabeth K Márquez  2 , Frank de Los Santos Ortiz  2 , Camilo A Correa-Cárdenas  2 , Maria Clara Duque  2 , Alberto Paniz-Mondolfi  3   4
Affiliations

Phylogenomic Evidence of Reinfection and Persistence of SARS-CoV-2: First Report from Colombia

Juan David Ramírez et al. Vaccines (Basel). .

Abstract

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.

Keywords: Colombia; SARS-CoV-2; genomic surveillance; reinfections.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Epidemiological investigation in the three patients. Gray color indicates positive RT-PCR; green indicates a negative PCR. The epidemiological investigation was conducted in 2020.
Figure 2
Figure 2
Phylogenomic reconstruction of the six genomes sequenced in this study compared to the 4171 genomes encompassing the global diversity of SARS-CoV2. The red dots and lines represent Patient 1 (persistence); the turquoise dots and lines represent Patient 2 (persistence); and the blue dots and lines represent Patient 3 (reinfection).
Figure 3
Figure 3
Phylogenetic relationships for the paired genome assemblies obtained from each patient. A zoom to which each of the analyzed genomes belongs was carried out to identify the geographical origin of the most closely related genomes: (A) Patient 1; (B) Patient 2; (C) Patient 3.
See this image and copyright information in PMC

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