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

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.

SUBMITTER: Ramirez JD

PROVIDER: S-EPMC8003345 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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

Ramírez Juan David JD Muñoz Marina M Ballesteros Nathalia N Patiño Luz H LH Castañeda Sergio S Rincón Carlos A CA Mendez Claudia C Oliveros Carolina C Perez Julie J Márquez Elizabeth K EK Ortiz Frank de Los Santos FLS Correa-Cárdenas Camilo A CA Duque Maria Clara MC Paniz-Mondolfi Alberto A

Vaccines 20210319 3

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, gen ...[more]

PMID: 33808687

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Project description:BackgroundThe degree of protective immunity conferred by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently unknown. As such, the possibility of reinfection with SARS-CoV-2 is not well understood. We describe an investigation of two instances of SARS-CoV-2 infection in the same individual.MethodsA 25-year-old man who was a resident of Washoe County in the US state of Nevada presented to health authorities on two occasions with symptoms of viral infection, once at a community testing event in April, 2020, and a second time to primary care then hospital at the end of May and beginning of June, 2020. Nasopharyngeal swabs were obtained from the patient at each presentation and twice during follow-up. Nucleic acid amplification testing was done to confirm SARS-CoV-2 infection. We did next-generation sequencing of SARS-CoV-2 extracted from nasopharyngeal swabs. Sequence data were assessed by two different bioinformatic methodologies. A short tandem repeat marker was used for fragment analysis to confirm that samples from both infections came from the same individual.FindingsThe patient had two positive tests for SARS-CoV-2, the first on April 18, 2020, and the second on June 5, 2020, separated by two negative tests done during follow-up in May, 2020. Genomic analysis of SARS-CoV-2 showed genetically significant differences between each variant associated with each instance of infection. The second infection was symptomatically more severe than the first.InterpretationGenetic discordance of the two SARS-CoV-2 specimens was greater than could be accounted for by short-term in vivo evolution. These findings suggest that the patient was infected by SARS-CoV-2 on two separate occasions by a genetically distinct virus. Thus, previous exposure to SARS-CoV-2 might not guarantee total immunity in all cases. All individuals, whether previously diagnosed with COVID-19 or not, should take identical precautions to avoid infection with SARS-CoV-2. The implications of reinfections could be relevant for vaccine development and application.FundingNevada IDEA Network of Biomedical Research, and the National Institute of General Medical Sciences (National Institutes of Health).

Dataset Information

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

Publications

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

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