Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child

Background:With the progression of the Coronavirus disease pandemic, the number of mutations in the viral genome has increased, showing the adaptive evolution of severe acute respiratory syndrome coronavirus 2 in humans and intensification in transmissibility. Long-term infections also allow the development of viral diversity. In this study, we report the case of a child with severe combined immu presenting a prolonged severe acute respiratory syndrome coronavirus 2 infection. We aimed to analyze 3 naso-oropharyngeal swab samples collected between August and December 2021 to describe the amino acid changes present in the sequence reads that may have a role in the emergence of new viral variants. Methods:The whole genome from clinical samples was sequenced through high throughput sequencing and analyzed using a workflow to map reads and then find variations/single-nucleotide polymorphisms. In addition, the samples were isolated in cell culture, and a plaque forming units assay was performed, which indicates the presence of viable viral particles. Results:The results obtained showed that the virus present in all samples is infectious. Also, there were 20 common mutations among the 3 sequence reads, found in the ORF1ab and ORF10 proteins. As well, a considerable number of uncommon mutations were found. Conclusions:In conclusion, we emphasize that genomic surveillance can be a useful tool to assess possible evolution signals in long-term patients.

Automated summary

In this study, a case of a child with severe combined immunodeficiency and prolonged severe acute respiratory syndrome coronavirus 2 infection was reported. The amino acid changes present in naso-oropharyngeal swab samples collected between August and December 2021 were analyzed to examine the emergence of new viral variants. Genomic surveillance using high throughput sequencing proved to be a useful tool in assessing possible evolution signals in long-term patients.