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Author Spotlight: Advancements in Multiplex Detection of Respiratory Viruses
Published on: November 10, 2023
Early pandemic molecular diversity of SARS-CoV-2 in children
Ahmed M Moustafa1, William Otto1, Xiaowu Gai2,3
1Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Insights
Early SARS-CoV-2 spread in Philadelphia involved diverse viral variants, with children showing varied genotypes. Whole genome sequencing revealed no significant genotype-associated clinical differences in pediatric patients.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- Community circulation of SARS-CoV-2 in the US began around February 2020.
- Philadelphia healthcare institutions initiated widespread testing for SARS-CoV-2 in March-April 2020.
Approach:
- Collected 169 SARS-CoV-2 samples (83 pediatric) from March-May 2020.
- Performed whole genome sequencing and utilized genotyping tools.
- Tracked viral variants and assessed genotype-associated clinical presentations and outcomes in children.
Key Points:
- Identified 13 major SARS-CoV-2 lineages during the April 2020 peak in Philadelphia.
- Detected at least 6 introductions of distinct viral variants.
- Observed greater viral genotype diversity in pediatric patients compared to adults.
Conclusions:
- Whole genome analysis revealed significant viral diversity and distinct variants during Philadelphia's initial SARS-CoV-2 outbreak.
- Most viral introductions were local, originating from nearby states.
- No evidence suggested genotype-specific clinical impacts in children, despite sample size limitations.
Background:
In the US, community circulation of the SARS-CoV-2 virus likely began in February 2020 after mostly travel-related cases. Children's Hospital of Philadelphia began testing on 3/9/2020 for pediatric and adult patients, and for all admitted patients on 4/1/2020, allowing an early glimpse into the local molecular epidemiology of the virus.
Methods:
We obtained 169 SARS-CoV-2 samples (83 from patients <21 years old) from March through May and produced whole genome sequences. We used genotyping tools to track variants over time and to test for possible genotype associated clinical presentations and outcomes in children.
Results:
Our analysis uncovered 13 major lineages that changed in relative abundance as cases peaked in mid-April in Philadelphia. We detected at least 6 introductions of distinct viral variants into the population. As a group, children had more diverse virus genotypes than the adults tested. No strong differences in clinical variables were associated with genotypes.
Conclusions:
Whole genome analysis revealed unexpected diversity, and distinct circulating viral variants within the initial peak of cases in Philadelphia. Most introductions appeared to be local from nearby states. Although limited by sample size, we found no evidence that different genotypes had different clinical impacts in children in this study.
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