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Insights from a workplace SARS-CoV-2 specimen collection program, with genomes placed into global sequence phylogeny
Owen P Leiser1, Deanna L Auberry2, Erica Bakker2
1Pacific Northwest National Laboratory, Chemical and Biological Signatures, Seattle, WA, United States of America.
Plos One
|April 28, 2023
Summary
Pacific Northwest National Laboratory analyzed SARS-CoV-2 specimens, finding a weak link between patient age and viral load. Viral sequencing revealed significant geographic mixing of virus strains, indicating widespread transmission.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- The National Virtual Biotechnology Laboratory (NVBL) was established by the Department of Energy in 2020 to combat COVID-19.
- Pacific Northwest National Laboratory (PNNL) developed a SARS-CoV-2 specimen collection and analysis program for symptomatic employees.
Purpose of the Study:
- To screen employee specimens for SARS-CoV-2.
- To sequence and analyze positive samples to understand viral characteristics and transmission dynamics.
Main Methods:
- Reverse-transcriptase quantitative PCR (RT-qPCR) for SARS-CoV-2 detection.
- Whole-genome sequencing and genotyping of positive samples.
- Phylogenetic analysis to investigate viral relationships and transmission patterns.
Main Results:
- Out of 688 specimens, 64 (9.3%) tested positive for SARS-CoV-2 via RT-qPCR.
- A weak statistical correlation was found between patient age and viral load (Ct values).
- Phylogenetic analysis indicated that many viral sequences had closest relatives outside Washington state, suggesting inter-regional viral mixing.
Conclusions:
- The study characterized SARS-CoV-2 strains from PNNL employees, providing insights into viral load and age.
- Findings highlight the interconnectedness of viral transmission across geographic regions.
- The research underscores the importance of genomic surveillance in understanding pathogen spread.
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