Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Area of Science:

• Genomics
• Bioinformatics
• Virology

Background:

• Genomic sequencing of SARS-CoV-2 is vital for identifying variants and informing public health strategies.
• The COVID-19 pandemic saw a surge in sequencing, enabling rapid variant detection and response.
• Current bioinformatic analysis of sequencing data is inconsistent across different groups.

Purpose of the Study:

• To highlight the discrepancies in SARS-CoV-2 genome sequences generated by different bioinformatic protocols.
• To propose standardized parameters and protocols for consistent bioinformatic analysis.
• To emphasize the importance of data consistency for pathogen surveillance.

Main Methods:

• Comparison of downstream bioinformatic protocols used on Illumina and Oxford Nanopore sequencing platforms.
• Analysis of raw sequence data from clinical samples to identify variations in generated consensus genomes.
• Characterization of discrepancies including single nucleotide polymorphisms, insertions, and deletions.

Main Results:

• Different bioinformatic workflows produced disparate SARS-CoV-2 virus sequences from the same sample.
• Variations included differences in single nucleotide polymorphisms and the inclusion/exclusion of insertions and deletions.
• These inconsistencies were observed across both Illumina and Oxford Nanopore sequencing platforms.

Conclusions:

• Lack of standardized bioinformatic analysis leads to significant discrepancies in SARS-CoV-2 genome sequences.
• Standardized protocols are essential for accurate variant identification and reliable pathogen surveillance.
• Consistent genomic data is fundamental for effective pandemic preparedness and public health decision-making.