Stability of SARS-CoV-2 Phylogenies

Abstract

The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors associated with lab-specific practices affect some sequences in the repositories. We find that some recurrent mutations in reported SARS-CoV-2 genome sequences have been observed predominantly or exclusively by single labs, co-localize with commonly used primer binding sites and are more likely to affect the protein coding sequences than other similarly recurrent mutations. We show that their inclusion can affect phylogenetic inference on scales relevant to local lineage tracing, and make it appear as though there has been an excess of recurrent mutation and/or recombination among viral lineages. We suggest how samples can be screened and problematic mutations removed. We also develop tools for comparing and visualizing differences among phylogenies and we show that consistent clade-and tree-based comparisons can be made between phylogenies produced by different groups. These will facilitate evolutionary inferences and comparisons among phylogenies produced for a wide array of purposes. Building on the SARS-CoV-2 Genome Browser at UCSC, we present a toolkit to compare, analyze and combine SARS-CoV-2 phylogenies, find and remove potential sequencing errors and establish a widely shared, stable clade structure for a more accurate scientific inference and discourse.Foreword:

Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic

“…Whereas UShER appears to be robust to a single systematic error present in fewer than five samples ( Figure 2), a single systematic error present in all 10 samples had a similar overall effect on placement accuracy as 50% missing data in error-free sequences. Consistent with our previous work 37,38 , addition of two perfectly correlated systematic errors can drastically affect UShER performance ( Figure S1). Systematic errors should be rigorously identified and removed before sample placements are performed.…”

“…Second, systematic error, where the same apparent variant is introduced into many sequences, are present in some SARS-CoV-2 sequences and have the potential to affect phylogenetic inference because they appear as inherited mutations 37,38 . Whereas UShER appears to be robust to a single systematic error present in fewer than five samples ( Figure 2), a single systematic error present in all 10 samples had a similar overall effect on placement accuracy as 50% missing data in error-free sequences.…”

“…Systematic errors should be rigorously identified and removed before sample placements are performed. We refer readers to methods that we developed previously to detect and eliminate such errors 37,38 and the UShER package includes a tool to remove known problematic positions when preparing input data.…”

“…Quantifying Uncertainty in Sample Placement: Quantifying uncertainty in phylogenetic placement is critical for accurately interpreting SARS-CoV-2 phylogenies where true phylogenetic signal is limited and sometimes even contradictory 36,37 . We developed functionality within UShER to report the number of equally parsimonious placements by default.…”

Phylogenetic analysis of SARS-CoV-2 data is difficult

“…Our singleton removal strategy is further justified by a recent study that has shown that lab-specific sequencing practices yield mutations that have been observed predominantly or exclusively by single labs. These can in turn affect the phylogeny reconstruction process (26). The authors provide regularly updated masking recommendations at https://github.com/W-L/ProblematicSites_ SARS-CoV2/blob/master/problematic_sites_ sarsCov2.vcf.…”