Inflection in prevalence of SARS-CoV-2 infections missing the N501Y mutation as a marker of rapid Delta (B.1.617.2) lineage expansion in Ontario, Canada
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Abstract
Background
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta lineage (B.1.617.2) was implicated in the SARS-CoV-2 surge in India. We sought to describe the rapid expansion of the Delta lineage in Ontario, Canada (population 15 million) using mutation profile information and confirmatory whole genome sequencing.
Methods
All laboratory-confirmed SARS-CoV-2 cases reported to Public Health Ontario between April 1 st and June 12 th 2021, with cycle threshold values ≤35, were eligible for screening for the N501Y and the E484K mutations. We classified cases via mutation screening as: (1) N501Y-/E484K- (wild-type/Delta), (2) Alpha (N501Y+/E484K-), (3) Beta/Gamma (N501Y+/E484K+), or (4) N501Y-/E484K+ (predominantly B.1.525, and B.1.1.318).
Results
The N501Y-/E484K- mutation profile went from having a 29% transmission deficit relative to Alpha (relative R e = 0.71, 95%CI: 0.64, 0.77) on April 1 st to having a 50% transmission advantage on June 12 th (relative R e = 1.50, 95%CI: 1.31, 1.71). Whole genome sequencing of N501Y-/E484K-cases (N=583) confirmed that the pattern of increasing relative reproduction number coincided with the replacement of wild-type with Delta variant (from 2.2% in early April, to 83% in late May).
Discussion
Delta is rapidly overtaking other SARS-CoV-2 variants in Ontario, and has a substantial transmission advantage. An inflection in the proportion of cases missing the N501Y mutation from rapidly decreasing to rapidly increasing, 3 may be an early warning signal for Delta lineage expansion.
Article activity feed
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SciScore for 10.1101/2021.06.22.21259349: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Limitations include potentially non-representative sampling for whole genome sequencing. For countries once dominated by Alpha, Beta, or Gamma lineages, an inflection in the proportion of cases missing the N501Y mutation from rapidly decreasing to rapidly increasing,3 may be an early warning signal for Delta lineage expansion.
Results …
SciScore for 10.1101/2021.06.22.21259349: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Limitations include potentially non-representative sampling for whole genome sequencing. For countries once dominated by Alpha, Beta, or Gamma lineages, an inflection in the proportion of cases missing the N501Y mutation from rapidly decreasing to rapidly increasing,3 may be an early warning signal for Delta lineage expansion.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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