Temporal Dynamics and Evolution of SARS-CoV-2 Demonstrate the Necessity of Ongoing Viral Genome Sequencing in Ontario, Canada.

Calvin Sjaarda ,Robert Slinger,Danielle Brabant-Kirwan,Tony Mazzulli,Ramzi Fattouh,Katya Douchant,Aaron Campigotto,Marc Desjardins,Samir N Patel,Samira Mubareka,Leanne Mortimer,Robert I Colautti,Nahuel Fittipaldi,Prameet M Sheth,Allison Mcgeer,Henry Wong,Andrew G Mcarthur,Bettina Hamelin,Jared T Simpson,Jennifer L Guthrie

doi:10.1128/msphere.00011-21

Abstract

Genome-wide variation in SARS-CoV-2 reveals evolution and transmission dynamics which are critical considerations for disease control and prevention decisions. Here, we review estimates of the genome-wide viral mutation rates, summarize current COVID-19 case load in the province of Ontario, Canada (5 January 2021), and analyze published SARS-CoV-2 genomes from Ontario (collected prior to 24 November 2020) to test for more infectious genetic variants or lineages. The reported mutation rate (∼10-6 nucleotide [nt]-1 cycle-1) for SARS-CoV-2 is typical for coronaviruses. Analysis of published SARS-CoV-2 genomes revealed that the G614 spike protein mutation has dominated infections in Ontario and that SARS-CoV-2 lineages present in Ontario have not differed significantly in their rate of spread. These results suggest that the SARS-CoV-2 population circulating in Ontario has not changed significantly to date. However, ongoing genome monitoring is essential for identification of new variants and lineages that may contribute to increased viral transmission.

Highlights

Rate of 1026 to 1024 substitutions per nucleotide per cell infection (s/n/c) is commonly observed in RNA viruses, compared to DNA viruses that mutate at a rate of ;1028 to 1026 s/n/c [12]
D614G MUTATION FREQUENCY One of the most prevalent variants observed in SARS-CoV-2 sequenced genomes is the adenine-to-guanine nucleotide substitution at position 23403, a nonsynonymous mutation resulting in an amino acid substitution from aspartic acid to glycine at position 614 in the spike protein
Given that the G614 variant was already prevalent in Ontario at the beginning of the pandemic and that the D614 variant has not been detected since May, it is likely that the second wave has likewise been dominated by the G614 variant of SARS-CoV-2, suggesting that increased case numbers corresponding to the second wave of COVID-19 are likely unrelated to the spike protein variant

Summary

Introduction

Rate of 1026 to 1024 substitutions per nucleotide (nt) per cell infection (s/n/c) is commonly observed in RNA viruses, compared to DNA viruses that mutate at a rate of ;1028 to 1026 s/n/c [12]. The low mutation rate and high transmission rate of SARS-CoV-2 have resulted in distinct genetic lineages that are shared across large geographic regions. D614G MUTATION FREQUENCY One of the most prevalent variants observed in SARS-CoV-2 sequenced genomes is the adenine-to-guanine nucleotide substitution at position 23403, a nonsynonymous mutation resulting in an amino acid substitution from aspartic acid to glycine at position 614 in the spike protein.

Results

Conclusion