Phylogenetic analysis of SARS‐CoV‐2 in the first few months since its emergence

Abstract

During the first months of SARS‐CoV‐2 evolution in a new host, contrasting hypotheses have been proposed about the way the virus has evolved and diversified worldwide. The aim of this study was to perform a comprehensive evolutionary analysis to describe the human outbreak and the evolutionary rate of different genomic regions of SARS‐CoV‐2. The molecular evolution in nine genomic regions of SARS‐CoV‐2 was analyzed using three different approaches: phylogenetic signal assessment, emergence of amino acid substitutions, and Bayesian evolutionary rate estimation in eight successive fortnights since the virus emergence. All observed phylogenetic signals were very low and tree topologies were in agreement with those signals. However, after four months of evolution, it was possible to identify regions revealing an incipient viral lineage formation despite the low phylogenetic signal, since fortnight 3. Finally, the SARS‐CoV‐2 evolutionary rate for regions nsp3 and S, the ones presenting greater variability, was estimated as 1.37 x 10 ‐3 and 2.19 x 10 ‐3 substitution/site/year, respectively. In conclusion, results from this work about the variable diversity of crucial viral regions and determination of the evolutionary rate are consequently decisive to understand essential features of viral emergence. In turn, findings may allow the first time characterization of the evolutionary rate of S protein, crucial for vaccine development. This article is protected by copyright. All rights reserved.

Evolutionary analysis of SARS-CoV-2 spike protein for its different clades

“…This is expected since the complete genome includes several genomic regions with a high degree of conservation, while the S region is one of the most rapidly evolving in the SARS-CoV-2 genome (Pereson et al 2020). Nonetheless, the spike evolution rate was quite similar to that obtained by analyzing this region during the first four months of the pandemic (Pereson et al 2020). Although the evolutionary rate of all clades was similar, the founding clades (L, O, V, and S) showed evolutionary rates slightly lower than the most recent and currently more distributed ones (G, GH, and GR).…”

“…The evolutionary rate of S protein estimated for all together clades was significantly higher than that previously reported by analyzing the entire genome (van Dorp et al 2020; Liu et al 2020). This is expected since the complete genome includes several genomic regions with a high degree of conservation, while the S region is one of the most rapidly evolving in the SARS-CoV-2 genome (Pereson et al 2020). Nonetheless, the spike evolution rate was quite similar to that obtained by analyzing this region during the first four months of the pandemic (Pereson et al 2020).…”

“…Even though some studies have determined the nucleotide evolutionary rate of SARS-CoV-2 using the entire genome (Giovanetti et al 2020; van Dorp et al 2020), those values are slower and do not represent the real mutation capacity of the S region alone. Only one study has reported the nucleotide evolutionary rate of the S genomic region in the first four months of the pandemic, but without differentiating the seven viral clades, which can be relevant in therapeutics and re-infections (Pereson et al 2020). Thus, the aim of this study was to determine the nucleotide evolutionary rate and the haplotype network of the S region for SARS-CoV-2 in general and for each of the seven genetic clades during the first nine months of pandemic.…”

Adaptation of advanced clinical virology assays from HIV-1 to SARS-CoV-2

“…Since the first sequence of SARS-CoV-2 was generated [ 22 ▪ ], more than 95 000 SARS-CoV-2 sequences have been deposited in the global initiative on sharing all influenza data (GISAID). Unlike HIV-1, which has high-level heterogeneity even within an infected individual with an estimated substitution rate of 0.8–1.7 × 10 −3 per site per year [ 66 – 68 ], SARS-CoV-2 sequences have a high-sequence identity with a substitution rate estimated to be 8.4 × 10 −4 –1.1 × 10 −3 per site per year at the population level [ 69 – 72 ]. This conservation has largely been attributed to the exoribonuclease (ExoN) activity of the nonstructural protein 14 (nsp14) as it was demonstrated that wild-type SARS-CoV has a mutation rate of 9.0 × 10 −7 substitutions per nucleotide per replication cycle [ 73 ].…”

Evolutionary analysis of SARS‐CoV‐2 spike protein for its different clades

“…Only one study has reported the nucleotide evolutionary rate of the S genomic region in the first four months of the pandemic, but without differentiating the seven viral clades, which can be relevant in therapeutics and re-infections. 15 Thus, the aim of this study was to determine the nucleotide evolutionary rate and the haplotype network of the S region for SARS-CoV-2 in general and for each of the seven genetic clades during the first nine months of the pandemic.…”