Genome evolution of SARS-CoV-2 and its virological characteristics

Abstract

Coronavirus disease of 2019 (COVID-19), which originated in China in 2019, shows mild cold and pneumonia symptoms that can occasionally worsen and result in deaths. SARS-CoV-2 was reported to be the causative agent of the disease and was identified as being similar to SARS-CoV, a causative agent of SARS in 2003. In this review, we described the phylogeny of SARS-CoV-2, covering various related studies, in particular, focusing on viruses obtained from horseshoe bats and pangolins that belong to Sarbecovirus, a subgenus of Betacoronavirus. We also describe the virological characteristics of SARS-CoV-2 and compare them with other coronaviruses. More than 30,000 genome sequences of SARS-CoV-2 are available in the GISAID database as of May 28, 2020. Using the genome sequence data of closely related viruses, the genomic characteristics and evolution of SARS-CoV-2 were extensively studied. However, given the global prevalence of COVID-19 and the large number of associated deaths, further computational and experimental virological analyses are required to fully characterize SARS-CoV-2.

Keywords: COVID-19; Comparative genomics; Coronavirus; SARS-CoV-2; Viral evolution.

Fig. 1

Phylogeny of orthocoronaviruses. Maximum likelihood (ML)-based phylogenetic tree of 61 orthocoronaviruses. Partial amino acid sequences of ORF1ab were used for the analysis. We generated the multiple alignment of the sequences using L-INS-i of MAFFT version 7.453 [9], and the amino acid substitution model LG+I+G was selected using ProtTest3 [10]. Based on the model, we constructed an ML tree using RAxML-NG [11] applying 1000 bootstrapping tests. GenBank or GISAID (that was indicated by asterisk (*)) accession number, strain name, and host of each virus are indicated for each branch terminal. CoVs obtained from humans or bats are shown in red or blue, respectively. A black or open circle corresponds to bootstrap values ≥ 95% or ≥ 80%, respectively. The scale is shown in the upper left

Fig. 2

Phylogeny of CoVs belonging to Sarbecoronavirus. ML-based phylogenetic tree of 41 CoVs belonging to Sarbecoronavirus including SARS-CoV-2. Whole genome sequences were used for the analysis. We generated the multiple alignment of the sequences using L-INS-i of MAFFT version 7.453 [9], and the nucleotide substitution model GTR+I+G was selected using ModelTest-NG [13]. Based on the model, we constructed an ML tree using RAxML-NG [11], applying 1000 bootstrapping tests. Please see Fig. 1 legend for the details of this figure

Fig. 3

Genomic structure of SARS-CoV-2. Schematic genomic structure of SARS-CoV-2 was shown based on the SARS-CoV-2 Wuhan-Hu-1 (NCBI Reference Sequence ID: NC_045512.2). The scale was shown on the top. Each ORF was illustrated based on the NCBI annotation of NC_045512.2, and a rectangle filled with black corresponds to a structural protein. The number in parentheses is the length of amino acid sequence (aa, amino acid). A gene name as well as rectangle colored in light blue was a hypothetical ORF which is not annotated NC_045512.2 currently. ORF3b is based on Konno et al. [15], and the others are based on Davidson et al. [16] and Jungreis et al. [17]