Global landscape of SARS-CoV-2 mutations and conserved regions

Abstract

Background: At the end of December 2019, a novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been identified in Wuhan, a central city in China, and then spread to every corner of the globe. As of October 8, 2022, the total number of COVID-19 cases had reached over 621 million worldwide, with more than 6.56 million confirmed deaths. Since SARS-CoV-2 genome sequences change due to mutation and recombination, it is pivotal to surveil emerging variants and monitor changes for improving pandemic management.

Methods: 10,287,271 SARS-CoV-2 genome sequence samples were downloaded in FASTA format from the GISAID databases from February 24, 2020, to April 2022. Python programming language (version 3.8.0) software was utilized to process FASTA files to identify variants and sequence conservation. The NCBI RefSeq SARS-CoV-2 genome (accession no. NC_045512.2) was considered as the reference sequence.

Results: Six mutations had more than 50% frequency in global SARS-CoV-2. These mutations include the P323L (99.3%) in NSP12, D614G (97.6) in S, the T492I (70.4) in NSP4, R203M (62.8%) in N, T60A (61.4%) in Orf9b, and P1228L (50.0%) in NSP3. In the SARS-CoV-2 genome, no mutation was observed in more than 90% of nsp11, nsp7, nsp10, nsp9, nsp8, and nsp16 regions. On the other hand, N, nsp3, S, nsp4, nsp12, and M had the maximum rate of mutations. In the S protein, the highest mutation frequency was observed in aa 508-635(0.77%) and aa 381-508 (0.43%). The highest frequency of mutation was observed in aa 66-88 (2.19%), aa 7-14, and aa 164-246 (2.92%) in M, E, and N proteins, respectively.

Conclusion: Therefore, monitoring SARS-CoV-2 proteomic changes and detecting hot spots mutations and conserved regions could be applied to improve the SARS-CoV-2 diagnostic efficiency and design safe and effective vaccines against emerging variants.

Keywords: Amino Acid; COVID-19; Emerging variants; Genome; SARS-CoV-2; Vaccines.

Fig. 1

Schematic view of the SARS-CoV-2 genome arrangement. SARS-CoV-2 is an enveloped single-stranded positive-sense RNA beta coronavirus with a polycistronic genome ~ 30 kb in length. SARS-CoV-2 genome encodes several non-structural proteins (ORF1a and ORF1b, that are processed into NSP1-16) at the 5′-end, in addition to structural proteins (S, E, M, and N), and multiple other accessory proteins (ORF3a, 6, 7a, 7b, 8, 9b, 9c and 10) at the 3′-end

Fig. 2

Overview of the study design. A Schematic describing the workflow of the study. B Illustration showing the number of SARS-CoV-2 samples. The number of analyzed SARS-CoV-2 samples are mentioned in bars

Fig. 3

Mutation rate of SARS-CoV-2 genome in different geographic areas. The graph reports SARS-CoV-2 frequency of one, two, three, and four more mutations in the SARS-CoV-2 genome by April 28, 2022, in seven geographic areas

Fig. 4

Heat maps of conserved genomic regions of SARS-CoV-2. SARS-CoV-2 genomes are divided into ten regions, and the frequency of mutations is in different regions worldwide. Nsp non-structural protein, S Spike protein, E Envelope protein, M Membrane protein, N Nucleocapsid protein

Fig. 5

Clustering analysis of SARS-CoV-2 proteins. Heat map and dendrogram illustration of SARS-CoV-2 proteins based on the frequency of mutations in ten different regions of SARS-CoV-2 genomes. A Spike. B Envelope. C Membrane, D Nucleocapsid and E NSP12. NTD, N-terminal domain; RBD, receptor-binding domain; FP, fusion peptide; HR, heptapeptide repeat sequence; TM, transmembrane; CT, cytoplasmic tail. LKR, serine-arginine (SR) rich-linker region; RBM, receptor binding motif; CP, cytoplasm domain; TMD α-helical transmembrane domain

Fig. 6

Dynamut prediction of molecular flexibility and destabilizing effect of common SARS-CoV-2 mutations. The protein rigidification and structural flexibility are highlighted in blue and red color, respectively. Light green represents wild-type and mutant residues of protein. A Spike mutation D614G. B Envelope mutation T9I. C Nucleoprotein mutation D63G. D NSP12 mutation 9323L. E Membrane mutations A63T, I82T and Q19E