Analysis of SARS-CoV-2 mutations in Mexico, Belize, and isolated regions of Guatemala and its implication in the diagnosis

Abstract

The genomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide are publicly available and are derived from studies due to the increase in the number of cases. The importance of study of mutations is related to the possible virulence and diagnosis of SARS-CoV-2. To identify circulating mutations present in SARS-CoV-2 genomic sequences in Mexico, Belize, and Guatemala to find out if the same strain spread to the south, and analyze the specificity of the primers used for diagnosis in these samples. Twenty three complete SARS-CoV-2 genomic sequences, available in the GISAID database from May 8 to September 11, 2020 were analyzed and aligned versus the genomic sequence reported in Wuhan, China (NC_045512.2), using Clustal Omega. Open reading frames were translated using the ExPASy Translate Tool and UCSF Chimera (v.1.12) for amino acid substitutions analysis. Finally, the sequences were aligned versus primers used in the diagnosis of COVID-19. One hundred and eighty seven distinct variants were identified, of which 102 are missense, 66 synonymous and 19 noncoding. P4715L and P5828L substitutions in replicase polyprotein were found, as well as D614G in spike protein and L84S in ORF8 in Mexico, Belize, and Guatemala. The primers design by CDC of United States showed a positive E value. The genomic sequences of SARS-CoV-2 in Mexico, Belize, and Guatemala present similar mutations related to a virulent strain of greater infectivity, which could mean a greater capacity for inclusion in the host genome and be related to an increased spread of the virus in these countries, furthermore, its diagnosis would be affected.

Keywords: SARS coronavirus; genetic variation; mutations.

Figure 1

Nucleotide variations and distribution identified in the SARS‐CoV‐2 genomic sequences from Mexico, Guatemala, and Belize

Figure 2

Mutations P4715L and G614G: (A) amino acid P4715 in red spheres, correspondent to residue 323 in RdRp protein of SARS‐CoV‐2. In blue spheres D760 and D761 active sites. In magenta sticks, V763, C622, N695, Y619, and F812 residues. These residues, lying 5 Å surrounding DD active site. In orange sticks, H295, C301, C306, and C310 residues (Zn⁺ ion binding site). Structure was downloaded from PDB (https://www.rcsb.org/) ID 6M71.pdb, and edited using UCSF Chimera, v.1.12. (B) Amino acid substitution D614G on spike (original model downloaded from rcsb.org, code 6VSB.pdb). G614 mutation is far away from important residues for attachment (RBD in green light spheres) and fusion (fusion peptides, red spheres, residues 788–806) with membrane. Visualization using Chimera UCSF, v.1.12

Figure 3

Spatial distribution of the mutation L84S in the ORF8 protein. L84P mutation is represented in red sticks and in wire light sea green color, R48, G50, L57, P56, Q72, and Y73. In yellow sticks, a probable Hg⁺ ion binding site