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.

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact

“…This approach has been reported previously to detect other virus mutations with clinical importance, such as the ones in the influenza virus (Bolotin et al, 2009;van der Vries et al, 2010;Wong et al, 2011;Hoang Vu Mai et al, 2019). A similar screening was also performed by analyzing SARS-CoV-2 mutations and evaluating their diagnosis implication (Hernańdez-Huerta et al, 2020).…”

Emerging SARS-CoV-2 variants of concern and potential intervention approaches

“…Another concern is a variant detected in France of a S deletion (ΔH69-V70) which has shown to be associated with S-gene target gene detection failure in three-target RT-PCR [48]. Several reports have targeted mutations in different open reading frames (ORFs) especially ORF8 position which was found in some isolates from Mexico, Belize and Guatemala as potentially leading to epitope loss and reduced sensitivity for serological testing [49][50][51].…”

Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation

“…Previous in vitro and simulation studies have found that G614 mutation is considered as more infectious variant than the D614 wildtype (Daniloski et al, 2020;Hou et al, 2020;Hu et al, 2020;Korber et al, 2020;Li et al, 2020;. Studies showed that D614G mutation is associated with antigenic epitopes (Gupta et al, 2020;Hernández-Huerta et al, 2020;Islam et al, 2020;Kim et al, 2020;Koyama et al, 2020;Saha et al, 2020; . CC-BY-NC 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.…”

“…The copyright holder for this preprint this version posted April 19, 2021. ; https://doi.org/10.1101/2021.04.12.21255337 doi: medRxiv preprint 9 2020), antibody neutralizing sensitivity (Goldman et al, 2020;Hu et al, 2020;Klumpp-Thomas et al, 2020;Li et al, 2020;Mansbach et al, 2020), infectivity (Daniloski et al, 2020;van Dorp et al, 2020;Hu et al, 2020;Korber et al, 2020;Li et al, 2020), transmission (van Dorp et al, 2020 and fatality (Hernández-Huerta et al, 2020). Plante et al 2020 have suggested that SARS CoV-2 G614 variant has roles in increasing upper respiratory viral loads, transmissions and survival fitness of the virus (Plante et al, 2020).…”