tetano
Editor, Senior Moderator
J Med Virol
. 2020 Oct 13.
doi: 10.1002/jmv.26591. Online ahead of print.
Analysis of SARS-CoV-2 mutations in Mexico, Belize and isolated regions of Guatemala and its implication in the diagnosis
Mar?a Teresa Hern?ndez-Huerta[SUP] 1 [/SUP], Laura P?rez-Campos Mayoral[SUP] 2 [/SUP], Carlos Romero D?az[SUP] 2 [/SUP], Margarito Mart?nez Cruz[SUP] 3 [/SUP], Gabriel Mayoral-Andrade[SUP] 2 [/SUP], Luis Manuel S?nchez Navarro[SUP] 4 [/SUP], Mar?a Del Socorro Pina Canseco[SUP] 2 [/SUP], Eli Cruz Parada[SUP] 3 [/SUP], Ruth Mart?nez Cruz[SUP] 2 [/SUP], Eduardo P?rez-Campos Mayoral[SUP] 2 [/SUP], Alma Dolores P?rez Santiago[SUP] 3 [/SUP], Gabriela V?squez Mart?nez[SUP] 3 [/SUP], Eduardo P?rez-Campos[SUP] 2 3 5 [/SUP], Carlos Alberto Matias-Cervantes[SUP] 2 [/SUP]
Affiliations
Abstract
Background: The genomic sequences of 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.
Aims: 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.
Methods: 23 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.
Results: 187 distinct variants were identified, of which 102 are missense, 66 synonymous and 19 non-coding. 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 US showed a positive E-value.
Conclusion: 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, further, its diagnosis would be affected. This article is protected by copyright. All rights reserved.
Keywords: SARS coronavirus; genetic variation; mutations.
. 2020 Oct 13.
doi: 10.1002/jmv.26591. Online ahead of print.
Analysis of SARS-CoV-2 mutations in Mexico, Belize and isolated regions of Guatemala and its implication in the diagnosis
Mar?a Teresa Hern?ndez-Huerta[SUP] 1 [/SUP], Laura P?rez-Campos Mayoral[SUP] 2 [/SUP], Carlos Romero D?az[SUP] 2 [/SUP], Margarito Mart?nez Cruz[SUP] 3 [/SUP], Gabriel Mayoral-Andrade[SUP] 2 [/SUP], Luis Manuel S?nchez Navarro[SUP] 4 [/SUP], Mar?a Del Socorro Pina Canseco[SUP] 2 [/SUP], Eli Cruz Parada[SUP] 3 [/SUP], Ruth Mart?nez Cruz[SUP] 2 [/SUP], Eduardo P?rez-Campos Mayoral[SUP] 2 [/SUP], Alma Dolores P?rez Santiago[SUP] 3 [/SUP], Gabriela V?squez Mart?nez[SUP] 3 [/SUP], Eduardo P?rez-Campos[SUP] 2 3 5 [/SUP], Carlos Alberto Matias-Cervantes[SUP] 2 [/SUP]
Affiliations
- PMID: 33049069
- DOI: 10.1002/jmv.26591
Abstract
Background: The genomic sequences of 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.
Aims: 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.
Methods: 23 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.
Results: 187 distinct variants were identified, of which 102 are missense, 66 synonymous and 19 non-coding. 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 US showed a positive E-value.
Conclusion: 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, further, its diagnosis would be affected. This article is protected by copyright. All rights reserved.
Keywords: SARS coronavirus; genetic variation; mutations.