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Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America.
Infect Genet Evol. 2020 11; 85:104557.IG

Abstract

SARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemic. The virus crossed the species barrier and established in the human population taking advantage of the spike protein high affinity for the ACE receptor to infect the lower respiratory tract. The Nucleocapsid (N) and Spike (S) are highly immunogenic structural proteins and most commercial COVID-19 diagnostic assays target these proteins. In an unpredictable epidemic, it is essential to know about their genetic variability. The objective of this study was to describe the substitution frequency of the S and N proteins of SARS-CoV-2 in South America. A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm. Forty-three sequences from 13 Colombian departments were obtained in this study using the Oxford Nanopore and Illumina MiSeq technologies, following the amplicon-based ARTIC network protocol. The substitutions D614G in S and R203K/G204R in N were the most frequent in South America, observed in 83% and 34% of the sequences respectively. Strikingly, genomes with the conserved position D614 were almost completely replaced by genomes with the G614 substitution between March to April 2020. A similar replacement pattern was observed with R203K/G204R although more marked in Chile, Argentina and Brazil, suggesting similar introduction history and/or control strategies of SARS-CoV-2 in these countries. It is necessary to continue with the genomic surveillance of S and N proteins during the SARS-CoV-2 pandemic as this information can be useful for developing vaccines, therapeutics and diagnostic tests.

Authors+Show Affiliations

Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Grupo de Parasitología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia. Electronic address: cefrancom@unal.edu.co.Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.Grupo de Microbiología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia.Grupo de Microbiología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia.Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Centro de Investigación en Salud para el Trópico-CIST, Universidad Cooperativa de Colombia, Santa Marta, 470003, Colombia.Programa Ciencias de la Biodiversidad, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá 111311, Colombia.Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.Dirección de Vigilancia en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.Dirección General, Instituto Nacional de Salud, Bogotá 111321, Colombia.Unidad de Secuenciación y Genómica, Grupo de Investigación Básica y Aplicada en Enfermedades Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32950697

Citation

Franco-Muñoz, Carlos, et al. "Substitutions in Spike and Nucleocapsid Proteins of SARS-CoV-2 Circulating in South America." Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 85, 2020, p. 104557.
Franco-Muñoz C, Álvarez-Díaz DA, Laiton-Donato K, et al. Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Infect Genet Evol. 2020;85:104557.
Franco-Muñoz, C., Álvarez-Díaz, D. A., Laiton-Donato, K., Wiesner, M., Escandón, P., Usme-Ciro, J. A., Franco-Sierra, N. D., Flórez-Sánchez, A. C., Gómez-Rangel, S., Rodríguez-Calderon, L. D., Barbosa-Ramirez, J., Ospitia-Baez, E., Walteros, D. M., Ospina-Martinez, M. L., & Mercado-Reyes, M. (2020). Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 85, 104557. https://doi.org/10.1016/j.meegid.2020.104557
Franco-Muñoz C, et al. Substitutions in Spike and Nucleocapsid Proteins of SARS-CoV-2 Circulating in South America. Infect Genet Evol. 2020;85:104557. PubMed PMID: 32950697.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. AU - Franco-Muñoz,Carlos, AU - Álvarez-Díaz,Diego A, AU - Laiton-Donato,Katherine, AU - Wiesner,Magdalena, AU - Escandón,Patricia, AU - Usme-Ciro,José A, AU - Franco-Sierra,Nicolás D, AU - Flórez-Sánchez,Astrid C, AU - Gómez-Rangel,Sergio, AU - Rodríguez-Calderon,Luz D, AU - Barbosa-Ramirez,Juliana, AU - Ospitia-Baez,Erika, AU - Walteros,Diana M, AU - Ospina-Martinez,Martha L, AU - Mercado-Reyes,Marcela, Y1 - 2020/09/17/ PY - 2020/06/15/received PY - 2020/08/31/revised PY - 2020/09/11/accepted PY - 2020/9/21/pubmed PY - 2020/12/15/medline PY - 2020/9/20/entrez KW - Non-synonymous substitutions KW - Nucleocapsid KW - SARS-CoV-2 KW - South America KW - Spike SP - 104557 EP - 104557 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect Genet Evol VL - 85 N2 - SARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemic. The virus crossed the species barrier and established in the human population taking advantage of the spike protein high affinity for the ACE receptor to infect the lower respiratory tract. The Nucleocapsid (N) and Spike (S) are highly immunogenic structural proteins and most commercial COVID-19 diagnostic assays target these proteins. In an unpredictable epidemic, it is essential to know about their genetic variability. The objective of this study was to describe the substitution frequency of the S and N proteins of SARS-CoV-2 in South America. A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm. Forty-three sequences from 13 Colombian departments were obtained in this study using the Oxford Nanopore and Illumina MiSeq technologies, following the amplicon-based ARTIC network protocol. The substitutions D614G in S and R203K/G204R in N were the most frequent in South America, observed in 83% and 34% of the sequences respectively. Strikingly, genomes with the conserved position D614 were almost completely replaced by genomes with the G614 substitution between March to April 2020. A similar replacement pattern was observed with R203K/G204R although more marked in Chile, Argentina and Brazil, suggesting similar introduction history and/or control strategies of SARS-CoV-2 in these countries. It is necessary to continue with the genomic surveillance of S and N proteins during the SARS-CoV-2 pandemic as this information can be useful for developing vaccines, therapeutics and diagnostic tests. SN - 1567-7257 UR - https://www.unboundmedicine.com/medline/citation/32950697/Substitutions_in_Spike_and_Nucleocapsid_proteins_of_SARS_CoV_2_circulating_in_South_America_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1567-1348(20)30388-9 DB - PRIME DP - Unbound Medicine ER -