Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between Janua...
- Autores:
-
Laiton Donato, Katherine
Franco Muñoz, Carlos
Álvarez Díaz, Diego Alejandro
Ruiz Moreno, Hector A.
Usme Ciro, José Aldemar
Prada, Diego A.
Reales Gonzalez, Jhonnatan
Corchuelo, Sheryll
Herrera Sepulveda, Maria T.
Naizaque, Julián Ricardo
Santamaría, Gerardo
Rivera, Jorge Alonso
Rojas, Paola
Hernandez Ortiz, Juan
Cardona, Andres
Malo, Diana
Prieto Alvarado, Franklin
Ruiz Gómez, Fernando
Wiesner, Magdalena
Ospina Martínez, Martha L.
Mercado Reyes, Marcela
- Tipo de recurso:
- Article of investigation
- Fecha de publicación:
- 2021
- Institución:
- Universidad Cooperativa de Colombia
- Repositorio:
- Repositorio UCC
- Idioma:
- OAI Identifier:
- oai:repository.ucc.edu.co:20.500.12494/45597
- Acceso en línea:
- https://hdl.handle.net/20.500.12494/45597
- Palabra clave:
- SARS-CoV-2
Variantes
Evolución
Colombia
SARS-CoV-2
Variants
Evolution
Colombia
- Rights
- openAccess
- License
- Atribución – Sin Derivar
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Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 |
| title |
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 |
| spellingShingle |
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 SARS-CoV-2 Variantes Evolución Colombia SARS-CoV-2 Variants Evolution Colombia |
| title_short |
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 |
| title_full |
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 |
| title_fullStr |
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 |
| title_full_unstemmed |
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 |
| title_sort |
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 |
| dc.creator.fl_str_mv |
Laiton Donato, Katherine Franco Muñoz, Carlos Álvarez Díaz, Diego Alejandro Ruiz Moreno, Hector A. Usme Ciro, José Aldemar Prada, Diego A. Reales Gonzalez, Jhonnatan Corchuelo, Sheryll Herrera Sepulveda, Maria T. Naizaque, Julián Ricardo Santamaría, Gerardo Rivera, Jorge Alonso Rojas, Paola Hernandez Ortiz, Juan Cardona, Andres Malo, Diana Prieto Alvarado, Franklin Ruiz Gómez, Fernando Wiesner, Magdalena Ospina Martínez, Martha L. Mercado Reyes, Marcela |
| dc.contributor.author.none.fl_str_mv |
Laiton Donato, Katherine Franco Muñoz, Carlos Álvarez Díaz, Diego Alejandro Ruiz Moreno, Hector A. Usme Ciro, José Aldemar Prada, Diego A. Reales Gonzalez, Jhonnatan Corchuelo, Sheryll Herrera Sepulveda, Maria T. Naizaque, Julián Ricardo Santamaría, Gerardo Rivera, Jorge Alonso Rojas, Paola Hernandez Ortiz, Juan Cardona, Andres Malo, Diana Prieto Alvarado, Franklin Ruiz Gómez, Fernando Wiesner, Magdalena Ospina Martínez, Martha L. Mercado Reyes, Marcela |
| dc.subject.spa.fl_str_mv |
SARS-CoV-2 Variantes Evolución Colombia |
| topic |
SARS-CoV-2 Variantes Evolución Colombia SARS-CoV-2 Variants Evolution Colombia |
| dc.subject.other.spa.fl_str_mv |
SARS-CoV-2 Variants Evolution Colombia |
| description |
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between January and April 2021, were processed for genome sequencing and lineage determination following the nanopore amplicon ARTIC network protocol and PANGOLIN pipeline. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes I95I, Y144T, Y145S and the insertion 146 N in the N-terminal domain, R346K, E484K and N501Y in the Receptor binding Domain (RBD) and P681H in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlantico, Bolivar, Bogotá D.C, and Santander that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage. |
| publishDate |
2021 |
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2021-08-14 |
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2022-07-07T14:21:26Z |
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2022-07-07T14:21:26Z |
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Artículos Científicos |
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http://purl.org/coar/resource_type/c_2df8fbb1 |
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1567-1348 |
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10.1016/j.meegid.2021.105038 |
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https://hdl.handle.net/20.500.12494/45597 |
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Laiton-Donato K, Franco-Muñoz C, Álvarez-Díaz DA, Ruiz-Moreno HA, Usme-Ciro JA, et al. (2021). Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. Infect Genet Evol. 95:105038. doi: 10.1016/j.meegid.2021.105038.https://repository.ucc.edu.co/handle/20.500.12494/45597 |
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1567-1348 10.1016/j.meegid.2021.105038 Laiton-Donato K, Franco-Muñoz C, Álvarez-Díaz DA, Ruiz-Moreno HA, Usme-Ciro JA, et al. (2021). Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. Infect Genet Evol. 95:105038. doi: 10.1016/j.meegid.2021.105038.https://repository.ucc.edu.co/handle/20.500.12494/45597 |
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https://www.sciencedirect.com/science/article/pii/S1567134821003361?via%3Dihub |
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Infection, Genetics and Evolution |
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Abdool Karim, S.S., de Oliveira, T., 2021 Mar 24. New SARS-CoV-2 variants — clinical, public health, and vaccine implications. N. Engl. J. Med. https://doi.org/10.1056/ NEJMc2100362 [Internet]. [cited 2021 Apr 30];NEJMc2100362. Bal, A., Destras, G., Gaymard, A., Stefic, K., Marlet, J., Eymieux, S., et al., 2021 Jan 21. Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/ 01 and other variants with spike deletion H69–V70, France, August to December 2020. Eurosurveillance 26 (3), 2100008 [Internet]. [cited 2021 May 4]. CDC, 2021. SARS-CoV-2 variants of concern as of 4 May 2021 [Internet] [cited 2021 May 4]. Available from: https://www.ecdc.europa.eu/en/covid-19/variants-concern. Davies, N.G., Abbott, S., Barnard, R.C., Jarvis, C.I., Kucharski, A.J., Munday, J.D., et al., 2021 Apr 9. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science (80-) 372 (6538) [Internet]. [cited 2021 Apr 30]. eabg3055. Garcia-Beltran, W.F., Lam, E.C., St. Denis, K., Nitido, A.D., Garcia, Z.H., Hauser, B.M., et al., 2021 Apr 29. Multiple SARS-CoV-2 variants escape neutralization by vaccineinduced humoral immunity. Cell 184 (9). https://doi.org/10.1016/j. cell.2021.03.013 [Internet]. 2372-2383.e9. Greaney, A.J., Loes, A.N., Crawford, K.H.D., Starr, T.N., Malone, K.D., Chu, H.Y., et al., 2021 Mar 10. Comprehensive mapping of mutations in the SARS-CoV-2 receptorbinding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 29 (3) [Internet]. [cited 2021 Apr 30]. 463–476.e6. Jeyanathan, M., Afkhami, S., Smaill, F., Miller, M.S., Lichty, B.D., Xing, Z., 2020. Immunological considerations for COVID-19 vaccine strategies [Internet] Nat. Rev. Immunol. Nat. Res. 20, 615–632 [cited 2021 Apr 30]. Laiton-Donato, K., Villabona-Arenas, C.J., Usme-Ciro, J.A., Franco-Munoz, ˜ C., Alvarez- ´ Díaz, D.A., Villabona-Arenas, L.S., et al., 2020 Dec 1. Genomic epidemiology of severe acute respiratory syndrome coronavirus 2, Colombia. Emerg. Infect. Dis. 26 (12), 2854–2862 [Internet]. [cited 2021 Apr 30]. Laiton-Donato, K., Usme-Ciro, J.A., Franco-Munoz, ˜ C., Alvarez-Díaz, ´ D.A., RuizMoreno, H.A., Reales-Gonz´ alez, J., et al., 2021 Mar 15. Novel highly divergent SARSCoV-2 lineage with the Spike substitutions L249S and E484K. medRxiv. https://doi. org/10.1101/2021.03.12.21253000 pre-print [Internet]. [cited 2021 May 7]; 2021.03.12.21253000. Liu, Z., VanBlargan, L.A., Bloyet, L.-M., Rothlauf, P.W., Chen, R.E., Stumpf, S., et al., 2021 Mar 10. Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Cell Host Microbe 29 (3) [Internet]. [cited 2021 May 1]. 477–488.e4. Noticias Coronavirus-Genoma [Internet]. [cited 2021 Apr 30]. Available from: http s://www.ins.gov.co/Noticias/Paginas/coronavirus-genoma.aspx. PAHO, 2021. Guidance for SARS-CoV-2 Samples Selection for Genomic Characterization and Surveillance - PAHO/WHO. Pan American Health Organization [Internet]. [cited 2021 May 7]. Available from: https://www.paho.org/en/documents/guida nce-sars-cov-2-samples-selection-genomic-characterization-and-surveillance. Rees-Spear, C., Muir, L., Sa, G., Heaney, J., Aldon, Y., Jl, S., et al., 2021 Jan 19. The impact of Spike mutations on SARS-CoV-2 neutralization 1. bioRxiv 4. https://doi. org/10.1101/2021.01.15.426849 [Internet]. 2021.01.15.426849. Available from:. [cited 2021 Mar 2] Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C.O., Finkin, S., et al., 2021 Feb 10. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature 592 (7855), 616–622 [Internet]. [cited 2021 Apr 30]. Available from: https ://www.nature.com/articles/s41586-021-03324-6. Wibmer, C.K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., et al., 2021 Apr 1. SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma. Nat. Med. 27 (4), 622–625 [Internet]. [cited 2021 Apr 30]. Available from: https://doi.org/10.1038/s41591-021-01285-x. Xie, X., Liu, Y., Liu, J., Zhang, X., Zou, J., Fontes-Garfias, C.R., et al., 2021 Apr 1. Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera. Nat. Med. 27 (4), 620–621 [Internet]. [cited 2021 May 1]. Available from: https://doi.org/10.1038/s41591-021-01270-4. |
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Michel Tibayrenc Universidad Cooperativa de Colombia, Facultad de Ciencias de la Salud, Medicina, Santa Marta |
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Laiton Donato, KatherineFranco Muñoz, CarlosÁlvarez Díaz, Diego AlejandroRuiz Moreno, Hector A.Usme Ciro, José AldemarPrada, Diego A.Reales Gonzalez, JhonnatanCorchuelo, SheryllHerrera Sepulveda, Maria T.Naizaque, Julián RicardoSantamaría, GerardoRivera, Jorge AlonsoRojas, PaolaHernandez Ortiz, JuanCardona, AndresMalo, DianaPrieto Alvarado, FranklinRuiz Gómez, FernandoWiesner, MagdalenaOspina Martínez, Martha L.Mercado Reyes, Marcela952022-07-07T14:21:26Z2022-07-07T14:21:26Z2021-08-141567-134810.1016/j.meegid.2021.105038https://hdl.handle.net/20.500.12494/45597Laiton-Donato K, Franco-Muñoz C, Álvarez-Díaz DA, Ruiz-Moreno HA, Usme-Ciro JA, et al. (2021). Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. Infect Genet Evol. 95:105038. doi: 10.1016/j.meegid.2021.105038.https://repository.ucc.edu.co/handle/20.500.12494/45597Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between January and April 2021, were processed for genome sequencing and lineage determination following the nanopore amplicon ARTIC network protocol and PANGOLIN pipeline. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes I95I, Y144T, Y145S and the insertion 146 N in the N-terminal domain, R346K, E484K and N501Y in the Receptor binding Domain (RBD) and P681H in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlantico, Bolivar, Bogotá D.C, and Santander that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage.https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000318507https://orcid.org/0000-0002-8093-0544https://scienti.minciencias.gov.co/gruplac/jsp/visualiza/visualizagr.jsp?nro=00000000008981jose.usmec@campusucc.edu.cohttps://scholar.google.com.co/citations?user=cU2KyT4AAAAJ&hl=en5Michel TibayrencUniversidad Cooperativa de Colombia, Facultad de Ciencias de la Salud, Medicina, Santa MartaMedicinaSanta Martahttps://www.sciencedirect.com/science/article/pii/S1567134821003361?via%3DihubInfection, Genetics and EvolutionAbdool Karim, S.S., de Oliveira, T., 2021 Mar 24. New SARS-CoV-2 variants — clinical, public health, and vaccine implications. N. Engl. J. Med. https://doi.org/10.1056/ NEJMc2100362 [Internet]. [cited 2021 Apr 30];NEJMc2100362.Bal, A., Destras, G., Gaymard, A., Stefic, K., Marlet, J., Eymieux, S., et al., 2021 Jan 21. Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/ 01 and other variants with spike deletion H69–V70, France, August to December 2020. Eurosurveillance 26 (3), 2100008 [Internet]. [cited 2021 May 4].CDC, 2021. SARS-CoV-2 variants of concern as of 4 May 2021 [Internet] [cited 2021 May 4]. Available from: https://www.ecdc.europa.eu/en/covid-19/variants-concern.Davies, N.G., Abbott, S., Barnard, R.C., Jarvis, C.I., Kucharski, A.J., Munday, J.D., et al., 2021 Apr 9. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science (80-) 372 (6538) [Internet]. [cited 2021 Apr 30]. eabg3055.Garcia-Beltran, W.F., Lam, E.C., St. Denis, K., Nitido, A.D., Garcia, Z.H., Hauser, B.M., et al., 2021 Apr 29. Multiple SARS-CoV-2 variants escape neutralization by vaccineinduced humoral immunity. Cell 184 (9). https://doi.org/10.1016/j. cell.2021.03.013 [Internet]. 2372-2383.e9.Greaney, A.J., Loes, A.N., Crawford, K.H.D., Starr, T.N., Malone, K.D., Chu, H.Y., et al., 2021 Mar 10. Comprehensive mapping of mutations in the SARS-CoV-2 receptorbinding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 29 (3) [Internet]. [cited 2021 Apr 30]. 463–476.e6.Jeyanathan, M., Afkhami, S., Smaill, F., Miller, M.S., Lichty, B.D., Xing, Z., 2020. Immunological considerations for COVID-19 vaccine strategies [Internet] Nat. Rev. Immunol. Nat. Res. 20, 615–632 [cited 2021 Apr 30].Laiton-Donato, K., Villabona-Arenas, C.J., Usme-Ciro, J.A., Franco-Munoz, ˜ C., Alvarez- ´ Díaz, D.A., Villabona-Arenas, L.S., et al., 2020 Dec 1. Genomic epidemiology of severe acute respiratory syndrome coronavirus 2, Colombia. Emerg. Infect. Dis. 26 (12), 2854–2862 [Internet]. [cited 2021 Apr 30].Laiton-Donato, K., Usme-Ciro, J.A., Franco-Munoz, ˜ C., Alvarez-Díaz, ´ D.A., RuizMoreno, H.A., Reales-Gonz´ alez, J., et al., 2021 Mar 15. Novel highly divergent SARSCoV-2 lineage with the Spike substitutions L249S and E484K. medRxiv. https://doi. org/10.1101/2021.03.12.21253000 pre-print [Internet]. [cited 2021 May 7]; 2021.03.12.21253000.Liu, Z., VanBlargan, L.A., Bloyet, L.-M., Rothlauf, P.W., Chen, R.E., Stumpf, S., et al., 2021 Mar 10. Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Cell Host Microbe 29 (3) [Internet]. [cited 2021 May 1]. 477–488.e4.Noticias Coronavirus-Genoma [Internet]. [cited 2021 Apr 30]. Available from: http s://www.ins.gov.co/Noticias/Paginas/coronavirus-genoma.aspx.PAHO, 2021. Guidance for SARS-CoV-2 Samples Selection for Genomic Characterization and Surveillance - PAHO/WHO. Pan American Health Organization [Internet]. [cited 2021 May 7]. Available from: https://www.paho.org/en/documents/guida nce-sars-cov-2-samples-selection-genomic-characterization-and-surveillance.Rees-Spear, C., Muir, L., Sa, G., Heaney, J., Aldon, Y., Jl, S., et al., 2021 Jan 19. The impact of Spike mutations on SARS-CoV-2 neutralization 1. bioRxiv 4. https://doi. org/10.1101/2021.01.15.426849 [Internet]. 2021.01.15.426849. Available from:. [cited 2021 Mar 2]Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C.O., Finkin, S., et al., 2021 Feb 10. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature 592 (7855), 616–622 [Internet]. [cited 2021 Apr 30]. Available from: https ://www.nature.com/articles/s41586-021-03324-6.Wibmer, C.K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., et al., 2021 Apr 1. SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma. Nat. Med. 27 (4), 622–625 [Internet]. [cited 2021 Apr 30]. Available from: https://doi.org/10.1038/s41591-021-01285-x.Xie, X., Liu, Y., Liu, J., Zhang, X., Zou, J., Fontes-Garfias, C.R., et al., 2021 Apr 1. Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera. Nat. Med. 27 (4), 620–621 [Internet]. [cited 2021 May 1]. Available from: https://doi.org/10.1038/s41591-021-01270-4.SARS-CoV-2VariantesEvoluciónColombiaSARS-CoV-2VariantsEvolutionColombiaCharacterization of the emerging B.1.621 variant of interest of SARS-CoV-2Artículos Científicoshttp://purl.org/coar/resource_type/c_2df8fbb1http://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionAtribución – Sin Derivarinfo:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2PublicationLICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://repository.ucc.edu.co/bitstreams/73b54378-7748-4030-b101-3755916727c1/download8a4605be74aa9ea9d79846c1fba20a33MD54ORIGINAL36. Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. Laiton-Donato et al 2021.pdf36. Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. 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