SARS-CoV-2 spread across the Colombian-Venezuelan border

Alberto Paniz-Mondolfi; Marina Muñoz; Carolina Florez; Sergio Gomez; Angelica Rico; Lisseth Pardo; Esther C. Barros; Carolina Hernández; Lourdes Delgado; Jesús E. Jaimes; Luis Pérez; Aníbal A. Teherán; Hala Alejel Alshammary; Ajay Obla; Zenab Khan; Jayeeta Dutta; Adriana van de Guchte; Ana S. Gonzalez-Reiche; Matthew M. Hernandez; Emilia Mia Sordillo; Viviana Simon; Harm van Bakel; Martin S. Llewellyn; Juan David Ramírez

doi:10.1016/j.meegid.2020.104616

SARS-CoV-2 spread across the Colombian-Venezuelan border

Título traducido de la contribución: El SARS-CoV-2 se extiende a través de la frontera colombo-venezolana

Alberto Paniz-Mondolfi, Marina Muñoz, Carolina Florez, Sergio Gomez, Angelica Rico, Lisseth Pardo, Esther C. Barros, Carolina Hernández, Lourdes Delgado, Jesús E. Jaimes, Luis Pérez, Aníbal A. Teherán, Hala Alejel Alshammary, Ajay Obla, Zenab Khan, Jayeeta Dutta, Adriana van de Guchte, Ana S. Gonzalez-Reiche, Matthew M. Hernandez, Emilia Mia SordilloViviana Simon, Harm van Bakel, Martin S. Llewellyn, Juan David Ramírez

Producción científica: Contribución a una revista › Artículo › revisión exhaustiva

14 Citas (Scopus)

Resumen

Introducción: Tanto Venezuela como Colombia adoptaron medidas de contención tempranas en respuesta a la pandemia de COVID-19. Sin embargo, la actual crisis humanitaria de Venezuela ha diezmado su sistema sanitario y ha obligado a millones de venezolanos a huir a través de su porosa frontera con Colombia. La extensa frontera compartida y el tránsito transfronterizo ilegal a través de senderos improvisados entre los dos países son grandes retos para las autoridades de salud pública. Informamos de los primeros genomas de SARS-CoV-2 de Venezuela y presentamos una instantánea del panorama epidemiológico del SARS-CoV-2 en la región fronteriza entre Colombia y Venezuela. Métodos: Secuenciamos y ensamblamos genomas virales a partir de ARN total extraído de muestras clínicas nasofaríngeas (NP), utilizando una línea de análisis basada en referencias personalizadas. Los tres ensamblajes obtenidos se sometieron a la tipificación mediante la herramienta "Pangolin" de asignación filogenética de linajes de brotes globales con nombre. Se obtuvo un total de 376 genomas de SARS-CoV-2 disponibles públicamente de la base de datos GISAID para realizar análisis genómicos comparativos. Además, se utilizó la cepa Wuhan-1 como referencia. Resultados: Encontramos que dos de los genomas de SARS-CoV-2 de Venezuela pertenecían al linaje B1, y el tercero al linaje B.1.13. Observamos una mutación puntual en el gen de la proteína Spike (sustitución D614G), de la que se ha informado previamente que está asociada a una mayor infectividad, en los tres genomas venezolanos. Además, tres mutaciones (sustitución R203K/G204R) estaban presentes en el gen de la nucleocápside (N) de un genoma venezolano. Conclusiones: La secuenciación genómica demuestra la similitud entre los linajes de SARS-CoV-2 de Venezuela y los virus recogidos en pacientes de zonas fronterizas de Colombia y de Brasil, lo que es coherente con el tránsito transfronterizo a pesar de las medidas administrativas que incluyen los cierres. La presencia de mutaciones asociadas a una mayor infectividad en los 3 genomas venezolanos que reportamos y en los genomas colombianos del SARS-CoV-2 de las zonas fronterizas vecinas puede plantear retos adicionales para el control de la propagación del SARS-CoV-2 en el complejo panorama epidemiológico de los países latinoamericanos. Las autoridades de salud pública deben seguir cuidadosamente el progreso de la pandemia y su impacto en las poblaciones desplazadas dentro de la región.

Título traducido de la contribución	El SARS-CoV-2 se extiende a través de la frontera colombo-venezolana
Idioma original	Inglés estadounidense
Número de artículo	104616
Publicación	Infection, Genetics and Evolution
Volumen	86
DOI	https://doi.org/10.1016/j.meegid.2020.104616
Estado	Publicada - nov. 4 2020

Áreas temáticas de ASJC Scopus

Microbiología
Ecología, evolución, comportamiento y sistemática
Biología molecular
Genética
Microbiología (médica)
Enfermedades infecciosas

ODS de las Naciones Unidas

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Paniz-Mondolfi, A., Muñoz, M., Florez, C., Gomez, S., Rico, A., Pardo, L., Barros, E. C., Hernández, C., Delgado, L., Jaimes, J. E., Pérez, L., Teherán, A. A., Alshammary, H. A., Obla, A., Khan, Z., Dutta, J., van de Guchte, A., Gonzalez-Reiche, A. S., Hernandez, M. M., ... Ramírez, J. D. (2020). SARS-CoV-2 spread across the Colombian-Venezuelan border. Infection, Genetics and Evolution, 86, Artículo 104616. https://doi.org/10.1016/j.meegid.2020.104616

@article{8dd7623a5ce5454186d4783c15caef52,

title = "SARS-CoV-2 spread across the Colombian-Venezuelan border",

abstract = "Introduction: Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuela's ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region. Methods: We sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages {\textquoteleft}Pangolin{\textquoteright} tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference. Results: We found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. Additionally, three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome. Conclusions: Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.",

author = "Alberto Paniz-Mondolfi and Marina Mu{\~n}oz and Carolina Florez and Sergio Gomez and Angelica Rico and Lisseth Pardo and Barros, {Esther C.} and Carolina Hern{\'a}ndez and Lourdes Delgado and Jaimes, {Jes{\'u}s E.} and Luis P{\'e}rez and Teher{\'a}n, {An{\'i}bal A.} and Alshammary, {Hala Alejel} and Ajay Obla and Zenab Khan and Jayeeta Dutta and {van de Guchte}, Adriana and Gonzalez-Reiche, {Ana S.} and Hernandez, {Matthew M.} and Sordillo, {Emilia Mia} and Viviana Simon and {van Bakel}, Harm and Llewellyn, {Martin S.} and Ram{\'i}rez, {Juan David}",

note = "Funding Information: This work was supported by the University of Glasgow , Scottish Funding Council and the Global Challenges Research Fund (GCRF) and GCRF Research Network EP/T003782/1 . Publisher Copyright: {\textcopyright} 2020 Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

year = "2020",

month = nov,

day = "4",

doi = "10.1016/j.meegid.2020.104616",

language = "English (US)",

volume = "86",

journal = "Infection, Genetics and Evolution",

issn = "1567-1348",

publisher = "Elsevier",

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Paniz-Mondolfi, A, Muñoz, M, Florez, C, Gomez, S, Rico, A, Pardo, L, Barros, EC, Hernández, C, Delgado, L, Jaimes, JE, Pérez, L, Teherán, AA, Alshammary, HA, Obla, A, Khan, Z, Dutta, J, van de Guchte, A, Gonzalez-Reiche, AS, Hernandez, MM, Sordillo, EM, Simon, V, van Bakel, H, Llewellyn, MS & Ramírez, JD 2020, 'SARS-CoV-2 spread across the Colombian-Venezuelan border', Infection, Genetics and Evolution, vol. 86, 104616. https://doi.org/10.1016/j.meegid.2020.104616

TY - JOUR

T1 - SARS-CoV-2 spread across the Colombian-Venezuelan border

AU - Paniz-Mondolfi, Alberto

AU - Muñoz, Marina

AU - Florez, Carolina

AU - Gomez, Sergio

AU - Rico, Angelica

AU - Pardo, Lisseth

AU - Barros, Esther C.

AU - Hernández, Carolina

AU - Delgado, Lourdes

AU - Jaimes, Jesús E.

AU - Pérez, Luis

AU - Teherán, Aníbal A.

AU - Alshammary, Hala Alejel

AU - Obla, Ajay

AU - Khan, Zenab

AU - Dutta, Jayeeta

AU - van de Guchte, Adriana

AU - Gonzalez-Reiche, Ana S.

AU - Hernandez, Matthew M.

AU - Sordillo, Emilia Mia

AU - Simon, Viviana

AU - van Bakel, Harm

AU - Llewellyn, Martin S.

AU - Ramírez, Juan David

N1 - Funding Information: This work was supported by the University of Glasgow , Scottish Funding Council and the Global Challenges Research Fund (GCRF) and GCRF Research Network EP/T003782/1 . Publisher Copyright: © 2020 Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/11/4

Y1 - 2020/11/4

N2 - Introduction: Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuela's ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region. Methods: We sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages ‘Pangolin’ tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference. Results: We found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. Additionally, three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome. Conclusions: Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.

AB - Introduction: Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuela's ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region. Methods: We sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages ‘Pangolin’ tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference. Results: We found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. Additionally, three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome. Conclusions: Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.

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SARS-CoV-2 spread across the Colombian-Venezuelan border

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