First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador

J. C. Fernandez-Cadena; M. Carvajal; E. Muñoz; B. Prado-Vivar; S. Marquez; S. Proaño; R. Bayas; J. J. Guadalupe; M. Becerra-Wong; B. Gutierrez; G. Morey-Leon; G. Trueba; M. Grunauer; V. Barragán; P. Rojas-Silva; D. Andrade-Molina; P. Cárdenas

doi:10.1016/j.nmni.2022.101001

First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador

J. C. Fernandez-Cadena
, M. Carvajal
, E. Muñoz
, B. Prado-Vivar
, S. Marquez
, S. Proaño
, R. Bayas
, J. J. Guadalupe
, M. Becerra-Wong
, B. Gutierrez
, G. Morey-Leon
, G. Trueba
, M. Grunauer
, V. Barragán
, P. Rojas-Silva
, D. Andrade-Molina^*
, P. Cárdenas^*

^*Corresponding author for this work

Laboratorio INTERLAB
Universidad San Francisco de Quito
University of Oxford
Universidad de Guayaquil
Hospital de los Valles
Universidad Espíritu Santo, Ecuador

Research output: Contribution to journal › Article › peer-review

Abstract

Background: COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. Methodology: A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. Results: The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. Conclusions: We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.

Original language	English
Article number	101001
Journal	New Microbes and New Infections
Volume	48
DOIs	https://doi.org/10.1016/j.nmni.2022.101001
State	Published - Jul 2022

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

COVID19
NGS
SARS-CoV-2
co-infection
genome sequencing

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10.1016/j.nmni.2022.101001

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Fernandez-Cadena, J. C., Carvajal, M., Muñoz, E., Prado-Vivar, B., Marquez, S., Proaño, S., Bayas, R., Guadalupe, J. J., Becerra-Wong, M., Gutierrez, B., Morey-Leon, G., Trueba, G., Grunauer, M., Barragán, V., Rojas-Silva, P., Andrade-Molina, D., & Cárdenas, P. (2022). First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador. New Microbes and New Infections, 48, Article 101001. https://doi.org/10.1016/j.nmni.2022.101001

@article{ef91fa1204164f968804358f6d720dab,

title = "First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador",

abstract = "Background: COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. Methodology: A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. Results: The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. Conclusions: We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.",

keywords = "COVID19, NGS, SARS-CoV-2, co-infection, genome sequencing",

author = "Fernandez-Cadena, \{J. C.\} and M. Carvajal and E. Mu{\~n}oz and B. Prado-Vivar and S. Marquez and S. Proa{\~n}o and R. Bayas and Guadalupe, \{J. J.\} and M. Becerra-Wong and B. Gutierrez and G. Morey-Leon and G. Trueba and M. Grunauer and V. Barrag{\'a}n and P. Rojas-Silva and D. Andrade-Molina and P. C{\'a}rdenas",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s)",

year = "2022",

month = jul,

doi = "10.1016/j.nmni.2022.101001",

language = "Ingl{\'e}s",

volume = "48",

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Fernandez-Cadena, JC, Carvajal, M, Muñoz, E, Prado-Vivar, B, Marquez, S, Proaño, S, Bayas, R, Guadalupe, JJ, Becerra-Wong, M, Gutierrez, B, Morey-Leon, G, Trueba, G , Grunauer, M , Barragán, V , Rojas-Silva, P, Andrade-Molina, D & Cárdenas, P 2022, 'First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador', New Microbes and New Infections, vol. 48, 101001. https://doi.org/10.1016/j.nmni.2022.101001

TY - JOUR

T1 - First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador

AU - Fernandez-Cadena, J. C.

AU - Carvajal, M.

AU - Muñoz, E.

AU - Prado-Vivar, B.

AU - Marquez, S.

AU - Proaño, S.

AU - Bayas, R.

AU - Guadalupe, J. J.

AU - Becerra-Wong, M.

AU - Gutierrez, B.

AU - Morey-Leon, G.

AU - Trueba, G.

AU - Grunauer, M.

AU - Barragán, V.

AU - Rojas-Silva, P.

AU - Andrade-Molina, D.

AU - Cárdenas, P.

PY - 2022/7

Y1 - 2022/7

N2 - Background: COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. Methodology: A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. Results: The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. Conclusions: We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.

AB - Background: COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. Methodology: A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. Results: The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. Conclusions: We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.

KW - COVID19

KW - NGS

KW - SARS-CoV-2

KW - co-infection

KW - genome sequencing

UR - https://www.scopus.com/pages/publications/85138440963

U2 - 10.1016/j.nmni.2022.101001

DO - 10.1016/j.nmni.2022.101001

M3 - Artículo

AN - SCOPUS:85138440963

SN - 2052-2975

VL - 48

JO - New Microbes and New Infections

JF - New Microbes and New Infections

M1 - 101001

ER -

First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador

Abstract

UN SDGs

Keywords

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