First Case of Within-Host Co-Infection of Different SARS-CoV-2 Variants in Ecuador

14 Pages Posted: 2 Apr 2022 Last revised: 25 Jun 2022

See all articles by Juan Carlos Fernandez-Cadena

Juan Carlos Fernandez-Cadena

INTERLAB

Mateo Carvajal

Universidad San Francisco de Quito (USFQ)

Erika Muñoz

affiliation not provided to SSRN

Belen Prado-Vivar

USFQ

Sully Marquez

Universidad San Francisco de Quito (USFQ)

Stefanie Proaño

affiliation not provided to SSRN

Rosa Bayas

affiliation not provided to SSRN

Juan Jose Guadalupe

Universidad San Francisco de Quito (USFQ)

Monica Becerra-Wong

Universidad San Francisco de Quito (USFQ)

Bernardo Gutierrez

Universidad San Francisco de Quito (USFQ)

Gabriel Morey León

Universidad de Guayaquil

Gabriel Trueba

Universidad San Francisco de Quito (USFQ)

Michelle Grunauer

Universidad San Francisco de Quito (USFQ)

Veronica Barragan

Universidad San Francisco de Quito (USFQ)

Patricio Rojas-Silva

Universidad San Francisco de Quito (USFQ)

Derly Andrade Molina

affiliation not provided to SSRN

Paul Cardenas

Universidad San Francisco de Quito (USFQ)

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 has 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.

Note:
Funding Information: This research was funded by USFQ and UEES.

Conflict of Interests: The authors declare no conflict of interest.

Ethical Approval: The study protocol was approved by the Institutional Review Board of the Universidad San Francisco de Quito P2020-022IN (CEISH No. 1234) and by the Ecuadorian Ministry of Public Health MSP- CGDES-2020-0121-O. The patient provided written informed consent for sample analysis and publication.

Keywords: SARS-CoV-2, COVID19, Co-infection

Suggested Citation

Fernandez-Cadena, Juan Carlos and Carvajal, Mateo and Muñoz, Erika and Prado-Vivar, Belen and Marquez, Sully and Proaño, Stefanie and Bayas, Rosa and Guadalupe, Juan Jose and Becerra-Wong, Monica and Gutierrez, Bernardo and Morey León, Gabriel and Trueba, Gabriel and Grunauer, Michelle and Barragan, Veronica and Rojas-Silva, Patricio and Andrade Molina, Derly and Cardenas, Paul, First Case of Within-Host Co-Infection of Different SARS-CoV-2 Variants in Ecuador. NMNI-D-22-00092, Available at SSRN: https://ssrn.com/abstract=4073194 or http://dx.doi.org/10.2139/ssrn.4073194

Juan Carlos Fernandez-Cadena

INTERLAB ( email )

Av. del Bombero Km 6,5 vía a la costa
Guayaquil, Guayas
Ecuador

Mateo Carvajal

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Erika Muñoz

affiliation not provided to SSRN ( email )

No Address Available

Belen Prado-Vivar

USFQ ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Sully Marquez

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Stefanie Proaño

affiliation not provided to SSRN ( email )

No Address Available

Rosa Bayas

affiliation not provided to SSRN ( email )

No Address Available

Juan Jose Guadalupe

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Monica Becerra-Wong

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Bernardo Gutierrez

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Gabriel Morey León

Universidad de Guayaquil

Cdla Universitaria
Guayaquil, EC090505
Ecuador

Gabriel Trueba

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Michelle Grunauer

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Veronica Barragan

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Patricio Rojas-Silva

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

Derly Andrade Molina

affiliation not provided to SSRN

No Address Available

Paul Cardenas (Contact Author)

Universidad San Francisco de Quito (USFQ) ( email )

Diego de Robles y Vía Interoceánic
Campus Cumbayá
QUITO, PICHINCHA 17-1200-84
Ecuador

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