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 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