Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved

Abstract

Este estudio realiza un análisis genómico sistemático de las coinfecciones por SARS-CoV-2 a lo largo de toda la pandemia, sin restringirse a periodos de cocirculación de linajes altamente divergentes. Se analizaron 7.609 genomas virales obtenidos entre marzo de 2020 y septiembre de 2022, identificándose inicialmente candidatos a coinfección mediante la detección de llamadas heterocigotas (HZ). Tras un riguroso proceso de validación bioinformática, filogenética, epidemiológica y genética del huésped, se confirmaron 14 casos robustos de coinfección (0,18%). Las coinfecciones se produjeron durante toda la pandemia e involucraron tanto cepas de distintos linajes (pre-Alpha, Delta y Omicron) como cepas del mismo sublinaje. La mayoría de los casos fueron clínicamente leves o asintomáticos, con una elevada proporción de pacientes no vacunados y relacionados con el entorno sanitario. La segregación de las cepas coinfectantes permitió aclarar brotes nosocomiales previamente difíciles de interpretar. El estudio demuestra que las coinfecciones por SARS-CoV-2 han sido un fenómeno constante durante la pandemia y subraya su relevancia para la vigilancia genómica, la epidemiología hospitalaria y la comprensión de los procesos de recombinación viral.

Background: SARS-CoV-2 recombinants involving the divergent Delta and Omicron lineages have been described, and one of them, "Kraken" (XBB.1.5), has recently been a matter of concern. Recombination requires the coexistence of two SARS-CoV-2 strains in the same individual. Only a limited number of studies have focused on the identification of co-infections and are restricted to co-infections involving the Delta/Omicron lineages.

Methods: We performed a systematic identification of SARS-CoV-2 co-infections throughout the pandemic (7609 different patients sequenced), not biassed towards the involvement of highly divergent lineages. Through a comprehensive set of validations based on the distribution of allelic frequencies, phylogenetic consistency, re-sequencing, host genetic analysis and contextual epidemiological analysis, these co-infections were robustly assigned.

Results: Fourteen (0.18%) co-infections with ≥ 8 heterozygous calls (8-85 HZs) were identified. Co-infections were identified throughout the pandemic and involved an equal proportion of strains from different lineages/sublineages (including pre-Alpha variants, Delta and Omicron) or strains from the same lineage. Co-infected cases were mainly unvaccinated, with mild or asymptomatic clinical presentation, and most were at risk of overexposure associated with the healthcare environment. Strain segregation enabled integration of sequences to clarify nosocomial outbreaks where analysis had been impaired due to co-infection.

Conclusions: Co-infection cases were identified throughout the pandemic, not just in the time periods when highly divergent lineages were co-circulating. Co-infections involving different lineages or strains from the same lineage were occurring in the same proportion. Most cases were mild, did not require medical assistance and were not vaccinated, and a large proportion were associated with the hospital environment.