Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient

Virology Journal

Research

Larry K. Kociolek¹  William J. Muller¹  Taylor A. Heald-Sargent¹  Maria Francesca Reyes Agnes²  Lacy M. Simons²  Ramon Lorenzo-Redondo²  Judd F. Hultquist²  Egon A. Ozer²  Arghavan Alisoltani² 

[1] Ann & Robert H. Lurie Children’s Hospital of Chicago, 60611, Chicago, IL, USA;Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, 60611, Chicago, IL, USA;Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, 60611, Chicago, IL, USA;

关键词: SARS-CoV-2;    Variants of concern;    Delta;    Omicron;    Superinfection;   

DOI  :  10.1186/s12985-023-02186-w

 received in 2023-06-30, accepted in 2023-09-18,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundPersistent SARS-CoV-2 infection in immunocompromised hosts is thought to contribute to viral evolution by facilitating long-term natural selection and viral recombination in cases of viral co-infection or superinfection. However, there are limited data on the longitudinal intra-host population dynamics of SARS-CoV-2 co-infection/superinfection, especially in pediatric populations. Here, we report a case of Delta-Omicron superinfection in a hospitalized, immunocompromised pediatric patient.MethodsWe conducted Illumina whole genome sequencing (WGS) for longitudinal specimens to investigate intra-host dynamics of SARS-CoV-2 strains. Topoisomerase PCR cloning of Spike open-reading frame and Sanger sequencing of samples was performed for four specimens to validate the findings. Analysis of publicly available SARS-CoV-2 sequence data was performed to investigate the co-circulation and persistence of SARS-CoV-2 variants.ResultsResults of WGS indicate the patient was initially infected with the SARS-CoV-2 Delta variant before developing a SARS-CoV-2 Omicron variant superinfection, which became predominant. Shortly thereafter, viral loads decreased below the level of detection before resurgence of the original Delta variant with no residual trace of Omicron. After 54 days of persistent infection, the patient tested negative for SARS-CoV-2 but ultimately succumbed to a COVID-19-related death. Despite protracted treatment with remdesivir, no antiviral resistance mutations emerged. These results indicate a unique case of persistent SARS-CoV-2 infection with the Delta variant interposed by a transient superinfection with the Omicron variant. Analysis of publicly available sequence data suggests the persistence and ongoing evolution of Delta subvariants despite the global predominance of Omicron, potentially indicative of continued transmission in an unknown population or niche.ConclusionA better understanding of SARS-CoV-2 intra-host population dynamics, persistence, and evolution during co-infections and/or superinfections will be required to continue optimizing patient care and to better predict the emergence of new variants of concern.

【 授权许可】

CC BY   
© The Author(s) 2023

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