Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient
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Published:2023-10-27
Issue:1
Volume:20
Page:
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ISSN:1743-422X
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Container-title:Virology Journal
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language:en
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Short-container-title:Virol J
Author:
Alisoltani Arghavan,Simons Lacy M.,Agnes Maria Francesca Reyes,Heald-Sargent Taylor A.,Muller William J.,Kociolek Larry K.,Hultquist Judd F.,Lorenzo-Redondo Ramon,Ozer Egon A.
Abstract
Abstract
Background
Persistent 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.
Methods
We 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.
Results
Results 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.
Conclusion
A 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.
Funder
Dixon Translational Research Grant made possible by the generous support of the Dixon Family Foundation
National Center for Advancing Translational Sciences
Northwestern University Cancer Center
NIH-supported Third Coast CFAR
National Institutes of Health
Walder Foundation Foundation’s Chicago Coronavirus Assessment Network (Chicago CAN) Initiative
Publisher
Springer Science and Business Media LLC
Subject
Infectious Diseases,Virology
Cited by
1 articles.
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