Identification and Characterization of Viral Reservoirs in Patients with Post-Acute Sequelae of SARS-CoV-2 Infection

Introduction: SARS-CoV-2 viral persistence may be a central contributor to the post-acute sequelae of SARS-CoV-2 infection (PASC) also known as Long COVID. Numerous studies have reported SARS-CoV-2 viral persistence in the post-acute setting. However, the presence and location of true causative SARS-CoV-2 viral reservoirs in Long COVID is unclear.

Objective: We will identify the viral reservoirs associated with Long COVID by systematically assessing autopsy tissue sites for viral replication, and genomically linking the virus present with the index infection.

Methods: The presence of candidate viral reservoirs will be determined in up to 100 decedents enrolled in the RECOVER Autopsy Cohort, including decedents with Long COVID and decedents in the post-acute phase without Long COVID. All tissue sites collected by the study protocol will be assessed in an unbiased manner using highly-sensitive transcriptomic profiling, including direct assessment of SARS-CoV-2 reverse strand, a marker of viral replication. The presence of replicating virus will be correlated with the patients' symptoms in an organ specific manner. For candidate viral reservoirs, viral genomic analyses will be conducted using Viral-NGS, and the viral variants in the reservoirs will be compared to the predominant variants at the time of index infections. The presence and location of virus in the reservoirs will be further characterized using ddPCR and in-situ hybridization. Global host response within the reservoirs will be determined by bulk RNA-Seq.

Results: Pending.

Conclusion/Discussion: This study entails an unbiased and thorough analysis of tissues throughout the body for the presence of SARS-CoV-2 viral reservoirs. Identification of these reservoirs will greatly enhance our understanding of this disorder and offer insights into the therapeutic options.

Key Topics:

• Biomarker, in-depth phenotyping assays and in vitro studies using tissue and other biospecimens
• Clinical manifestations of chronic viral infections, biological pathways, immune-autoimmune disorders, systems, organs, or diseases
• Linking autopsy findings with pathobiological mechanisms of Long COVID to guide targeted interventions
• Viral persistence/reactivation