Virus World

Background

Methods

Findings

Interpretation

Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks, give rise to highly divergent lineages and contribute to cases with post-acute COVID-19 sequelae (long COVID). However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. We refer to these as ‘persistent infections’ as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all.

Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We estimate that 0.1–0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people. This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution. Using viral sequence data, individuals with persistent SARS-CoV-2 infections were identified, and had higher odds of self-reporting long COVID, in a large community surveillance study.

Published in Nature (Feb. 21, 2024):

https://doi.org/10.1038/s41586-024-07029-4 

With an estimated 65 million individuals suffering from Long COVID, validated therapeutic strategies as well as non-invasive biomarkers are direly needed to guide clinical management. We used blood digital transcriptomics in search of viral persistence and Long COVID diagnostic biomarkers in a real-world, general practice-based setting with a long clinical follow-up. We demonstrate systemic SARS-CoV-2 persistence for more than 2 years after acute COVID-19 infection. A 2-gene biomarker, including SARS-CoV-2 antisense RNA, correctly classifies Long COVID with 93.8% sensitivity and 91.7% specificity. Specific immune transcripts and immunometabolism score correlate to systemic viral load and patient-reported anxiety/depression, providing mechanistic links as well as therapeutic targets to tackle Long COVID.

Available in medRxiv (Jan. 17, 2023):

 https://doi.org/10.1101/2024.01.14.24301293 

Lancet study solidifies evidence of long-term viral persistence after COVID; demonstrates urgency of sustained research into the chronic health consequence of the virus. 

Medford MA, April 8, 2024 – Research published today in Lancet Infectious Disease and supported by PolyBio Research Foundation provides the strongest evidence yet that the COVID virus can persist for months or years after infection. The findings, published by a UC San Francisco/Harvard Medical School team, found that proteins created by the virus were still present for up to 14 months in a quarter of people tested. This demonstrates SARS-CoV-2 viral persistence as an urgent area of research underlying a breadth of chronic disease after COVID. “The fact that every new SARS-CoV-2 infection has the potential to become chronic is perhaps the single most concerning aspect of this virus” says Dr. Amy Proal, President of PolyBio. “We have compelling data that viral persistence is much more common than recognized which could have major health implications.”

Solid Evidence of Persistent Infection

The researchers analyzed blood samples from 171 people who had been infected with the virus. Using a novel ultra-sensitive blood test, they found that proteins from the virus were still present up to one year after infection in up to 25% of people. These findings greatly bolster evidence that the coronavirus can linger in tissue and organs, even after recovery from acute infection.

The likelihood of detecting the COVID proteins indicative of persistent virus was about twice as high among those who were hospitalized for COVID as it was for those who were not. It was also higher for those who were not hospitalized but reported being sicker. The researchers note that viral proteins identified in the study could not have been a result the COVID vaccine, since nearly all study participants had not received the shots prior to the blood collection. In addition, proteins were only rarely found in banked blood obtained from over 200 people before the pandemic, confirming the accuracy of the blood test used in the research.

“Finding COVID-19 proteins floating in the bloodstream for more than a year following initial infection was a surprise to most of us and is the product of new molecular tools. This finding now firmly informs the next step in our research agenda — is persistence of the SARS-CoV-2 virus responsible for causing people’s current symptoms in Long COVID or medical events they may have in the future?” says Jeffrey N. Martin, Head of the Division of Clinical Epidemiology at University of California, San Francisco who co-led the study.

Martin is part of a multi-disciplinary collaboration behind the findings. The blood test used to find viral proteins was created by Harvard Medical School’s David Walt – founder of biotech companies that have transformed technologies across biomedical research. The blood samples were provided by volunteers in the UCSF Long-term Impact of Infection with Novel Coronavirus (LIINC) study. The UCSF team contains experts who helped make HIV/AIDS a treatable disease and pivoted their infrastructure into Long COVID via LIINC in April of 2020. The UCSF team is part of PolyBio’s LongCovid Research Consortium – a privately funded global collaborationof scientists working rapidly to document SARS-CoV-2 persistence in Long COVID, with data channeled into clinical trials. In a seminal Nature paper, the Consortium delineated a roadmap for the study of SARS-CoV-2 persistence that is being executed by dozens of international teams. However, with an estimated 18 million adults and 5.8 million children suffering from Long COVID, government investment is also needed. SARS-CoV-2 has even been found in the lymph nodes of children months after COVID, suggesting persistent infection can begin early in life. “COVID persistence could contribute to Long COVID in both adults and children” says Michael Peluso, MD, principal investigator of LIINC and an infectious disease researcher in the UCSF School of Medicine. “We must rapidly keep studying that possibility.”

About PolyBio 

PolyBio Research Foundation is a 501(c)3 transforming how complex chronic conditions like Long COVID are studied, diagnosed, and treated. PolyBio conceptualizes research projects that identify root cause drivers of chronic conditions and builds collaborative teams to make the projects a reality. PolyBio is supported by numerous donors including Kanro – a philanthropic fund to support open source scientific research established by Vitalik Buterin, creator of Ethereum.

Research published in The Lancet Infectious Diseases (April 8, 2024):

https://doi.org/10.1016/S1473-3099(24)00211-1

During the COVID-19 pandemic it was widely described that certain individuals infected by SARS-CoV-2 experience persistent disease signs and symptoms, Long COVID, which in some cases is very severe with life changing consequences. To maximize our chances of identifying the underpinnings of this illness, we have focused on 121 of the most severe cases from >1000 patients screened in specialized clinics in Sweden and Belgium. We restricted this study to subjects with objective measures of organ damage or dysfunction, >3 months following a verified, but mild- to-moderate SARS-CoV-2 infection.

By performing systems-level immunological testing and comparisons to controls fully convalescent following a similar mild/moderate COVID-19 episode, we identify elevated serological responses to SARS-CoV-2 in severe Long COVID suggestive of chronic antigen stimulation. Persistent viral reservoirs have been proposed in Long COVID and using multiple orthogonal methods for detection of SARS-CoV-2 RNA and protein in plasma we identify a subset of patients with detectable antigens, but with minimal overlap across assays, and no correlation to symptoms or immune measurements. Elevated serologic responses to SARS-CoV-2 on the other hand were inversely correlated with clonally expanded memory CD8+ T cells, indicating that restrained clonal expansion enables viral persistence, chronic antigen exposure and elevated IgG responses, even if antigen-detection in blood is not universally possible.

Preprint in medRxiv (Feb. 13, 2024):

 https://doi.org/10.1101/2024.02.11.24302636