What the Study Revealed

The research is spearheaded by Rudolf Jaenisch, a biology professor at MIT and a founding member of the Whitehead Institute for Biomedical Research, recognized for his work in gene modification. Other contributors hail from the same institute and Harvard University, ensuring a high level of expertise and credibility.

1. Chimeric Transcripts

By reviewing existing datasets of gene profiles from cells infected with SARS-CoV-2, the study identified chimeric transcripts—hybrid combinations of human and SARS-CoV-2 genes—present in lung, heart, brain, and stomach cells and organoids. Chimeric transcripts were also found in lung fluid samples from COVID-19 patients. This suggests that SARS-CoV-2 genes can integrate with human genes, forming a chimeric gene. In biological terms, a chimera refers to an organism containing genetic material from multiple sources.

This supports the idea that the human genome can produce SARS-CoV-2-human chimeric transcripts, which may be transcribed into new proteins.

2. LINE-1 and HIV-1 RT

HIV-1 reverse transcriptase (RT) is associated with the human immunodeficiency virus type 1 (HIV-1), while long interspersed element 1 (LINE-1) consists of ancient viral remnants that constitute about 17% of the human genome. Both HIV-1 RT and LINE-1 can integrate specific viral genes into the human genome.

The researchers enhanced LINE-1 or HIV-1 RT activity in human cells before infecting them with SARS-CoV-2. They confirmed the presence of SARS-CoV-2 genes (specifically those coding for the nucleocapsid protein) in the human cell nucleus, a phenomenon absent in uninfected cells. In cells with lower expressions of LINE-1 or HIV-1 RT, SARS-CoV-2 genes were also found but at diminished levels.

These analyses confirm that both LINE-1 (which is normally expressed in human cells) and HIV-1 RT can facilitate the integration of SARS-CoV-2 genes into the human genome.

3. Focus on LINE-1 and Gene-Protein Transcription

The research further investigated which genes are transcribed into proteins within human cells and discovered that the gene coding for the SARS-CoV-2 nucleocapsid protein was involved in the transcription activities. These transcription activities correlated with LINE-1 expression.

Continuing, the study revisited gene profile datasets of human cells infected with SARS-CoV-2 to check for an increase in LINE-1 expression. The results showed a direct correlation between LINE-1 expression and the presence of SARS-CoV-2-human chimeric transcripts. Additionally, traces of SARS-CoV-2 genes were found in the genomic analysis of these datasets.

The findings indicate that human cells infected with SARS-CoV-2 experience increased LINE-1 expression, which facilitates the integration of SARS-CoV-2 genes. These integrated genes can then lead to the creation of SARS-CoV-2-human chimeric transcripts, which are transcribed into new proteins.

4. The Role of Cytokines

Given that COVID-19 is marked by cytokine storms, the researchers sought to determine if inflammation would trigger LINE-1 expression. By exposing human cells to cytokines produced by immune cells, they confirmed that LINE-1 expression indeed increased. This suggests that inflammatory cytokines can amplify LINE-1 expression, in addition to the effects of SARS-CoV-2 infection.

Contextualizing the Findings

1. Limitations of the Study

As with all research, findings must be viewed in light of their limitations. This study was conducted solely in cultured human cells and utilized public datasets, necessitating further validation in animal models.

Moreover, the study induced high levels of LINE-1 and HIV-1 RT in the human cells. In cells with normal levels of these elements, the genomic integration of SARS-CoV-2 genes was not as effective.

One critique from an expert in HIV-1 raised concerns about how experimental conditions can be optimized for genomic integration, implying that similar efficiency may not occur in living organisms. Keeping this in mind, let’s delve into the broader implications of this research.

2. Potential for Viral Reactivation

The authors noted, “We found that LINE-1 expression can be induced by SARS-CoV-2 infection or cytokine exposure, indicating a molecular mechanism that may account for SARS-CoV-2 retro-integration in patients.” They suggest that integrated SARS-CoV-2 sequences could be transcribed, potentially explaining why viral sequences remain detectable long after initial infection, even in the absence of infectious virus.

There are instances where individuals test positive for SARS-CoV-2 again after two consecutive negative results, despite symptom resolution and discharge from the hospital. Due to the brief interval between negative and subsequent positive tests and enforced quarantine, scientists suspect reactivation rather than reinfection. Although there are verified reinfection cases, these typically occur much later, requiring exposure to a different variant of SARS-CoV-2.

The current preprint provides initial evidence supporting the idea that SARS-CoV-2 could reactivate, shedding light on the curious case of a second positive test following two negative results. However, similar to other viruses known for reactivation, subsequent reactivations often result in milder illnesses due to factors such as immune memory or reduced virulence of the pathogen, which aligns with certain suspected cases of COVID-19 reactivation.

The study found evidence of only fragments of SARS-CoV-2 genes—specifically those coding for the nucleocapsid—integrating into the human genome, rather than the entire viral genome. Thus, the transcription process of this integrated SARS-CoV-2 should not yield infectious virions, as the authors clarify.

3. Distinguishing Between Infectious and Non-Infectious Reactivation

Most RNA viruses, including coronaviruses, replicate in the cytoplasm of cells rather than in the nucleus where the genome resides. An exception to this is HIV-1, which can enter the nucleus and replicate there, integrating its genes into the human genome through HIV-1 RT, allowing it to persist in the body indefinitely.

However, the critical distinction is that HIV-1 genomic integration encompasses the entire viral genome, producing infectious virions. Thus, HIV-1 reactivation can result in a new infection. In contrast, the current preprint indicates that only certain segments of SARS-CoV-2 integrate into the human genome, suggesting that SARS-CoV-2 would only partially reactivate in a non-infectious manner.

According to Science, “The work, currently reported in a preprint, implies that the pandemic pathogen mimics HIV and other retroviruses by integrating its genetic material—but crucially, just fragments—into human chromosomes. Because not all parts of the coronaviral genome are integrated, it cannot produce infectious RNA or DNA, making it likely a biological dead end.”

4. Concerns About Persistent Immune Activation

The authors raised the question of whether such SARS-CoV-2 genomic integration could produce proteins that might activate the immune system, potentially complicating COVID-19 clinical outcomes.

Yet, it's equally plausible that this immune activation could be advantageous for the host. LINE-1 comprises a significant portion of the human genome, and scientists theorize it may confer an evolutionary benefit. “From an evolutionary standpoint, retro-integration of viral RNA via LINE-1 could represent an adaptive mechanism to maintain antigen expression, potentially enhancing protective immunity,” the authors stated. Essentially, expressing fragments of the virus intermittently could aid in sustaining immune memory.

Conversely, retro-integration might be harmful, potentially leading to severe immune responses such as a cytokine storm or autoimmune reactions. Another possibility is that proteins synthesized from these integrated genes could simply be discarded as cellular waste.

At present, little is understood about the health implications (if any) of such SARS-CoV-2 genomic integration.

5. Rethinking Diagnostic Tests

If SARS-CoV-2 genomic integration proves harmless to the host—meaning no infectious virions or detrimental immune responses—current SARS-CoV-2 diagnostic tests may require reevaluation.

The authors noted, “The dependence on PCR tests to measure the impact of treatments on viral replication and load may not accurately reflect treatment efficacy, as PCR tests might detect viral transcripts from sequences stably integrated into the genome rather than infectious virus.”

Science concurred, stating, “If true and common, this phenomenon could lead to serious implications, from false signals of active infection to misleading results in COVID-19 treatment studies.”

6. Questions of Permanent DNA Changes

Should the genomic integration of SARS-CoV-2 resemble that of HIV-1, it could be permanent. However, this remains speculative, and further research is necessary. More importantly, it is crucial to determine whether such genomic integration could result in future health issues.

Another contentious question is whether SARS-CoV-2 genomic integration can be inherited by offspring, similar to human herpesvirus type 6 (HHV-6), which integrates into genome telomeres and can be passed down. However, HHV-6's genetic inheritance is harmless and does not provoke immune responses.

Fortunately, most viruses lack this capability; HHV-6 is currently the only one confirmed to do so. Even HIV-1 can only be transmitted non-genetically, such as through maternal blood to the child. Thus, it is likely that SARS-CoV-2 cannot be inherited in this way.

Short Abstract

This article analyzes a newly released preprint from reputable experts that presents findings requiring careful interpretation. The study indicates that SARS-CoV-2 infection and cytokine exposure can elevate LINE-1 expression in human cells. LINE-1 subsequently integrates parts of SARS-CoV-2 genes into the human genome, which can be transcribed into chimeric transcripts and translated into new proteins. This groundbreaking finding holds significant implications for understanding viral reactivation, revising current diagnostic tests, and assessing the potential short-term and long-term health effects of SARS-CoV-2 genomic integration.

Thanks to Robin Whittle.

1st March 2021 update: A more recent preprint, “Host-virus chimeric events in SARS-CoV-2 infected cells are infrequent and artifactual,” from Purdue University and the National Institutes of Health in the U.S., has drawn opposite conclusions, suggesting that chimeric transcripts in SARS-CoV-2 infected cells are mere background noise. While they did identify evidence of chimeric transcripts, these were not significantly more prevalent than normal cellular activity. Conflicting findings in science are not uncommon, indicating a need for further research to clarify the issue of SARS-CoV-2 genomic integration.