Persistence of viral RNA following acute infection

By Dr. Sanchari Sinha Dutta, Ph.D.Jun 6 2022Reviewed by Danielle Ellis, B.Sc.

Professor Diane Griffin from the Johns Hopkins Bloomberg School of Public Health, USA, has recently explained the persistence mechanism of viral RNA in the human body after clinical recovery from acute infection. The article has been published in the journal PLOS BIOLOGY.

Background

Viruses require a continuous chain of transmission between infected and susceptible individuals to persist. After acute infection, DNA viruses, such as Herpes viruses, can undergo a latent phase wherein no infectious virions are produced. DNA viruses adopt this strategy to persist in the human body. These viruses can reactivate after months, years, or decades to produce infectious virions and subsequently infect a new group of susceptible individuals.

RNA viruses that cause acute infections by transiently producing infectious virions require an efficient transmission process to persist in the human population. However, in some cases, viral RNA remains in the human body even after eliminating infectious virions. In coronavirus disease 2019 (COVID-19) patients, detectable levels of viral RNA have been observed after acute infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Such long-term presence of viral RNA might be associated with the prolonged manifestation of symptoms commonly known as long COVID.

Existing literature indicates that viral RNA mostly persists in “immune-privileged” sites, such as the brain, eyes, and testes. In addition, viral RNA can be present in the blood, joints, respiratory and gastrointestinal tracts, kidney, and lymphoid tissue.

Form of viral RNA that persists in the system

Viral RNA detected in clinical samples by reverse transcription-polymerase chain reaction (RT-PCR) is often present in degraded or fragmented form. However, studies have shown that full-length viral RNA can eventually resume productive replication in the absence of host immune control.

Because RNA viruses replicate primarily in the cytoplasm, it is most likely that viral RNA persists in this site. For nonretroviral RNA viruses, reverse transcription by cellular enzymes facilitates their persistence as endogenous viral elements. In the cytoplasm, the RNA of negative-stranded viruses is protected by the ribonucleocapsid. Similarly, positive-stranded viruses associate with membranous structures to protect the RNA.

Mechanisms facilitating viral RNA persistence

The innate immune system acts as the first line of defense to recognize and eliminate viral RNA. Innate immune responses include induction of interferon response and production of interferon-stimulated antiviral proteins that help eliminate viral RNA from the body. However, for the complete elimination of infected cells, the production of virus-specific antibodies and T cells (adaptive immune response) is required.   

Acquisition of escape mutations in viral RNA sequences through positive selection is regarded as the major mechanism of immune evasion. Because of these mutations, the production of infectious virions can be suppressed, facilitating the survival of infected cells and the persistence of viral RNA.

Specifically, certain mutations that appear in the viral RNA may reduce the assembly of infectious virions and surface expression of viral protein so that the virus can escape immune cell-mediated recognition and elimination. These mutations help the virus transmit viral RNA to uninfected cells without producing infectious virions.

Furthermore, host-induced adaptive immune responses may trigger the elimination of infectious virus through noncytolytic mechanisms that allow the survival of the infected cell. Viral RNA can persist in cells that are survived. Collectively, these processes help maintain a detectable viral RNA pool even after recovery from acute infection.

Clinical consequences of viral RNA persistence

Viral RNA is capable of inducing innate immune responses and chronic inflammation. Despite not being replicated or assembled to form infectious virions, viral RNA can be translated to synthesize viral proteins, leading to chronic stimulation of adaptive immune responses.

Clinical consequences of such chronic immune stimulation depend on the site of viral RNA persistence. Studies have shown that the long-term presence of alphavirus RNA in synovial tissues is associated with chronic inflammation and joint pain. Similarly, the prolonged presence of enterovirus RNA in the myocardium has been associated with cardiac abnormalities.

In severe COVID-19 patients, SARS-CoV-2 RNA has been detected in the blood during recovery. This indicates the systemic spread of the infection that might be responsible for the induction of long-COVID. A state of hyperinflammation and vascular injury has been documented in COVID-19 patients presenting various symptoms even three months after acute infection.

Long-term stimulation of adaptive immune responses in the lymphoid tissue could benefit the hosts in terms of inducing durable immunity against reinfection. Infection with the measles virus has been associated with long-lasting immunity because of the persistence of viral RNA in the lymphoid tissues. In contrast, induction of only short-lived immunity has been observed in SARS-CoV-2 infection due to a lack of RNA persistence in the lymphoid tissue.