Could Covid-19 Awaken Hidden Viruses In Your Body? What A New Study Says

Most people think of a viral infection as a fight between one virus and the immune system. However, the human body can carry several viruses for years without causing any illness. Some viruses can stay largely inactive and controlled by the immune system. They may become active again when the body is under major stress, such as during severe illness. A new study published in Nature suggests that Covid-19 may be one such trigger.

Researchers found that several long-hidden viruses became active again in people hospitalised with Covid-19. These findings are important because viral reactivation was seen even in people who did not have obviously suppressed immune systems. The study also found links between viral reactivation, more severe Covid-19 and some long-term health problems. However, the researchers say that the study does not prove that these viruses cause severe Covid-19 or long Covid.

What Does It Mean When A Virus 'Wakes Up'?

Some viruses do not completely leave the body after the first infection. Instead, they can stay in a quiet or inactive state and are normally kept under control by the immune system. Herpesviruses are a well-known example. When the body experiences stress, serious illness or changes in immune activity, these viruses can sometimes begin producing viral material again. This is known as viral reactivation. It does not necessarily mean that a person develops a new infection. But, a virus already present in the body becomes active again.

What Did The New Study Find?

The researchers analysed data from 1,154 people hospitalised with Covid-19 across 20 US hospitals. The participants were enrolled between May 2020 and March 2021 and were followed during their hospital stay and for up to 12 months afterwards. Researchers examined blood, nasal swabs and, in some mechanically ventilated patients, samples from the airways.

Using genetic sequencing, they searched for evidence of viruses other than SARS-CoV-2. They detected viral material from several chronic viruses, including Epstein-Barr virus (EBV), cytomegalovirus (CMV), herpes simplex virus 1 (HSV-1) and members of the Anelloviridae family. Overall, 47.9% of participants with available data showed evidence of at least one viral reactivation during the acute phase of Covid-19. The viruses did not all behave in the same way. EBV tended to reactivate early in the illness. HSV-1 and CMV were more likely to appear later, showing that different viruses may respond to the stress of Covid-19 at different stages.

Joann Diray Arce, PhD, who leads the PVP-Data Management and Analysis Core and is the lead of the study's Clinical and Data Coordinating Center, said, "This is the largest and most comprehensive biomarker study of Covid-19, in which we followed more than one thousand patients, collected more than 200,000 samples, and generated more than 1 billion data points over the course of a year for this public resource."

Which Viruses Were Involved?

One of the better-known viruses detected was Epstein-Barr virus, which is extremely common and can cause infectious mononucleosis. Researchers also found cytomegalovirus, another widespread virus that can remain in the body for life.

HSV-1, the virus commonly linked to cold sores, was also detected. Another important group was Anelloviridae, a large family of viruses that is common in humans but is still poorly understood. The study found that these viruses could become detectable during Covid-19 even when a person did not have obvious long-term immune suppression.

Can This Explain More Severe Covid-19 And Long Covid?

The study found that reactivation of several chronic viruses was linked to higher Covid-19 severity. For example, viral signals from Anelloviridae, CMV, EBV and HSV-1 were associated with different measures of disease severity and complications. Some viral signals were also associated with worse long-term outcomes among certain severely ill patients.

However, there is an important distinction between association and cause. The researchers cannot say that the reactivated viruses directly made Covid-19 worse. 

“This association with long Covid is an interesting finding as millions around the world suffer from this chronic condition,” says Ofer Levy, MD, PhD, Physician scientist, director of the Precision Vaccines Program (PVP) at Boston Children's. 
“Having new insight as to the molecular and viral associations with long Covid could point the way to better understanding and ultimately better diagnostics and treatments.”

Levy added, “Although many no longer think of Covid being a problem, up to 50,000 Americans died of Covid in 2025-2026 respiratory season and some estimates suggest over 10 million U.S. adults suffer from long Covid. We need to help these patients recover with the best outcomes.”

“Moreover, sooner or later, there may be another coronavirus pandemic, which means we need to learn all the lessons we can from Covid-19 to be better prepared,” he Said. 

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