During the past two winters, the use of face masks, avoidance of crowds, and other measures to prevent COVID-19 resulted in a dramatic downturn in the infection numbers for many common winter respiratory viruses, including the flu. But all indications are that this winter in the Northern Hemisphere will be different. The number of flu infections is going up, and according to the US Centers for Disease Control and Prevention (CDC), the current hospitalization rate for the disease in the US is higher than it has been at this time of the year in the past decade. Respiratory syncytial virus (RSV) infections are currently also on the rise.
These trends, together with the continued COVID-19 pandemic, have triggered predictions of a “tripledemic” this winter in which communities are buffeted by outbreaks of multiple respiratory viruses simultaneously. What happens if, in this pathogenic soup, more than one virus infects an individual at the same time?
“People thought about this way back in the 1950s and 60s,” says Yale School of Medicine immunologist Ellen Foxman, as they observed that an initial viral infection sometimes protected against a second simultaneous infection in cell cultures. Back then, though, this couldn’t be analyzed in human populations, “because we didn’t have good tests for these viruses until about the past 10 to 15 years, when PCR became a way of testing for viruses.” All we knew is that everyone gets sick in the winter, says Foxman.
See “Is COVID-19 Seasonal?”
Thus, “most of what we know about virus infection, virus pathogenesis, [and] virus epidemiology is based on the one virus-one disease approach, and that’s not real,” says Pablo Murcia, a virologist at the MRC-University of Glasgow Centre for Virus Research. Multiple viruses cocirculate in the environment and illnesses caused by coinfections may occur—we know little about how individuals respond to them, he says. Studies on viral interactions have been rather rare, but they are slowly becoming more common.
Evidence of what happens when viruses interact is gradually accumulating based on population, individual, and cellular data. In some cases, infections can compound and cause worse symptoms than each on its own. But viruses frequently negatively interact, a phenomenon known as viral interference.
It is “quite important” to improve our understanding of these interactions, says Murcia, as this will help us grasp how viruses are transmitted in real life. Moreover, by unraveling the mechanisms that viruses use to interfere with other pathogens, we may find new approaches to treating patients.
From populations to hosts to cells
In the second half of the 20th century, not only did evidence of how one virus can block another begin to emerge in the lab, but certain epidemiological patterns of respiratory virus outbreaks suggested the existence of viral interference. For example, data from Norway from 1974 to 1981 showed that RSV and flu infections did not reach their epidemic peaks at the same time, and an analysis of studies conducted in the 1970s in India and Nepal found that a single adenovirus type tends to predominate in a given village, often excluding others. More recently, researchers reported that the usual seasonal epidemic of common respiratory viruses was delayed during the flu epidemic in 2009–2010 in Beijing and France.
Most of what we know about virus infection, virus pathogenesis, [and] virus epidemiology is based on the one virus-one disease approach, and that’s not real.—Pablo Murcia, MRC-University of Glasgow Centre for Virus Research
With the possibilities opened up by the use of new PCR technologies, Murcia and his colleagues analyzed 44,230 cases of respiratory illnesses in Scotland between 2005 and 2013. The analysis was based on data of patients simultaneously tested for 11 viruses—including rhinovirus, influenzas A and B, RSV, and seasonal coronaviruses. Of all the patients who tested positive for at least one virus, 11 percent of them had a coinfection—most commonly of two viruses, but some patients harbored up to five viruses at the time of sample collection.
The results offer a glimpse at the frequency of coinfections at the host level and add evidence of positive and negative interactions between these viruses. Specifically, statistical analyses of the prevalence of each pair of viruses at the population level revealed strong signs of positive interactions between different parainfluenza viruses, which cause respiratory infections in infants and young children, and between metapneumovirus and RSV—both also quite common in young children. In contrast, negative interactions cropped up between influenza B and adenoviruses and between rhinoviruses and influenza A virus.
Infections with rhinoviruses, which are the most common culprit behind the common cold, have also been found to block flu infections in other studies, including one led by Foxman. Renee Chan, a cell biologist at the Chinese University of Hong Kong, and her colleagues studied this interaction at the population, individual, and cellular levels, confirming a negative interaction between the two viruses at all of them. The phenomenon needs to be studied at all these three levels in order to confirm it actually occurs, she says.
One of the key mechanisms of the observed interference is a nonspecific immune response to the first virus, which puts an individual into an antiviral state that offers protection against some other would-be invaders.
The innate immune system takes up arms
In recent years, the development of organoid models has shed additional light on how viral interference works. In lab experiments with respiratory viruses, “you want the tissue that’s getting infected to be as close as possible to what we have in our airway,” says Foxman. To achieve this, her team uses organoids made of stem cells induced to form human airway epithelium. “They differentiate into a tissue that looks a lot like the tissue that lines our airway,” she explains.
In studies published in 2020 and 2021, Foxman and her colleagues reported that an initial infection of rhinovirus induced a strong and rapid innate immune response that prevented a subsequent infection with influenza or SARS-CoV-2 in an organoid model.
“The body has these specialized sensors that just sense structures that a lot of viruses have in common, and it doesn’t matter the details of which virus it is,” explains Foxman. For example, detection of viral RNA causes infected cells to secrete interferons, molecules that alert neighbors that there is a virus around. As a result, this release upregulates what are collectively known as interferon stimulated genes (ISGs) that encode antiviral proteins, she says, some of which “block the virus from entering the cells, some block viruses from leaving the cell, others will just shut off all the cellular machinery that the virus needs to reproduce.”
“Many different viruses can turn on this response, and many different viruses are also prevented from growing once this response is on,” notes Foxman, who is a coinventor on patent applications for biomarkers to study the interferon response in the airway.
Based on lab experiments and mathematical models, researchers have also hypothesized that direct competition may play a role, with viruses contending with one another for cells to infect, cell surface receptors, or cellular resources. Yet, within hosts, this competition may be tied up with the immune response, notes Stacey Schultz-Cherry, a virologist at St. Jude Children’s Research Hospital in Memphis, Tennessee. That’s because, by replicating faster, a virus that gains an edge in the competition could extend its lead by causing the host to enter into an antiviral state that “can really limit that second virus or third virus from coming in and actually infecting in that environment.”
When viral interference fails
Whether a virus interferes with a second infection depends, however, on many factors—several of them related to the immune response itself: how the viruses involved trigger the interferon response and also how they respond to it, the timing of infection, and the host’s ability to produce this innate response.
For instance, “vulnerable populations, whether it be pregnant women, the elderly, or people with high body mass index” often show weakened innate immune responses, says Schultz-Cherry. Thus, the question is whether these populations are more susceptible to coinfections.
Any time you have expansion of the paradigm of how you understand disease pathogenesis, [this] opens up the door to interventions that you’ve never even thought of.—Ellen Foxman, Yale School of Medicine
The timing of the infections also matters, most sources tell The Scientist. “Let’s say somebody had flu and it got in their lungs and they had some tissue damage” from it, says Foxman. That person may still be recovering from this damage when they get a second virus once “all the interferon effect is gone.” This would be a plausible scenario where a second infection may actually make things worse, “because the tissue isn’t in its normal healthy, resilient state.”
But even within infections occurring simultaneously, “my best guess,” Foxman adds in a follow-up email, “is that interference rather than potentiation is more likely if the first infection is mild and rapidly induces a robust host innate immune response.”
Given that it’s only been around for a few years, even less is known about coinfections involving SARS-CoV-2. Yet the immune hallmarks of the disease give some clues about how these play out. Deficient interferon production has been linked to an increased vulnerability to SARS-CoV-2, so researchers wonder whether patients with less interferon response are more prone to getting coinfections, or to suffering more severe disease if they do. There’s some epidemiological data and animal research pointing toward potential interactions between flu and SARS-CoV-2 that could worsen clinical outcomes. For instance, even as researchers observed that influenza-positive patients had a lower risk for acquiring SARS-CoV-2, the clinical outcome was more severe in cases where coinfection did occur than in those in which only one of the two viruses was detected. Golden Syrian hamsters coinfected with SARS-CoV-2 and influenza also had more lung damage after a coinfection compared to animals infected by either of the two viruses.
However, Murcia emphasizes that so far, we don’t know much about how SARS-CoV-2 interacts with other viruses in real life. This will be the first winter in the Northern Hemisphere in which many coinfections of SARS-CoV-2 and other viruses could occur, and yet, it may take “multiple seasons” of people mixing normally to actually observe clear patterns of interaction, he notes.
Learning from viral interference
With so many open questions remaining, all sources agree on the importance of improving our understanding of viral interactions. Doctors and public health professionals need to track coinfections far more often, because the evidence indicates that they do impact how “viruses behave within the human body . . . and how severe disease you might get,” says Hana Dobrovolny, a computational biophysicist who studies viral infections at Texas Christian University. Once researchers understand better how frequent coinfections are, as well as their associated clinical outcomes, we can use that information to improve how patients infected by these viruses are treated, she says.
“Any time you have expansion of the paradigm of how you understand disease pathogenesis, [this] opens up the door to interventions that you’ve never even thought of,” Foxman concurs.
For instance, vaccines and antiviral drugs are important for public health, yet we have both for COVID-19 and flu and “they’re still both huge public health problems,” Foxman notes. We need additional complementary strategies that come at the problem from a different angle, she says.
Based on the accumulating evidence that rhinoviruses—which sometimes do not induce any symptoms—interfere with other respiratory viruses, Chan posits that viruses causing asymptomatic infections may be key players in viral interference, adding that more efforts should be made to monitor and understand how these viruses may provide natural protection from other pathogens and what pathways they induce.
Yet Foxman says it’s unlikely that viral interference will prevent us from seeing high respiratory virus circulation this winter. If anything, the phenomenon might mean that “we won’t get the peak wave of each one all at the same time,” she says, but rather “they could be staggered.”
In any case, it is important to continue to take precautionary measures, including vaccination, she adds, since “you don’t need two viruses to get sick.” While the insights gleaned about viral interference are “not yet actionable,” she notes, “there are established technologies that we know can actually benefit you right now.”
Other Interactions in the Dish
Some lab experiments have revealed interactions of viruses within cells with unclear relevance to the real world. For instance, a coinfection with influenza A and a human parainfluenza type favors the growth of the flu virus in vitro, an effect attributed to the cell fusion abilities of the parainfluenza virus.
Early this year, Murcia also showed that human lung cells coinfected with influenza A and RSV churn out hybrid viral particles that harbor components of both parental viruses and are better at evading antibodies against flu. “Whether that happens in real life, we don’t know,” says Murcia, nor do we know whether these particles “make disease more severe or less severe.”