By Dan Hurley

Veteran virus trackers say they are chronicling something never before seen — the suppression of virtually every common respiratory and gastrointestinal virus besides the novel coronavirus. They theorize that is largely due to global shutdowns, mask-wearing and a host of other health protocols aimed at stemming the spread of the coronavirus.

These other viruses — including influenza A, influenza B, parainfluenza, norovirus, respiratory syncytial virus (RSV), human metapneumovirus — all appear to be circulating at or near levels lower than ever previously measured. The same is true for the respiratory bacteria that cause pertussis, better known as whooping cough, and pneumonia.

“It’s crazy,” said Lynnette Brammer, who leads the Centers for Disease Control and Prevention Domestic Influenza Surveillance team. “This is my 30th flu season. I never would have expected to see flu activity this low.”

In 2019, during the third week of December, before the coronavirus struck the United States, the CDC’s network of clinical labs reported that 16.2 percent of the 29,578 samples tested were positive for influenza A. During the same week in 2020, the rate was 0.3 percent.

An online map of flu activity maintained by the CDC offers striking visual evidence of the effect. In 2020, for the week ending Dec. 19, the map of the United States is a sea of green, showing “minimal” levels in every state. For the corresponding week in 2019, most states were red (“high”) or deep blue (“very high”).

Another virus, enterovirus D68 — linked to a polio-like paralysis seen mostly in children — has likewise been greatly reduced. As recently as August, CDC officials warned doctors and parents to be on the lookout for cases of the polio-like condition, known as acute flaccid myelitis. Outbreaks of the condition have peaked in a peculiar every-other-year cycle for six years, with 120 cases across the United States in 2014, 153 in 2016, and 240 in 2018. But in 2020, the CDC confirmed just 29 cases.

“We haven’t had any specimen positive for [enterovirus] D68 … at our site in Colorado since July, and my colleagues around the country also saw very little,” said Kevin Messacar, a pediatric infectious-disease physician at Children’s Hospital Colorado in Aurora. “We also have not seen significant influenza or RSV on our wards in Colorado. All the most common childhood infections that land children in the hospital — influenza, croup, bronchiolitis — we are not seeing.”

As welcome as the absence of these other viruses is during a pandemic, epidemiologists say they see a potentially dangerous consequence after coronavirus cases eventually decline — a rebound that could be frightfully large given the relaxation of social distancing and lowered immunity to other pathogens.

“The best analogy is to a forest fire,” said Bryan Grenfell, an epidemiologist and population biologist at Princeton. “For the fire to spread, it needs to have unburned wood. For epidemics to spread, they require people who haven’t previously been infected. So if people don’t get infected this year by these viruses, they likely will at some point later on.”

The possibility of a rebound is not merely theoretical: It appears to be happening already in Australia. Official reports showed historically low levels of flu-like illness among children and adults beginning in May, usually the start of flu season in that hemisphere. The sharp decline in cases came as the country imposed strict shutdown measures. But in the last few months, after the coronavirus was virtually obliterated and the country ended those restrictions, the number of flu cases among children aged 5 and younger began to soar, rising sixfold by December, when such cases are usually at their lowest.

“That’s an important cautionary tale for us,” Messacar said. “Just because we get through the winter and don’t see much RSV or influenza doesn’t mean we’ll be out of the woods.”

A breathtaking picture of the extent of the collapse of viral and bacterial infections can be seen in a single chart created and maintained by BioFire, a company that provides diagnostic tests for viral and bacterial infections to over 2,500 U.S. health-care providers. The chart shows positivity rates for 13 respiratory viruses and bacteria during the past two years.

A year ago at this time, nearly 60 percent of samples taken from patients with flu-like symptoms came back positive for one of the pathogens. But beginning in March of this year, when the coronavirus prompted shutdowns and school closings, the percent of samples positive for any other pathogen took a Grand Canyon-worthy plunge, bottoming out in May at about 6 percent. Even now, at the time of year when respiratory infections typically begin to peak, just 18 percent of samples are positive for any respiratory virus or bacteria.

Individual charts maintained by the CDC show similarly stark declines in national rates of infection for RSV, norovirus, metapneumovirus and parainfluenza, as well as for other types of coronaviruses.

The question, of course, is why SARS-CoV-2, the virus that causes covid-19, continues to spread like wildfire when so many other viruses have been crushed. The primary answer, epidemiologists say, goes back to that “wildfire” metaphor. Nobody on Earth had been exposed to SARS-CoV-2 before its emergence last year in China, and so we were all fully susceptible. (Similarly, the indigenous populations of North and South America were devastated when Europeans brought with them not just smallpox, but also chickenpox, cholera, influenza, measles, and other pathogens to which they had never been exposed.)

Viruses that have circulated for years, by contrast, are “endemic,” or always present at a base level. Because many of us have previously been exposed and therefore have developed immunity to them, social distancing can more easily cut the chain of transmission.

“A little bit of social distancing can greatly reduce the infectivity of common pathogens,” said Lindsay Meyers, who worked for BioFire for 19 years and created its online charts before leaving the company in the summer. “Whereas with a pandemic pathogen, when everyone is susceptible, you need much stricter social distancing to contain.”

Epidemiologists use the term “nonpharmaceutical interventions” to describe the range of behavior changes, such as social distancing, that people use to lower their risk of infection. In a paper published in the Dec. 1 issue of the Proceedings of the National Academy of Sciences, Grenfell and colleagues noted that such behavior changes during the 1918 flu pandemic may have lowered the transmission of measles by 38 percent.

But the focus of the paper was on the likely outcome in 2021 and beyond after the coronavirus pandemic dissipates and such practices are relaxed. Using mathematical models, they focused on the likely effect on respiratory syncytial virus, or RSV, a common and very contagious virus that infects most children before their second birthday, and causes over 200,000 hospitalizations and 14,000 deaths in normal years.

“The bottom line is that while we have these controls in place, there is a slow buildup of susceptibility to these other viruses,” said Rachel Baker, a postdoctoral researcher in Grenfell’s department and first author of the paper. “The numbers [of infections] were pretty stable for 30 years, but in 2020 it disappeared. We need to be aware that future large outbreaks might be coming.”

Social distancing is probably not the only factor suppressing endemic pathogens. Walgreens, for instance, has seen “unprecedented demand” for flu vaccine shots this season, according to Kevin Ban, chief medical officer of the pharmacy chain.

Vaccines, unfortunately, are not available for most other viruses. But another powerful factor, called viral interference, could also play an important role in limiting infections. In a paper published Oct. 1 in the Lancet Microbe, Ellen Foxman of Yale University reported that a prior rhinovirus infection greatly reduces the chances of contracting influenza A. The reason, she found, is that infection with one virus prompts the body’s immune system to release interferon, which blocks replication of all viruses.

“The interferon response is one of the body’s best defenses against respiratory viruses,” Foxman said. “As soon as it gets turned on by one virus, any other virus that comes along and tries to grow in the respiratory tract can’t.”

The body’s response to SARS-CoV-2, in other words, could be blocking the spread of other viruses. Its response to other pathogens might produce similar protection: Foxman points to temporary breaks in the spread of influenza during the 1918 pandemic, as well as during the 2009 H1N1 swine flu pandemic, as possibly due to viral interference from rhinovirus.

Viral interference could also help explain a deep mystery about the coronavirus: why so few children are getting severely sick from it. As it happens, one of the only endemic viruses still circulating widely now is rhinovirus, which typically causes the common cold. And according to Meyers, “Rhinovirus is circulating only in pediatric populations. It’s been wiped out in adults.”

To be clear, no one is suggesting that people should intentionally infect themselves with rhinovirus to protect themselves from SARS-CoV-2.

“I do not advocate people going out infecting themselves with anything,” Foxman said flatly.

But when the pandemic is finally brought under control by the vaccines now being rolled out, will it be safe for most people to toss their face masks and return to “normal” life?

“It’s a real possibility that we’re going to see increased outbreaks of the endemic infections,” said Ben Lopman, an epidemiologist in Emory University’s Rollins School of Public Health. “If people haven’t gotten infected this year, because of actions taken to prevent covid-19, there’s a real risk of bigger outbreaks when we go back to normal.”

Besides larger-than-normal numbers of endemic infections, Lopman added, some of those infections could be more severe than normal, again because of waning immunity.

Even so, he emphasized, “It’s certainly a good thing that we’re keeping these other infections in check right now, when our hospitals are filled with covid-19 patients. But we’re learning that the effects of the pandemic are complex. They’re going to be long-lasting. And we’re going to find that they extend beyond just the disease that SARS-CoV-2 causes.”

Of course, predicting the future effect of a once-in-a-century pandemic is an uncertain business.

“This is something that hasn’t happened in our lifetime,” said Messacar, the Colorado pediatrician. “We know there will be more children and adults susceptible to enterovirus D-68, influenza, parainfluenza, RSV. But what will actually happen in reality, we don’t know.”

Foxman expressed similar reluctance to make a firm prediction.

“The decline in respiratory viruses has really been fascinating,” she said. “It’s incredible. We’ve never had a natural experiment like this before. What the consequence will be for the short and long term remains to be seen.”

Only one thing is a certainty, she added. “Eventually these viruses will come back. They always find a way.”