Social isolation has stopped the outbreak, but many people are still getting sick from other viruses.
As scientists are discovering, many viruses are lurking quietly in the human body, hiding in the lungs, blood and nervous system, or living in a host of gut microbes.
Some thrive in the body, while others attack the body’s cells, tissues and organs.
Biologists estimate that there are 38 trillion viruses living in each human body, 10 times as many as bacteria.
Some viruses can cause disease, but many just coexist with humans.
In late 2019, for example, researchers at the University of Pennsylvania discovered a new class of Redondoviridae virus in the respiratory tract. It contains 19 viral strains, a few of which have been linked to periodontal or lung disease, but others may help fight respiratory diseases.
A steady stream of new research clearly shows that we’re not just made up of human cells;
Instead, our body is more like a superorganism, made up of human cells and symbiotic bacteria, fungi and, most abundantly, viruses.
The latest data suggest that up to half of the biological matter in the human body is not produced by human cells.
A decade ago, researchers were barely aware of the large number of viruses in the human body.
Today, however, we think of large viral groups as part of a much larger human microbiome.
This microbiome is made up of a large number of passive and active invading microbes that occupy almost every corner of the human body.
We’ve been mapping the virus community for 10 years now, and the more we look at it, the more we see that viruses are like our partners, and that they can have a positive or negative impact on our daily lives.
Recent research suggests that we can even use viruses to improve our own health.
For example, researchers at Rockefeller University in the United States have purified an enzyme from a virus that kills methicillin-resistant Staphylococcus bacteria in patients.
The results were so encouraging that the US Food and Drug Administration (FDA) has designated the enzyme as a “breakthrough therapy”.
The treatment is currently in phase 3 clinical trials.
An abundance of viruses
Viruses need to invade host cells to reproduce, and they are adept at taking advantage of all the options offered by the body.
Around 2013, scientists found the virus in the skin, respiratory tract, blood and urine.
But I, Chandrabali Ghose and others found the virus in an even more surprising place — in a September 2019 paper, we detected it in the cerebrospinal fluid of healthy adults.
These viruses belong to several different families and are not associated with any known disease.
We also found the same virus in plasma, joint fluid and breast milk.
Scientists know that some rare infectious viruses (herpes virus in particular) can sneak into the cerebrospinal fluid.
The central nervous system, which is usually thought of as a sterile environment, is somehow overrun by multiple viral populations.
What is a virus?
A virus is an extremely tiny particle made up of a protein shell and its inner strand of RNA, or DNA.
They can only replicate with the help of host cells.
Viruses can be identified in three ways: shape (A), host (B), and genetic material (C).
Viruses seem to accumulate in our bodies as soon as we are born.
Studies have shown that a variety of viruses are present in the intestines of babies shortly after birth, suggesting that the viruses may have come from the baby’s mother, and that some of them enter the baby’s body through breast milk.
As babies grow into weeks or months, the number of some of these viruses declines.
Other viruses, from the air, water, food and other people, get into their bodies.
The virus grows in number and diversity and persists in the body for years by infecting cells.
The virus is relatively stable in adults compared to babies.
As we age, the Anelloviridae family (200 species) is present in almost everyone’s body, just as bacteria are in our bodies.
Many of the viruses that live in our bodies do not attack human cells.
Instead, they attack some bacteria in the human microbiome.
These viruses, called bacteriophages, lurk inside bacteria, using their organelles to replicate themselves and often burst out of them to infect more bacteria, killing the host bacteria in the process.
Bacteriophages are almost everywhere in nature.
If you look closely, they can be found in soil, in any water environment from the ocean to your home faucet, and in extreme environments such as acidic minerals, the Arctic and hot springs.
You can even spot viruses floating around in the air.
They are there to look for the bacteria that live in them.
For phages, the human body is just another hunting ground, and infecting and attacking the bacteria in it is their purpose.
In 2017, Sophie Nguyen and Jeremy Barr, then working at San Diego State University, demonstrated that many phages can penetrate the mucous membranes on the surface of some organs to enter the body and find their final site of settlement.
Several laboratory studies have shown that phages can penetrate the mucous membranes of the human gut, lungs, liver, kidneys and even the brain.
But once phages randomly enter places where few bacteria exist, such as the central nervous system, they may fail to replicate and eventually die out.
The group of viruses in the human body
Different parts of the body have very different groups of viruses.
Melissa Ly of the University of California, San Diego, and I have also shown that by comparing the viral groups of unrelated people, it is possible to determine whether any of them are living together.
Different people can have very different viral groups, and cohabiting people seem to share about 25 percent of their viral groups.
The virus can spread not only among family members through typical transmission methods such as coughing, but also through daily contact, sharing of sinks, toilets, tables and food.
Although we only looked at a small number of people, the data shows that roommates who are not in a relationship share the same percentage of viruses as roommates who are in a romantic relationship.
Intimate contact doesn’t seem to have much effect on this, just living in the same space is enough.
Shira Abeles of the University of California, San Diego, has found huge differences in the virus in the mouths of men and women, which may be caused by different hormonal components in their bodies, but no one has been able to prove a link.
We did find that there was a lot of variation in the group of viruses among different populations because of geographical location.
For example, populations in Western countries tend to be less diverse than those in other countries, and these differences may be related to diet and the environment.
While many viruses in the human body infect bacteria, a small number also infect cells directly in human tissues.
These viruses may be in a minority, as the body’s immune system suppresses them.
Iwijn De Vlaminck, then at Stanford University, showed that certain types of viruses rise sharply when a person’s immune system is challenged — for example, when the recipient of an organ has to take immunosuppressive drugs to avoid organ rejection.
The observations show that under normal circumstances, our immune system can suppress the virus, but when people’s immune system is suppressed, the virus can multiply unchecked.
We can also see this opportunism in Novel Coronavirus.
Patients infected with novel coronavirus, especially those with severe illness, are likely to develop complications.
The most common is secondary bacterial pneumonia, or bacteremia, which is caused by an increase in bacteria in the blood.
Viruses that lurk in humans, such as human Epstein-Barr virus and Cytomegalovirus, can be reactivated.
When the immune system is focused on fighting novel coronavirus, patients may be more vulnerable to other viruses.
Although many phages are predators, they probably live in harmony with their host bacteria and don’t explode inside them.
When some phages infect bacteria, they integrate their genomes into the bacteria’s genome.
While some phages multiply immediately, killing the host bacteria, others simply persist in the body, as if in a quiet, dormant state.
This may be a survival strategy: when the host bacterium divides, it needs to make a copy of its own genome, as well as a copy of the phage’s genome.
In this mode, the survival of the host determines the survival of the phage, so the phage has some benefit in keeping the host alive.
It’s clear why this strategy is good for phages, but it’s not clear that it’s good for bacteria.
For whatever reason, many bacteria in the human body seem to have adapted to living with parasitic bacteriophages.
Some viruses are less well understood, some may be harmless, and they are in almost everyone’s body, such as Crassphage.
When the time is right, these dormant phages wake up and produce lots of progeny, killing their host cells.
Sometimes, some phages leave the bacteria with the bacteria’s genes, which can sometimes benefit them when they infect the next bacterium.
For example, I discovered that phages in saliva carry genes that help bacteria evade the body’s immune system.
Some phages even carry genes that help the bacteria resist some antibiotics.
Phages don’t need such genes themselves, since antibiotics can’t kill them, but when they give the genes to the host bacteria, they help the bacteria survive — and the phages survive.
We often see similar gene transfer phenomena, such as horizontal transfer of drug-resistant genes from one bacterium to another.
Phages can also further protect their hosts.
As a pathogenic bacterium, Pseudomonas aeruginosa usually causes pneumonia and leads to a variety of diseases.
People with lung diseases like cystic fibrosis can’t completely clear their lungs of bacteria, even when given antibiotics that kill the bacteria.
Some Pseudomonas aeruginosa incorporate filamentous phages into their genomes.
In 2019, a team led by Elizabeth Burgener, Paul Bollyky and others at Stanford University found that filamentous phages can help Pseudomonas aeruginosa hide from antibiotics by forming a protective outer layer of carbohydrates and proteins on the outside of cells.
This allows them to hide in place until the antibiotic has been completely metabolized in the body, then continue to multiply and cause infection.
Trying to use viruses that live in the human body to improve health is not itself a very new idea.
We found that something similar is already happening naturally, as phages move around the human body looking for suitable bacteria to host, some of them attach to the mucosal surfaces of cells in the nose, throat, stomach and intestines.
Although phages cannot replicate in these cells, they can lie in wait for an intrusive host to pass by.
In theory, this process could protect us from certain diseases.
Suppose you eat food contaminated with salmonella. As the bacteria pass through the stomach, phages on the surface of the stomach membrane infect the bacteria and kill them before they can cause disease.
In this way, phages can actually act as part of the immune system, helping us fight off some of the bacteria that are harmful to us.
No one has confirmed this yet, but in 2019 a Finnish research team showed that phages that stick to the mucus of pigs and rainbow trout can live for seven days, during which time they help the animals fend off a class of bacteria that infects them.
The human virus group Our bodies are full of viruses that come and go and stay in our bodies for years.
Some families of viruses, such as the herpesviridae family, cause a variety of diseases.
One phage that is getting a lot of attention is crAssphage, which was discovered in 2014 by Bas Dutih of the Radboude Institute in the Netherlands.
Since then, research has shown that these phages inhabit the vast majority of the world’s human population, in addition to traditional hunter-gatherers.
It is very rare for a virus to spread so widely, and no one has yet found a link to a disease.
Scientists think it can control the spread of a common intestinal bacterium called Bacteroides.
Some physicians have expressed interest in the potential for phages to resist a proliferation of drug-resistant bacteria.
Phages were discovered more than a hundred years ago, when doctors tried to use them to treat pathogenic bacteria, but without great success.
Antibiotics replaced phage therapy in most parts of the world in the 1940s because they were more effective and easier to use.
Now, some medical researchers are doing new work on phages, such as researchers at Rockefeller University who are using a phage enzyme to fight methicillin-resistant Staphylococcus aureus (MRSA) infections.
For years, many doctors were afraid to use bacteriophages because they didn’t know whether the human immune system could overreact to them, leading to life-threatening inflammation.
Bacteriophages used for therapy need to be grown with bacteria, which can cause a strong immune response in humans if they are not completely removed before phage therapy is used.
Today, we have more advanced phage purification methods that have largely alleviated concerns about adverse reactions.
What really limits phage therapy for infectious diseases is the difficulty of finding an effective virus.
For years, researchers have been scouring the natural habitats of phages, trying to find ones that can fight pathogens that cause humans.
Viruses are known to be abundant in feces, saliva, and sputum, and some researchers are aware that local sewage treatment plants may also be one of the most abundant sources of phages.
A few similar phages have been used in experimental treatments.
In 2016, Robert Schooley of the University of California, San Diego, oversaw a landmark case.
In this case, doctors successfully treated the school’s professor, Tom Patterson, who had suffered multiple organ failure after being infected with Acinetobacter baumannii, using phages from sewage and environmental sources.
Viruses improve human health
As we learn more about the role played by the various viruses in the human virogroup, it may be possible to develop more treatments.
Although it will take us a long time to figure out what the human virus group is, it is necessary when you consider what has been achieved in the last decade.
A decade ago, many scientists thought the microbiome was just a collection of tiny organisms passively distributed in the gut.
But we now know that while some parts of the microbiome are indeed stable, others are active and constantly changing.
And the part that seems to be most active right now is the virus.
In 2018, a study of donated brain tissue from people who died of Alzheimer’s disease showed high levels of the herpes virus in their brains.
Then, in May 2020, the Tufts and M.I.T. researchers infected the brain-like tissue they had developed in the lab with Herpes simplex virus 1, which became filled with amyloid plaques, similar to the brain-destroying structures found in the brains of Alzheimer’s patients.
We were surprised to learn that some familiar viruses could play an unexpected and crucial role.
As research continues, we may discover new strains of viruses that affect human health and develop new ways of using viruses to manipulate the microbiome and protect people from disease.
If humans can figure out how to manage bad viruses and use good ones, we might be able to transform ourselves into more powerful superorganisms.
David Pride is an infectious disease specialist and associate professor of pathology at the University of California, San Diego.
His laboratory focuses on the role of the microbial community in human homeostasis, health and disease.