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HomeHealthExplainer: Virus variants and strains - Science News for Students

Explainer: Virus variants and strains – Science News for Students

Viruses, like the one in this illustration, borrow the machinery of a cell to reproduce. But sometimes copying errors occur, leading to changes in the virus’s genetic material. The new form is known as a variant — and sometimes it’s changed enough to become a new strain.
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Some virus experts might not consider viruses to be alive. Yet viruses can reproduce. To do so, they hijack the cells of a host. They borrow the “machinery” in the host’s cells to copy the virus’ genetic code. Those host cells may spit out hundreds or thousands — even millions — of copies of the original virus. These new viruses then go on to infect more cells. Maybe the host will also sneeze out the viruses or otherwise release some to infect other potential hosts. And those hosts might be anything from people or plants to bacteria.
But each time a virus is copied, there’s some risk the host’s cell will make one or more errors in the genetic code of that virus. These are known as mutations. Each new one alters the genetic blueprint of the virus a bit. Mutant viruses are known as variants of the original.
Many mutations won’t affect how a virus works. Some might be bad for the virus. Others might improve how well the virus can infect a cell, or help the virus evade its host’s immune system. A mutation might even allow the virus to resist the effects of some therapy. Scientists refer to such new-and-improved variants as strains.
Keep in mind that all strains of a virus are variants. Not all variants, however, are different enough to qualify as a new strain.
And although coronavirus variants made news throughout much of the COVID-19 pandemic, any virus runs the risk of spawning new variants through mutation.
Indeed, mutations are one basis of evolution. Mutations that don’t benefit an organism (or virus), often die out. But those that make an organism more fit — better adapted to its environment — tend to become more dominant.
Anthony Fauci heads the National Institute of Allergy and Infectious Diseases. It’s in Bethesda, Md. Every time a virus infects someone, viral copying — also known as replication — goes on. And as each new copy is made, he notes, there’s the risk of a new variant developing. He spoke August 12 on National Public Radio’s Morning Edition to discuss concerns about the coronavirus.  
“A virus will not mutate if you don’t allow it to replicate,” he explained. “And when you have people getting infected and spreading it through the community, the virus has ample opportunity to do that.” Let enough people get infected, and “sooner or later,” he said, a more dangerous form of the virus may evolve. That’s why virus experts have been pushing vaccines, use of masks and social distancing. These cut the risk of new infections, which will limit the risk of new copying errors.
Scientists refer to some new versions of the coronavirus as “variants of concern.” Compared to the original virus, these variants might infect or spread between people more easily, respond less well to treatments or impair how well vaccines work against the virus. A more serious class of viruses are so-called “variants of high consequence.” Treatments or precautions work far less well against these viruses than they had against earlier forms of the virus. For instance, the new variants might resist current vaccines. They may not show up well in current tests. They might even cause more severe disease.
As of August 2021, no coronavirus variants of high consequence have emerged anywhere in the world. But there were four variants of concern. As one after another evolved, scientists began referring to them with letters of the Greek alphabet: alpha, beta, gamma and delta.
That last one has been especially troubling. According to the U.S. Centers for Disease Control and Prevention, or CDC, the delta variant spreads much faster than other variants. It seems to cause more severe disease. It also responds less well to treatment with lab-grown antibodies. The good news: COVID-19 vaccines appear to work well at limiting severe disease or death from this variant.
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The influenza virus mutates rapidly. The new strains spawned by those changes are one reason people need flu shots every year. The latest flu vaccines have been developed to target new variants.
Variants usually develop within a host because viruses are error-prone. This is especially true for RNA viruses, such as coronaviruses and flu viruses. And some variants may prove better suited to reach particular target tissues. That’s what Holly Hughes and her team found. Hughes works for the CDC in Fort Collins, Colo. There she focuses on decrypting the genetic code of viruses.
She was part of a team that did this for EEEV. That’s short for the eastern equine encephalitis (En-seff-uh-LY-tis) virus. Hughes notes that it is “one of the deadliest mosquito-borne diseases in the United States.” Few people become infected by this virus. But about a third of those individuals die. And those who survive can be left with long-term physical or mental problems.
Hughes’ team sampled the virus from a woman who got EEEV during a 2019 epidemic — and didn’t survive. The researchers turned up a number of EEEV variants in her blood. The team also sampled fluid from around her brain and spinal cord. To their surprise, only one variant had made it to the brain. The others hadn’t crossed the body’s blood-brain barrier. That’s important, Hughes notes. All of the EEEV copied by the woman’s brain cells would now carry this variant’s genetics.
This seems to suggest that a mix of variants in the blood allows EEEV “to infect different areas of the body,” says Hughes. Her team shared its findings in the July 2021 Emerging Infectious Diseases.
While EEEV cases are rare, rabies infections are not. According to the World Health Organization, rabies kills an estimated 59,000 people each year. Some 95 percent of these deaths occur in Africa and Asia, especially India. Although dog bites are the leading source of human infections, other animals carry the virus too. Indeed, some variants of rabies virus are well-suited to infect particular hosts. These include racoons, bats, foxes and skunks
Ryan Wallace, who works for the CDC in Atlanta, Ga., studies rabies. He led a 2014 project that looked at how often variants of the virus cross over from rabies-infected animals to other species in the United States.
Scientists had thought rabies variants tended to be linked to one primary species. Such species are known as its “reservoirs.” In their study, Wallace and his team looked for crossovers into species other than the reservoir. And this proved surprisingly common, they found. For instance, between 1990 and 2011, some 67,058 raccoons were found with the raccoon variant. Another 30,876 other rabid animals also were infected with the raccoon variant.
Crossovers to other species by the raccoon variant “was unexpectedly high,” they reported. Skunks are a major source of rabies. However, compared to skunks, this study found “raccoons were four times more likely to transmit rabies to other species.”
This finding makes a good case for vaccinating pets, Wallace and his coworkers argue. Why? The spillover of a rabies variant from one species to another can lead the virus to adapt into new strains. These can now more readily attack new host species. The good news: For now, the rabies shots given to dogs and cats work against all U.S. rabies variants.
allergy: The inappropriate reaction by the body’s immune system to a normally harmless substance. Untreated, a particularly severe reaction can lead to death.
antibodies: Any of a large number of proteins that the body produces from B cells and releases into the blood supply as part of its immune response. The production of antibodies is triggered when the body encounters an antigen, some foreign material. Antibodies then lock onto antigens as a first step in disabling the germs or other foreign substances that were the source of those antigens.
bacteria: (singular: bacterium) Single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside other living organisms (such as plants and animals). Bacteria are one of the three domains of life on Earth.
blood-brain barrier: A barrier of tightly packed cells that carefully regulate what molecules can — and can’t — enter the brain. The barrier protects the brain from foreign substances in the blood and helps to maintain a constant environment for brain cells.
cell: The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Most organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell. (
coronavirus: A family of viruses named for the crown-like spikes on their surface (corona means “crown” in Latin). Coronaviruses cause the common cold. The family also includes viruses that cause far more serious infections, including SARS and COVID-19.
COVID-19: A name given to the disease that caused a massive global outbreak. It first emerged in December 2019 and is caused by a new coronavirus known as SARS-CoV-2. Symptoms can include pneumonia, trouble breathing, feeling too tired to walk more than a few steps, fever, headaches, low blood-oxygen levels, blood clots and brain “fog.”
develop: To emerge or to make come into being, either naturally or through human intervention, such as by manufacturing.
emerging infectious disease: A disease that suddenly has begun infecting increasing numbers of people or other organisms and could increase dramatically, more so in the near future.
encephalitis: An inflammation of the brain, usually caused by a viral infection. The disease can impair movement, clarity of thinking and other facets of brain function. In severe cases, this condition can lead to death.
environment: The sum of all of the things that exist around some organism or the process and the condition those things create. Environment may refer to the weather and ecosystem in which some animal lives, or, perhaps, the temperature and humidity (or even the placement of things in the vicinity of an item of interest).
epidemic: A widespread outbreak of an infectious disease that sickens many people (or other organisms) in a community at the same time. The term also may be applied to non-infectious diseases or conditions that have spread in a similar way.
evolution: (v. to evolve) A process by which species undergo changes over time, usually through genetic variation and natural selection. These changes usually result in a new type of organism better suited for its environment than the earlier type. The newer type is not necessarily more “advanced,” just better adapted to the particular conditions in which it developed. Or the term can refer to changes that occur as some natural progression within the non-living world (such as computer chips evolving to smaller devices which operate at an ever faster speed).
focus: (in behavior) To look or concentrate intently on some particular point or thing.
genetic: Having to do with chromosomes, DNA and the genes contained within DNA. The field of science dealing with these biological instructions is known as genetics. People who work in this field are geneticists.
host: (in biology and medicine) The organism (or environment) in which some other thing resides. Humans may be a temporary host for food-poisoning germs or other infective agents. (v.) The act of providing a home or environment for something.
immune system: The collection of cells and their responses that help the body fight off infections and deal with foreign substances that may provoke allergies.
impair: (n. impairment) To damage or weaken in some way.
infect: To spread a disease from one organism to another. This usually involves introducing some sort of disease-causing germ to an individual.
infection: (adj. infectious) A disease that can spread from one organism to another. It’s usually caused by some type of germ.
inflammation: (adj. inflammatory) The body’s response to cellular injury and obesity; it often involves swelling, redness, heat and pain. It also is an underlying feature responsible for the development and aggravation of many diseases, especially heart disease and diabetes.
mutation: (v. mutate) Some change that occurs to a gene in an organism’s DNA. Some mutations occur naturally. Others can be triggered by outside factors, such as pollution, radiation, medicines or something in the diet. A gene with this change is referred to as a mutant.
National Institute of Allergy and Infectious Diseases: Initially created as a small lab in 1887 at a hospital in New York City, it now is headquartered in Bethesda, Md. Developed to explore the new science of bacteriology, it became part of the National Institutes of Health in 1948. Today it works to better understand, treat and prevent all types of infectious and immunity-affecting diseases.
organism: Any living thing, from elephants and plants to bacteria and other types of single-celled life.
pandemic: An epidemic that affects a large proportion of the population across a country or the world.
physical: (adj.) A term for things that exist in the real world, as opposed to in memories or the imagination. It can also refer to properties of materials that are due to their size and non-chemical interactions (such as when one block slams with force into another).
primary: An adjective meaning major, first or most important. (In reference to colors). The basic hues that can combine to make all other colors. For mixing light, the primary colors are red, green, and blue. (in elections) A preliminary, early U.S. election to select a limited number of candidates (typically one for each open office) who will represent their political party on the printed ballot in an upcoming national election.
rabies: A virus that is transmitted from mammals such as bats, raccoons, skunks and dogs — sometimes to people. Rabies is found on every continent except Antarctica, and is spread by contact with the saliva of an infected host. A vaccine exists. Without a vaccination, nearly every infected person will die.
replication: (in biology) The copying of genetic material as a microbe or virus begins to reproduce. (in experimentation) Getting the same result as an earlier test or experiment — often an earlier test performed by someone else. Replication depends upon repeating every step of a test, step by step. If a repeated experiment generates the same result as in earlier trials, scientists view this as verifying that the initial result is reliable. If results differ, the initial findings may fall into doubt. Generally, a scientific finding is not fully accepted as being real or true without replication.
reservoir: A large store of something. Lakes are reservoirs that hold water. People who study infections refer to the environment in which germs can survive safely (such as the bodies of birds or pigs) as living reservoirs.
social distancing: A term for the intentional separation of people to limit the chance that a disease can be passed from one to another.
species: A group of similar organisms capable of producing offspring that can survive and reproduce.
spinal cord: A cylindrical bundle of nerve fibers and associated tissue. It is enclosed in the spine and connects nearly all parts of the body to the brain, with which it forms the central nervous system.
strain: (in biology) Organisms that belong to the same species that share some small but definable characteristics. For example, biologists breed certain strains of mice that may have a particular susceptibility to disease. Certain bacteria or viruses may develop one or more mutations that turn them into a strain that is immune to the ordinarily lethal effect of one or more drugs.
therapy: (adj. therapeutic) Treatment intended to relieve or heal a disorder.
tissue: Made of cells, it is any of the distinct types of materials that make up animals, plants or fungi. Cells within a tissue work as a unit to perform a particular function in living organisms. Different organs of the human body, for instance, often are made from many different types of tissues.
transmit: (n. transmission) To send or pass along.
vaccine: (v. vaccinate) A biological mixture that resembles a disease-causing agent. It is given to help the body create immunity to a particular disease. The injections used to administer most vaccines are known as vaccinations.
variant: A version of something that may come in different forms. (in biology) Members of a species that possess some feature (size, coloration or lifespan, for example) that make them distinct. (in genetics) A gene having a slight mutation that may have left its host species somewhat better adapted for its environment.
virus: Tiny infectious particles consisting of RNA or DNA surrounded by protein. Viruses can reproduce only by injecting their genetic material into the cells of living creatures. Although scientists frequently refer to viruses as live or dead, in fact no virus is truly alive. It doesn’t eat like animals do, or make its own food the way plants do. It must hijack the cellular machinery of a living cell in order to survive.
World Health Organization: An agency of the United Nations, established in 1948, to promote health and to control communicable diseases. It is based in Geneva, Switzerland. The United Nations relies on the WHO for providing international leadership on global health matters. This organization also helps shape the research agenda for health issues and sets standards for pollutants and other things that could pose a risk to health. WHO also regularly reviews data to set policies for maintaining health and a healthy environment.
Journal:​ ​​H.R. Hughes et al. Fatal human infection with evidence of intrahost variation of eastern equine encephalitis virus, Alabama, USA, 2019. Emerging Infectious Diseases. Vol. 27, July 2021, p. 1886. doi: 10.3201/eid2707.210315.
Meeting:​​ A.S. Lauring and P.N. Malani. Variants of SARS-CoV-2. JAMA. August 13, 2021. doi JAMA. Published online August 13, 2021. doi:10.1001/jama.2021.14181.
Journal:​ R.M. Wallace et al. Right place, wrong species: A 20-year review of rabies virus cross species transmission among terrestrial mammals in the United States. PLOS ONE. Vol. 9, October 8, 2014, p, e107539. doi: 10.1371/journal.pone.0107539.
Journal:​ ​​ M.K. Sudarshan et al. Assessing burden of human rabies in India: results of a national multi-centre epidemiological survey. International Journal of Infectious Diseases. Vol. 11, January 2007, p. 29. doi: 10.1016/j.ijid.2005.10.007.
Janet Raloff is the editor of Science News for Students. Prior to this, she was an environmental reporter for Science News, specializing in toxicology. To her never-ending surprise, her daughter became a toxicologist.
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