Today, many virological terms are used by people who do not understand their meaning. These include journalists, doctors, scientists, lawyers and people from all walks of life. Under normal circumstances, the misuse of the word is rare and therefore irrelevant. However, since we are in the midst of a viral pandemic that affects almost everyone, I will try to explain what is meant by a viral isolate, variant, and strain.
Many terms used in virology are poorly defined. They have no universally accepted definition, and no "Bible" with their correct meaning. Since each of us has been trained by other virologists, we hear them use the term in certain contexts, and copy their usage—whether it is correct or not. I learned a lot of good things from my mentors, but also a lot of wrong things.
However, certain terms shall have specific meanings. Some of my colleagues will certainly disagree with some of my definitions, others will. Thanks to the latter. I also recognize that very few people will read this and it will have little impact. Maybe one day a high school student will search some term and come across it. Mainly so that I can jot down my thoughts in an orderly manner.
Every term in virology that comes to mind has to do with attempts to sequence the vast variety of viruses in the virome. Today, most of them derive their meaning from viral genomes: the DNA or RNA that encodes the production of new virus particles. This reliance on genomes is relatively new: until the 1980s, we didn't have genome sequences; therefore, most categories were based on other properties, such as the size of the virus particle, whether it had a membrane, the type of symmetry, and so on. Today, it's all about the genome. Whether you think this myopia is a good idea is not the subject of this article.
let's start with terminologyVirus isolate, since it is the easiest to define. An isolate is the name we give to a virus that we isolate from an infected host and spread in culture. The first SARS-CoV-2 isolates were isolated from pneumonia patients in Wuhan in late 2019. A small amount of fluid was injected into their lungs, removed, and placed on top of the cultured cells. The virus in the fluid multiplies in the cells, and voila, we have our first virus isolates.
Virus isolate is a very basic term that simply means that a virus has been isolated from an infected host. One isolate is from one host. We can isolate my virus, or yours, or the neighbor's down the street. Viral isolates were not available from most patients. Although SARS-CoV-2 has infected millions of people, we don't have millions of isolates, maybe thousands. We do have genome sequences from many people that can be inferred to represent isolates from each individual -- but in most cases the infectious virus was not isolated from an individual patient.
Isolates are given names so their origin is known. For example, one of the earlier isolates of SARS-CoV-2 is called BetaCoV/Wuhan/WIV04/2019. The isolate name consists of the Betacoronavirus genus followed by the city, isolate number and year. SARS-CoV-2 is the name of the virus; it is not an isolated name. Isolates of other viruses have also been precisely named. I really like the very detailed nomenclature of influenza viruses, as follows: virus name/antigenic type/host of origin (if not human/geographic origin/serial number/last two digits (or all four digits) of year of isolation/blood Lectin subtype neuraminidase subtype. Examples include Influenza A/Duck/Germany/1868/68 (H6N1) or Influenza A/Chicken/Vietnam/NCVD-404/2010 (H5N1).
Avirus variantis an isolate whose genome sequence differs from the reference virus. It was not inferred whether changes in the genome sequence resulted in any changes in the virus phenotype. Throughout the era of viral genome sequencing, the meaning of variants has become blurred, since nearly every isolate can have slightly different genome sequences. This was the case with SARS-CoV-2: almost every sequence from a different person is slightly different. By the end of 2020, any SARS-CoV-2 sequence from any two people would differ by approximately 10 out of 30,000 nucleotide changes. They are both variants, but the term is rarely used in this context. Since then, however, viral genomes with many more changes have been identified. These are called "variants of concern" (VOCs) because these changes are thought to confer new phenotypic properties, such as increased fitness. It's a good thing British scientists called them VOCs because now the media has to call them variants.
Unfortunately, following in the footsteps of scientists who should have known better, the mainstream media has been using the term "strain" to describe what a true variation is. This practice occurs in every viral outbreak: there is a new, more (fill in the blank with your favorite phenotype) strain of Ebola, Zika, and now SARS-CoV-2. It started in early 2020 and found variants with a single amino acid change in the spike protein, from a D to a G at position 614. The media said it was a new, more transmissible strain. But the use of the strain is incorrect: it is a variant, and remains so to this day.
Avirus strainare variants with distinct and stable phenotypic characteristics. These characteristics can only be determined through the results of experiments performed in the laboratory, in cultured cells and animals, as well as observations in infected humans. The name of the strain did not come easily: of course it could not simply be given by a journalist! asJens Kuhn wrote, "The designation of virus variants as strains will be the responsibility of an international expert group." The strain of SARS-CoV-2 is named more than once: there is only one strain of the virus. Incorrect use of the term does not change that fact. As you can imagine, it may take some time for the international panel to agree on anything.
Viral strains are few and far between: a name that is much needed but rarely given. A retrovirologist recently assured me that there is only one strain of HIV-1. The Lansing strain of poliovirus is derived from a human isolate that was passaged 99 times in mice until it acquired the ability to infect that species. This strain has distinctly different properties from the human strain.
There are other terms to describe viruses, but they are more confusing than controversial, and they are not commonly used. the termserotypeUsed to describe viruses of the same species that differ antigenically. There are three serotypes of poliovirus; if you are infected with type 1, the immunity you develop will not protect you from type 2 or 3. The same is true for the four serotypes of dengue virus and hundreds of rhinovirus serotypes. Today, the genome sequence of the virus is used to infer whether isolates are serologically distinct. the termgenotypeUsed to describe the genetic makeup of viruses. For example, the hepatitis C virus is placed into different genotypes based on the overall properties of its genome. For other viruses, the termcladeused to. A clade is a group of organisms consisting of an ancestor and its descendants, as shown in the phylogenetic tree below. SARS-CoV-2 isolates and HIV-1 isolates were placed into clades based on phylogenetic trees constructed from their genome sequences.
I think virological terms should be used accurately and consistently. During the pandemic, terms such as isolate, strain and variant are often used incorrectly, creating confusion. I don't believe the public or scientists will agree with any nomenclature. Rest assured, if you misuse isolate, variant or strain, I will correct you according to my dictionary.
FAQs
What is the difference between a virus variant and a virus strain? ›
Viruses with mutations in their genetic code are called variants. Variant refers to the differences in the genetic code from that of the original virus, but strain refers to a different physical property or behaviour exhibited by the virus.
What is the difference between a strain and an isolate? ›A Strain is a genetic variant or subtype of an organism. A Clone is a copy of a cell produced asexually from one ancestor or stock, to which they are genetically identical. An Isolate is an organism collected from a specific sample material (like a effluent/water sample or a stool sample etc.)
What are the two methods used for isolation of viruses? ›This chapter outlines the two most commonly used methods of virus isolation—namely, tissue cultures and embryonated eggs.
What are the strains of viruses? ›A strain is a genetic variant (not to be confused with a viral variant) or subtype of microorganism (that could be a virus, but it also applies to bacteria and fungi). This is the kind of definition to which biologists abide ––it is the scientific, biological term.
How does a virus create a variant? ›When a virus replicates, and the end copy has differences (in DNA or RNA), those differences are mutations. Variant. When you accumulate enough mutations, you get a variant.
What are the three coronavirus strains? ›| Human coronavirus name | Illness |
|---|---|
| SARS-CoV | Severe acute respiratory syndrome (SARS) |
| MERS-CoV | Middle East respiratory syndrome (MERS) |
| HCoV-NL63 | Usually mild respiratory illness |
| HCoV-229E |
The different types of strain are longitudinal, lateral, shear and volumetric.
How do you know which strain of COVID you got? ›When you receive a COVID-19 test, you won't find out which variant caused your infection. That's because COVID-19 tests only detect the presence of the virus – they don't determine the variant. Genomic sequencing looks at the genetic code of the virus to determine which variant caused the infection.
What are the two types of strain? ›Just like stress, there are two types of strain that a structure can experience: 1. Normal Strain and 2. Shear Strain. When a force acts perpendicular (or "normal") to the surface of an object, it exerts a normal stress.
What are the steps of virus isolation? ›The three-step isolation procedure combines filtration with a positively charged nylon membrane, ultrafiltration and clean-up of the viral RNA with a silica based membrane. Detection of the viral RNA is accomplished by reverse-transcription polymerase chain reaction (RT-PCR).
What is the purpose of virus isolation? ›
Virus Isolation is a highly relevant and important testing method used assist in the diagnosis of viral infections, including those of emerging, re-emerging, and novel viral pathogens.
What are the three isolation techniques? ›Three routine PBMC isolation techniques were evaluated, focusing on cell recovery and viability, population composition, and cell functionality. The techniques comprised the classic Ficoll approach, isolation by CPTs, and isolation by SepMate tubes with Lymphoprep.
What are variants of a virus such as Covid? ›Variants Are Expected
Viruses constantly change through mutation and sometimes these mutations result in a new variant of the virus. Some changes and mutations allow the virus to spread more easily or make it resistant to treatments or vaccines. As the virus spreads, it may change and become harder to stop.
Omicron's subvariants are considered to be especially efficient spreaders of the disease, and while scientists are still learning about XBB. 1.5, they say it is the most transmissible strain of the virus so far.
What type of virus is the coronavirus? ›Coronavirus disease (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus. Most people infected with the virus will experience mild to moderate respiratory illness and recover without requiring special treatment.
Why does COVID mutate so much? ›Virus mutation happens quickly over weeks to months due to the high number of viruses and infected people. Since it was first discovered, SARS-CoV2 has been acquiring two mutations in its genome (complete set of DNA) every two weeks.
Which viruses mutate the fastest? ›RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate.
Are SARS and COVID the same? ›Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus first identified in Wuhan, China, in December 2019. It became a pandemic throughout 2020 and into 2021. Infection with SARS-CoV-2 leads to a potentially severe respiratory illness called COVID-19.
Are SARS and COVID related? ›Content: COVID-19 seems not to be very different from SARS regarding its clinical features. However, it has a fatality rate of 2.3%, lower than that of SARS (9.5%) and much lower than that of MERS (34.4%).
What family of viruses does coronavirus belong to? ›What are the 4 sources of strain? ›
Agnew described four characteristics of strains that are most likely to lead to crime: 1) strains are seen as unjust, 2) strains are seen as high in magnitude, 3) strains are associated with low social control, and 4) strains create some pressure or incentive to engage in criminal coping.
What type of strain is the most common? ›What are the most popular weed strains? The most popular weeds strains are sativas and indicas. Sativa strains are known for their uplifting, energizing effects that can be used to combat fatigue or depression while also providing a sense of creativity in some people who use it during the day time hours.
What is an example of strain? ›I strained my back trying to lift the couch. Too much computer work strains the eyes. He strained a muscle in his leg.
Can you get Omicron twice? ›Is it possible to get Omicron twice? The Omicron variant spreads easier than other variants of coronavirus, and people can get it twice. Reinfection is possible even if a person has already had this virus or is fully vaccinated.
How is Omicron different from Delta? ›Transmissibility. And while the Omicron variant may be somewhat milder, it also spreads more easily than earlier variants, including the Delta variant. Researchers suspected this early on, based on Omicron's high number of mutations (there are about 50 altogether; 36 in the virus' spike protein alone).
Can you get a different strain of Covid if you just had it? ›Studies suggest that reinfection with SARS-CoV-2 with the same virus variant as the initial infection or reinfection with a different variant are both possible; early reinfection within 90 days of the initial infection can occur.
What are the classes of strain? ›Strain is the ratio of the change in length of a material to the original, unaffected length. The four different types of strain are axial, bending, shear, and torsional.
How do you classify a strain? ›- Grade I (Mild): Tissue is stretched.
- Grade II (Moderate): Involves stretching and some tearing of tissue.
- Grade III (Severe): Complete tearing of tissue.
Plant species
Experts suggest that there are over 700 strains of cannabis. One of the most important characteristics of a cannabis strain is the THC content.
The viral entry can be divided into four steps: attachment, penetration, cytoplasmic trafficking, and uncoating.
Can a virus replicate without a host? ›
As viruses are obligate intracellular pathogens they cannot replicate without the machinery and metabolism of a host cell.
What is the life cycle of a virus? ›The viral life cycle can be divided into several major stages: attachment, entry, uncoating, replication, maturation, and release.
Does quarantining a virus get rid of it? ›So while the virus may not spread across your device, quarantining the infected file in and of itself will not clean it of viruses. It is, however, possible to quarantine and then clean the file.
What is the difference between quarantining viruses and removing viruses? ›Remove deletes the file from your PC. Quarantine moves the file to a safe location and blocks it so it can't run.
When is the right time for collection of virus isolation? ›In general, specimens for virus isolation should be collected within 4 days after onset of illness as virus shedding decreases rapidly after that time.
What are the 7 categories of isolation? ›- Introduced seven isolation precaution categories with color-coded cards: Strict, Respiratory, Protective, Enteric, Wound and Skin, Discharge, and Blood.
- No user decision-making required.
- Simplicity a strength; over isolation prescribed for some infections.
Behavioral isolation occurs when two populations that are capable of interbreeding develop differences in courtship rituals or other behaviors. Geographic isolation occurs when two populations are separated by geographic barriers such as rivers, mountains, or bodies of water.
What type of isolation technique is most effective? ›- Plating- This includes the dilution of a mixture of microbes until only few is left in the suspension. ...
- Streaking - This method is the most widely used technique in the isolation of microbes. ...
- Single technique - This technique is the most ideal method in obtaining pure culture.
How long do omicron symptoms last? Most people who test positive with any variant of COVID-19 typically experience some symptoms for a couple weeks. People who have long COVID-19 symptoms can experience health problems for four or more weeks after first being infected, according to the CDC.
What medicine helps with Covid? ›Managing COVID-19 symptoms
Most people with COVID-19 have mild illness and can recover at home. You can treat symptoms with over-the-counter medicines, such as acetaminophen (Tylenol) or ibuprofen (Motrin, Advil), to help you feel better. Learn more about what to do if you are sick.
What is a virus that can affect various parts of the body and has multiple strains? ›
Enterovirus infections affect many parts of the body and may be caused by any of several different strains of enterovirus. Enterovirus infections are caused by many different viruses.
What is the most contagious virus in human history? ›Bubonic and Pneumonic Plagues. Perhaps the most notorious of all infectious diseases, the bubonic and pneumonic plagues are believed to be the cause of the Black Death that rampaged through Asia, Europe and Africa in the 14th century killing an estimated 50 million people.
Which diseases have the highest R0? ›- Measles – 12-18.
- Chickenpox – 10-12.
- Polio – 10-12.
- HIV/AIDS – 2-5.
- SARS – 0.19-1.08.
- MERS – 0.3-0.8.
- Common Cold – 2-3.
- Ebola – 1.56-1.9.
The highest R0 for the variants Alpha (1.22), Beta (1.19), Gamma (1.21), Delta (1.38) and Omicron (1.90) were reported from Japan, Belgium, the United States, France and South Africa, respectively. The estimated basic reproduction numbers and growth rates for each variant are tabulated below.
Why do some people not get COVID? ›It's possible that it's not a mutation in one gene, but a combination of mutations in multiple genes, that render a small number of people immune to COVID. Targeting multiple genes without causing any unwanted side-effects can be tricky and would make it much harder to harness this knowledge for anti-COVID drugs.
Is COVID-19 a DNA or RNA virus? ›Coronaviruses (CoVs) are positive-stranded RNA(+ssRNA) viruses with a crown-like appearance under an electron microscope (coronam is the Latin term for crown) due to the presence of spike glycoproteins on the envelope.
Is SARS a DNA or RNA virus? ›The SARS-CoV is a novel coronavirus with a large ( approximately 30 thousand nucleotides) positive-sense, single-stranded RNA containing 14 functional open reading frames (ORFs) of which 2 large ORFs constitute the replicase gene which encodes proteins required for viral RNA syntheses.
What does it mean when a virus has variants? ›Variants Are Expected
Viruses constantly change through mutation and sometimes these mutations result in a new variant of the virus. Some changes and mutations allow the virus to spread more easily or make it resistant to treatments or vaccines.
Variant: A variant is a viral genome (genetic code) that may contain one or more mutations.
What is the difference between a strain and a variety? ›What is the difference between variety and strain ? In botanical nomenclature, variety is a taxonomic rank below that of species and subspecies but above that of form. A strain is a genetic variant or subtype of a microorganism, that is to say a virus or bacterium or fungus.
What is the difference between variation and mutation? ›
The main difference between mutation and variation is that mutation is an alteration in the nucleotide sequence of a gene whereas variation is any difference between individuals of a particular species.
Why COVID mutates so fast? ›Key points: Most coronaviruses don't normally mutate much, but the COVID-19 coronavirus does. Surprisingly, the virus takes advantage of anti-virus enzymes witin human cells to mutate and produce new strains more frequently than expected.
Which variants of COVID exist? ›What COVID-19 variant are we on? Currently, the dominant variant nationwide is XBB.1.5, with 39.9% of cases, followed by XBB.1.16, with 18.2% of cases, and XBB.1.9.1 with 12.5% of cases. "The original omicron variant is gone now," says Dr. Rupp.
What is an example of a variant? ›A variant is another version of something. You could say chimps and apes and gorillas are variants in the primate family. Words often have variants, spellings that vary from region to region or country to country. The British colour and the American color are variants.
What is a variant in medical terms? ›(VAYR-ee-unt) An alteration in the most common DNA nucleotide sequence. The term variant can be used to describe an alteration that may be benign, pathogenic, or of unknown significance. The term variant is increasingly being used in place of the term mutation.
What are the 4 types of strain? ›Hint: There are three types of strain namely normal or longitudinal strain, shearing strain and volumetric or bulk strain which have been categorized on the basis of type of distortion produced by them.
What are the 4 major types of strain? ›The four types of strain are longitudinal strain, lateral strain, volumetric strain and shear strain.
What are the 3 types of genetic variation? ›The genetic diversity has three different sources: mutation, recombination and immigration of genes.
Does variation lead to mutation? ›Genetic variations can arise from gene variants (also called mutations) or from a normal process in which genetic material is rearranged as a cell is getting ready to divide (known as genetic recombination). Genetic variations that alter gene activity or protein function can introduce different traits in an organism.
Do all mutations lead to variation? ›Not all genetic mutations lead to genetic disorders. Some genetic mutations don't have any effect on your health and well-being. This is because the change in the DNA sequence doesn't change how your cell functions.