Alpha variant

 A form of the COVID-19 virus that was first detected in Great Britain in November, 2020. Twice as infectious as the “wild type” virus originating in China in 2019, the Alpha variant quickly replaced it throughout the United States in the spring of 2021, only to be replaced in turn the following summer by the even more infectious Delta variant.

Antibody

A protein “label” placed on foreign cells that marks them for destruction by your immune system. Produced by B cells that circulate in your blood, your body has at least a few that will bind to any conceivable invading virus or bacterium.

Antigen

A foreign substance. When your body’s immune defenses circulating in your bloodstream encounter an antigen (typically a protein on the surface of a microbe or virus) they react by proliferating and secreting antibodies that bind to the antigen, marking it for destruction.

B cell

The circulating cells of your immune system that produce antibodies. Each B cell is able to manufacture only one specific antibody (there are LOTS of kinds of B cells). When activated by a pathogen encounter, a B cell begins to churn out its antibody, which mark any other pathogens for destruction.

Booster shot

 An additional inoculation of a vaccine administered six or more months after initial vaccination, to induce another wave of antibody formation, often increasing antibody levels a hundred-fold.

Breakthrough infection

The infection of an individual who has been vaccinated against the infecting virus. An example: a person fully vaccinated (two shots spaced a month apart) with the Pfizer anti-COVID-19 vaccine, who subsequently becomes infected with the COVID-19 virus (typically the antibody-evading Delta strain).

Community transmission

Transmission of a virus like COVID-19 from one member of a community to another member of that same community. Typically, rates of community transmission are high only when many members of a community are already infected.

Coronavirus

A kind of respiratory virus named for their crown (corona) of surface “spike” proteins protruding outward from its surface – seen in cross section, it is like a crown. If you breath in these viruses, they can grow in your lungs and lead to respiratory illness. Some 20% - 30% of common colds are caused by coronaviruses. Three are far more deadly: SARS, MERS, and COVID-19. All three are bat viruses that have passed to humans.

COVID-19

A coronavirus closely related to SARS that appeared in China in December, 2019. The name COVID means Corona Virus Disease. The number 19 refers to the year this virus first appeared. Infected individuals do not immediately show symptoms, and 30% never do, so infections spread rapidly, particularly  in urban areas.

CRISPR

A molecular tool used to edit genes. The Nobel prize was awarded in 2019 for its discovery. The tool is composed of two molecules that work together. One part is a nucleotide sequence manufactured by the investigator to guide the CRISPR tool to a specific gene sequence; the other part is a DNA-cutting enzyme. When a cut is made at the target sequence, the hole that results is filled in with whatever sequence the investigator floods into the reaction.

Delta variant

 A highly infectious form of the COVID-19 virus that can evade the antibodies produced by COVID-19 vaccination, resulting in many “breakthrough” infections of fully-vaccinated individuals. Because the Delta variant does not evade T cells, such breakthrough infections do not usually lead to serious illness.

DNA

Deoxyribo Nucleic Acid, the stuff genes are made of. Each DNA molecule is composed to two long chains of subunits called nucleotides, the two chains wound around each other – a double helix. There are four kinds of subunits (A,T, G,C). The sequence of these four letters encodes the message of a gene, much as the sequence of the 24 letters of the English alphabet encode the definition of DNA you are reading.

Endemic

Native to a place. A disease is endemic when it occurs constantly in a geographic area. Thus influenza (“flu”) is endemic in the United States because this virus infects large numbers of people every year; malaria is not endemic because it does not.

Endocytosis

The way an animal cell is able to “gobble up” a nearby molecule or virus. The  cell’s membrane surrounds the object, then the membrane’s edges fuse together to enclose the object within the cell.

Genome

All the genes and other DNA of an organism. Your genes contain the information that determines certain things about you, like your biological/assigned sex and the color of your hair and eyes. Genes are made of portions of long molecules in the cell called DNA. Like lines of computer code, the string of chemical subunit in the long DNA molecule encode a set of instructions. These instructions are used by the cell to guide its manufacture of proteins — what each protein is like, as well as when, where, and how much of each protein is made. These proteins are the tools used by the growing body during development to make you you.

COVID-19 Genome

The COVID-19 genome is large for a virus, with 30,000 letters encoding 29 different proteins. Four of them make up the protein coat of the virus (including the spike), while the rest stabilize the virus genes and help them replicate.

Genomic surveillance

The routine random selection of COVID-19 cases for sequencing of the virus. Each sequence is then compared to the “base” sequence (the sequence of nucleotides of the original virus from China) and any differences noted as mutations.  A particular constellation of mutations serve to identify particular COVID-19 variants.

Herd Immunity

 If enough members of a population are immune to infection (say, because they are vaccinated), these vaccinated individuals (the “herd”) form a protective wall around each still-vulnerable (not-yet-vaccinated) individual, preventing the virus from reaching that person. The greater the r0 value of the virus, the greater the proportion of the herd that must be vaccinated for the defensive wall to be effective.

Immune escape

The ability of a variant to avoid recognition by antibodies, typically those produced by a previous infection or a vaccine. Thus the Omicron variant possesses a cluster of mutations affecting the portion of the COVID-19 spike protein to which antibodies bind; these mutations change the shape of the spike there, and so prevent antibody binding. The variant is said to have “escaped” a person’s immune protection. Note that antibody escape of this sort does not imply escape from T cells, which recognize a different portion of the virus.

Immune response

Your body’s defense against infection. Circulating in your bloodstream are a variety of different kinds of white blood cells that work together to identify and kill foreign invaders. B cells produce antibodies that recognize anything foreign and label them for killing by “cell-eating” macrophages; T cells recognize things foreign and themselves kill the invaders. How do these cells “know” something is foreign? At birth, there are LOTS of different B and T cells, but in early development any B or T cell that recognizes anything in your body is eliminated. What is left are those B cells and T cells that don’t recognize anything that is “you” — so anything they do recognize must be foreign!

Long COVID

Some people with COVID-19 have lingering symptoms for months after acute infection. Symptoms often include shortness of breath and fatigue, and can sometimes also involve a wide range of debilitating problems with the heart, lungs and other organs. As many as a third of COVID-19 survivors develop some kind of lingering symptoms. Experts have coined a new term for long COVID: post-acute sequelae SARS-CoV-2 infection (PASC).

Mandate

An official order to do something, from the Latin mandatum, ‘something commanded’. Thus a face mask mandate is an official requirement that everyone wear a face mask.

MERS

Eight years ago a new deadly kind of coronavirus abruptly appeared in Saudi Arabia. Labeled Middle East Respiratory Syndrome (MERS), is like many coronaviruses a bat virus, which in this instance had been spread to humans by camels (God alone knows how the bat-to-camel transfer happened!). Some 2000 cases of MERS were reported over two years before the outbreak subsided; 36% of them died of the infection.

Mutation

A change in a gene. Often a mutation results from a copying mistake during DNA replication, the wrong “letter” being inserted in the message, changing its meaning.

Omicron variant

A variant of the COVID-19 coronavirus discovered in southern Africa in November, 2021. Containing over 50 mutations from the original form of COVID-19, 30 of them in the spike protein, the Omicron variant is highly contagious although not as virulent as the Delta variant, and is able to partially escape the vaccines developed for the original form. At the peak of United States infections in early 2022, over 800,000 people a day were being infected with the Omicron variant.

Pandemic

A world-wide outbreak of a deadly disease. An outbreak is called an epidemic when there is a sudden increase in cases. The rapid spread of COVID-19 in Wuhan, China (a large city, its population of 11 million far exceeds New York City’s 8 million) became an epidemic by January,  2020.  The virus proceeded to spread across several countries, and then world-wide. In March 2020  COVID-19 was classified as a pandemic. 

PCR

The Polymerase Chain Reaction uses heat to separate the DNA double helix into single stands of DNA, then cools the solution to allow the enzyme DNA polymerase to slide along each single strand adding nucleotides as it goes, until it is double-stranded again. Then heat and repeat the cycle. One duplex becomes 2, 2 then becomes 4, which the becomes 8…  you can soon get millions of copies!  PCR plays important roles in crime detection, allowing the DNA of a single hair to be amplified enough to identify the person it came from. It also plays a key role in identifying the COVID-19 virus in nose-swab samples, the gold standard in COVID testing.

Placebo

A substance designed to have no therapeutic value. Thus in clinical trials of a vaccine, some patients are administered a salt solution instead of the vaccine, as a placebo control.

r0

The number of individuals an infected individual is likely to infect. Any value of r0 greater then 1.0 will cause the infection to spread. The coronavirus COVID-19 has evolved progressively greater values of r0, from 2.5 (initial “wild type” strain) to 4-5 (Alpha variant) to 8-10 (Delta variant).

Receptor

 The door molecules use to enter animal cells. Typically a protein on the cell surface that acts like the trip on a bear trap – when a molecule encounters the receptor protein and fits correctly, the receptor protein responds by altering its shape, triggering endocytosis.

SARS

The deadly coronavirus Severe Acute Respiratory Syndrome (SARS) appeared in China in 2002. The outbreak infected 8,098 people, killing just under 10% of them. Because the virus made people very sick quickly, it didn’t spread before symptoms appeared. Immediately quarantining infected people stopped the spread in its tracks, and within a few months it was eliminated from the human population. No known transmission of SARS has occurred since 2004.

Spike protein

Protruding out from the COVID-19 virus particle’s “skin” are a host of protein spikes. Each spike is a large protein (a 1,200 amino acid chain) to which sugar molecules are attached (what biochemists call a  “glycoprotein”). When a COVID-19 particle encounters a human cell, the globular head of the spike protein interacts with a protein on the human cell surface called ACE2. This binding initiates entry into the cell, where the virus particle disassembles and begins to reproduce.

Spillback

The passage of a virus from humans to an animal species. The majority of white-tailed deer in Iowa, for example, are infected with the omicron variant of COVID-19, a spillback from humans. Dogs and cats have become infected with human strains of COVID-19, as well as minks, ferrets, lions, tigers and many other animal species, all examples of spillback.

Spillover

The passage of a virus from an animal species to humans. COVID-19 is thought to have passed from Chinese bats to humans, for example. Spillover has also occurred in Danish commercial minks, which transmitted COVID-19 acquired from humans (spillback) back to humans (spillover). It is not known if deer or pet dogs and cats might reinfect humans in the same fashion.

T cell

A key component of your immune system defense against infection, T cells circulate in your bloodstream, constantly scanning every cell they encounter for “foreign” proteins. Because virus-infected cells display bits of the virus on their surfaces, the T cells are able to identify virus-infected human cells, and proceed to kill them.

Vaccine

Injecting a harmless microbe or genes ( a “vaccine”) into someone to protect them from future infection. At the heart of every vaccine is an antigen, a molecule which provokes your immune system to generate antibodies directed against the virus. There are five general ways to present the COVID-19 antigen to patients:

•  Recombinant vector vaccines are made of  the spike protein gene inserted into a harmless virus. Infected with this, patients will manufacture the spike protein, inducing antibodies to be made against it. Examples: Oxford/AstraZenica, Johnson&Johnson

•  Live attenuated virus vaccines are made of damaged (and so not infectious) COVID-19 particles. Infected with this, patients make antibodies to the spike proteins on the damaged virus particles. Example: CaronaVac (China)

•  Inactivated virus vaccines are made of heat-killed virus particles. Injected, the spike proteins on their surface induce the patient to manufacture antibodies directed against COVID-19 spike proteins. Example: Sinopharm (China)

•  Subunit vaccines are made of the spike protein itself. Injected, they induce antibody formation directly. Examples: Novavax, Sanofi

•  Nucleic acid vaccines are made of the COVID-19 genes themselves. Injected into a patient, they cause the manufacture of spike proteins, which in turn cause the production of antibodies directed against the spike protein. Examples: Pfizer, Moderna

Virus

Tiny infectious particles. Although people  frequently refer to viruses as live or dead, in fact no virus is alive. A virus is just a combination of two chemicals, a nucleic acid (DNA or RNA) encased within a protective protein coat. Viruses can reproduce only by injecting their genetic material into the cells of living creatures.