BIO-RAD

Virus Detection and Transmission Kit(Coronavirus)
Catalog #17008261EDU

Student Guide
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Table of Contents

Contents
Outbreak of a Respiratory Disease........................................................................................................ 1
Activity 1: Learning about Virus Biology, Pathophysiology, and Detection....................................... 2
Part 1: Patient Symptom Review......................................................................................................... 2
			 Focus Questions............................................................................................................................ 3
Part 2: Learning about Viruses, Pathophysiology, and Detection...................................................... 4
		 The Biology of Viruses........................................................................................................................ 4
		 Mechanisms of Infection and Disease................................................................................................. 5
			 How Viruses Infect the Human Body.............................................................................................. 5
			 How Viruses Cause Disease (Pathophysiology).............................................................................. 6
		 Two Common Viruses........................................................................................................................ 7
			 Coronavirus (CoV).......................................................................................................................... 7
			 Norovirus (NoV).............................................................................................................................. 8
			 Focus Questions............................................................................................................................ 9
		 Detecting Viruses in Patient Samples................................................................................................ 10
			 Focus Questions.......................................................................................................................... 11Part 3: Patient Diagnosis.................................................................................................................... 12
		 About the PLS-CoV Test.................................................................................................................. 12
			 Focus Questions.......................................................................................................................... 14		 Patient Data..................................................................................................................................... 15
			 Focus Questions.......................................................................................................................... 16
Activity 2: Detecting Infections............................................................................................................ 17Part 1: Pre-Laboratory Questions...................................................................................................... 17Part 2: Patient Sample Analysis by Agarose Gel Electrophoresis................................................... 18
		Protocol........................................................................................................................................... 19
Part 3: Analysis................................................................................................................................... 20
Part 4: Collecting Class Data............................................................................................................. 21
Activity 3: Building a Transmission Model.......................................................................................... 22
Part 1: Understanding the Chain of Infection.................................................................................... 22
		 Chain of Infection............................................................................................................................. 22
		Reservoirs........................................................................................................................................ 23
		 Portals of Entry and Exit................................................................................................................... 24
		 Modes and Routes of Transmission.................................................................................................. 24
		 Host Susceptibility............................................................................................................................ 25
		 Focus Questions.............................................................................................................................. 26
Part 2: Creating a Transmission Model............................................................................................. 27
		Instructions...................................................................................................................................... 27

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Activity 4: Mitigating Risk..................................................................................................................... 33
		 Public Health Response................................................................................................................... 33
Part 1: Understanding Response Strategies to Disease Outbreaks................................................ 34				 The Epidemic Curve......................................................................................................................... 34				 Other Risks of Uncontrolled Spread.................................................................................................. 35
		 Focus Question................................................................................................................................ 35
		 Prevention Strategies....................................................................................................................... 35
Part 2: Developing a Response Strategy for the AnyTown PLS Outbreak...................................... 37				 Focus Questions.............................................................................................................................. 37
Appendix A: Naming Viruses and the Diseases They Cause............................................................ 39
Glossary................................................................................................................................................. 40
References............................................................................................................................................. 43ii

Student Guide

Outbreak of a Respiratory Disease
A new respiratory disease has been reported recently in the region surrounding AnyTown, USA.
Called Pneumonia-Like Syndrome1 (PLS), this disease is spreading rapidly and causes symptoms
that include shortness of breath, cough, severe body aches, and high fever. PLS has led to numerous
hospitalizations, and patients are not responding to standard treatments for pneumonia or influenza(the flu).
Scientists have applied the latest genome sequencing methods to find that PLS is caused by acoronavirus (CoV) they call PLS-CoV. Coronaviruses are a large family of viruses that can cause
illnesses that range in severity, from a common cold to COVID-19. PLS-CoV is considered a “novel”
coronavirus because its genomic sequence is quite different from all other strains previously foundin nature. Because PLS-CoV is novel, little is known about how it spreads, how it causes disease, or
how it should be treated. There is no vaccine and no immunity within the population, so everyone issusceptible to infection.
As PLS-CoV spreads, doctors, researchers, and clinicians are working as quickly as possible tounderstand the pathophysiology of PLS-CoV and to find the most effective treatments. Molecularbiologists have used the PLS-CoV genome sequence to develop a diagnostic test that can detect
PLS-CoV infections. Virologists, molecular biologists, epidemiologists, and public health officials arealso working together to understand the nature of this virus and how it spreads.
Figuring out the mode of transmission will be key to deciding the best way to keep the spread undercontrol.
In this series of activities, you will gain insights into the variety and range of expertise needed todiagnose, study, and mitigate virus outbreaks.
• You will begin as an emergency room physician, where you will diagnose two patients who havedifferent symptoms that are consistent with PLS• When one of the patients tests positive for PLS-CoV infection, you will then move into the roleof a medical lab scientist and perform a PLS-CoV diagnostic test on samples collected from othersuspected cases• Next, to determine the mode of transmission of this virus, you work as an epidemiologist andconsider all the data you have about an outbreak of PLS at a local restaurant• Finally, you take on the role of a public health official who must decide whether to take immediate
action to control the spread of this disease and the best means of doing so

Please note this is a fictitious disease spread by a fictitious virus. For information about how viruses and the diseases theycause are named, refer to Appendix A.
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Student Guide

Activity 1
Learning about Virus Biology, Pathophysiology, and Detection
In this activity, you will learn about viruses, how they infect humans and cause disease, and thechallenges doctors may face when diagnosing patients based on symptoms alone. You will thenexplore how diagnostic tests work and how they can help doctors make a definitive diagnosis.

Part 1: Patient Symptom Review
It is late in the evening of Sunday, June 8, and you are an emergency room (ER) physician at AnyTown
Hospital. Two patients arrive at the ER within an hour of each other. Both are experiencing symptoms
that are characteristic of Pneumonia-Like Syndrome (PLS) (Figure 1).
• Patient A, a 23-year-old male, has a nagging, dry cough, body aches, and fever of 104°F.
• Patient B, a 46-year-old female, has a nagging cough and severe congestion.
Fever
Congestion

Cough
Body aches

Figure 1. Patients A (left) and B (right).

As the ER physician, you examine both patients. Pneumonia is an infection that inflames the air sacs
in one or both lungs. It can be caused by a bacterial, viral, or fungal infection. You’d like to determine
whether the patients are suffering from a bacterial or a viral infection, or whether the source of their
symptoms is something else, such as allergies. You find their lungs sound clear of any infection,and there are no signs of bacterial infection in the patients’ ears or throats. Based on the patients’
symptoms and the recent concern over the regional uptick in PLS cases, you suspect both patients
may be suffering from a viral infection, possibly PLS-CoV.
Review the symptom chart (Table 1) and answer the Focus Questions that follow.

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Table 1. Symptom chart for several respiratory ailments. For this activity, consider only these ailments. In
reality, there may be many other causes for the respiratory symptoms of Patients A and B.
Symptoms

PLS (PneumoniaLike Syndrome)

Common Cold

Influenza (Flu)Allergies

Fever or chills

CommonSometimes

Common

Never

Cough

CommonCommonCommonSometimes

Congestion or runnynose

CommonCommonCommonCommonSneezing

Rare

Sometimes

Sometimes

CommonShortness of breath ordifficulty breathing

CommonRare

CommonSometimes(asthma-related)

Fatigue

CommonSometimes

CommonSometimes

Muscle or body aches

CommonSometimes

CommonNever

HeadacheCommonSometimes

Sometimes

Rare

Sore throat

CommonCommonCommonRare

Nausea or vomiting

Sometimes

Never

Sometimes

Sometimes (possible
with food allergies)

Diarrhea

Sometimes

Never

Sometimes

Sometimes (possible
with food allergies)

Diagnostic tests
available

Yes

No

Yes

Yes

Treatments available

Unknown;patient isolation
recommended

Over-the-counter
analgesics,
decongestants, andcough suppressantsPrescription antivirals andover-the-counter analgesics,
decongestants, and coughsuppressantsOver-the-counter
antihistamines,
decongestants

Focus Questions
Based on each patient’s symptoms, which respiratory ailment(s) in Table 1 might they have? Whichwould you rule out as unlikely, and why?

Based on the patients’ symptoms, which diagnostic test(s) would you order for each patient?

PLS is a new and potentially lethal viral disease that is spreading rapidly. What are potential
outcomes from not testing/determining the actual cause:• For the patient?

• For the community?

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Part 2: Learning about Viruses, Pathophysiology, and Detection
The Biology of Viruses
Viruses are everywhere. They infect all life forms, from bacteria to plants to animals, in every
ecosystem on Earth. In fact, viruses are the most numerous biological entities. Millions of types ofviruses are believed to exist, but only 9,000 virus species have been described in detail.
We are exposed to viruses every day, though certain environments or actions can increase the likelihoodof exposure or infection. The study of viruses is called virology, and it is a subspeciality of microbiology.
Viruses cannot move on their own, have no metabolism (they do not “eat” anything), and they cannot
reproduce by themselves. Instead, viruses infect living cells and hijack the reproductive and metabolic
machinery of those cells to make more copies of themselves. In doing this, viruses can cause disease.
Virus particles are made up of the same types of molecules that characterize all living cells: proteins,
lipids, carbohydrates, and nucleic acids. At their most basic, they consist of nucleic acid surrounded
by a protein coat known as a capsid (the capsid + genome combination is called a nucleocapsid).
Some viruses may also have a membrane that surrounds the nucleocapsid, called an envelope,and they may contain enzymes needed to infect host cells. A complete viral particle with all thecomponents needed for host cell infection is called a virion (Figure 2).
Viruses contain all the genetic material needed for host cells to make new virions, and this fullcomplement of genetic material is known as its genome. Whereas the genomes of some viruses, likechickenpox and smallpox, are made of DNA like those of humans (a virus that has a DNA genome
is classified as a DNA virus), others are made of RNA (RNA virus). Because of their propensity tomutate, RNA viruses are usually the ones we hear about as emerging and causing concern over (new)diseases. These mutations help viruses adapt to new host species.
A virus’s genomic sequence is its molecular fingerprint. Scientists use a virus’s genomic sequence todetermine its identity and its genetic relatedness to other known viruses.
Enveloped

Non-enveloped

Envelope proteins
DNA or RNA
genomeNucleocapsid

Lipid envelope

Protein capsid

Figure 2. Structure of a virion. Non-enveloped viruses (left) do not have the lipid membrane that enveloped
viruses (right) have.

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CareerSpotlight

Virologist
Virologists are research scientists who study viruses. They work in academic, industrial, orgovernment institutions and contribute to core knowledge about viral biology — their genetic
makeup, structure, hosts, infection cycle, etc. This knowledge guides the work done by doctors,
pathologists, and others to prevent and rapidly respond to viral disease outbreaks.
Entry-level technician positions are available to those with a college degree; postgraduate degrees
and research experience are needed for those wanting to run their own research programs.

Mechanisms of Infection and Disease
How Viruses Infect the Human Body
When viruses infect cells, they hijack those cells to turn them into virus-making factories. This process
has many variations, but in general, the key stages of infection include the following:• Virus enters the body — viruses enter the human body through a portal of entry (Figure 3A),
		usually the eyes, respiratory tract (including mouth, nose, lungs), urogenital tract, gastrointestinal
		 (alimentary) tract, or skin (for example, through a needle or insect or animal bite)• Virus attaches to a host cell — cells of the respiratory, gastrointestinal, skin, and genital tissues
		 are the most common sites of infection. There, proteins on the cell surface (receptors) interact with		 proteins on the outside of the virus; the specific interaction between a viral protein and a host cell		 receptor protein determines which species a virus can infect (Figure 3B, step 1)• Virus penetrates the host cell — once a virus binds a receptor, it deposits its genome into the host		 cell. The way this happens depends on the virus: some inject their DNA directly into the cell,		 others are taken up by endocytosis, or (as in the case of enveloped viruses) through fusion of the		 lipid envelope with the host cell membrane (Figure 3B, step 2)• Virus replicates — the virus takes control of the host cell and directs it to express the viral genes
		 to produce viral proteins and assemble more virions (Figure 3B, steps 3–5)
• Progeny viruses exit the host cells — the hundreds to thousands of progeny virions then leave the		 host cell (a process that often leads to cellular damage or death) to infect other cells (Figure 3B,		 step 6). Progeny virions may infect neighboring cells to cause a localized infection, or they can		 spread through bodily fluids into different organs• Virus sheds into the environment — virions eventually spread to a portal of exit (for example, the		 respiratory, gastrointestinal, and urogenital tracts and blood) and are released into the environment;		 the virus then goes on to be transmitted to another person to set up a new infection cycle

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Student Guide

Conjunctiva

1. Attachment

Eyes
Nose
ThroatArthropod

6. Release

Capillary

2. Penetration
Respiratory
tract

Gastrointestinal
tract

Scratch,injury3. Release of viral genome
and replication

5. Virion assembly

Urinogenital
tract
Skin

4. Viral protein expression

A

Anus

B

Figure 3. Portals of entry into a human host (A) and the stages of viral infection of a host cell (B).

How Viruses Cause Disease (Pathophysiology)
For most people most of the time, the immune system can handle a viral infection. In some cases,
though, viral infections can cause disease in several ways:• Damage caused by the virus — viruses can destroy infected host cells by interrupting cellular		 functions, by releasing enzymes and other proteins that degrade cellular components, or by lysing
		 the cell to cause the release of progeny virions. This can cause damage to tissues and organs and		 make us sick. Some viruses, like the human papilloma virus (HPV), can also integrate their DNA
		 into the host to cause damage later in the form of cancer or other diseases• Damage caused by the immune system — as viruses infect a host, they stimulate the immune
		 system, which then destroys the virus and infected cells; if this response goes too far, it may also		 lead to severe pathological consequences to the host, like excessive inflammation or targeted		cell death• Damage caused by a secondary infection — cells, tissues, and organs that are damaged by		 a virus or immune response may become more vulnerable to secondary infections. For example,
		 a common cold can be the result of a viral infection, but a patient may develop a bacterial infection
		 like bronchitis, sinusitis, or pneumonia as a secondary effect6

Student Guide

Two Common Viruses
This activity centers around a coronavirus outbreak. However, two distinct groups of viruses arepresented here to demonstrate how different viruses can behave differently in the human body.

Coronavirus (CoV)Coronaviruses (CoVs) have risen to fame and notoriety as a group of viruses that can cause serious
respiratory syndromes in humans. In fact, there are many different types of CoVs, and they arecommon in many different mammals and in birds. When they infect humans, some strains of CoV cancause colds or other mild respiratory (nose, throat, lung) illnesses. Others, however, can cause serious
respiratory diseases, including severe acute respiratory syndrome (SARS, caused by SARS-CoV),
Middle East respiratory syndrome (MERS, caused by MERS-CoV), and coronavirus disease 2019
(COVID-19, caused by severe acute respiratory syndrome coronavirus 2, or SARS-CoV-2).
Refer to Appendix A for information about how viruses and the diseases they cause are named.
CoVs are RNA viruses that have a lipid envelope. CoV virions are spherical, have an average diameterof 125 nm, and are named for their appearance: “corona” means “crown,” and the virus’s outer layers
are covered with spike proteins that surround them like a crown (Figure 4). These spike proteins help
virions bind to and infect cells by acting as molecular “keys to the host cell” — they bind to receptor
proteins on the surface of the host cell, which allows the virus to enter the host cell. Beneath these
spikes is the lipid envelope, which can be disrupted by detergents and alcohols.

Figure 4. SARS-CoV particle. Negative stain electron microscopy of a SARS-CoV virion. Note the characteristicclub-shaped projections surrounding the periphery of the virion. Source: C.D. Humphrey, CDC (https://www.cdc.
gov/sars/lab/images.html).

Two of the most famous CoVs, SARS-CoV and SARS-CoV-2, infect humans primarily through therespiratory tract and by binding with the ACE2 receptor protein. ACE2 receptors are found all over thehuman body but are particularly dense in intestinal epithelial cells, the lungs, blood vessels, endothelial andsmooth cells of the blood vessels and heart, and the tubular epithelial cells of the kidneys (Figure 5).

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Student Guide
Norovirus (NoV)
Noroviruses (NoVs) are another group of RNA viruses. Unlike the CoVs, however, they are notenveloped by lipids, and this makes them more stable on surfaces. The NoV protein coat helps itwithstand detergents and even acids. Strong disinfectants like bleach are needed to disrupt andinactivate NoVs.
NoV virions are 30–40 nm in diameter, and humans and other mammals serve as natural hosts.
Upon infection, NoVs bind to histo-blood group antigens (HBGAs), which line the gastrointestinal
tract (Figure 5). Also referred to as the winter vomiting bug or just stomach bug, NoVs are the mostcommon cause of gastroenteritis (infectious diarrhea), which is characterized by non-bloody diarrhea,
vomiting, stomach pain, and sometimes fever or headaches.

1

Coronavirus(Lipid envelope)3

Norovirus(Protein coat)

4

2

2

3

5

SARS-CoV-2
ACE2 receptor
1

HBGA receptor

Low

2

3

4

5
High

Figure 5. Viral pathogenesis. Different viruses target different tissues based upon receptor preference.
Noroviruses bind to HBGA receptors, which occur primarily in the gastrointestinal tract. The SARS-CoV-2 virus
binds to ACE2 receptors, which are found in various tissues and organs throughout the body. In this image,the color of ACE2 receptor sites reflects the relative abundance of those receptors (for example, there are higher
levels of ACE2 receptors in the lungs and gastrointestinal tract than in the liver or brain).

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Focus Questions
Would you call a virus a “living cell”? Why or why not?

Using the information in Figure 5, explain why SARS-CoV-2 can cause symptoms other thanrespiratory distress (for example, gastrointestinal symptoms).

Which virus would you expect to remain intact longer on a doorknob: a CoV or a NoV?

CareerSpotlight

Pathologist
Pathologists are medical doctors who specialize in the causes, nature, and effects of disease.
Pathologists hold medical degrees (MD) with a specialty in pathology and work mostly in hospitals
and medical, academic, or industrial laboratories. Though pathologists are a part of a patient’s
healthcare team and are integral to patient diagnosis and treatment, they may never actually meetthe patient.

CareerSpotlight

Histotechnician and histotechnologist
Histotechnicians and histotechnologists are medical laboratory technicians who prepare tissue
samples for examination by a pathologist. Histotechnicians are trained to prepare samples foranalysis under a microscope. Histotechnologists may also perform testing on tissues and alternative
preparation methods, and they may supervise other staff. Histotechnicians and histotechnologists
work in hospitals or clinical pathology labs, research laboratories, doctors’ offices, forpharmaceutical companies, or for government agencies.
Histotechnicians need vocational education, an associate degree (from a community college), or ahigh school diploma and two years of related work experience. To become a histotechnologist, youwill need to have a college degree and certification.

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Detecting Viruses in Patient Samples
Diagnosing patients based on their symptoms alone can be difficult. Different conditions often cause
similar symptoms, and those symptoms may overlap with other medical conditions. For example, a stuffy
nose and sneezing may be caused by the common cold or by allergies. When diagnosing a viral infection,a doctor considers all the symptoms a patient is experiencing as well as their recent activity and exposure
history.
To make a conclusive diagnosis, doctors often also rely on a diagnostic test. Diagnostic tests exist for avariety of infections (for example, bacterial, fungal, protist). This activity focuses on the diagnosis of viral
infections. There are two general types of diagnostic tests for viral infections:• Antigen or antibody tests — use antibodies to detect the presence of virus particles, viral proteins,		 or a patient’s own antibodies against the infection:
		• An antigen test uses antibodies to detect virus particles or viral proteins in patient samples; it			 can detect an active infection (an example is the at-home rapid antigen test used to detect
			SARS-CoV-2/COVID-19)
		• An antibody test uses antibodies to detect other antibodies in patient samples; it can detect			 whether a person has had an infection in the past
• PCR-based tests — use PCR amplification to detect the presence of a viral genome in the patient’s
		 bodily fluids or tissues:		• PCR tests for DNA viruses		• Reverse-transcription PCR (RT-PCR) tests for RNA viruses; they include an added step to convert
			 the RNA into DNA before PCR (Figure 6)

Many copies of target region of DNA

1. RNA isolation from sample
PCR primers

3. PCR amplification

DNA

DNA

2. Reverse transcription
RNA (from the virus)

Figure 6. Reverse-transcription PCR (RT-PCR). RT-PCR uses an enzyme called reverse transcriptase to reverse
the transcription process and convert RNA back into DNA. The DNA then serves as the template in a PCR. In thisdiagram, the purple arrows on the DNA represent primers, short sequences of DNA that direct PCR amplification ofa specific target region on the DNA.

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Focus Questions
Antigen tests are also used to test for pregnancy. In these tests, the antigen being detected
is human chorionic gonadotropin (HCG), a protein hormone whose presence in urine over acertain level indicates a pregnancy. Can a PCR-based test be used to detect HCG?

Which of the four types of tests listed above could you use to test for an active CoV or NoV
infection?

CareerSpotlight

Medical Laboratory Professional
Medical laboratory science professionals perform laboratory analyses that help physicians in patient
diagnosis, treatment, monitoring, and disease prevention. Their training and expertise can include
clinical chemistry, hematology, immunology, microbiology, and molecular biology. They consult withother members of a healthcare team.
Medical laboratory technicians often have an associate degree or certification and perform thecollection, processing, and analysis of biological specimens. Medical laboratory scientists have a
4-year college degree and certification and therefore a deeper theoretical knowledge base. They
perform laboratory procedures and help interpret the results, consult with medical teams, conduct
research, and develop new test methods.

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Part 3: Patient Diagnosis
As the ER physician, you suspect that Patient A and Patient B may be infected with the novel
coronavirus, PLS-CoV, but their symptoms also do not rule out influenza. You order diagnostic tests
for influenza and for PLS-CoV.
About the PLS-CoV Test
The AnyTown Hospital has access to the new RT-PCR test that can detect the presence of PLS-CoV inhuman samples.
The lab technician collects small samples of cells from the nasopharynx of Patients A and B using
nasopharyngeal swabs (Figure 7). This a common sample collection method for tests that detectbacteria or viruses that cause respiratory infections.

Nasal cavity
Swab
Nasopharynx

ThroatFigure 7. Collection of a sample using a nasopharyngeal swab.

After the sample is collected, a medical laboratory technician performs the PLS-CoV RT-PCR test. This
test uses PCR amplification of two genes (Table 2):• A gene specific to the virus PLS-CoV — the test detects the N gene, which encodes the		 nucleocapsid protein of PLS-CoV. The test is designed to detect only a specific section of the		N gene of PLS-CoV. It will not detect N genes from any other CoVs that may be present• A gene found in all human samples — in this case, GAPDH is used; this serves as a control to		 confirm successful extraction and amplification of nucleic acids from human samples

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Student Guide
Table 2. Target regions of the PLS-CoV diagnostic test.
Target region

Band size

Purpose

PLS-CoV N gene

~530 bp

Detects presence of PLS-CoV

Human GAPDH gene~250 bp

Control: confirms that nucleic acid was successfullycollected and extracted from a human source

In this test, two sets of primers are mixed in the same tube with the sample: one set will bind to andamplify the GAPDH gene, and one set will bind to and amplify the N gene. In this way, technicians canlook for both genes in the same sample.
Following PCR, the medical laboratory technician analyzes the samples by agarose gel electrophoresis.
The term electrophoresis refers to the movement of charged molecules in response to an electricfield, which can be used to separate them. In this case, the technique is used to separate DNA pieces
by size (Figure 8) and allows them to be visualized.

–

Agarose gel

Large DNAfragments
Movement

Wells(where samples are loaded)

Small DNAfragments+
Figure 8. Agarose gel electrophoresis. By convention, the rectangular spaces across the top of a gel represent
the wells into which samples are loaded. The negatively charged DNA fragments migrate through the gel toward
the positive pole (anode) when a voltage is applied. The straight path the DNA fragments follow through the gel
is called a lane. Smaller fragments migrate more quickly through the gel matrix and so they move farther into thegel than larger fragments.

For the PLS-CoV test, the technician loads the RT-PCR products (DNA fragments) into an agarose gelslab. The agarose gel is in an electrophoresis cell and covered in a conductive buffer solution. Whenthe technician starts the electrophoresis, current flows between the electrodes at each end of thechamber (Figure 8). The negatively charged electrode (cathode) is closest to the sample wells, andwhen electrophoresis starts, the DNA fragments move toward the positively charged electrode (anode)
because DNA carries a net negative charge.

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Student Guide
As the DNA fragments move, the agarose gel acts as a sieve, or a matrix of holes. Smaller DNA
fragments move more easily than larger ones, so the smaller DNA fragments travel farther than larger
ones (Figure 8). The relative size of fragments contained in each band can be found by measuring how
far each band has traveled from the wells.
An analogy for gel electrophoresis is a situation where all the desks and chairs in a classroom are
randomly pushed together. An individual student can wind their way through the maze quickly andwith little difficulty, but four students holding hands would require more time and have difficulty
working their way through the maze. Smaller chains of students will move (migrate) through the maze
more quickly, and so move farther through the maze in each period than larger chains.
The nasopharyngeal swab sample from all patients contains any infecting virus as well as some humancells that have sloughed off during sample collection. In this PLS-CoV test, if the RNA sample was
successfully collected, extracted, and amplified:• All human patient samples should have a band for the GAPDH gene
• Only patients infected with PLS-CoV will also have the N gene band, which is specific to PLS-CoV

Focus Questions
In the PLS-CoV test, which target region — the N gene or GAPDH gene — would produce
a band that would move farther than the other by agarose gel electrophoresis? Why?

How many bands would you expect to see in a sample collected from a person who is
infected with PLS-CoV?

In the gel at right, the first lane has a molecular weight ruler (MWR),
which is a set of DNA fragments of known size. These fragments
are used to estimate the size of DNA fragments in the samples.
In the second lane, draw and label the bands you would expect
to see in the PLS-CoV tests for:
• The amplified N gene target• The amplified GAPDH gene target
1,000 bp
700 bp500 bp200 bp100 bp14

MWR

Student Guide
Patient Data
Now that you understand how the PLS-CoV test works, you move into the role of medical lab scientist
at AnyTown Hospital. You will review the test results for Patients A and B (Figure 9) and communicate
the test results back to the ER physician.
Your analysis includes the following samples:• MWR — molecular weight ruler with DNA fragments 1,000, 700, 500, 200, and 100 bp• (–) Control — this control has only the GAPDH gene; it simulates a sample from a person who is		 not infected with PLS-CoV• (+) Control — this control has both the N and the GAPDH genes; it simulates a sample from a		 person who is infected with PLS-CoV• NTC (no-template control) — this control is a sample that has only the PCR primers and no		DNA template• Patient A

Patient B

Patient A

NTC(+) Control(–) Control

MWR• Patient B

1,000 bp
700 bp500 bp200 bp100 bpFigure 9. Agarose gel electrophoresis of the controls and patient samples from the PLS-CoV diagnostic
test. This gel shows the bands obtained from an RT-PCR test, including primers that amplify the PLS-CoV N geneand the human GAPDH gene. MWR = molecular weight ruler; (–) control = control sample containing the human
GAPDH gene; (+) = positive control sample containing both the N and GAPDH genes;
NTC = no-template control (containing no template DNA); A = sample from Patient A; B = sample from patient B.

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Focus Questions
Is either patient infected with the virus? How do you know?

Is either patient not infected with the virus? How do you know?

What would you conclude from a sample if it did not have the GAPDH band?

What would you conclude from an analysis in which there was a band in the NTC lane?

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Activity 2
Detecting Infections
As the medical lab scientist at AnyTown Hospital, you reported the confirmed case of PLS-CoV
infection to local public health officials. The next day, the officials took a detailed patient history for
Patient A and, to contain the spread of PLS-CoV, they initiated contact tracing to notify all known
contacts of Patient A of their exposure and ask them to be tested.
Before he showed up with symptoms at the AnyTown Hospital in the late evening of June 8, Patient A
had been at the AnyTown Restaurant for lunch. At the time, he was experiencing only a mild cough, butby the evening, his symptoms had worsened, and he was in the ER. After notification from the hospitalof the positive case, the public health officials contacted the AnyTown Restaurant to track down theother customers and staff who were in the restaurant for lunch on June 8. The officials interviewed andcollected nasopharyngeal swabs from each person for diagnostic testing.
In this activity, you act as a medical lab technician and use DNA gel electrophoresis to analyze the
PCR samples of all the people who were in the restaurant at the same time as Patient A. You will then
combine your results with results from your classmates to figure out which, if any, other restaurant staff
and patrons are infected with the novel CoV, PLS-CoV.

Part 1: Pre-Laboratory Questions
You have four of the restaurant staff/patron samples for your analysis. You will combine your results withthose from your class to get a complete picture of the infection status of all restaurant staff and patrons.
Your analysis will include the samples listed in Table 3. Before you begin, fill in the Purpose column inTable 3 with the details of each sample in your analysis.
Table 3. Samples included in the PLS-CoV diagnostic test.
SampleDescription

MWR

Molecular weight ruler(–)

Control sample containing the
GAPDH gene(+)

Control sample containing boththe N and GAPDH genes

NTC

No-template control(water; no DNA)

Restaurant samples

Four staff/patron samples
designated by a number

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Student Guide

Part 2: Patient Sample Analysis by Agarose Gel Electrophoresis
Student workstation

Quantity

Molecular weight ruler (MWR), 20 µl

1

GAPDH control (–), 10 µl

1

N gene and GAPDH positive control (+), 10 µl

1No-template control (NTC), 10 µl

1Samples from restaurant staff and patrons, 10 µl

4

TAE electrophoresis buffer

300 ml100x Fast Blast DNA Stain (if using)

50 ml

1% TAE agarose gel with 8 wells

1

Horizontal gel electrophoresis chamber

1Power supply (may be shared)

1

Microcentrifuge tube rack1

Micropipet and tips

1

Gel staining tray (optional)

1

Waste container

118Student Guide

Protocol1

Running DNA on an Agarose Electrophoresis Gel

2

3

4

5

6

7

8

1. Sketch your agarose gel setup to the right. Label each ➜of the eight wells with the sample that will be loaded.
2. Place a 1% TAE agarose gel into the electrophoresis
chamber. Be sure that the gel is oriented so that thewells are closest to the black (–) electrode, or cathode.
3. Fill the electrophoresis chamber with enough TAE
buffer to cover the gel by about 2 mm.

➜

1

4. Using a fresh pipet tip for each sample, load 10 µl ofeach DNA sample and 20 µl of MWR into each gel
according to the table below.
Lane Sample
1		 MWR, 20 µl
2		 (–), 10 µl
3		 (+), 10 µl
4		 NTC, 10 µl
5		 Restaurant patron or staff sample, 10 µl
6		 Restaurant patron or staff sample, 10 µl
7		 Restaurant patron or staff sample, 10 µl
8		 Restaurant patron or staff sample, 10 µl➜

5. Place the lid on the electrophoresis chamber and➜connect the electrical leads to the power supply, red to
red and black to black.
6. Turn on the power and run the gel. Ask your instructor
for the run conditions.
7. When the electrophoresis run is completed, turn off
the power and remove the lid from the chamber.
8. Carefully remove the gel from the electrophoresis
chamber and transfer it as directed by your instructor.
Be careful — the gel is very slippery.

➜

9. Stain and/or visualize your gel as directed by yourinstructor.

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Part 3: Analysis
1. Complete the table and sketch your electrophoresis results. Label the bands of the molecular		 weight ruler using the sizes shown in Figure 9.
Lane

Sample

1
2
3
4
5
6
7
8

2. State the results of the control samples and describe what you can conclude from them.

3. Record your restaurant staff/patron results below.
Person ID

20

Infection Status (Positive/Negative/Undetermined)

Student Guide

Part 4: Collecting Class Data
Gather the results from other groups in your class. In the table below, record the infection status for all
who were in the restaurant.
Table 4. Class results.
PersonInfection Status (Positive/Negative)

Person

A1

C6

A2

C7

A3

E1

A4

E2

B1

E3

B2

E4

B3

E5

B4

F1

B5

F2

B6

F3

B7

F4

B8

F5

C1

F6

C2

W1

C3

W2

C4

K1

Infection Status (Positive/Negative)

C5

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Student Guide

Activity 3
Building a Transmission ModelIn this activity, you assume the role of epidemiologist. You will integrate all the diagnostic test datawith other information about the restaurant patrons and staff to figure out how PLS-CoV spreadthroughout the restaurant.
CareerSpotlight

Epidemiologist
Epidemiologists study how disease outbreaks start, how diseases are transmitted, and how toeffectively mitigate spread. This involves collecting and analyzing data, communicating findings,
and working with other programs and agencies to decide courses of action. Their findings influence
regulatory, private, and public policy.
Epidemiologists typically earn a postgraduate, master’s degree in public health, focusing on
epidemiology. Epidemiologists find employment at state or local health departments, hospitals,
colleges, universities, and federal government agencies, such as the Centers for Disease Control
and Prevention (CDC).

Part 1: Understanding the Chain of Infection
To stop a contagious disease from spreading, you first need to find out how it is spreading. Infectious
disease control and prevention rely on understanding the chain of infection.
Chain of Infection
When epidemiologists talk about infectious diseases like PLS, they describe a chain of infection that
includes six points (Figure 10):
• Infectious agent — the pathogen (for example, virus, bacterium, fungus); this activity focuses on		 the virus PLS-CoV as the infectious agent• Reservoir — the environment in which the infectious agent lives (for example, people, animals,
		insects, etc.)• Portal of exit — the point at which the infectious agent leaves the reservoir; in humans, this refers		 to where on the body the infectious agent leaves• Mode of transmission — the way the infectious agent moves on to a new host
• Portal of entry — where on the body the infectious agent enters a new host• Susceptible host — person who can be infected22

Student Guide
Infectious agent

Susceptible
hostReservoi
Reservoir

Chain of Infection

Portal of entry

Portal of exit

Mode oftransmission

Figure 10. Chain of infection. In epidemiology, a chain of infection has six main points.

The chain of infection can be broken wherever it is vulnerable, most often at:• Controlling or eliminating the pathogen at transmission, for example by stopping the pathogen
		 (in this case, PLS-CoV) from spreading• Protecting portals of entry — preventing the pathogen from entering a host, for example by		 wearing a mask
• Increasing host’s defenses — making the host more resilient to infection, for example by		 vaccinating the hostReservoirs
A reservoir is where a pathogen lives, replicates, and spreads. Reservoirs include:• Humans — the reservoirs for many infectious diseases, humans can carry infections and		 pass them on to others while being symptomatic (showing physical symptoms of disease) or		asymptomatic (showing no symptoms but still carrying and transmitting viruses)• Animals and insects — infectious diseases transmitted from animals/insects to humans are		 referred to as zoonotic diseases• Environment — soils, water, and contaminated foods may also harbor pathogens that can		 spread to humans
Identifying reservoirs can be a critical component of fighting pathogen-caused disease. For example,
it was possible to eradicate smallpox because humans were the only reservoir for the smallpox virus.
Naturally occurring smallpox was eradicated after the last human case was identified and isolated. It ismuch more difficult to control or eradicate viruses that have multiple reservoirs or hosts.

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Student Guide
Portals of Entry and Exit
To cause disease, a pathogen must access tissues and cells through a portal of entry. To spread toothers (for disease transmission to occur), it must leave the host through a portal of exit (refer to How
Viruses Infect the Human Body, Activity 1).
The portals of exit and entry may be the same in a host. For example, a virus may exit from the nose or
mouth when a person exhales, talks, laughs, or sneezes. It may then enter the nose or mouth of a newhost when that person inhales. Or the portals of entry and exit might be different. For example, virions
may exit one person through their feces or vomit, be carried along on unwashed hands to food, water,or utensils and enter a new host through its mouth.
Modes and Routes of Transmission
Viruses can move between individuals in many ways that are categorized as either direct or indirect(Table 5).
• Direct transmission occurs directly between individuals through direct, person-to-person
		 contact or droplets• Indirect transmission typically occurs via an intermediate such as a surface, a vector like		mosquitoes, or airborne particles; the reservoir and new host do not need to be near each other		 for transmission to occur
Some viruses may use more than one mode of transmission.
Table 5. Modes of transmission.
DirectIndirectContact• Skin-to-skin contact like holding hands• Direct exchange of bodily fluids throughkissing or sexual intercourse

Fomites (contaminated inanimate objects) like door handles,
cell phones, shared drinking glasses, surfaces, or other objects

Droplets from sneezing, coughing, or eventalking; these droplets are large (>5 µm),
have a limited range of transmission, andquickly fall to the groundContaminated food or water
Vectors such as mosquitoes or ticks
Aerosols/airborne small liquid droplets (<5 µm) from sneezing,
coughing, or even talking; these droplets can remain suspended
in the air for extended periods of time (up to several hours)

Whether a virus has a lipid envelope or not is a key factor in determining its route of transmission.
Enveloped viruses require an intact lipid envelope to be able to infect, and they must remain in a wet
environment to keep the lipid envelope intact. So enveloped viruses typically spread through respiratory
droplets in a respiratory-aerosol route or in blood via insect bites, injection, or even organ donations.
When infected people exhale, talk, laugh, sing, cough, or sneeze, they spray mucus and other bodily
fluids that can contain viruses or other pathogens (Figure 11). These fluid drops vary in size from larger
liquid droplets (>5 µm) to smaller liquid aerosols (<5 µm)2. Whereas the larger droplets have a shorter
range for transmission because they quickly fall to the ground, smaller liquid aerosols can remainsuspended in the air (airborne) for longer periods of time and so accumulate in the air and travel for
greater distances, especially when there is poor ventilation.
There is no absolute cutoff in size to help distinguish a droplet from an aerosol; this is a topic of debate among experts(Nicas et al. 2005, Siegel et al. 2007, Tellier, 2009, Gralton et al. 2011).
2

24

Student Guide
Small aerosols are more susceptible to be inhaled deep into the lungs to cause infection in the lower
respiratory tract, while large droplets tend to be trapped and cause infections in the upper airways.

Figure 11. Droplet and airborne transmission. When an infected person exhales, talks, coughs, or sneezes,
virus-laden drops are transported through the air, where a potential host may inhale them to initiate a new
infection. The smaller the droplet, the farther it may drift. Larger droplets (>5 µm) tend to fall quickly out of
the air and so require direct transmission through direct contact, or indirect transmission as they fall on andcontaminate surfaces (fomites). In contrast to droplets, aerosols are much smaller (<5 µm), can linger in air forhours and travel beyond 1 to 2 m from the infected individual who exhales them, causing new infections at both
short and long ranges.

Virus-containing droplets and aerosols can also be generated from nonrespiratory activities, such as
toilet flushing or vomiting.
Non-enveloped viruses can withstand extremes of pH, detergents, and dryness. They can even
withstand the harsh pH and detergent conditions within the gastrointestinal tract and so can betransmitted through a fecal-oral route, in which virions enter through the mouth and exit through feces
to contaminate another surface and infect others.
Host Susceptibility
Once a virus enters a host, the susceptibility of that host depends on multiple factors that include
species (some viruses can infect only a particular species while others can affect a broader range), age(the youngest and/or oldest in a population will be most susceptible), and overall health and immunity
status (whether the host has been vaccinated against infection or has been infected previously).
Understanding whether host susceptibility is tied to age or sex, for example, can help public officers
understand how best to control spread. Host susceptibility can also be a target for prevention
strategies like vaccination or therapies.
For pathogens that spread from person to person, once a susceptible person becomes infected, they
become a new source for subsequent spread.

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Student Guide
Focus Questions
Droplet and aerosol transmission both involve viruses (or other pathogens) that are suspended
in bodily fluids. Why, then, is droplet transmission considered direct and aerosol transmission
considered indirect?

Enveloped viruses have exterior lipid membranes that can dry out in the environment. Which of
the modes of transmission listed in Table 5 is least likely for enveloped viruses, and why?

26

Student Guide

Part 2: Creating a Transmission Model
Public health officials need to know how PLS-CoV is transmitted to figure out how to keep furthertransmission in check. Your task is to analyze the complete set of data from the patient and restaurant
information supplied by your teacher, and to propose an explanation for how it spread.
Instructions
1. On the restaurant diagram:		a. Mark which restaurant staff and patrons were positive (use the class results).

		 b. Add other information from the patient cards that you think might be relevant.
			 What did they eat? Did they move about the restaurant?
2.
		
		
		

Propose a mode and route of transmission for PLS-CoV at the restaurant. Closely
examine the restaurant layout, seating chart, patient movement, and other available
data. Remember PLS-CoV is a novel coronavirus and so may have a different mode oftransmission from other CoVs.

3. Explain how the evidence supports your proposal.

4. Build a model to propose how PLS-CoV may have spread through the AnyTown
		 Restaurant. Include as many of the six points of the chain of infection in your model		 as you can.
		 a. Can you confidently pinpoint the source(s) of the infection? If yes, who/what was it			 and how do you know? If no, what other information would you need?

5. Considering your model, do any of the positive or negative test results surprise you?
		 How might you explain those results?

6. How might you test your model of how the virus spread?

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Student Guide

Activity 4
Mitigating Risk
It is now June 15 in AnyTown, and PLS is spreading rapidly through the town and surrounding region.
Since the initial diagnosis of Patient A, dozens more patients have been hospitalized with PLS, anda handful are in the AnyTown Hospital intensive care unit (ICU). Doctors are still struggling to findeffective treatments.
In this activity, you take on the role of Director for the AnyTown Department of Public Health. After
reviewing the goals and strategies for mitigation, it will be your responsibility to decide whether to takemeasures to slow further spread of the PLS-CoV virus in AnyTown and what those measures might be.

CareerSpotlight

Public Health Director
Public health directors manage local, state, and even national public healthcare programs andorganizations with the goal of improving the health and well-being of a population. Public healthdirectors ensure that laws are adhered to as they design and monitor emergency response plans
and hold hearings on public health issues. Public health directors have a master’s degree or Ph.D.
in Public Health and a state license to practice medicine.

Public Health Response
The public health response to a disease outbreak depends on several factors, including whether thevirus is novel (for example, PLS-CoV) or common (for example, flu), whether effective treatments areavailable, contagiousness and severity of the disease caused, and the populations that are affected(severe disease in young children, for example, can be more alarming because treatments may be lessavailable and their bodies more vulnerable to long-term damage).
Novel, highly contagious viruses like PLS-CoV are of particular concern because impacted populations
will have no pre-existing immunity. This means the effects of infection may be severe and any available
therapies may not be effective. These factors can combine to overwhelm local healthcare facilities,
leaving a community unable to respond to other health emergencies or supply preventive care.
When outbreaks of novel viruses occur, epidemiologists and public health officials work together
to figure out the best course of action. Epidemiologists tend to focus on figuring out the mode oftransmission of a novel virus because once they know how it is transmitted, they will be able todecide what measures to put in place to keep it from spreading. Public health officials work with theepidemiologists, local hospitals, and other agencies to decide which measures to put in place andhow to monitor the public health threat from the virus.
Often, there is no clear course of action. Public health officials must weigh the need and efficacy ofcontrol measures against their unintended impacts on society, such as effects on local economies andon the overall health and well-being of the population.

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Student Guide

Part 1: Understanding Response Strategies to Disease Outbreaks
In person-to-person transmission, once a susceptible host is infected, they become a source oftransmission to another susceptible host. One infected person can potentially transmit to morethan one susceptible host. Infectious diseases that spread easily from person to person are called
contagious diseases.
The Epidemic Curve
An epidemic curve shows the number of illnesses detected in an outbreak over time (Figure 12). If
an infectious disease spreads uncontrollably through a population, the number of infections tends
to rise rapidly, followed by a theoretical steep decline as the disease eventually finds fewer people
to infect. Though the total amount of time for the infection to pass through may be short, the total
number of infected and sick patients at the peak of an outbreak may overwhelm the capacity of local
health systems. This concerns public health officials because it could impact the ability of patients toreceive care and of noninfected citizens to access their regular healthcare. Eventually, illness may also
hit doctors and nurses and impact other essential services upon which a society depends, including
police and fire, teachers, grocery store workers, etc.
If, however, protective measures are put in place to control or reduce the rate of spread, the number of
infections could theoretically be lowered to a level that does not exceed the health system’s capacity.
This decreases the risk of overwhelming the health services and gives more time for treatments andvaccines to be developed. In this scenario, the total number of infections might be spread out over alonger period; that is, the infection curve would be “flattened” (Figure 12).

Number of cases

For more information and a graphic illustration of this phenomenon, visit www.washingtonpost.com/
graphics/2020/world/corona-simulator.

Healthcare
system capacity

Without
protective measures

With
protective measures

Time since first case

Figure 12. The epidemic curve. The epidemic curve plots the total number of cases of a disease over time. Without
protective measures, a highly contagious disease causes the number of infections to increase quickly to a level that
may exceed the capacity of a healthcare system. Implementing protective measures can slow the spread of diseaseand can keep the number of infections within the boundaries of the healthcare system’s capacity.

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Student Guide
Other Risks of Uncontrolled Spread
As viruses spread, they replicate, and their genes undergo random changes, or genetic mutations.
Over time, these genetic copying errors can lead to changes in how the virus behaves (which species
or tissues it infects, for example) and to how our bodies respond to it. Eventually, the changed virus
might be able get through our immune response undetected. Such antigenic drift causes people who
may have immunity from previous infections or vaccination to lose that immunity and be reinfected.
The changes may also make the virus less susceptible to treatments or existing vaccines.
Antigenic drift is one of the reasons why influenza and COVID-19 vaccines must be reviewed andupdated to keep up with the viruses as they change.

Focus Question
What are some other risks to the economy and/or society associated with having high numbersof people sick or quarantined? Consider all the types of products and services that are needed
to keep a community functioning.

Prevention Strategies
To reduce the risk associated with a disease outbreak, the most suitable strategy depends on thespecific chain of infection. Epidemiologists and public health officials usually focus on the segment in
the infection chain that is most susceptible to intervention.
Epidemiologists also consider the length of time people are sick and how long previous outbreaks ofsimilar diseases have lasted. For example, an outbreak may be connected to a single contamination ofa food or water source. Mitigation in this case might involve identifying and eradicating the source ofcontamination. However, outbreaks of novel respiratory viruses can last for several years before they
are contained.
Table 6 summarizes several common strategies that can be put into place at the individual orcommunity level. Some can be applied either to all people or only to specific groups (for example,
only to sick patients or those testing positive for the infection, or to large groups of people vs smallergroups).

30

Student Guide
Table 6. Common mitigation strategies for infectious diseases.
Strategy

Description

Isolation/quarantine

Physically isolate individuals who are infected (isolation) or who havebeen exposed (quarantine)

Travel restriction

Limit movement of an entire population, regardless of infection status

Social distancing

Reduce close contact in public settings

Closing schools

Move to online education, if possible

Canceling community events

Cancel concerts, sporting events, conferences, or other large
assemblies of people

Spacing guidelines

Add guidelines to create space between people as they wait in line,
sit at tables, etc.

Surface sanitization

Disinfect surfaces in areas where people congregate

Personal protective equipment (PPE)

Use clothing and other physical barriers to pathogen spread

Face mask or shield

Cover the nose and mouth or face; different degrees of filtration canbe added with masks

Gown

Wear a disposable, sanitary gown to cover clothing

GlovesWear disposable, sanitary gloves to protect hands

Recalls

Stop sales of and ask consumers to return items that may becontaminated with a pathogen

Air filtration and ventilation

Employ mechanisms of improving indoor air quality and purity:
ventilation improves air flow, filtration improves purity

Environmental monitoring

Test environmental reservoirs for pathogen presence; for example,
test air or wastewater samples for presence of a pathogen

Testing

Perform diagnostic tests on the public to diagnose or monitor for
infection; can be used to clear people for attendance at mass
gatherings, work, or school

Pharmaceutical interventions

Use and develop medications that can treat symptoms or prevent
infection

Vaccination

Primes the immune system, reduces number of susceptible hosts

Medication (antivirals)

Treat symptoms, reduce replication of viruses, and use othermechanisms for treating disease

Vector control

Inhibit movement or activity of pathogen-containing insects, animals,
or other hosts or reservoirs

Each strategy has its pros and cons and may not be 100% effective. For example, isolating a
population may be effective at reducing spread, but it will have unintended consequences on theability of society to function. Often, a layered approach (the use of more than one strategy) is best.
This is particularly true in the case of a novel virus like PLS-CoV, where it may be difficult to predict theoutcomes and efficacy of any one approach.

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Student Guide

Part 2: Developing a Response Strategy for the AnyTown PLS OutbreakIn this activity, in your role as an AnyTown public health official, you must decide which measures,
if any, you will put in place to slow the spread of disease and mitigate its effects on the healthcare
system and society.

Focus Questions
PLS-CoV is a novel virus, and the first decision to make is whether AnyTown should introduce
prevention measures to contain its spread. If you were the Public Health Director, what otherinformation would you need to be able to make this decision?
• Information about PLS-CoV and/or PLS disease:• Information about the AnyTown community and surrounding region:

32

Student Guide
List three different strategies the population of AnyTown could use to reduce their personal riskof PLS-CoV infection. Consider the nature of PLS-CoV, the mode of transmission you found in
Activity 3 for PLS-CoV, and the prevention strategies in Table 6.

• Briefly explain how each strategy works to minimize risk.

• Are there any drawbacks to each strategy that might prevent people from using them?

List three different prevention methods you could implement at the community level.

• Briefly explain how each strategy works to minimize the spread of PLS.

• What are some potential societal and economic impacts of each of the three strategies?

Describe a way in which three of the personal and/or community-level strategies might be used
together to maximize effectiveness.

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Student Guide
How might your personal and community-wide mitigation proposals change because of thefollowing new findings during a PLS-CoV outbreak or epidemic?

• New, additional, and significant mode of transmission — spread by fomites:• New treatment — a new medication becomes available that reduces symptoms and		hospitalization rates:• Vaccine — a vaccine becomes available that reduces transmission and/or disease severity:

34

Appendix A

Appendix A
Naming Viruses and the Diseases They Cause
The International Committee on Taxonomy of Viruses (ICTV) gives official names to novel viruses
according to genetic structure. The World Health Organization (WHO), in its International Classificationof Diseases (ICD), gives names to virus-caused diseases.
In the past, viruses and the diseases they caused were often named according to the regions inwhich they were first found (“Norwalk Virus”), according to animal source (“Swine Flu”), or otherconsiderations. This inconsistent system was not only uninformative, but it also created unintended
negative impacts on trade, travel, tourism, or animal welfare and sometimes caused offense to certain
cultural, social, national, regional, professional, and ethnic groups.
The current method is more informative because it names viruses according to their closest genetic
relatives, which can provide insights into their behavior. It also names diseases according tosymptoms or other aspects that enable discussion on disease spread, transmission, transmissibility,
severity, and treatment.
As a recent example, the ICTV named “severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)”
because the virus is genetically related to the coronavirus (CoV) responsible for the SARS (severe
acute respiratory syndrome) outbreak of 2003. While related, the two viruses are different. The WHOannounced “COVID-19” as the name of this new disease on 11 February 2020, following guidelines
previously developed with the World Organization for Animal Health (OIE) and the Food and Agriculture
Organization of the United Nations (FAO). COVID-19 is an acronym for “coronavirus disease of 2019”.

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Glossary

Glossary
Aerosols — fine spray of respiratory droplets produced by exhalation and consisting of saliva, mucus,
and other matter from respiratory tract surfaces; generally smaller in size than droplets, aerosols spread
farther and can remain suspended in the air for much longer than droplets; transmission through aerosols,
therefore, is considered an indirect mode of transmission.
Agarose gel electrophoresis — technique or process by which charged molecules like DNA are
separated in an electrical field (see Electrophoresis); an agarose gel matrix is used to slow the movementof larger molecules relative to smaller ones.
Airborne — mode of transmission involving aerosols; occurs when bacteria or viruses travel in droplet
nuclei that have been aerosolized.
Antibody test — diagnostic test that uses antibodies to detect the presence of other antibodies in thepatient’s bloodstream (to indicate a previous infection, for example).
Antigen test — diagnostic test that uses antibodies to detect the presence of an antigen (a virus or otherpathogen, for example); designed to detect an active infection.
Antigenic drift — accumulation of mutations in genes that encode surface proteins of viruses that thehost’s antibodies recognize; results in a new strain of virus not effectively inhibited by the antibodies thatprevented infection by recognized strains and makes it easier for the virus to spread through a partiallyimmune population.
Asymptomatic infection — infection that does not result in symptoms; an infected individual who does
not show symptoms of the infection.
Capsid — protein coat that surrounds the genetic material of a virus.
Contagious diseases — infectious diseases that spread easily from person to person.
Containment — action of keeping something harmful under control or within limits.
Direct transmission — movement of an infectious agent like a virus between two hosts in a manner thatinvolves direct contact between the hosts and/or reservoir.
Droplets — liquid respiratory emissions produced by exhalation and consisting of saliva, mucus, andother matter from respiratory tract surfaces; generally larger in size than aerosols, droplets do not remainsuspended in air as long as aerosols; transmission through droplets is considered a direct mode oftransmission.
DNA virus — virus with a DNA genome.

36

Glossary
Electrophoresis — movement and separation of molecules in an electrical field; positively charged
particles move toward negatively charged poles, and vice versa.
Envelope — in reference to virus structure, the lipid covering of certain groups of viruses.
Epidemic curve — statistical chart used in epidemiology to visualize the onset of a disease outbreak; also
known as an epi curve or epidemiological curve.
Eradicate — destroy completely, get rid of, put an end to.
Fecal-oral route — route of transmission of a disease in which pathogens pass in fecal particles from one
person to the mouth of another person.
Genome — the complete set of genetic information of an organism (or virus).
Genome sequencing — determination of the nucleotide sequence of a genome.
Indirect transmission — movement of an infectious agent like a virus between two hosts in a mannerthat involves indirect contact between the hosts and/or contact with an intermediate surface or vector.
Infectious agent — pathogen; any organism or agent that can produce disease (can include viruses,bacteria, fungi, protists, algae, and other organisms).
Isolation — separation of an infected individual from others.
Mitigation — reduction of something harmful or the reduction of its harmful effects.
Mode of transmission — in epidemiology, the mechanism by which a pathogen like a virus moves fromone host (or reservoir) to another.
Mutate — undergo a change in the genetic code; such a change may or may not result in a physicalchange.
Nasopharyngeal swab — method of collecting a sample of nasal secretions from the back of the noseand throat.
Nucleocapsid — capsid (protein coat) of a virus with the enclosed nucleic acid.
Pathophysiology — process by which an infection (for example, by a virus, bacterium, fungus, etc.)
causes disease.
PCR test — polymerase chain reaction; diagnostic test designed to detect the presence of DNA byamplification of that DNA by PCR.

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Glossary
Portal of entry —path through which an infectious agent like a virus enters its host.
Portal of exit — path through which an infectious agent like a virus leaves its host.
Quarantine — separation of a potentially infectious person from the general population.
Reservoir — in epidemiology, refers to the habitat in which the infectious agent normally exists.
Respiratory-aerosol route — route of transmission of a disease in which pathogens pass from one
person in respiratory droplets or aerosols to the mouth or nose another person.
Respiratory droplet — small aqueous excretion produced by exhalation and consisting of saliva, mucus,
and other matter from respiratory tract surfaces; generally larger in size than aerosols, droplets tend to
fall out of the air relatively quickly and so do not spread farther than a few meters; transmission throughdroplets, therefore, is considered direct transmission.
Reverse-transcription PCR (RT-PCR) test — diagnostic test designed to detect the presence of RNA;requires a reverse transcription step to convert the RNA to DNA before amplification by PCR.
RNA virus — virus with an RNA genome.
Susceptible host — host organism that is vulnerable to infection.
Symptomatic infection — infection that results in symptoms; an infected individual that shows
symptoms of the infection.
Virion — viral particle that exists independently of a host cell; consists of the genome, protein capsid, andin some cases, lipid envelope.
Virology — subfield of microbiology, the study of viruses and their structure, classification, evolution,mechanisms of infection and reproduction, pathophysiology, and detection.
Zoonotic — viruses, bacteria, fungi, and other microbes that can spread from animals to cause diseasein humans.

38

Appendix A

References
Gralton J et al. (2011). The role of particle size in aerosolised pathogen transmission: A review. J Infect62, 1–13.
Nicas M et al. (2005). Toward understanding the risk of secondary airborne infection: emission of
respirable pathogens. J Occup Environ Hyg 2, 143–54.
Siegel J et al. (2007). Guideline for Isolation Precautions: Preventing Transmission of Infectious Agentsin Health Care Settings. Am J Infect Control 35, S65–164.
Tellier R (2009). Aerosol transmission of influenza A virus: a review of new studies. J R Soc Interface
Suppl 6, S783–90.

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Canada 1 905 364 3435 China 86 21 6169 8500 Czech Republic 00 800 00 24 67 23 Denmark 00 800 00 24 67 23 Finland 00 800 00 24 67 23
France 00 800 00 24 67 23 Germany 00 800 00 24 67 23 Hong Kong 852 2789 3300 Hungary 00 800 00 24 67 23 India 91 124 4029300 Israel 0 3 9636050
Italy 00 800 00 24 67 23 Japan 81 3 6361 7000 Korea 82 080 007 7373 Luxembourg 00 800 00 24 67 23 Mexico 52 555 488 7670
The Netherlands 00 800 00 24 67 23 New Zealand 64 9 415 2280 Norway 00 800 00 24 67 23 Poland 00 800 00 24 67 23 Portugal 00 800 00 24 67 23
Russian Federation 00 800 00 24 67 23 Singapore 65 6415 3188 South Africa 00 800 00 24 67 23 Spain 00 800 00 24 67 23 Sweden 00 800 00 24 67 23
Switzerland 00 800 00 24 67 23 Taiwan 886 2 2578 7189 Thailand 66 2 651 8311 United Arab Emirates 36 1 459 6150 United Kingdom 00 800 00 24 67 23

Life ScienceGroup

10000164966 Ver A

US/EG

23-02600723

Sig 0123