Unit 2

SARS-CoV-2 origins and how humans are infected

This is a new curriculum. We are refining the materials and teaching support according to teacher feedback. If you have any questions or comments, please use the contact form on the Get Help page and we will respond promptly. Thanks for your patience and understanding!

Lesson 2.1

How did SARS-CoV-2 infect humans?

This lesson explores how the COVID-19 pandemic originated when the SARS-CoV-2 virus first infected humans.

Lesson Objectives

By the end of the lesson, you will be able to…

  • Define a reservoir and intermediate host in viral infections.
  • Explain how the amino acid sequence of coronavirus spike proteins can be used to track virus transmission between animals.
  • Infer how SARS-CoV-2 was transmitted across animal species based on the amino acid sequence of the spike protein in different viral strains.

2.11-2.12 How are infections transmitted? Animal to human transmission: Zoonosis (7 slides)

How do humans become infected with a pathogen like SARS-CoV-2? You’re going to start with a quick review of the ways different pathogens are transmitted and then zoom into transmission from animals, or zoonosis. You’ll learn about how the horseshoe bat is critical to coronavirus infections.

2.13 How did coronaviruses come to infect humans? (17 slides)

This section takes a closer look at the animal reservoirs for coronaviruses and you’ll explore the current puzzle about where exactly SARS-CoV-2 came from. Why do we even care? You’ll find out!

2.14 How does SARS-CoV-2 infect humans? The Spike protein (13 slides)

Before you can use Spike protein mutations to track SARS-CoV-2 on its journey across species, you need to know which parts of the Spike protein will give you the best information. This section focuses on where you will be looking.

2.15 Tracking zoonosis across the species barrier (25 slides)

Now, you’ll do an activity to try to figure out where SARS-CoV-2 went after bats – into civets, pangolins or both! This data was taken from very new studies and you will be the first to do this exercise.

2.16 Where do pangolins fit in? (26 slides)

Finding pangolins infected with SARS-CoV-2 has led to intense speculation that they could be the intermediary host. You’ll apply your new skills at mutation analysis to deduce whether that’s possible.

2.17 Vocab review

2.18 Apply your new knowledge!
Read the following news article about the search for an intermediate host for SARS-CoV-2 and answer the questions on your worksheet. You can find the link here.


2.18 Reading worksheet

Lesson 2.2

How did COVID-19 travel around the world?

This lesson focuses on how phylogenetic analysis of different SARS-CoV-2 isolates helps us understand how the COVID-19 pandemic spread around the world.

Lesson Objectives

By the end of the lesson, you will be able to…

  • Describe what a viral isolate is.
  • Interpret a phylogenetic tree to determine a virus lineage.
  • Explain how phylogenetic trees can be used to track viral spread.

2.21 Global travel in the age of COVID-19 (11 slides)

International travel is so easy that epidemics can rapidly become pandemics, which are more widespread. COVID-19 was first identified in Wuhan, China, but within months had traveled all over the world. In this section, you’ll explore just how easy it is to get from Wuhan to practically anywhere in the world.

2.22 Tracking infectious disease spread (10 slides)

Tracking SARS-CoV-2 spread across the world can be done using phylogenetic analysis – sequencing virus isolates collected in different places at different times. In this section, you’ll learn what phylogenetic analysis means and how to set up a phylogenetic tree.

2.23 Tracking SARS-CoV-2 spread (30 slides)

Now that you’re able to interpret phylogenetic trees, you’ll work with a database to determine how SARS-CoV-2 came to Austria.

Take a break after slide 18!

2.24. Using clades to track SARS-CoV-2 around the world (14 slides)

Virus isolates that descend from a common ancestor can be grouped into clades, then clade maps can be used to trace how viruses evolve globally. Now, you’ll use the clade map being developed in real time by Nextstrain.org to trace how SARS-CoV-2 traveled around the world.

2.25. How did SARS-CoV-2 come to the U.S.? (18 slides)

You’ll continue to use the clade map, this time to figure out how SARS-CoV-2 came to the U.S. Did it just come from China, and did stopping flights into the U.S. help curtail its arrival at all?

2.26 Vocab review

2.27 Apply your new knowledge!

Study the New York Times interactive infographic here to understand how and when SARS-CoV-2 came to the U.S. and traveled within its borders. Complete your reading worksheet.


2.27 Reading worksheet

Lesson 2.3

How is SARS-CoV-2 transmitted between people?

This lesson focuses on virus transmission from person to person, particularly through the air. It evaluates risk factors and describes ways to minimize infection.

Lesson Objectives

By the end of the lesson, you will be able to…

  • Explain how SARS-CoV-2 can be transmitted through the air and through fomites.
  • Differentiate between droplets and aerosols.
  • Analyze data and make conclusions about where SARS-CoV-2 is most likely to be found in the environment indoors and in outdoor public spaces.
  • Make recommendations about how businesses could operate while preventing  SARS-CoV-2 transmission among patrons and employees.

2.31-2.32 Routes of Pathogen Transmission (38 slides)

This first section sets the stage by reviewing how pathogens are transmitted from person to person. Then, in the second part, you’ll learn how an argument about the nature of droplets vs. aerosols has impeded our understanding about SARS-CoV-2 transmission.

You can take a break in the middle of this section!

2.33 SARS-CoV-2 and aerosol transmission (26 slides)

Finding out that SARS-CoV-2 travels in aerosols as well as droplets was a game-changer in terms of understanding why it is so infectious. In this section, you’ll work through a couple of the papers published in spring 2020 that provided this critical information.

2.34 Ways to Minimize Transmission (17 slides)

Realizing that SARS-CoV-2 is highly infectious and that it can be transmitted through aerosols makes it imperative that we act to minimize transmission. In this section, you’ll evaluate different methods and their limitations.

2.35 Back to work! (20 slides)

In this last section, you’ll examine another risk factor for SARS-CoV-2 infection – inadequate ventilation. First, you’ll examine two of the case studies that provided this information, then you’ll evaluate several scenarios in which it leads to infection and what can be done to minimize risk. Finally, you’ll bring it all together by constructing your own scenario and recommendations, based on your own experiences.

2.36 Vocab review

2.37 Apply your new knowledge!

Read the following news article about how being in isolation for a long period of time is hard to sustain and complete your reading worksheet.
The link is here.


2.37 Reading worksheet

Lesson 2.4

When is SARS-CoV-2 infectious and how can we tell?

This lesson focuses on how we can know whether a person infected with SARS-CoV-2 will pass it on, and how we can tell we’ve been infected.

Lesson Objectives

By the end of the lesson, you will be able to…

  • Describe how the Minimal Infectious Dose (MID) determines if a successful infection will occur.
  • Explain the importance of the latent and infectious periods in how we can control whether an infection is transmitted.
  • Consider multiple pieces of information to determine how likely it is that a person will be infected with SARS-CoV-2 in various scenarios.
  • Explain how testing for SARS-CoV-2 is carried out, and its limitations.

2.41 How much SARS-CoV-2 is needed to cause an infection? (16 slides)

A key question in dealing with SARS-CoV-2 infectivity is how much virus is needed to cause disease. This section focuses on how the minimal infectious dose is measured and the limitations of the measurement. Will ‘humanized’ mice be the solution?

2.42 How does time of exposure impact infection with SARS-CoV-2? (9 slides)

The MID is not the only factor that determines whether an infection will be successful. The other ingredient is time. In this short section, you’ll evaluate scenarios that illustrate how time affects infection, and also learn about the impact superspreaders can have.

2.43 When is an infected person infectious? (41 slides)

A key question in infection control is how long after infection it takes to become infectious, and when does infection disappear? Now, you’ll learn about the different stages of infection and why asymptomatic transmission presents such a challenge to infection control.

Take a break after slide 18!

2.44 How likely am I to be infectious? (9 slides)

You’ve learned that how likely an infected person will pass on the infection depends on how much virus they transmit and when they are infectious. In this short section, you’ll evaluate a few scenarios as to whether you’d be likely to infect others.

2.45 How can I know if I’m infected? (21 slides)

Testing for the presence of SARS-CoV-2 is the only way to know for sure that infection has occurred. But are tests reliable? Here you’ll learn about how tests for SARS-CoV-2 work. You’ll review PCR and explore the limitations of testing.

2.46 Asymptomatic transmission: a case study (10 slides)

Asymptomatic transmission is a major public health challenge that has been very controversial. Here you’ll explore the first case study that was published to suggest it would be a big factor in the COVID-19 pandemic.

2.47 Vocab review

2.48 Apply your new knowledge!

Read the following news article about how asymptomatic transmission of SARS-CoV-2 was originally missed and answer the questions on your reading worksheet.
The link is here.


2.48 Reading worksheet