Based on the information provided, the scenario that would put me at the highest risk of being infected by the SARS-CoV-2 virus from the infected student in the crowded classroom would be: - Sitting or standing very close to the infected student for a prolonged period of time, especially if we were talking face-to-face without any face masks. This would allow the virus to spread more easily through respiratory droplets released into the air by the infected student through coughing, sneezing, talking or breathing. - Touching surfaces like desks or doorknobs that the infected student had recently touched and then touching my own eyes, nose or mouth without practicing appropriate hand hygiene in between. This could allow the virus to

1. 2019-2020
Coronavirus Outbreak
Rachel Mackelprang, Ph.D.

2. Ground Zero
Photo: https://www.sciencemag.org/
news/2020/01/novel-human-virus-
pneumonia-cases-linked-seafood-
market-china-stir-concern
• ~11 million people
• Central China’s political, economic, financial, commercial, cultural and
educational center
• Major transportation hub

3. The Early Days
Dec 30th 2019: First hints of trouble: Local media reports that the Wuhan
Municipal Health Commission asked local hospitals to report unusual
cases of pneumonia.
https://www.sciencemag.org/news/2020/01/novel-human-virus-pneumonia-cases-linked-seafood-market-china-stir-concern
https://www.theguardian.com/environment/2020/jan/30/make-coronavirus-ban-on-chinese-wildlife-markets-permanent-says-environment-expert-aoe
Chen et al. 2020. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a
descriptive study. The Lancet. 395:507-513

4. The Early Days
Dec 30th 2019: First hints of trouble: Local media reports that the Wuhan
Municipal Health Commission asked local hospitals to report unusual
cases of pneumonia.
Dec 31st 2019: Authorities announce 27 cases of pneumonia linked to
Huanan Seafood Market. Seven of the 27 were in serious condition.
https://www.sciencemag.org/news/2020/01/novel-human-virus-pneumonia-cases-linked-seafood-market-china-stir-concern
https://www.theguardian.com/environment/2020/jan/30/make-coronavirus-ban-on-chinese-wildlife-markets-permanent-says-environment-expert-aoe
Chen et al. 2020. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a
descriptive study. The Lancet. 395:507-513

5. The Early Days
Dec 30th 2019: First hints of trouble: Local media reports that the Wuhan
Municipal Health Commission asked local hospitals to report unusual
cases of pneumonia.
Dec 31st 2019: Authorities announce 27 cases of pneumonia linked to
Huanan Seafood Market. Seven of the 27 were in serious condition.
https://www.sciencemag.org/news/2020/01/novel-human-virus-pneumonia-cases-linked-seafood-market-china-stir-concern
Jan 1st 2020: Huanan Market is closed
https://www.theguardian.com/environment/2020/jan/30/make-coronavirus-ban-on-chinese-wildlife-markets-permanent-says-environment-expert-aoe
Chen et al. 2020. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a
descriptive study. The Lancet. 395:507-513

6. The Early Days
Dec 30th 2019: First hints of trouble: Local media reports that the Wuhan
Municipal Health Commission asked local hospitals to report unusual
cases of pneumonia.
Dec 31st 2019: Authorities announce 27 cases of pneumonia linked to
Huanan Seafood Market. Seven of the 27 were in serious condition.
https://www.sciencemag.org/news/2020/01/novel-human-virus-pneumonia-cases-linked-seafood-market-china-stir-concern
Jan 1st 2020: Huanan Market is closed
https://www.theguardian.com/environment/2020/jan/30/make-coronavirus-ban-on-chinese-wildlife-markets-permanent-says-environment-expert-aoe
Jan 3rd 2020: Determined that disease is most likely caused by an
unknown virus
Chen et al. 2020. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a
descriptive study. The Lancet. 395:507-513

7. The Early Days
Dec 30th 2019: First hints of trouble: Local media reports that the Wuhan
Municipal Health Commission asked local hospitals to report unusual
cases of pneumonia.
Dec 31st 2019: Authorities announce 27 cases of pneumonia linked to
Huanan Seafood Market. Seven of the 27 were in serious condition.
https://www.sciencemag.org/news/2020/01/novel-human-virus-pneumonia-cases-linked-seafood-market-china-stir-concern
Jan 1st 2020: Huanan Market is closed
https://www.theguardian.com/environment/2020/jan/30/make-coronavirus-ban-on-chinese-wildlife-markets-permanent-says-environment-expert-aoe
Jan 3rd 2020: Determined that disease is most likely caused by an
unknown virus
Jan 7th 2020: Causative agent determined to be a novel coronavirus
Chen et al. 2020. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a
descriptive study. The Lancet. 395:507-513

8. The Early Days
Dec 30th 2019: First hints of trouble: Local media reports that the Wuhan
Municipal Health Commission asked local hospitals to report unusual
cases of pneumonia.
Dec 31st 2019: Authorities announce 27 cases of pneumonia linked to
Huanan Seafood Market. Seven of the 27 were in serious condition.
https://www.sciencemag.org/news/2020/01/novel-human-virus-pneumonia-cases-linked-seafood-market-china-stir-concern
Jan 1st 2020: Huanan Market is closed
https://www.theguardian.com/environment/2020/jan/30/make-coronavirus-ban-on-chinese-wildlife-markets-permanent-says-environment-expert-aoe
Jan 3rd 2020: Determined that disease is most likely caused by an
unknown virus
Jan 11th 2020: First death reported
Jan 7th 2020: Causative agent determined to be a novel coronavirus
Chen et al. 2020. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a
descriptive study. The Lancet. 395:507-513

9. The Early Days
Dec 30th 2019: First hints of trouble: Local media reports that the Wuhan
Municipal Health Commission asked local hospitals to report unusual
cases of pneumonia.
Dec 31st 2019: Authorities announce 27 cases of pneumonia linked to
Huanan Seafood Market. Seven of the 27 were in serious condition.
https://www.sciencemag.org/news/2020/01/novel-human-virus-pneumonia-cases-linked-seafood-market-china-stir-concern
Jan 1st 2020: Huanan Market is closed
https://www.theguardian.com/environment/2020/jan/30/make-coronavirus-ban-on-chinese-wildlife-markets-permanent-says-environment-expert-aoe
Jan 3rd 2020: Determined that disease is most likely caused by an
unknown virus
Jan 11th 2020: First death reported
Jan 23rd 2020: Wuhan enters general quarantine. All transport modes
in and out of Wuhan are suspended.
Jan 7th 2020: Causative agent determined to be a novel coronavirus
Chen et al. 2020. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a
descriptive study. The Lancet. 395:507-513

10. The First Cases
Huang et al. 2020. Clinical feature of patients infected with 2019 novel coronavirus in Wuhan,
China. The Lancet. 395:495-506

11. What are coronaviruses?
Coronaviruses are nothing new. They are widespread in humans and
other animals

12. What are coronaviruses?
Coronaviruses are nothing new. They are widespread in humans and
other animals
Electron micrograph:
Scott Camazine/Almay
Named for the crown or “corona”
of club-shaped spikes

13. What are coronaviruses?
Coronaviruses are nothing new. They are widespread in humans and
other animals
Electron micrograph:
Scott Camazine/Almay
Named for the crown or “corona”
of club-shaped spikes
Four strains of coronavirus that
commonly affect humans. They
cause ~20% of common colds.

14. What are coronaviruses?
Coronaviruses are nothing new. They are widespread in humans and
other animals
Electron micrograph:
Scott Camazine/Almay
Named for the crown or “corona”
of club-shaped spikes
Four strains of coronavirus that
commonly affect humans. They
cause ~20% of common colds.
Since 2003, 3 “spillovers” of an
animal coronavirus to humans
have occurred.

15. What are coronaviruses?
Coronaviruses are nothing new. They are widespread in humans and
other animals
Electron micrograph:
Scott Camazine/Almay
Named for the crown or “corona”
of club-shaped spikes
Four strains of coronavirus that
commonly affect humans. They
cause ~20% of common colds.
Since 2003, 3 “spillovers” of an
animal coronavirus to humans
have occurred.
• Severe Acute Respiratory Syndrome
(SARS-CoV)
• Middle East Respiratory Syndrome
(MERS-Cov)
• 2019 novel coronavirus. Virus name:
SARS-CoV-2, name of disease:
COVID-19

16. Relationships between coronaviruses
Zhou et al. 2020. Discovery of a novel coronavirus associated with the recent pneumonia outbreak in
humans and its potential bat origin. bioRxiv preprint. https://doi.org/10.1101/2020.01.22.914952.

17. Relationships between coronaviruses
Zhou et al. 2020. Discovery of a novel coronavirus associated with the recent pneumonia outbreak in
humans and its potential bat origin. bioRxiv preprint. https://doi.org/10.1101/2020.01.22.914952.
Common human coronaviruses.

18. Relationships between coronaviruses
Zhou et al. 2020. Discovery of a novel coronavirus associated with the recent pneumonia outbreak in
humans and its potential bat origin. bioRxiv preprint. https://doi.org/10.1101/2020.01.22.914952.
Common human coronaviruses.
SARS

19. Relationships between coronaviruses
Zhou et al. 2020. Discovery of a novel coronavirus associated with the recent pneumonia outbreak in
humans and its potential bat origin. bioRxiv preprint. https://doi.org/10.1101/2020.01.22.914952.
Common human coronaviruses.
SARS
MERS

20. Coronavirus replication
Liang et al. 2018. Development of small-molecule MERS-
CoV inhibitors. Viruses 10:721

21. Coronavirus facts
Source: https://commons.wikimedia.org/wiki/File:3D_medical_animation_corona_virus.jpg
Fun facts
ssRNA (+sense)
32 kb
Largest known RNA virus genome
Mutate and change at a high rate
https://asm.org/Articles/2020/January/2019-Novel-Coronavirus-2019-nCoV-Update-Uncoating

22. Spillover: Huanan Seafood Market
Photo credit: https://www.bangkokpost.com/world/1842814/china-
seals-off-more-cities-as-virus-toll-climbs
Photo: SAM⼩小K/Weibo
https://www.theguardian.com/environment/2020/jan/30/make-coronavirus-ban-on-chinese-wildlife-markets-permanent-says-environment-expert-aoe
Before Huanan seafood market was closed on January 1st, it
contained dozens of species of animals, including live wolf pups,
salamanders, golden cicadas, civets and bamboo rats
List of prices for a vendor at the market

23. Animal Origins
Bats and Pangolins are the prime
suspects, but bats are the more
likely source.
Zhang et al. 2020. Pangolin homology associated with 2019-
nCoV. Biorxiv. https://www.biorxiv.org/content/
10.1101/2020.02.19.950253v1.full.pdf
Photos: shutterstock
https://www.nature.com/articles/d41586-020-00548-w

24. Animal Origins
Bats and Pangolins are the prime
suspects, but bats are the more
likely source.
96%
sequence
similarity
Zhang et al. 2020. Pangolin homology associated with 2019-
nCoV. Biorxiv. https://www.biorxiv.org/content/
10.1101/2020.02.19.950253v1.full.pdf
Photos: shutterstock
https://www.nature.com/articles/d41586-020-00548-w

25. Animal Origins
Bats and Pangolins are the prime
suspects, but bats are the more
likely source.
96%
sequence
similarity
Zhang et al. 2020. Pangolin homology associated with 2019-
nCoV. Biorxiv. https://www.biorxiv.org/content/
10.1101/2020.02.19.950253v1.full.pdf
Photos: shutterstock
However, SARS and the sequence
from its animal source (bats via palm
civets) were 99.8% similar. More work
needs to be done to ID the source of
COVID-19.
https://www.nature.com/articles/d41586-020-00548-w

26. Official counts as of March 9th, 10:25am EDT
Source: NY Times

27. Official counts as of March 9th, 10:25am EDT
Map: NY Times
Li et al. 2020. Estimating the scale of COVID-19 epidemic in the United
States: simulations based on air traffic directly from Wuhan, China.
medRxiv preprint. https://doi.org/10.1101/2020.03.06.20031880

28. Official counts as of March 9th, 10:25am EDT
Map: NY Times
These data (i.e. 500+ US cases) represent official numbers. Many have not been officially
tested and/or have mild symptoms. The actual number of US cases is likely in the
thousands to tens of thousands.
Li et al. 2020. Estimating the scale of COVID-19 epidemic in the United
States: simulations based on air traffic directly from Wuhan, China.
medRxiv preprint. https://doi.org/10.1101/2020.03.06.20031880

29. Official counts as of March 9th, 10:25am EDT
Source: NY Times

30. How the virus was contracted
Source: NY Times March 9th 10:25am EDT

31. Genetic Epidemiology
https://nextstrain.org/ncov
These screen captures are from an amazing interactive website.

32. Genetic Epidemiology
https://nextstrain.org/ncov
These screen captures are from an amazing interactive website.

33. How is it spread?
Through the
air by
coughing or
sneezing
Touching a
surface with
the virus on
it, then
touching your
mouth, nose,
or eyes
Close
personal
contact, such
as touching
or shaking
hands

34. How is it spread?

35. How is it spread?
Can linger in the air for ~30 min

36. How long does the virus live on a surface?
https://www.scmp.com/news/china/science/article/3074351/coronavirus-can-travel-twice-far-official-safe-distance-and-stay

37. How long does the virus live on a surface?
https://www.scmp.com/news/china/science/article/3074351/coronavirus-can-travel-twice-far-official-safe-distance-and-stay

38. How long does the virus live on a surface?
The length of time it can linger on a surface depends on factors
such as material and temperature, but could be 2-3 days.
https://www.scmp.com/news/china/science/article/3074351/coronavirus-can-travel-twice-far-official-safe-distance-and-stay

39. How is it spread?
https://www.nytimes.com/2020/03/02/health/coronavirus-how-it-spreads.html

40. How is it spread?
You walk into a crowded classroom. Another student is infected
by SARS-CoV-2. What puts you at the most risk of being infected
by that person?
https://www.nytimes.com/2020/03/02/health/coronavirus-how-it-spreads.html

41. How is it spread?
You walk into a crowded classroom. Another student is infected
by SARS-CoV-2. What puts you at the most risk of being infected
by that person?
Four factors likely to play a role
(1) How close you get
(2) How long you are near the person
(3) Whether that person projects viral droplets on you
(4) How much you touch your face
https://www.nytimes.com/2020/03/02/health/coronavirus-how-it-spreads.html

42. How is it spread?
https://www.scmp.com/news/china/science/article/3074351/coronavirus-can-travel-twice-far-official-safe-distance-and-stay

43. How easily is it spread?
R0 (pronounced “R naught”) is the basic reproduction number, an
estimate of the number of people who catch the virus from a single
infected person.
del Rio et al. 2020. COVID-19—New insights on a rapidly changing epidemic. JAMA. doi:10.1001/jama.
2020.3072
Animation website: https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html

44. How easily is it spread?
R0 (pronounced “R naught”) is the basic reproduction number, an
estimate of the number of people who catch the virus from a single
infected person.
The current estimate for SARS-CoV-2 is between 2 and 3
del Rio et al. 2020. COVID-19—New insights on a rapidly changing epidemic. JAMA. doi:10.1001/jama.
2020.3072
Animation website: https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html

45. How easily is it spread?
R0 (pronounced “R naught”) is the basic reproduction number, an
estimate of the number of people who catch the virus from a single
infected person.
The current estimate for SARS-CoV-2 is between 2 and 3
del Rio et al. 2020. COVID-19—New insights on a rapidly changing epidemic. JAMA. doi:10.1001/jama.
2020.3072
Animation website: https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html

46. How easily is it spread?
R0 (pronounced “R naught”) is the basic reproduction number, an
estimate of the number of people who catch the virus from a single
infected person.
The current estimate for SARS-CoV-2 is between 2 and 3
del Rio et al. 2020. COVID-19—New insights on a rapidly changing epidemic. JAMA. doi:10.1001/jama.
2020.3072
Animation website: https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html

47. How easily is it spread?
R0 (pronounced “R naught”) is the basic reproduction number, an
estimate of the number of people who catch the virus from a single
infected person.
The current estimate for SARS-CoV-2 is between 2 and 3
del Rio et al. 2020. COVID-19—New insights on a rapidly changing epidemic. JAMA. doi:10.1001/jama.
2020.3072
Animation website: https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html

48. How easily is it spread?
R0 (pronounced “R naught”) is the basic reproduction number, an
estimate of the number of people who catch the virus from a single
infected person.
The current estimate for SARS-CoV-2 is between 2 and 3
del Rio et al. 2020. COVID-19—New insights on a rapidly changing epidemic. JAMA. doi:10.1001/jama.
2020.3072
Animation website: https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html

49. How easily is it spread?
R0 (pronounced “R naught”) is the basic reproduction number, an
estimate of the number of people who catch the virus from a single
infected person.
The current estimate for SARS-CoV-2 is between 2 and 3
del Rio et al. 2020. COVID-19—New insights on a rapidly changing epidemic. JAMA. doi:10.1001/jama.
2020.3072
Animation website: https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html

50. Compare with the seasonal flu
Animation website: https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html
SARS-CoV-2: R0= 2.6 Flu: R0= 1.3

51. How deadly is the virus?
https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html

52. How deadly is the virus?FatalityRate
Average number of people infected by each sick person
https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html
Note the
log scale

53. How deadly is the virus?FatalityRate
Average number of people infected by each sick person
https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html
Note the
log scale
Estimates range between 0.1% and 3%

54. How deadly is the virus?FatalityRate
Average number of people infected by each sick person
Caveat: Very difficult to determine lethality of new virus. Worst cases are usually
detected first, which can skew estimates. People with mild illness may never visit a
doctor
https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html
Note the
log scale
Estimates range between 0.1% and 3%

55. How long does it take to show symptoms?
Incubation period: based on pooled analysis of confirmed
COVID-19 cases reported between Jan 4th and Feb 24th
Lauer et al. 2020. The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported
confirmed cases: estimation and application. Annals of Internal Medicine. DOI: 10.7326/M20-0504
Mean: 5.1 days
CI: 4.5 to 5.8 days

56. Symptoms

57. How can I protect myself and others?
Use common sense. Don’t panic
Stay home if you are sick