Newer version is available: https://www.slideshare.net/RachelMackelprang/novel-coronavirus-information

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

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

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

The Early Days
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.

The Early Days
cases of pneumonia.
Jan 1st 2020: Huanan Market is closed

The Early Days
cases of pneumonia.
Jan 3rd 2020: Determined that disease is most likely caused by an
unknown virus

The Early Days
cases of pneumonia.
unknown virus
Jan 7th 2020: Causative agent determined to be a novel coronavirus

The Early Days
cases of pneumonia.
unknown virus
Jan 11th 2020: First death reported

The Early Days
cases of pneumonia.
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.

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

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

other animals
Electron micrograph:

Scott Camazine/Almay
Named for the crown or “corona”
of club-shaped spikes

other animals

Four strains of coronavirus that
commonly affect humans. They
cause ~20% of common colds.

other animals

Since 2003, 3 “spillovers” of an
animal coronavirus to humans
have occurred.

other animals

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

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
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

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

SARS
MERS

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

Animal Origins
likely source.
96%
sequence
similarity
10.1101/2020.02.19.950253v1.full.pdf

Animal Origins
likely source.
96%
sequence
similarity
10.1101/2020.02.19.950253v1.full.pdf
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.

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

How Coronavirus Hijacks Your Cells
By Jonathan Corum and Carl Zimmer: https://www.nytimes.com/interactive/2020/03/11/science/how-
coronavirus-hijacks-your-cells.html
Named after the crownlike spikes that protrude from its surface
It is enveloped in a bubble of oily lipid molecules, which falls apart upon
contact with soap.

It attaches to cells in the upper respiratory system via a protein called
ACE2

It infects cells by fusing its lipid membrane with the membrane of the cell.
Once inside, it release its ssRNA genome.

The infected cell translates the RNA into protein
Viral protein
Viral RNA

As the infection progresses, the host’s cellular machinery churns out new
spikes and proteins that will form more copies of the virus
Cell nucleus

New copies of the virus are assembled and carried to the outer edges of
the cell

Each infected cell can release millions of copies of the virus before the cell
finally breaks down and dies.

How many people have been infected?
There are several sites providing live (or near live) updates
Johns Hopkins: https://www.arcgis.com/apps/opsdashboard/index.html#/
bda7594740fd40299423467b48e9ecf6
New York Times: https://www.nytimes.com/interactive/2020/world/coronavirus-
maps.html?action=click&pgtype=Article&state=default&module=styln-
coronavirus&variant=show&region=TOP_BANNER&context=storyline_menu
https://thewuhanvirus.com/

Ofﬁcial counts as of March 10th, 5:04pm EDT
Source: NY Times

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

Map: NY Times
These data (i.e. 900+ 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

How the virus was contracted
Source: NY Times March 10th 5:04pm EDT

Genomic Epidemiology
Information and ﬁgures from Trevor Bedford (https://bedford.io/blog/) and the awesome
Nextstrain project (https://nextstrain.org/ncov)
Genomic epidemiology: use of genetic sequences of pathogens to
understand patterns of transmission spread.

On average, there is a 7 day interval from one infection to the next

On average, there is a 7 day interval from one infection to the next
On average, the virus mutates ~2 times per month. This means that ~every other step in
the transmission chain will have a mutation.

Genomic technologies allow us to sequence the viral genomes
from infected individuals. We can use the sequence to reconstruct
how the infections are connected.

The big picture as of March 10th

The earliest infections (purple—left side of the tree) are from Wuhan.

All these genomes have a common ancestor in late Nov/early Dec.

All these genomes have a common ancestor in late Nov/early Dec.
Suggests the virus emerged recently in humans!

First USA Cases

First USA Cases
First USA case was called “USA/WA1/2020” from a traveller returning
from Wuhan. Sample was taken in mid-January

First USA Cases
It has an identical genome to the virus Fujian/8/2020 sampled in Fujian (SE coast
of mainland China), suggesting a close relationship.

First USA Cases
The second Washington case (USA/WA2/2020–sampled in late February) was
identical to the the first, but with three additional mutations.

First USA Cases
The second Washington case (USA/WA2/2020–sampled in late February) was
identical to the the first, but with three additional mutations.
This is exactly what is expected for a virus circulating for 5 weeks.

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

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

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

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.

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

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?

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

How is it spread?

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

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

Compare with the seasonal ﬂu
SARS-CoV-2: R0= 2.6 Flu: R0= 1.3

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

How deadly is the virus?FatalityRate
Average number of people infected by each sick person
Note the
log scale

Note the
log scale
Estimates range between 0.1% and 3%

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
Note the
log scale
Estimates range between 0.1% and 3%

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

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

How does soap help get rid of SARS-CoV-2?
Slide credit: Dr. Roland Hatzenpichler
Lipid membrane

SLS competes with lipids and
“punches holes” into the
membrane

and

It substitutes interactions of virus
proteins/membrane with
molecules on skin
Lipid membrane

Sodium lauryl sulfate (SLS, C12), the
main detergent in hand soap, is an
amphipathic (has hydrophilic and
hydrophobic part) molecule. Just like
lipids!
membrane

and

molecules on skin
Lipid membrane

Sodium lauryl sulfate (SLS, C12), the
main detergent in hand soap, is an
amphipathic (has hydrophilic and
hydrophobic part) molecule. Just like
lipids!
membrane

and

molecules on skin
Wash your hands frequently!
Lipid membrane

Really—wash your hands and stop touching your
face
Image credit: @BrodHiggins

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