2019_nCoV/SARS‐CoV‐2:

rapid classification of beta

coronaviruses and
identification of Traditional
Chinese Medicine as
potential origin of zoonotic
coronaviruses
Supervisor :- Rowida Al momani
Done by :- Esraa Hasa , Baker Kutkut
ABSTRACT
• The wide spread of the current coronavirus ( COVID-19) brought us back to define its
origin, since it is still difficult to identify its host and decoding sequence, and because
the sequences of the different types of Betacoronavirus are considered diverse.
Scientists noted that the unencrypted flanks of the viral genome can be used to separate
the four known subtypes of the beta-corona virus. Only by means of conservation,
laboratories can trace the targeted sequence of the genome in order to define the types
and subtypes of the virus. It is also demonstrated that only 253 major sourced noncoding
sequences of Sarbecovirus are enough to determine the similarities of genetic base
among the species and the sub- genomes. Investigations, conducted to understand the
origin of the corona virus, were made in China, on bats used for trade, however, as a
result, several genomes of coronavirus were obtained from bats. Furthermore, these
bats are used traditionally in China for medicine and trade purposes. However, these
bats are likely to hold high risks of zoonotic coronavirus epidemics
Significance of the study
• The significance of the study lies in the fact that the study of the
noncoding upstream and downstream flanks of coronavirus genomes
will help to determine the origin of the species of the beta
coronavirus and find about its correct sequence relationships
Introduction
• Coronavirus is similar to SARS- CoV which was found in bats.
• SARS- CoV was transmitted from bats to humans by means of an intermediate host
• MERS‐CoV was also found similar and was transmitted to human from camels, while its origin might be from
bats
• COVID-19 is another virus of the same species found to cause flue symptoms accompanies with mild acute
cough and high temperature
• Coronaviruses can be found on specific hosts or a range of hosts
• It is assumed that COVID-19 is found in bats and might have jumped to another animal which was sold alive in
the animal market in Wuhan/ China. It is assumed that Pangolin is the suspected animal
• The virus transmitted to the zero case from Wuhan city in the animal market and now it is transmitted from a
human to another
• since with the reappearance of this new class of coronaviruses, Several studies were conducted and 2019-
nCoV was found to be 96% genome-identical to a bat coronavirus; the same study revealed that said virus
belongs to the SARS-CoV15 species. Thus, it is speculated that SARS-CoV was transmitted to humans from
exotic animals in markets
General of Coronaviruses
Coronaviruses are divided into three genera:
1.  Alphacoronavirus,
2.  Betacoronavirus 
3.  Gammacoronavirus.
SARS, MERS and 2019_nCoV are members
of Betacoronavirus, which is divided into the
subgenera:
4.  Embecovirus, 
5. Hibecovirus,
6.  Merbecovirus, 
7. Nobecovirus 
8.  Sarbecovirus.
All coronaviruses have a genome consisting
of a positive‐sense single‐strand RNA
molecule.
Genome of Coronavirus
• The identification of the viral genome is important for the
international scientific community because it allows to follow the
modifications that the virus can undergo over time and in different
countries; Besides helping to understand how the virus is spreading
around the world, this type of information is useful for the
development of vaccines and diagnostic tests.
• Comparative analysis of the genome with that of other viruses allows
us to identify which mutations make SARS-CoV-2 different and which
ones resemble other viruses.
• The viral genome sequence is still unknown
Genome of the Code of Coronavirus
• Symptoms
• Considering the clinical symptoms of the patients, how do we know
when we talk about a suspicious case, a probable case or a confirmed
case of 2019-nCoV? According to the WHO: a suspected case is a
patient with severe acute respiratory infection (fever, cough, and
requiring hospital admission)
A number of drugs are being developed and tested for the novel
coronavirus
 
The US Food and Drug Administration (FDA) approved limited
emergency use for chloroquine and hydroxychloroquine as a treatment
for COVID-19.
 
RemdesivirAnebola drug that was found to be ineffective is now being
tested in two phase III randomised clinical trials in Asian countries and
it was reported that upon administeration to a coronavirus patient in
the US, appeared to have improved the clinical condition.
Favilavir, the first approved coronavirus drug in China
 
Why Covid-19 infections
?affect people differently

Age: In the US, 31-59% of

adults ages 75 to 84
diagnosed with the virus
had symptoms severe
enough to be
hospitalized, compared to
14-21% of confirmed
patients ages 20 to 44,
according to the CDC
Other medical conditions: People with conditions like heart disease, diabetes, and cancer may be more likely to have severe symptoms of Covid-19, which can lead
to a higher risk of death, than people with no underlying medical conditions. People with underlying medical conditions are also more frequently hospitalized with
the virus
- Gender: Researchers in China found that 58% of patients hospitalized with Covid-19 were male; there was a similar imbalance in patients in the US and Italy, too
- Blood type: A preliminary study conducted in China found that patients with type A blood had more severe symptoms than those with type O blood
Transmission
Respiratory transmission: it is mainly transmitted between people through
"respiratory droplets" when symptomatic people sneeze or cough This idea, that
large droplets of virus-laden mucus are the primary mode of transmission, guides
the CDC's advice to
maintain at least a 6-foot distance between you and other people

Contact transmission: it does seem to be possible however it couldn't be

ascertainedwhether the virus is contracted via a contaminated surface.

Aerosol transmission: there's no clear data whether the virus is commonly

transmitted via aerosols
Method
• The attempt to understand the nature of the virus and its
characteristics:
1- attempt to identify a DNA target
2- detect the unknown members of the Betacoronavirus,
3- identify commonality between members of the subgenera
phylogenitic analysis of upstream flank of the genome
4- The series of viruses were compared by multiple alignment of
nucleotide sequences(protein‐coding nucleotide sequences were
compared)
Comparison between genomes
Results
• lack of homologous DNA sequences based on based on 50 genome
sequences
• the phylogenetic signal and conservation was actually present in
noncoding regions of the viral genomes.
• n case of coronavirus these are mostly restricted to the 5’‐ and 3‐‘end
flanks, as all open reading frames are tightly packed
• a more extensive comparison was performed, this time with either
the 5’‐ or the 3’‐end noncoding flanks, obtained from 31 whole
genome sequences covering all subspecies of Betacoronavirus 
Variable genomes identified of  5’‐ or the 3’‐end
noncoding flanks, obtained from 31 whole
genome sequences 
 The phylogenetic trees
obtained

Both fragments could separate the

four subspecies, and an
unclassified bat isolate from
Cameroon could be identified as a
member of the Nobecovirus.
Another unclassified virus isolated
from a Nigerian bat showed high
similarity with the only other fully
sequenced member
of Hibecovirus, at least for its 5’‐
flank 
Final results
• 2019_nCoV naturally propagates in bats, but the bat species in which
the population mainly resides was unknown at the time of writing.
The food market of Wuhan may or may not have been selling bats for
food;
conclusion
• both SARS-CoV and MERS-CoV (the other two coronaviruses that have
recently caused epidemic outbreaks) jumped into the human species
through intermediary species, civets and camels, respectively, leading
to the suspicion that the same has occurred. happened at the origin
of COVID-19. That intermediary host has not yet been identified