Novel Coronavirus (2019-nCoV)

Karakteristik dan Penyebarannya

Ida Parwati
Department of Clinical Pathology and Laboratory Medicine
Dr. Hasan Sadikin General Hospital
Faculty of Medicine Universitas Padjadjaran
BANDUNG

20200213 COVID 19_PERSI JABAR

Outline
• Epidemiology/Penyebaran novel corona virus (2019 ncoV/COVID 19)
• Relation to previous epidemiology
• Characteristic COVID 19
• Pemeriksaan di Litbangkes

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WHO

• On January 30, 2020, the International Health Regulations Emergency

Committee of the World Health Organization declared the outbreak a:

“public health emergency of international concern external icon”

(PHEIC)

an alarm it reserves for events that pose a risk to multiple countries

and which requires a coordinated international response

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LAPORAN WHO

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12 February 2020

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 COVID 19

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Karakteristik COVID 19s (2019-nCoV)
• Virus corona adalah zoonosis (ditularkan dari
hewan dan manusia)
• Merupakan virus single-strand, positive-sense
RNA, panjang genom bervariasi dari 26 to 32 kb
• Penamaan ”Novel” pada jenis virus ini karena
merupakan virus yang baru, belum diketahui
secara jelas.
• Transmisi virus melalui droplet namun diduga
dapat melalui airborne

www.thelancet.com Published online January 29, 2020 https://doi.org/10.1016/S0140-6736(20)30251-8

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Phylogenetics and taxonomy
• SARS-CoV-2 belongs to the broad family of viruses known as coronaviruses. It is a
positive-sense single-stranded RNA (+ssRNA) virus. Other coronaviruses are
capable of causing illnesses ranging from the common cold to more severe
diseases such as Middle East respiratory syndrome (MERS). It is the seventh
known coronavirus to infect people, after 229E, NL63, OC43, HKU1, MERS-CoV,
and SARS-CoV.
• Like the original SARS coronavirus, the SARS coronavirus 2 is a member of the
subgenus Sarbecovirus (Beta-CoV lineage B). Its RNA sequence is approximately
30,000 bases in length.
• By 12 January, five genomes of 2019-nCoV had been isolated from Wuhan and
reported by the Chinese Center for Disease Control and Prevention (CCDC) and
other institutions; the number of genomes increased to 81 by 11 February. A
phylogenic analysis of the samples shows they are "highly related with at most
seven mutations relative to a common ancestor", implying that the first human
infection occurred in November or December 2019.

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Klasifikasi novel Coronavirus (2019-nCoV)

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Veterian Key Chapter 62 Coronaviridae.2016
• Full-length genome sequences were obtained from five
patients at the early stage of the outbreak. They are almost identical to each
other andshare 79.5% sequence identify to SARS-CoV
• 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus.
• novel CoV uses the same cell entry receptor, ACE2, as SARS-CoV.

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COVID-19/novel Coronavirus (2019-nCoV)
• The receptor-binding domain of betacoronaviruses, which directly engages
the receptor, is commonly located in the C-terminal domain of S1, as in
SARS-CoV29 for lineage B, and MERS-CoV30,31 and BatCoV HKU4,32 for
lineage C

• Through phylogenetic analysis of the receptor-binding domain of four

different lineages of betacoronaviruses

• 2019-nCoV was closer to bat-SL-CoVZC45 and bat-SL-CoVZXC21 at the

whole-genome level, the receptor-binding domain of 2019-nCoV fell within
lineage B and was closer to that of SARS-CoV

www.thelancet.com Published
20200213 COVID online
19_PERSI JABARJanuary 29, 2020 https://doi.org/10.1016/S0140-6736(20)30251-8
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The molecular biology of coronavirus, Adv. Virus Res page (48)
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The molecular biology of coronavirus, Adv. Virus Res page (48)
https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200130-sitrep-10-ncov.pdf?sfvrsn=d0b2e480_2
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Reservoir
• Animals sold for food were originally suspected to be the reservoir or intermediary
hosts of SARS-CoV-2 because many of the first individuals found to be infected by
the virus were workers at the Huanan Seafood Market, such markets are considered
to be incubators for novel pathogens. However, some researchers have suggested
that the it may not be the original source of viral transmission to humans.
• Research into the origin of the 2003 SARS outbreak has resulted in the discovery of
many SARS-like bat coronaviruses, most originating in the Rhinolophus genus of
horseshoe bats. SARS-CoV-2 falls into this category of coronaviruses closely related
to SARS-CoV. Two genome sequences from Rhinolophus sinicus show a resemblance
of 80% to 2019-nCoV. A third virus genome from Rhinolophus affinis, "RaTG13"
collected in Yunnan province, has a 96% resemblance to 2019-nCoV.
• Researchers from Guangzhou claim to have found a "99% identical" viral genome in
a pangolin sample. Pangolins are scaled mammals protected by Chinese law, but
poaching and trading for traditional medicine remains common. As of 12 Feb 2020,
the sequence remains unavailable, and all information comes from a university
announcement. 20200213 COVID 19_PERSI JABAR
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PERBANDINGAN KARAKTERISTIK
Middle East
Wuhan coronavirus
respiratory
(2019-nCoV)
syndrome (MERS)
First reported in December
Origin 2019 in Wuhan, China.
Likely from touching or
eating an infected, as yet
Transmission unidentified animal. Human-
to-human transmission
occurs through close contact.
Around 500 confirmed; 17
deaths as of Jan. 22. Some
Cases victims were older males
with preexisting conditions.
Cases reported mainly in
Wuhan, as well as other parts Arabia. Others in about two
Current status of China and Asia. One case dozen countries, including
reported in U.S.
Severe acute Common cold
respiratory caused by
syndrome (SARS) coronavirus
Four coronavirus strains are
First reported in 2012 in First reported in 2002 in
Saudi Arabia. southern China.
thought to be responsible for
15-30% of common colds.
Often from touching infected
Believed to have spread from
camels or consuming their
bats, which infected Close contact with infected
milk or meat. Limited
transmission between
civets.Transmitted mainly humans or touching a surface
between humans through that carries the virus.
humans through close
close contact.
contact.
2,494 confirmed cases; 858 Millions each year. Generally
8,098 cases; 774 deaths.
deaths (as of Nov. 30, 2019).
Mortality rate of about 10%.
nonlethal with rare
Mortality rate of 34%. exceptions.
All cases linked to Arabian
Peninsula, with 80% in Saudi
No new cases reported since
Circulates year-round, but
2004. 87% of previous cases
more common in fall/winter.
in China and Hong Kong.
U.S. Cases and deaths have
been declining since 2016.
Cases as of Jan. 22.
20200213 COVID 19_PERSI JABAR Source: World Health Organization, U.S.CDC and Wuhan Municipal
Health Commission Credit: Daniel Wood/NPR
Pemeriksaan COVID 19 di LITBANGKES
Menggunakan 2 protokol dari:

1. US CDC: rRT-PCR
2. Cara kovensional menggunakan 2 target gen:
- Gen N (nucleocapsid)
- gen RdRp (RNA-dependent RNA polymorphism)

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 Top WHO official warns world may be
‘dangerously unprepared’ for next pandemic
as coronavirus outbreak spreads
Published Mon, Feb 3 202010:45 AM ESTUpdated Mon, Feb 3 202012:14 PM EST

NATURE EDITORIAL 11 February 2020

As coronavirus spreads, the time to think

about the next epidemic is now!

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