ArticlePDF Available
Vol.31, No.2, December 2019 -3 -
Review Article
Introduction
Coronaviruses infect both humans and animals.
Since the 1960s, globally endemic human
coronaviruses have been identified as frequent
causes of respiratory infections such as the common
cold and responsible for all 10-20% of respiratory
tract infection in adults.
A novel coronavirus, designated 2019-nCoV, was
identied as the cause of a cluster of pneumonia cases
in Wuhan, a city in the Hubei province of China,
at the end of 2019. Epidemiologic investigation
in Wuhan identied an initial association with a
seafood market where most patients had worked or
visited.(1) On January 30, 2020, the World Health
Organization declared the outbreak a “public health
emergency of international concern” (PHEIC).
The current outbreak of this novel coronavirus
researched an unfortunate milestone record with
the death count officially exceeding that of the
SARS outbreak. As of Monday (09.02.2020), latest
data indicate this novel coronavirus has killed 910
people in about a month and a half, with 40573
cases worldwide. As number of conrmed cases
and deaths have been raising continuously, details
of the novel coronavirus in several aspects are still
not very clear. Very recently, WHO has named the
disease COVID-19, short for “coronavirus disease
2019.”
Epidemiology
Currently, it has been reported in all provinces in
China and 25 countries worldwide.
Virology
Coronaviruses are large enveloped, positive single-
stranded RNA viruses that can be divided into four
genera, namely alpha, beta, delta and gamma. A
host-derived membrane surrounds the genome,
which is encased in a helical nucleocapside. As
they are positive-sense single-stranded RNA
viruses, they do not need to carry enzymes to
initiate infection.(2) The virus genome has been
sequenced and these results in conjunction with
other reports show that it is 75-80% identical to
the SARS-CoV and even more closely related to
several bat coronaviruses.(3)
Alpha and beta coronaviruses are found in
both humans and animals. Gamma and delta
coronaviruses have only been identied in animals.
Coronaviruses are widespread among birds and
mammals, with bats being host to the largest variety
of genotypes.
Human Coronaviruses
Following four viruses have been identified as
common causes for respiratory tract diseases in
human after initial detection coronavirus in 1960.
229E (alpha coronavirus)
NL63 (alpha coronavirus)
OC43 (beta coronavirus)
HKU1 (beta coronavirus)
As a result of genetic recombination occurs between
members of the same or different coronavirus
groups, new viruses emerge from the animal
reservoirs and subsequently jump to human. There
are three new coronaviruses have been emerged as
a result of this genetic recombination up to now.
MERS-CoV (beta coronavirus) - Middle
East Respiratory Syndrome (MERS)
SARS-CoV (beta coronavirus) - severe
acute respiratory syndrome (SARS)
2019-nCoV (beta coronavirus) - 2019 novel
coronavirus acute respiratory disease
Covid-19
N. Suganthan1
1Department of Medicine, Faculty of Medicine, University of Jaffna.
Corresponding author: N Suganthan, email: drn.suganthan@yahoo.com, https://orcid.org/0000-0001-7905-6709, Invited review
article by the editorial team
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted
use, distribution and reproduction in any medium provided the original author and source are credited
DOI: http://doi.org/10.4038/jmj.v31i2.72
- 4 - Jana Medical Journal
Experience learnt from SARS and MERS
SARS
SARS was rst reported in 2003, when it emerged
in China. The illness spread by close person-to-
person contact to countries in North America,
South America, Europe, and greater Asia before
the global outbreak was contained later in 2003.
Common symptoms of SARS included fever,
cough, dyspnea, and occasionally watery diarrhea.
A viral pneumonia that rapidly progresses to
respiratory failure. Of infected patients, 20% to
30% required mechanical ventilation and 9.6%
died, with higher fatality rates in older patients and
those with medical comorbidities. 8098 individuals
were infected and 774 died. There have been no
reported cases since 2004.(4,5,6)
MERS
An acute viral respiratory tract infection caused
by the novel beta coronavirus MERS-CoV, rst
identied in Jordan and Saudi Arabia in 2012. Cases
have been limited to the Arabian Peninsula and its
surrounding countries, and to travelers from the
Middle East or their contacts. MERS shares many
clinical features with SARS such as severe atypical
pneumonia. Patients with MERS have prominent
gastrointestinal symptoms and often acute kidney
failure. November 2019, MERS-CoV has caused
a total of 2494 cases and 858 deaths, the majority
in Saudi Arabia. MERS necessitates mechanical
ventilation in 50% to 89% of patients with a case
fatality rate of 36%.(7,8,9)
Transmission and incubation period of
2019-nCoV
Coronaviruses are zoonotic and rarely, animal
coronaviruses can infect people and then spread
between people such as with MERS, SAR and now
with 2019-nCoV. Human-to-human transmission
has been confirmed and transmission from
asymptomatic individuals during the incubation
period may occur. Ro (reproduction number)
estimate is 1.4 to 2.5, meaning that every person
infected could infect between 1.4 and 2.5 people.
In comparison, measles has an RO of 12-18 and
SARS had a similar RO as the 2019-nCoV. The
viral incubation period is estimated at ~5 days
(95% condence interval, 4 to 7 days). Chinese
authorities have reported that the incubation period
may be longer (up to 14 days).(8)
Routes of transmission
It is transmitted by the direct contact with infected
secretions or large aerosol droplets.
Where did it start?
Both SARS and MERS are thought to have
originated from bats, then spread through civets
and camel respectively, to humans. Even though the
initial source of2019-nCoV is still not known, but
rst cases were linked to a seafood or wet market
in the city of Wuhan, capital of the central Hubei
province.(10)
Case denitions for surveillance
The case denitions are based on the information
currently available and might be revised as new
information accumulates. Countries may need
to adapt case denitions depending on their own
epidemiologic situation.(11)
Suspect case
A. Patient with severe acute respiratory infection
(fever, cough, and requiring admission to hospital),
AND with no other etiology that fully explains the
clinical presentation AND a
history of travel to or residence in China during the
14 days prior to symptom onset,
OR
B. Patient with any acute respiratory illness AND at
least one of the following during the 14 days prior
to symptom onset:
a. a) contact with a conrmed or probable case
of 2019-nCoV infection, or
b. b) worked in or attended a health care
facility where patients with conrmed or
probable 2019-nCoV acute respiratory
disease patients were being treated.
Probable case
Probable case: A suspect case for whom testing for
2019-nCoV is inconclusive or is tested positive
using a pan-coronavirus assay and without
laboratory evidence of other respiratory pathogens.
Conrmed case
A person with laboratory conrmation of 2019-
nCoV infection, irrespective of clinical signs and
symptoms. (11)
Vol.31, No.2, December 2019 - 5 -
Clinical features of Covid-2019
The 2019 coronavirus (2019-nCoV) infection
may be asymptomatic or may result in an acute
respiratory disease. Covid-19 may present with
mild, moderate, or severe illness; the latter includes
severe pneumonia, ARDS, sepsis and septic shock.
Early recognition of suspected patients allows
for timely initiation of infection prevention and
control. Males are more commonly aected, and
the median age range of patients is 49 to 59 years.
Nearly all reported cases have occurred in adults
(median age 59 years).
Frequently reported signs and symptoms at the
illness onset include fever (83-98%), cough (76-
82%), and myalgia or fatigue (11-44%). Less
commonly reported symptoms include sputum
production, headache, haemoptysis and diarrhea.
The fever course among the patients with 2019-
nCoV infection is not fully understood. It could be
prolonged and intermittent. There are no specic
signs or symptoms that would suggest Covid-19
compared symptoms and signs of respiratory
illnesses caused by other viruses.(12,13)
Investigations and conrmation of the diagnosis
In the FBC, lymphopenia (63%) appears as a
prominent laboratory abnormality along with
leukopenia in 9-25% , leukocytosis in 24-30% and
thrombocytopenia in 12%. Elevated transaminases
were noted in 37% of whom extreme elevations are
rare. Inammatory markers are elevated in majorly
(CRP- 68%, ESR-84%) and procalcitonin is normal
in most. Chest X-ray and CT ndings show bilateral
inltrate in 75% and unilateral involvement in 25%.
2019-nCoV is not detected by standard respiratory
viral panels. Lower respiratory specimens
likely have a higher diagnostic value than upper
respiratory tract specimens for detecting 2019-
nCoV infection. WHO recommends that lower
respiratory specimens such as sputum, endotracheal
aspirate, or bronchoalveolar lavage be collected
for 2019-nCoV testing where possible. If it is
not possible, upper respiratory tract specimens
such as a nasopharyngeal aspirate or combined
nasopharyngeal and oropharyngeal swabs should
be collected. Specimen testing is performed using
a real time reverse transcription PCR (rRT-PCR)
assay for 2019-nCoV. Turnaround time for the PCR
assay testing is about 24-48 hours.
Treatment
There is no specic anti-viral treatment
recommended. Main stay of treatment consists of
promptly implement infection control measures,
supportive care to relieve symptoms and support
organ function.
Infection prevention and control (IPC) measures is
a critical and integral part of clinical management
of patients and should be initiated at the point
of entry of the patient to hospital. Standard
precautions should always be routinely applied
in all areas of health care facilities. Standard
precautions include hand hygiene; use of PPE to
avoid direct contact with patients’ blood, body
uids, secretions (including respiratory secretions)
and non-intact skin. Standard precautions also
include prevention of needle-stick or sharps injury;
safe waste management; cleaning and disinfection
of equipment; and cleaning of the environment.
(see table 1)(14)
Table 1: IPC measures
At triage Give suspect patient a medical mask
Direct patient to separate area, an isolation room if
available
Keep at least 1meter distance between suspected patients
and other patients.
Instruct all patients to cover nose and mouth during
coughing or sneezing with tissue or flexed elbow for
others.
Perform hand hygiene after contact with respiratory
secretions
- 6 - Jana Medical Journal
Apply droplet precauons
Use a medical mask if working within 1-2 meters of the
patient.
Place patients in single rooms, or group together those
with the same etiological diagnosis.
If an etiological diagnosis is not possible, group patients
with similar clinical diagnosis and based on epidemiological
risk factors, with a spatial separation.
When providing care in close contact with a patient with
respiratory symptoms (e.g. coughing or sneezing), use eye
protection (face-mask or goggles)
Limit patient movement within the institution
Apply contact precauons
Use PPE (medical mask, eye protection, gloves and gown)
when entering room and remove PPE when leaving.
If possible, use either disposable or dedicated equipment
(e.g. stethoscopes, blood pressure cus and thermometers).
If equipment needs to be shared among patients, clean and
disinfect between each patient use.
Ensure that health care workers refrain from touching
their eyes, nose, and mouth with potentially contaminated
gloved or ungloved hands.
Avoid contaminating environmental surfaces that are not
directly related to patient care (e.g. door handles and light
switches).
Ensure adequate room ventilation. Avoid movement of
patients or transport. Perform hand hygiene.
Apply airborne precauons
during aerosol generaon
procedures
Ensure that healthcare workers performing aerosol-
generating procedures (i.e. open suctioning of respiratory
tract, intubation, bronchoscopy, cardiopulmonary
resuscitation) use PPE, including gloves, long-sleeved
gowns, eye protection, and t-tested particulate respirators
(N95 or equivalent, or higher level of protection).
Whenever possible, use adequately ventilated single
rooms when performing aerosol-generating procedures,
meaning negative pressure rooms with minimum of 12
air changes per hour or at least 160 litres/second/patient
in facilities with natural ventilation.
Avoid the presence of unnecessary individuals in the room.
Care for the patient in the same type of room after
mechanical ventilation commences.
Vol.31, No.2, December 2019 - 7 -
Provide standard supportive management for
respiratory disease and complications, including
advanced organ support if indicated.(14)
Supplementary Oxygen Therapy (target
SpO2 ≥90% in non-pregnant adults and
SpO2 ≥92-95 % in pregnant patients)
Conservative uid management
Antipyretics and /or Analgesics
Administer appropriate empiric
antimicrobials within ONE hour of
identication of sepsis
Empiric therapy includes a neuraminidase
inhibitor for treatment of inuenza when
there is local circulation or other risk factors
Other supportive care such as intubation,
mechanical ventilation, non-invasive
ventilation etc)
Close monitoring for signs of deterioration.
Do not routinely give systemic
corticosteroids for treatment of viral
pneumonia or ARDS outside of clinical
trials unless they are indicated for another
reason septic shock or other disease
processes (acute exacerbation of COPD,
etc).(13)
Managing sepsis and septic shock – follow
surviving sepsis guideline
Anti-viral drugs
Potential treatments against the novel coronavirus
include remdesivir, which was tested against
Ebola, and Kaletra, a combination of the antivirals
lopinavir and ritonavir. First case of covid-19 in
USA was treated with intravenous remdesivir with
favorable outcome.(15) However, it needs further
studies to recommend these drugs to prescribe
routinely for this condition.
Prognosis
At present, it is dicult to predict the mortality
of Covid-19 as it has been fluctuating due to
information come in. However, WHO estimated it
between 2-3%. (see table 2)
Table 2: Case fatality rate of selected viral diseases
Disease Case fatality rate
pH1N1 0.02-0.4%
Cocid-19 2-3%
SARS 10%
MERS 37%
Ebola virus 63%
Prevention
There is no vaccine available currenlty. It has begun
developing a vaccine and hope to begin a phase 1
trial within 3 months. So, spread of 2019-nCoV
infection can be controlled or reduced from person-
to-person by doing the following
Wash hands often with soap and water for at
least 20 seconds. If soap and water are not
available, use alcohol-based hand sanitizer
containing at least 60% alcohol.
Avoid touching your eyes, nose, or mouth
with unwashed hands.
Avoid close contact with people who are
sick.
Stay home when you are sick.
Cover your cough or sneeze with a tissue,
then throw the tissue in the trash.
Clean and disinfect frequently touched
objects and surfaces.(16,17)
Masks are Not Routinely Advised for public
for a healthy person, routinely wearing a mask
while out in public is unlikely to be helpful. In
addition, masks have to be changed every 20
minutes and they become moist and ineective
when worn through the day. Masks should instead
be reserved to be worn if you have symptoms of
respiratory tract infection to reduce transmission
of virus.
References
1 Report of clustering pneumonia of unknown
etiology in Wuhan City. Wuhan Municipal
Health Commission, 2019. (http://wjw
.wuhan .gov .cn/ front/ web/ showDetail/
2019123108989).
- 8 - Jana Medical Journal
2 de Wilde AH, Snijder EJ, Kikkert M, van
Hemert MJ. Host factors in coronavirus
replication. Curr Top Microbiol Immunol.
2018;419:1-42. doi:10.1007/82_2017_25
3 Zhou P, Yang X-L, Wang X-G, et al.
Discovery of a novel coronavirus associated
with the recent pneumonia outbreak in
2 humans and its potential bat origin.
bioRxiv, January 23, 2020.
4 World Health Organization. Consensus
document on the epidemiology of severe
acute respiratory syndrome(SARS).https://
www.who.int/csr/sars/en/WHOconsensus.
pdf.
5 Severe Acute Respiratory Syndrome
(SARS). Centers for Disease Control and
Prevention. https://www.cdc.gov/sars/
index.html Accessed January 31, 2020.
6 SARS Basics Factsheet. Centers for Disease
Control and Prevention. https://www.cdc.
gov/sars/about/fs-sars.html Accessed
January 31, 2020.
7 World Health Organization. Middle East
respiratory syndrome coronavirus (MERS-
CoV).https://www.who.int/en/news-room/
fact-sheets/detail/middle-east-respiratory-
syndromecoronavirus-(mers-cov).
8 World Health Organization. WHO
MERS global summary and assessment
of risk. Aug2018. https://www.who.int/
csr/disease/coronavirus_infections/risk-
assessment-august-2018.pdf.
9 Middle Eastern Respiratory Syndrome:
Interim Guidance for Health Professionals.
Centers for Disease Control. https://
www.cdc.gov/coronavirus/mers/interim-
guidance.html#evaluation Accessed
January 25, 2020.
10 World Health Organization. Novel
Coronavirus (2019-nCoV) situation
reports. https://www.who.int/emergencies/
diseases/novel-coronavirus-2019/
situation-reports.
11 Global Surveillance for human infection
with novel coronavirus (2019-nCoV):
interim guidance, 31 January 2020.
https://apps.who.int/iris/bitstream/
handle/10665/330857/WHO-2019-
nCoV-SurveillanceGuidance-2020.3-eng.
pdf?sequence=1&isAllowed=y
12 2019 Novel Coronavirus. Centers for
Disease Control and Prevention. https://
www.cdc.gov/coronavirus/2019-ncov/
index.html Accessed January 31, 2020.
13 Interim Clinical Guidance for
Management of Patients with Conrmed
2019 Novel Coronovirus (2019-nCoV)
Infection. Centers for Disease Control
and Prevention. https://www.cdc.gov/
coronavirus/2019-ncov/hcp/clinical-
guidance-management-patients.
html Accessed January 31, 2020.
14 Clinical management of severe acute
respiratory infection when novel
coronavirus (nCoV) infection is suspected
Interim guidance. January 14, 2020.
https://www.who.int/docs/default-source/
coronaviruse/clinical-management-of-
novel-cov.pdf
15 Holshue ML, DeBolt C, Lindquist S, et
al; Washington State 2019-nCoV Case
Investigation Team. First case of 2019 novel
coronavirus in the United States. N Engl
J Med. Published online January 31, 2020.
doi:10.1056/NEJMoa2001191
16 2019 Novel Coronavirus: Prevention and
Treatment. Centers for Disease Control
and Prevention. https://www.cdc.gov/
coronavirus/2019-ncov/about/prevention-
treatment.html Accessed February 2, 2020.
17 Handwashing: Clean Hands Save Lives/
How to Wash Your Hands. Centers for
Disease Control. https://www.cdc.gov/
handwashing/show-me-the-science-
handwashing.html Accessed February 2,
2020.
Chapter
The world has been put to a standstill by the COVID-19 pandemic, which has been caused by the SARS-CoV-2 (initially called 2019-nCoV) infecting agent. Moreover, this pandemic is spreading like a wildfire. Even the developed nations are running short of hospital beds and ventilators to treat the critically ill. Considering the total population of the world and the pace at which this pandemic is spreading, it not possible to hospitalize all the positive patients with intensive care facilities. In the chapter, the authors present a machine learning-based approach that will categorize the COVID-19 positive patients into five different categories, namely asymptomatic, mild, moderate, severe, and critical. The proposed system is capable of classifying the COVID-19-affected patients into five distinct categories using selected features of age, gender, ALT, hemoglobin, WBC, heart disease, hypertension, fever, muscle ache, shortness of breath with 97.5% accuracy.
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Discovery of a novel coronavirus associated with the recent pneumonia outbreak in 2 humans and its potential bat origin. bioRxiv
  • P Zhou
  • X-L Yang
  • X-G Wang
Zhou P, Yang X-L, Wang X-G, et al. Discovery of a novel coronavirus associated with the recent pneumonia outbreak in 2 humans and its potential bat origin. bioRxiv, January 23, 2020.
  • Factsheet Sars Basics
SARS Basics Factsheet. Centers for Disease Control and Prevention. https://www.cdc. gov/sars/about/fs-sars.html Accessed January 31, 2020.
Middle Eastern Respiratory Syndrome: Interim Guidance for Health Professionals
Middle Eastern Respiratory Syndrome: Interim Guidance for Health Professionals. Centers for Disease Control. https:// www.cdc.gov/coronavirus/mers/interimguidance.html#evaluation Accessed January 25, 2020.
Handwashing: Clean Hands Save Lives/ How to Wash Your Hands
Handwashing: Clean Hands Save Lives/ How to Wash Your Hands. Centers for Disease Control. https://www.cdc.gov/ handwashing/show-me-the-sciencehandwashing.html Accessed February 2, 2020.