novel coronavirus infection

8/12/2019 Novel Coronavirus Infection

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سو هصو هل



Dr.AL ANOUD ABDULLAH AL-JIFRI

Chairman of Infection & Prevention Department

Infectious Diseases ConsultantKFH, Madinah , MOH



What is coronavirus.

Diseases of coronavirus.

Mode of transmission.

Clinical presentation.

IPC strategies.

Management.



CDC continues to work closely with the WHO and other partnersto better understand the public health risk presented by recently

reported cases of infection with a novel coronavirus (nCoV).

As of May 16, 2013, 40 laboratory-confirmed cases have been

reported to WHO :

30 from Saudi Arabia,

2 from Qatar,

2 from Jordan,

3 from the United Kingdom,

one from the United Arab Emirates,

and 2 from France.

Among the 40 cases, 20 were fatal.



Baltimore classification is a classification system that places viruses into one of

seven groups depending on a combination of their nucleicacid (DNA or RNA), strandedness (single-stranded or

double-stranded), Sense, and method of replication.

Named after David Baltimore, a Nobel Prize-winning biologist

http://en.wikipedia.org/wiki/File:DavidBaltimore2008.JPG



Virus Family Examples (common names)

AdenoviridaeAdenovirus, Infectious canine hepatitis

virus

Papovaviridae Papillomavirus, Polyomaviridae,

Parvoviridae Parvovirus B19, Canine parvovirus

Herpesviridae

Herpes simplex virus, varicella-zoster

virus, cytomegalovirus, Epstein-Barr

virus

Poxviridae

Smallpox virus, cow pox virus, sheep pox

virus, orf virus, monkey pox virus,

vaccinia virus

Hepadnaviridae Hepatitis B virus




Reoviridae Reovirus, Rotavirus

Picornaviridae

Enterovirus, Rhinovirus, Hepatovirus,

Cardiovirus, Aphthovirus, Poliovirus,

Parechovirus, Erbovirus, Kobuvirus, Teschovirus,

Coxsackie

Caliciviridae Norwalk virus

Togaviridae Rubella virus, alphavirus

Arenaviridae Lymphocytic choriomeningitis virus

FlaviviridaeDengue virus, Hepatitis C virus, Yellow fever

virus

OrthomyxoviridaeInfluenzavirus A, Influenzavirus B,

Influenzavirus C, Isavirus, Thogotovirus




Paramyxoviridae

Measles virus, Mumps virus, Respiratory

syncytial virus, Rinderpest virus, Canine

distemper virus

Bunyaviridae California encephalitis virus, Hantavirus

Rhabdoviridae Rabies virus

Filoviridae Ebola virus, Marburg virus

Coronaviridae Corona virusAstroviridae Astrovirus

Bornaviridae Borna disease virus

Arteriviridae Arterivirus, Equine Arteritis Virus

Hepeviridae Hepatitis E virus



Are species in the genera of virus belonging to the

subfamily Coronavirinae in the family

Coronaviridae.

The name "coronavirus" is derived from the Latin

corona, meaning crown or halo, and refers to the

characteristic appearance of virions under electron

microscopy (E.M.) with a fringe of large, bulbous

surface projections creating an image

reminiscent of the solar corona.



Human coronaviruses were first identified

in the mid 1960s.



Coronaviruses primarily infect the upper

respiratory and gastrointestinal tract of

mammals and birds. In chickens, the Infectious bronchitis virus (IBV), a

coronavirus, targets not only the respiratory tract

but also the uro-genital tract.

The virus can spread to different organs throughout

the chicken.



4-5 different currently known strains of coronaviruses

infect humans.

The most publicized human coronavirus, SARS-CoV

which causes SARS, has a unique pathogenesis because it

causes both upper and lower respiratory tract infections

and can also cause gastroenteritis.



The five coronaviruses that can infect people are:

alpha coronaviruses 229E and NL63

beta coronaviruses OC43, HKU1,SARS-CoV (thecoronavirus that causes severe acute respiratory

syndrome).



Genus: Alphacoronavirus; type species: Alphacoronavirus 1

Species: Alpaca coronavirus, Alphacoronavirus 1, Human coronavirus

229E , Human Coronavirus NL63, Miniopterus Bat coronavirus 1,Miniopterus Bat coronavirus HKU8, Porcine epidemic diarrhea virus,

Rhinolophus Bat coronavirus HKU2, Scotophilus Bat coronavirus 512 Genus Betacoronavirus; type species: Murine coronavirus

Species: Betacoronavirus 1, Human coronavirus HKU1, Murine

coronavirus, Pipistrellus Bat coronavirus HKU5, Rousettus Bat

coronavirus HKU9, Severe acute respiratory syndrome-related

coronavirus, Tylonycteris Bat coronavirus HKU4, hCoV-EMC Genus Deltacoronavirus; type species: Bulbul coronavirus HKU11

Species: Bulbul coronavirus HKU11, Munia coronavirus HKU13, Thrush

coronavirus HKU12 Genus Gammacoronavirus; type species: Avian coronavirus

Species: Avian coronavirus, Beluga whale coronavirus SW1



Coronaviruses cause colds in humans primarily in

the winter and early spring seasons.

In the United States, people usually get infectedwith human coronaviruses in the fall and winter .



Most people will get infected with human

coronaviruses in their life time.

Young children are most likely to get

infected.

However, anybody can have multiple

infections in life time , and typically lead to

the common cold in adults and children.



What is the new human coronavirus?

The new virus strain is the human beta-coronavirus

EMC (HCoV-EMC)

It is different from other coronaviruses that have

been found in people before.

This particular novel coronavirus is rare but causes

serious illness, including death.



The virus may have

originated in an animal,

such as bats, but thatinvestigation is still

ongoing.

CDC is still learning

about this new virus.

http://www.google.ca/url?sa=i&rct=j&q=coronavirus&source=images&cd=&cad=rja&docid=UTUIQ7aU5qcIRM&tbnid=CI9rcTQYbCY6wM:&ved=0CAUQjRw&url=http://www.nature.com/nature/journal/v495/n7440/fig_tab/495176a_F1.html&ei=3wSZUcf2N8OfO_P9gfAI&bvm=bv.46751780,d.ZWU&psig=AFQjCNEq2ligTEiCouXK9XNTLB-aIglUgw&ust=1369068663142819

http://www.google.ca/url?sa=i&rct=j&q=coronavirus&source=images&cd=&cad=rja&docid=UTUIQ7aU5qcIRM&tbnid=CI9rcTQYbCY6wM:&ved=0CAUQjRw&url=http://www.nature.com/nature/journal/v495/n7440/fig_tab/495176a_F1.html&ei=3wSZUcf2N8OfO_P9gfAI&bvm=bv.46751780,d.ZWU&psig=AFQjCNEq2ligTEiCouXK9XNTLB-aIglUgw&ust=1369068663142819



This novel coronavirus is from the same large

family of viruses that includes the SARS virus.

Both viruses are capable of causing severe disease. However, one of the key differences between the

two is that this novel coronavirus doesn’t seem

to get passed from person to person easily, whilethe SARS virus did.



SARS CORONAVIRUS

NCOV

Group: Group IV ((+)ssRNA)

Order: Nidovirales

Family: Coronaviridae

Genus: Coronavirus

Species: SARS coronavirus

Group: Group IV ((+)ssRNA)

Order: Nidovirales

Family: Coronaviridae

Subfamily: Coronavirinae

Genera

• Alphacoronavirus •Betacoronavirus •Deltacoronavirus

•Gammacoronavirus



• The ways that human coronaviruses spread have

not been studied very much, except for SARS.

• However, it is likely that human coronaviruses

spread from an infected person to others through:

The air by coughing and sneezing

Close personal contact, such as touching or

shaking hands.



These viruses may also spread by touching

contaminated objects or surfaces then

touching mouth, nose, or eyes.



• Human coronaviruses usually cause mild

to moderate upper-respiratory tract

illnesses of short duration.

• Symptoms may include runny nose,

cough, sore throat, and fever.



• These viruses can sometimes

cause lower-respiratory tract

illnesses, such as pneumonia.

• This is more common in peoplewith cardiopulmonary disease

or compromised immune

systems, or the elderly. • (Sudden ,severe, acute

respiratory illness )



Pneumonia has been the most common

clinical presentation.

5 patients developed Acute Respiratory

Distress Syndrome (ARDS).

Renal failure, pericarditis and disseminated

intravascular coagulation (DIC) have also

occurred.



clinical syndromes include :

Severe pneumonia

Acute Respiratory Distress Syndrome

Sepsis

Severe sepsis

Septic shock



Probable Case

• A person fitting the definition above of a “Patient Under Investigation”,

with clinical, radiological, or histopathological evidence of pulmonary

parenchymal disease (e.g. pneumonia or the Acute Respiratory Distress

Syndrome, ARDS) but no possibility of laboratory confirmation either

because the patient or samples are not available or no testing is available

for other respiratory infections;

AND

• Close contact with a laboratory-confirmed case;AND

• Not already explained by any other infection or aetiology, including all

clinically indicated tests for community-acquired pneumonia according to

local management guidelines.



Confirmed Case

• A person with laboratory confirmation of infection

with the novel coronavirus.



Close contact includes:

Anyone who provided care for the patient,

including a health care worker or family member,

or who had other similarly close physical contact.

Anyone who stayed at the same place (e.g. lived

with, visited) as a probable or confirmed case

while the case was symptomatic.



In general, SARS begins with high fever (temperature

>100.4°F [>38.0°C]).

other symptoms may include :headache, an overall feeling

of discomfort ,and body aches.

Some people also have mild respiratory symptoms at the

onset.

About 10-20% of patients have diarreah.

After 2-7 days SARS patient may develop a dry cough.

Most patients develope pnemonia.



Preventing or limiting infection transmission in

health-care settings requires the application of

procedures and protocols referred to as “controls”. Include the following:

A. Administrative controls.

B. Environmental and engineering controls.

C. Personal protective equipment (PPE).



These are the first priority of IPC strategies.

They provide the infrastructure of policies and

procedures to prevent, detect, and control infectionsduring health care.

To be effective, IPC measures must anticipate

the flow of patients from the first point ofencounter until discharge from the facility.



Includes:

1) Establishment of sustainable IPC

infrastructures and activities.

2) Education of HCWs.

3) Prevention of overcrowding in waiting

areas, providing dedicated waiting areas for

the ill and placement of hospitalized

patients.



8) Rapid identification of patients with

ARI and patients suspected of nCoV

infection, with prompt application of

appropriate precautions, and

implementation of source control.▪ Clinical triage should be used for early

identification of all patients with ARIs.



Identified ARI patients should be placed in an area

separate from other patients, and additional IPC

precautions has to be promptly implemented. Clinical and epidemiological aspects of the cases

should be evaluated as soon as possible.

The investigation should be complemented bylaboratory evaluation.



These include :

basic health-care facility infrastructures.

1. Ensuring adequate environmental ventilation in all

areas within a health-care facility

2. Adequate environmental cleaning.

Spatial (locative) separation of at least 1 m should be

maintained between each ARI patient and others,

including HCWs (when not using PPE).

Both controls can help reduce the spread of some

pathogens during health care



Consistent use of available PPE and

appropriate hand hygiene help reduce the

spread of infection.



1 . Standard Precautions:

A cornerstone for providing safe health care and

reducing the risk of further infection.

Most transmissions occur in the absence of basic IPC

precautions and before a specific infection is suspected or

confirmed; hence, the routine application of measures to

prevent spread of acute respiratory infections (ARI) when

caring for symptomatic patients is essential to reduce

spread of any ARI in health-care settings.



Include :

Hand hygiene.

Use of PPE to avoid direct contact with patients’

blood, body fluids, secretions (including respiratory

secretions) and non-intact skin.

PPE should include the use of:

• facial protection by means of either a medical mask

and eye-visor or goggles, or a face shield;

&

• a gown and clean gloves.



Cleaning and

disinfection of the

environment (due to the

detection of SARS CoV

RNA by PCR on

surfaces in rooms

occupied by SARS

patients).



Prevention of needle-stick or sharps injury.

Safe waste management.

Cleaning, disinfection and, where applicable,

sterilization of patient-care equipment and

linen.



There are

currently no

vaccinesavailable to

protect you

against humancoronavirus

infection.



All individuals, including visitors and HCWs, in

contact with patients with ARI should:

1. Perform hand hygiene before and after contact withthe patient and his or her surroundings and

immediately after removal of a medical mask.

2. Wear a medical mask when in close contact (i.e.

within approximately 1 m) and upon entering the

room or cubicle of the patient. (Droplet precautions)



3. Wear eye protection (i.e. goggles or a face

shield)

4. Wear a clean, non-sterile, long-sleeved

gown; and gloves (some procedures may

require sterile gloves)



If any HCW have an illness caused by?

human coronaviruses, he/she can help

protect others by:

Staying home while they are sick.

Avoiding close contact with others.

Covering mouth and nose when coughing or

sneezing.



Limit the number of HCWs, family

members and visitors in contact with a

patient with probable or confirmed nCoV

infection. Family members and visitors in contact

with a patient should be limited to those

essential for patient support and should be

trained on the risk of transmission and on

the use of the same infection control

precautions as HCWs who are providing

routine care.



All individuals, including visitors and HCWs hasto:

1. Perform hand hygiene before and after contact

with the patient and his or her surroundings andimmediately after removal of PPE.

2. Wear a medical mask .

3. Wear eye protection (i.e. goggles or a face

shield).4. Wear a clean, non-sterile, long-sleeved gown;

and gloves (some procedures may require sterile

gloves).



Use either disposable equipment or dedicated

equipment (e.g. stethoscopes, blood pressure cuffs

and thermometers).If equipment needs to be shared among patients,

clean and disinfect it between each patient use.

HCWs should refrain from touching their eyes,nose or mouth with potentially contaminated

gloved or ungloved hands.



Place patients with probable or confirmed nCoV infectionin adequately ventilated single rooms or Airborne

Precaution rooms.

if possible, situate the rooms used for isolation (i.e.

single rooms) in an area that is clearly segregated from

other patient-care areas.

When single rooms are not available, put patients with the

same diagnosis together.

If this is not possible, place patient beds at least 1 m

a art.



For patients with probable or confirmed nCoV infection:

a) Avoid the movement and transport of patients out of the

isolation room or area unless medically necessary.

b) Use designated portable X-ray equipment and other

important diagnostic equipment.

c) If transport is required, use routes of transport that minimize

exposures of staff, other patients and visitors.

d) Notify the receiving area of the patient's diagnosis and

necessary precautions as soon as possible before the patient’s

arrival.

!!!!!!!



aerosol-generating procedures are

Any medical procedure (tracheal intubation ,

tracheotomy, non-invasive ventilation and manualventilation,bronchoscopy) that can induce the

production of aerosols of various sizes, including

small (< 5 mkm) particles.



f) Has to done in a negative pressure room

g) Perform procedures in an adequately ventilated room; i.e.

minimum of 6 to 12 air changes per hour in facilities

with a mechanically ventilated room and at least 60

liters/second/patient in facilities with natural ventilation

h)limit the number of persons present in the room to theabsolute minimum required for the patient’s care and

support



The duration of infectivity for nCoV infection is

unknown.

Isolation precautions should be used during theduration of symptomatic illness and continued for

24 hours after the resolution of symptoms.

Patient information (e.g. age, immune status andmedication) should also be considered in situations

where there is concern that a patient may be

shedding the virus for a prolonged period.



All specimens should be regarded as

potentially infectious

HCWs who collect or transport clinical specimens

should adhere rigorously to Standard Precautions to

minimize the possibility of exposure to pathogens.



1. Wear appropriate PPE

2. Trained in safe handling practices and spill

decontamination procedures.

3. Place specimens for transport in leak-proof specimen bags(secondary container) that have a separate sealable pocket for

the specimen (i.e. a plastic biohazard specimen bag), with the

patient’s label on the specimen container (primary container),and a clearly written request form.



4. Ensure that health-care facility laboratories adhere toappropriate biosafety practices and transport requirements.

5. Deliver all specimens by hand whenever possible.

6. Do not use pneumatic-tube systems

to transport specimens.

7. State the name of the (suspected) ARI of potential

concern clearly on the accompanying request form.

Notify the laboratory as soon as possible that the

specimen is being transported.



• Laboratory tests can be done to confirm infectionsecondary to human coronaviruses.

• Specific laboratory tests may include:

a) Virus isolation in cell culture.

b) Polymerase chain reaction (PCR) assays that are

more practical and available commercially.

c) Serological testing for antibodies to human

coronaviruses.• Nose and throat swabs are the best specimens for detecting

common human coronaviruses.

• Serological testing requires collection of blood specimens.



Specimen Type and Priority

• To increase the likelihood of detecting infection,

it is recommended to collect multiple specimensfrom different sites at different times after

symptom onset, if possible.

• As of November 27, 2012, consider lower

respiratory tract and stool specimens a priority

for collection and testing.



• For short periods (≤ 72 hours), most specimens should be

held at 2-8oC rather than frozen

• For delays exceeding 72 hrs, freeze specimens at -70oC

as soon as possible after collection (with exceptions noted

below).

• Label each specimen container with the patient’s ID

number, specimen type and the date the sample was

collected.



A.

Lower respiratory tract: • Broncheoalveolar lavage, tracheal aspirate, pleural fluid

• Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection

cup or sterile dry container.

• Refrigerate specimen at 2-8oC up to 72 hrs; if exceeding 72 hrs, freezeat -70oC and ship on dry ice.

• Sputum

• Have the patient rinse the mouth with water and then expectorate

deep cough sputum directly into a sterile, leak-proof, screw-capsputum collection cup or sterile dry container.

• Refrigerate specimen at 2-8oC up to 72 hrs; if exceeding 72 hrs, freeze

at -70oC and ship on dry ice.



Nasal Aspirates

Collect 2-3 mL into a sterile, leak-proof, screw-cap

sputum collection cup or sterile dry container.

Refrigerate specimen at 2-8oC up to 72 hrs; if exceeding

72 hrs, freeze at -70oC and ship on dry ice.



Serum

• For eventual serum antibody testing: Serum specimens should be collected

during the acute stage of the disease, preferably during the first week after

onset of illness, and again during convalescence, ≥ 3 weeks later.•

Children and adults

• Collect 1 tube (5-10 mL) of whole blood in a serum separator tube. Allow the

blood to clot, centrifuge briefly, and separate sera into sterile tube container.

The minimum amount of serum required for testing is 200 μL. Refrigeratespecimen at 2-8oC and ship on ice- pack; freezing and shipment on dry ice is

permissible.• Infants

• A minimum of 1 cc of whole blood is needed for testing of pediatric patients.

If possible, collect 1 cc in an EDTA tube and in a serum separator tube. If only

1cc can be obtained, use a serum separator tube.



EDTA blood (plasma)

Collect 1 tube (10 mL) of heparinized (green-top) or

EDTA (purple-top) blood.

Refrigerate specimen at 2-8oC and ship on ice-pack; do

not freeze.



Collect 2-5 grams of stool specimen (formed

or liquid) in sterile, leak-proof, screw-cap

sputum collection cup or sterile dry container. Refrigerate specimen at 2-8oC up to 72 hrs; if

exceeding 72 hrs, freeze at -70oC and ship on

dry ice.



Respiratory

Specimens

Test for other

respiratory pathogens

If POSITIVE for other

respiratory pathogens:

1.Testing for novel CoVmay not be required

2.Contact CDC for

consultation

If NEGATIVE for other respiratory

pathogens:

1.Prepare multiple sample aliquots

(≥200 μL) for retention at -70°C andshipping to CDC

2.Notify your local/state health

department and CDC

3.Contact CDC for approval to send

specimen aliquot for novel CoV



• Respiratory pathogens to be considered for testing by molecular

or antigen detection methods (not by viral culture) include:

• 1) influenza A, influenza B, respiratory syncytial virus,

human metapneumovirus, human parainfluenza viruses,

adenovirus, human rhinovirus and other respiratory viruses.

• 2) Streptococcus pneumoniae, Legionella pneumophila, and

other pathogens that cause severe lower respiratory infections.



Routine confirmation of cases of novel

coronavirus infection will be based on

detection of unique sequences of viral RNAby real-time reverse-transcriptase

polymerase chain reaction (RT-PCR) and

sequencing.



To consider a case as laboratory-confirmed, one of

the following conditions must be met:

Positive PCR assays for at least two differentspecific targets on the novel coronavirus genome

OR

One positive PCR assay for a specific target onthe novel coronavirus genome and an additional

different PCR product sequenced, confirming

identity to known sequences of the new virus

INTERPRETATION OF LABORATORY RESULTS



A positive PCR assay for a single specific target

without further testing is considered presumptive

evidence of novel coronavirus infection.

INTERPRETATION OF LABORATORY RESULTS



No virus-specific prevention or treatment (e.g. vaccine

or antiviral drugs) is available.

Only supportive management of patients who have acute

respiratory failure and septic shock as a consequence of

severe infection.

Because other complications have been seen (renal

failure, pericarditis, DIC) clinicians should monitor for

the development of these and other complications of

severe infection and treat them according to local

management guidelines.



Section 1 focuses on the early recognition and management of

patients with SARI and includes early initiation of supportive

and infection prevention and control measures, and therapeutics.

Section 2 focuses on management of patients who deteriorate and develop severe respiratory distress and ARDS.

Section 3 focuses on the management of patients who

deteriorate and develop septic shock .

Section 4 focuses on ongoing care of the critically ill patient

and best practices to prevent complications.



Yes.

WHO and CDC have not issued travel health

warnings for any country related to novelcoronavirus.

novel coronavirus infection

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