Coronavirus disease (COVID 19): Introduction, Sample Collection

Coronavirus disease (COVID 19): Introduction, Sample Collection, Transportation, Lab Requirement for This Test and Testing Algorithm

Introduction of Coronavirus disease (COVID -19)

Coronavirus disease 2019 or COVID -19 is a viral disease and its causative agent is Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whereas the provisional name 2019 novel coronavirus (2019-nCoV). It is a positive-sense single-stranded RNA virus and strain was first discovered in Wuhan, China, so it is sometimes referred to as the “Wuhan virus” or “Wuhan coronavirus”. Classification of this virus is as-

Realm: Riboviria

Kingdom: Orthornavirae

Phylum: Pisuviricota

Order: Nidovirales

Family: Coronaviridae

Genus: Betacoronavirus

Subgenus: Sarbecovirus

Species: Severe acute respiratory syndrome-related coronavirus

Strain: Severe acute respiratory syndrome coronavirus 2

Primary reservoir bat whereas an intermediate animal reservoir such as a pangolin is also thought to be involved in its introduction to humans. The virus is primarily spread between people through close contact and via respiratory droplets produced from coughs or sneezes. It mainly enters human cells by binding to the receptor angiotensin-converting enzyme 2 (ACE2).

WHO periodically updates the Global Surveillance for human infection with coronavirus disease (COVID-19) document which includes case definitions.

Suspect Case for Coronavirus disease (COVID -19)
A patient with acute respiratory illness (fever and at least one sign/symptom of respiratory disease (e.g., cough, shortness of breath), AND with no other etiology that fully explains the clinical presentation AND a history of travel to or residence in a country/area or territory reporting local transmission (See situation report) of COVID-19 disease during the 14 days prior to symptom onset.
A patient with an acute respiratory illness AND having been in contact with a confirmed or probable COVID- 19 case (see definition of contact) in the last 14 days prior to the onset of symptoms;
A patient with a severe acute respiratory infection (fever and at least one sign/symptom of respiratory disease (e.g., cough, shortness breath) AND requiring hospitalization AND with no other etiology that fully explains the clinical presentation.

Probable Case for Coronavirus disease (COVID -19)

A suspect case for whom testing for COVID-19 is inconclusive. • Inconclusive being the result of the test reported by the laboratory

Confirmed Case of Coronavirus disease (COVID -19)

A person with laboratory confirmation of COVID-19 infection, irrespective of clinical signs and symptoms.

Sample Collection for Coronavirus disease (COVID -19)

Specimens of choice are upper Or lower respiratory specimens that Include:
nasopharyngeal or oropharyngeal aspirates or washes
nasopharyngeal or oropharyngeal swabs.
broncheoalveolar lavage
tracheal aspirates and
sputum.
Procedure of oropharyngeal swab (throat swab) collection
Ask the subject to open his or her mouth wide open.
Depress the tongue.
Swab the posterior pharynx behind the tonsils with one applicator swab stick.
Avoid the tonsils
Place the swabs immediately into sterile tubes containing 2-3 ml of viral transport media and break the applicator stick.
If a second applicator swab is available in the same packet, use it to collect nasal swabs.
Put both swab sticks in the same virus transport medium (VTM) tube.

Specimen Collection Methods

Collect specimen in virus transport medium (VTM).
Arrange for transportation in a way the sample is received within 24 hours.
Store collected specimen at 2 – 4° C (refrigerator) till ready for transportation.
NEVER STORE THE SAMPLE AT FREEZER COMPARTMENT(-20° C) as it may degrade the sample quality.

Transportation of specimen

Transport specimen in 3 layers packaging system maintaining cold chain (2-4° C). Submit specimen with appropriate form fill up issued by WHO or CDC inappropriate testing site.

Sample Packaging for Coronavirus disease (COVID -19)

Layer 1: Put VTM with the specimen in a zip lock bag.
Layer 2: Place the zip lock bag in an airtight container lined with absorbent material(cotton).
Layer-3: Place this air-tight container in an icebox/vaccine box with an ice pack in all four corners as shown above image.
Sample rejection criteria if any
The sample is transported without maintaining a cold chain.
The sample is received without proper form fill up.
Unlabeled sample.

Laboratory requirements for COVID-19 test

For biosafety practices in the laboratory, testing on clinical specimens from patients meeting the suspected case definition should be performed in appropriately equipped laboratories by staff trained in the relevant technical
and safety procedures.
National guidelines on laboratory biosafety should be followed in all circumstances.
There is still limited information on the risk posed by COVID-19, but all procedures should be undertaken based on a risk assessment.
Specimen handling for molecular testing would require BSL-2 or equivalent facilities.
Attempts to culture the virus require BSL-3 facilities at a minimum.

Testing algorithm of SARS-CoV-2

Perform specimen tests for E gene (screening) and RdRp gene (Wuhan specific). If both E gene and RdRp gene are positive, report as positive. If E gene-positive and RdRp gene negative, test for secondary confirmatory assay (N gene). If both E gene and N gene-positive, report dispatch as positive for SARS-CoV-2.Perform specimen tests for E gene (screening) and RdRp gene (Wuhan specific). If both E gene and RdRp gene are negative, report dispatch as negative for SARS-CoV-2 or novel coronavirus.

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