Novel Coronavirus Preparedness and Response Plan- fbg-2

Title
Collection, Receiving, Processing and Transport of Specimens Containing Risk Group 3 Organisms
Including COVID-19
Intended Use
This SOP was developed to guide laboratory users and personnel on the steps required for
collecting, processing, packaging and transporting of specimens containing risk group 3 organisms,
including COVID-19, to be investigated.
Introduction
From time to time there have been global outbreaks of risk group 3 organisms such as
Chikungunya, West Nile Virus and Coronaviruses. A new strain of coronavirus was detected on
January 2020, after several persons were identified with an unusual type of pneumonia.
Coronaviruses (CoV), so named for their “crown-like” appearance, are a large family of viruses, the
Coronaviridae family, genus Betacoronavirus. Coronaviruses are enveloped single stranded,
positive sense RNA virus. The Coronaviruses have the longest genome of the RNA viruses. The
novel Coronavirus is closely associated with two other respiratory coronaviruses, the Severe Acute
Respiratory Syndrome (SARS - CoV) in 2003 and Middle East Respiratory Syndrome (MERS- CoV)
in 2012. Researchers have now confirmed that though the original source of the virus has not been
identified, transmission of the virus occurs from person to person through respiratory droplets.
Infections are purported to spread during the incubation or in asymptomatic patients. Persons may
have mild illness, but the illness may progress to severe acute respiratory distress syndrome and
even death. Diagnosis of this infection is based on the detection of viral RNA in clinical specimens,
namely respiratory samples, thus real time RT PCR is the method of choice. There are no test
methods available at present at PMH and therefore, specimens need to be transported to a
reference lab, either locally, regionally or to the United States for confirmation. The specimen
collection, processing and transport procedures herein should be strictly followed when handling
these types of organisms.
Collection of Specimens For COVID-19
Clinical specimens should be collected from any patient under investigation for COVID-19 as
defined by the WHO surveillance reference, 2020. Rapid collection and testing is a priority and
although testing of other respiratory viruses will be included in the initial workup.
Appropriate Specimen Types
The main specimen required for the initial workup listed in order of priority:
a. Lower Respiratory specimens including: bronchoalveolar lavage, tracheal aspirates, and
sputum
b. Upper Respiratory Tract specimens - nasopharyngeal or oropharyngeal aspirates or
washes, nasopharyngeal or oropharyngeal swabs
o Swab specimens should be collected only on swabs with a synthetic tip (such as
polyester or Dacron®) with aluminium or plastic shafts. Swabs with calcium
alginate or cotton tips with wooden shafts are not acceptable.
c. Serum (red top tube or serum separator tube)
d. Urine may also be collected (sterile urine collection cup
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