Page 7 - NIH Bulletin Vol. 16 December 2020

SPECIAL EDITION: BATTLING COVID-19

REAL TIME RT-PCR

Currently the gold standard for
laboratory testing of COVID-19 is
Real Time RT-PCR. This platform of
testing is available for many different
pathogens and hence was quickly
developed as the first line of testing in
many countries.

Virology Unit, Institute for Medical
Research (IMR) first developed the
assay on 11 January 2020 by designing
primers and probes based on the
availability of COVID-19 full genome
sequences available in GISAID (Global
Initiative for Sharing All Influenza Data)
database after Chinese scientists first
shared the data. By 21 January 2020, Designing DNA sequences of the primers and probes to be used in the diagnostic test for COVID-19.
the reagents to identify the virus
had arrived at the IMR laboratory.
Concurrently, University Malaya On 22 January 2020, the IMR shared with the National Public Health
Medical Centre (UMMC) shared the researchers had successfully optimised Laboratory (NPHL), which successfully
RNA extracts from a killed virus isolate the real-time RT-PCR protocol for identified the first confirmed case of
belonging to the same family as the the COVID-19. With that, IMR was the COVID-19 among close contacts. IMR
COVID-19 virus. The extract was then first laboratory in Malaysia to perform also identified the first positive case
used as a positive control for the test. testing on COVID-19. The reagent was among patients-under-investigations
(PUI) from the same cluster. With this
development, Virology Unit IMR led
the laboratory diagnosis of COVID-19.
Initially for interpretation of positive
RT-qPCR of a clinical sample, our
laboratory followed WHO guidelines
(Corman et al 2020) which was first
shared in January 2020 where a
positive RT-qPCR is determined when
a screening target (envelope gene)
and a confirmatory target (RdRp) were
detected. Moving forward to address
possibility of mutations, as per revised
WHO guidelines, our protocol now
Designing DNA sequences of the primers and probes to be used in the diagnostic test for includes two targets with at least one
COVID-19. confirmatory target.

VIRAL ISOLATION

Viral isolation is another gold standard IMR. Only trained and competent staff Generation sequencing (NGS) which
method for the diagnosis of COVID-19. are allowed to work in BSL3 laboratory can be used to identify genetic
The method involved inoculating due to the different SOP that must sequence of the virus and strains.
clinical sample into Vero E6 cells be strictly followed. These include
from suspected COVID-19 patients or correct sequence of donning and The Virology Unit receives clinical
confirmed COVID-19 patients from doffing PPE, preparations of culture samples from various clusters as well
different clusters to study molecular medium, processing and inoculation as post-mortem samples that were
epidemiology of the viruses in of clinical samples, observation on the inoculated into Vero-E6 cells. There
Malaysia. As COVID-19 is a risk group signs of cytopathic effect (CPE) which were several successful viral isolations
3 virus, all viral isolation work must be indicated virus growth and identifying stored in virus bank for further use.
carried out only in a Biosafety Level 3 and harvesting virus for subsequent
laboratory (BSL3) which is available in tests including RT-qPCR and Next

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