Education

Dr. Miswar Fattah, MSi 1997 : SMAK Depkes Makassar

Makassar, 6th June 1978 2002 : Chemistry - UNHAS
2006 : Master of Science in Clinical Chemistry,
Biomedicine- UNHAS
2012 : Doctor of Medicine - UNHAS

Current position

1. Specialty & Research Laboratory Manager, Prodia Clinical Laboratory 2018- Now
2. PATELKI : Vice President 2017-Now & Member of Collegium PATELKI 2015 - Now
3. IACC: Member scientific committe, Indonesian Association for Clinical Chemistry 2013- Now
4. President of ASEAN Association of Clinical Laboratory Scientist (AACLS) 2018-2020
5. Corresponding Member Scientific Committee Asia Pacific Federation for Clinical Chemistry (APFCB)
2010 – Now
LABORATORY TESTING RELATED COVID-19

DPP PATELKI Webinar

Jakarta, 03th April 2020

Dr. Miswar Fattah, MSi

Vice Presdient PATELKI
Specialty & Research Laboratory
Prodia Clinical Laboratory
miswarfattah@gmail.com
Outline
01 Introduction: COVID-19, Structure of 2019-NCOV & Diagnosis

02 Nucleic Acid Testing related COVID-19 test

03 Antibody Testing & Other testing related COVID-19

04 Potential preanalytical & analytical

vulnerabilities in the laboratory diagnosis of COVID-19
KEY EVENTS IN THE 2019-NCOV OUTBREAK

3th march 2020

1st Case report in
Indonesia

Modiefied from Seah I et al. 2020. Eye, pp. 1–3

SEVEN COVS THAT CAN INFECT HUMAN AND CAUSE
RESPIRATORY DISEASES

HCoV- HCoV- HCoV- SARS- MERS- SARS-

HKU1
229E OC43 NL63 CoV CoV CoV2
Rabi, F.A., Al Zoubi, M.S., Kasasbeh, G.A., Salameh, D.M., Al-Nasser, A.D., 2020. Pathogens 9, 231.
NAMING VIRUS AND DISEASE

Gorbalenya AE et al. 2020. Nature Microbiology. 5(4):536–44

 9,5% 6,26%

Coronavirus COVID-19 (2019-nCoV) [WWW Document], n.d. URL https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 (accessed 4.3.20).
MAIN STRUCTURE OF CORONAVIRUSES
LABORATORY TEST FOR COVID-19
LABORATORY TESTING RELATED OUTBREAK

Patient Epidemiology
management & Control
Perspective outbreak
THE DRAMATIC IMPACT OF THE RAPID DETECTION OF INFECTIOUS DISEASES
IN CONTROLLING AND PREVENTING AN OUTBREAK

Nguyen T et al. 2020. Micromachines. 11(3):306

 PRIORITIZATION FOR TESTING SHOULD BE GIVEN TO:
the first symptomatic
individuals in a closed setting
(e.g. schools, long-term living
facilities, prisons,
symptomatic health workers 3 hospitals)
(including emergency
services and non-clinical staff) 2

1 people who are at risk of

developing severe disease and
vulnerable populations, who
will require hospitalization and
Laboratory testing strategy recommendations for COVID-19: interim guidance, 22 March 2020.
advanced care for COVID-19
https://apps.who.int
CORRESPONDENCE BETWEEN DEVELOPMENT OF VIRAL LOAD DURING SARS-
COV-2 INFECTION, CLINICAL COURSE AND POSITIVITY OF RRT-PCR ASSAYS

G. Lippi, A.-M. Simundic, M. Plebani, Clinical Chemistry and Laboratory Medicine (CCLM). 1 (2020), doi:10.1515/cclm-2020-0285.
 Unclear
Mechanism of
Disease

Different target Diagnostic tool

of Gene under develop
High potencial
False Negative
Common problem
in diagnostics new
disease outbreak
High Potencial
False Positive
Not yet Lack of
standardize standardization
method of sampel type

Unclear
Sampling,
storage,
handling sample
Protocol
 RACING TO DEVELOP COVID-19 TESTS

HE tissue Electron microscope Viral Culture NGS RT PCR, LAMP

Chemiluminoscence
Rapid Lateral Flow ELISA Spesific Antibody Protein Isolation
Autoanalyzer

“If you have a sequence today, you have a PCR tomorrow”

GLOBAL DATA SEQUENCE OF 2019-NCOV

Released Genome Sequences - 2019 Novel Coronavirus Resource. https://bigd.big.ac.cn 3th April 2020
Type of Biomarkers

Pharmaco- Monitoring
Predictive, Early Diagnosis,
genetics & Therapy &
Risk, detection & Confirmatory
susceptibility & Staging
Targeted Prognostic
Screening
Therapy
DIFFERENT TYPE OF ANALYTE LABORATORY TESTING RELATED COVID-19

RNA Host Respons

Antigen Antibody Potencial
ORFla/b Gene CBC
N Protein IgM CRP
Succebility
N Gene
E Gene S Protein IgG D Dimer ACE2 Gene
S Gene IgA SGOT HLA Gene
Albumin
LDH, etc

rRTPCR, LAMP, ELISA, Immuno- ELISA, Immuno- Enzymatic, Genotyping

chromatography, colorimetry, microarray, RTPCR,
NGS chromatography flowcytometry,
Chemiluminoscence Sanger Seq, NGS
immnoassay impedance
NUCLEIC ACID TESTING (RNA SARS CORONA 2)

Upper airway Lower airway

Other
specimens specimens
Nasopharyngeal swabs Sputum Blood

Feces
Nasal swabs Airway secretion
Urine
Nasopharyngeal Bronchoalveolar lavage
secretions fluid Conjunctival secretions

collected by a healthcare professional, If both NP and OP swabs both are collected, they should be combined in a
single tube to maximize test sensitivity and limit testing resources
SAMPLE TYPE: CDC RECOMENDATION FOR INITIAL DIAGNOSTIC
TESTING FOR COVID-19

Nasopharyngeal specimen (NP)

Oropharyngeal (OP) specimen

collected by a
healthcare
nasal mid-turbinate (NMT) swab
professional

anterior nares specimen

lower respiratory tract specimens (sputum or BAL)

If both NP and OP swabs both are collected, they should be combined in a single tube to maximize test
sensitivity and limit testing resources
SAMPLE TYPE INDONSIAN GUIDELINE

Kementerian Kesehatan Republik Indonesia. www.kemkes.go.id

Kementerian Kesehatan Republik Indonesia. www.kemkes.go.id
THE ETIOLOGICAL DIAGNOSIS OF SARS-COV-2 INFECTION IS
CURRENTLY BASED ON:

Collection of an upper Analysis of the sample by

respiratory specimen (real-time) reverse
(i.e.,nasopharyngeal AND transcription
oropharyngeal swabs) polymerase chain
reaction (rRT-PCR)
https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelinesclinical-specimens.html
Gold standard for Diagnosis COVID-19
Real-time reverse transcription polymerase
chain reaction (rRT-PCR) is the current gold
Additional confirmatory
standard for diagnosing suspected cases of screening: N gene
COVID-19

Confirmatory screening:

Gene target
RdRP gene
for Diagnosis
COVID-19
First line screening:
E gene
Institute Gene targets
China CDC, China ORF1ab and N
Institut Pasteur, Paris, France Two targets in RdRP
US CDC, USA Two targets in N gene (previusly 3)
National Institute of Infectious Pancorona and multiple targets, Spike
Diseases, Japan protein
Charité, Germany RdRP, E, N
HKU, Hong Kong SAR ORF1b-nsp14, N
National Institute of Health, Thailand N
COMPARISON WHO VS. CDC METHOD FOR RTPCR SARC CORONA 2
Jung YJ et al. 2020. Comparative analysis of primer-probe sets for the laboratory confirmation of SARS-CoV-2. Microbiology
RELATIVE POSITIONS OF AMPLICON TARGETS ON THE SARS CORONAVIRUS
AND THE 2019 NOVEL CORONAVIRUS GENOME

Corman VM et al. 2020. Euro Surveill. 25(3):

DIFFERENT TARGET GENE

Corman VM et al. 2020. Euro Surveill. 25(3):

VARIATION DYNAMICS FOR SARS COV-2 GENE
COMPARATIVE ANALYSIS OF PRIMER-PROBE SETS FOR THE
LABORATORY CONFIRMATION OF SARS CORONA 2

Jung YJ et al. 2020. Comparative analysis of primer-probe sets for the laboratory confirmation of SARS-CoV-2. Microbiology
CRITERIA FOR A CASE TO BE CONSIDERED AS LABORATORY-
CONFIRMED BY VALIDATED NAAT ASSAYS ACCORDING TO THE WHO:

IFCC Information Guide on COVID-19 - IFCC. www.ifcc.org

FAVORABLE TECHNOLOGY DETECTION RELATED SARS COV-2

• Closed System
Molecular • More Safety & Standardize
• Open system
Based testing • Easy & Faster to develop new test

• Rapid immunochromatigraphy
Immunoassay • Faster results, Easy to use
• ELISA or Chemiluminoscence
Based testing • More standardize & possible to Quantify
DIFFERENT TYPE OF ANALYTE LABORATORY TESTING RELATED COVID-19

RNA Host Respons

Antigen Antibody Potencial
ORFla/b Gene CBC
N Protein IgM CRP
Succebility
N Gene
E Gene S Protein IgG D Dimer ACE2 Gene
S Gene IgA SGOT HLA Gene
Albumin
LDH, etc

rRTPCR, LAMP, ELISA, Immuno- ELISA, Immuno- Enzymatic, Genotyping

chromatography, colorimetry, microarray, RTPCR,
NGS chromatography flowcytometry,
Chemiluminoscence Sanger Seq, NGS
immnoassay impedance
LEVELS OF IGM, IGA, AND IGG ANTIBODIES AGAINST SARS-COV-2
IN PLASMA SAMPLES AFTER SYMPTOM ONSET

L. Guo et al., Clin. Infect. Dis. (2020), doi:10.1093/cid/ciaa310.

L. Guo et al., Clin. Infect. Dis. (2020), doi:10.1093/cid/ciaa310.
ANTIBODY IGG & IGM IN SEVERE COVID-19 PATIENTS

J. Zhao et al., Clin Infect Dis, doi:10.1093/cid/ciaa344.

SEROLOGICAL TESTING FOR SARS CORONA 2
• There has been much debate regarding the current value of
serological testing in COVID-19 diagnosis and monitoring.
• Serologic based tests are not currently recommended by the CDC,
NHS or other health organizations.
• There is general concern regarding their use in the acute phase of
infection as they detect infection too late in the course of illness
(usually more than 7-10 days) and they also may cross-react
with serologic responses to seasonal coronaviruses.
• However, there is anticipated value in using improved serological
testing in the future for public and occupational health
monitoring and assessment
IFCC Information Guide on COVID-19 - IFCC. www.ifcc.org
SEROLOGICAL TESTING FOR SARS CORONA 2

• For serum antibody monitoring, according to the

“Handbook of Covid-19 Prevention and Treatment”
(Zhejiang University School of Medicine)
• Serum lgM is detectable 10 days after symptom onset
• Serum lgG is detectable 12 days after symptom onset.
• A positive interpretation has been defined as a positive
lgM, or an increased lgG titer > 4 times than that in the
acute phase.

IFCC Information Guide on COVID-19 - IFCC. www.ifcc.org

J. Zhao et al., Clin Infect Dis, doi:10.1093/cid/ciaa344.
THE POSITIVE DETECTION RATE IS SIGNIFICANTLY INCREASED
WHEN COMBINED IGM ELISA ASSAY WITH PCR

L. Guo et al., Clin. Infect. Dis. (2020), doi:10.1093/cid/ciaa310.

pdspatklin. Alur Px Rapid Test Covid-19 PDS PatKLIn. PDSPATKLIN. www.pdspatklin.or.id
 RAPID TEST
ANTIBODY
GUIDELINE

Kementerian Kesehatan Republik Indonesia. www.kemkes.go.id

RAPID TEST ANTIGENE
GUIDELINE

Kementerian Kesehatan Republik Indonesia. www.kemkes.go.id

TESTS FOR SARS–COV-2/COVID-19 AND POTENTIAL USES
Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of
Diagnostic Testing for SARS–CoV-2/COVID-19

R. Patel et al., mBio. 11 (2020), doi:10.1128/mBio.00722-20.

IFCC Information Guide on COVID-19 - IFCC. www.ifcc.org
RECOMMENDED TEST
LIST:
FREQUENT LABORATORY ABNORMALITIES IN PATIENTS WITH
COVID-19 INCLUDE:
• Lymphopenia (35-75%)
•  C reactive protein (CRP 75-93%)
•  Lactate dehydrogenase (LDH; 27-92%)
•  Erythrocyte sedimentation rate (ESR; up to 85%)
•  D-dimer (36-43%)

•  Albumin (50-98%)
•  Hemoglobin (41-50%)
MAJOR PREDICTORS OF COVID-19 SEVERITY ARE:
•  Lymphocyte count
•  Albumin

•  Neutrophil count
•  Lactate dehydrogenase (LDH)
•  Aminotransferases
•  Cardiac biomarkers (e.g., cardiac troponins)
•  D-dimer
•  Procalcitonin
•  C reactive protein (CRP)

Lippi G, Plebani M. Laboratory abnormalities in patients with COVID-2019 infection. Clin Chem Lab Med. 2020 Mar 3.
PREANALYTICAL

General
• Lack of identification/misidentification
• Inadequate procedures for specimen (e.g. swab) collection, handling,
transport

• Collection of inappropriate or inadequate material for quality or volume

Storage • Presence of interfering substances

• Manual (pipetting) errors

Specific • Sample contamination

• Testing in patients receiving antiretroviral therapy

G. Lippi, A.-M. Simundic, M. Plebani, Clinical Chemistry and Laboratory Medicine (CCLM). 1 (2020), doi:10.1515/cclm-2020-0285.
POTENTIAL PREANALYTICAL AND ANALYTICAL VULNERABILITIES IN THE
LABORATORY DIAGNOSIS OF CORONAVIRUS DISEASE 2019 (COVID-19) USING
(REAL TIME) RT-PCR.

Lack of
Testing carried out Use of non-
Active viral harmonization of
outside of the adequately
recombination primers and
diagnostic window validated assays
probes

Insufficient or Misinterpretation
Instrument Non-specific PCR
inadequate of expression
malfunctioning annealing
material profiles

G. Lippi, A.-M. Simundic, M. Plebani, Clinical Chemistry and Laboratory Medicine (CCLM). 1 (2020), doi:10.1515/cclm-2020-0285.
WHY MIGHT COVID-19 TESTS FAIL?

They may have no major There may have been a

They may be in the early
respiratory symptoms, so problem with sample
stage of the disease with
there could be little collection, meaning there
a viral load that is too
detectable virus in the was very little sample to
low to be detected.
patient’s throat and nose. test.

There may have been There may have been

poor handling and technical issues inherent
shipping of samples and in the test, e.g. virus
test materials. mutation.
CURRENT SARS-COV-2 NOMENCLATURE FOR LABORATORY
STANDARIZATION (POST ANALYTIC)
• Virus: Severe acute respiratory syndrome coronavirus 2 (SARS
coronavirus 2; SARS-CoV-2)
• Species: SARS-related coronavirus
• Disease: COVID-19 (based on Coronavirus disease 2019)

the Logical Observation Identifiers Names and Codes (LOINC) terms

for SARS-CoV-2 lab tests have SARS coronavirus 2 in
the Component because the tests are looking for the virus, not the
disease
LOINC MULTIAXIAL HIERARCHY

SARS-CoV-2/COVID-19 LOINC Meeting| March 2020

Coronavirus COVID-19
HOW TO PREVENT

` 2m

If you have fever

WASH COVER AVOID CLEAN STOP DISTANCE
or cough you should stay at your hands well and your mouth and nose touching eyes, nose, and disinfect shaking hands or yourself at least 2

home regardless of your often to avoid

contamination
with a tissue or sleeve
when coughing or
or mouth with
unwashed hands
frequently touched
objects and surfaces
hugging when saying
hello or greeting other
meters (6 feet) away
from other people,
travel or contact history. sneezing and discard
tissue
people. especially those who
might be unwell.

SYMPTOMS

FEVER COUGH SHORTNESS BREATHING

(High Temperature) OF BREATH DIFFICULTIES
 EVALUASI PEMBICARA PATELKI
www.bit.ly/kuisionerPNTP
Nama: Miswar Fattah
Judul: Laboratory testing related covid-19
Nama Acara: WEBINAR COVID-19
Penyelenggara: DPP PATELKI