dr. miswar fattah, msi 1997 : smak depkes makassar th …
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Education
Current position
Dr. Miswar Fattah, MSiMakassar, 6th June 1978
1997 : SMAK Depkes Makassar 2002 : Chemistry - UNHAS
2006 : Master of Science in Clinical Chemistry, Biomedicine- UNHAS
2012 : Doctor of Medicine - UNHAS
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, MSiVice Presdient PATELKISpecialty & Research LaboratoryProdia Clinical Laboratorymiswarfattah@gmail.com
Introduction: COVID-19, Structure of 2019-NCOV & Diagnosis 01
Nucleic Acid Testing related COVID-19 test02
Antibody Testing & Other testing related COVID-1903
Potential preanalytical & analytical
vulnerabilities in the laboratory diagnosis of COVID-1904
Outline
KEY EVENTS IN THE 2019-NCOV OUTBREAK
3th march 20201st 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-229E
HCoV-OC43
HCoV-NL63
HKU1SARS-CoV
MERS-CoV
SARS-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
Coronavirus COVID-19 (2019-nCoV) [WWW Document], n.d. URL https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 (accessed 4.3.20).
9,5% 6,26%
MAIN STRUCTURE OF CORONAVIRUSES
LABORATORY TEST FOR COVID-19
LABORATORY TESTING RELATED OUTBREAK
Patient management Perspective
Epidemiology & Control 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:
people who are at risk of developing severe disease and vulnerable populations, who will require hospitalization and advanced care for COVID-19
1
2
3symptomatic health workers (including emergencyservices and non-clinical staff)
the first symptomatic individuals in a closed setting(e.g. schools, long-term living facilities, prisons,hospitals)
Laboratory testing strategy recommendations for COVID-19: interim guidance, 22 March 2020. 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.
High potencial False Negative
High Potencial False Positive
Common problem in diagnostics new disease outbreak
Unclear Mechanism of
Disease
Diagnostic tool under develop
Lack of standardization of sampel type
Unclear Sampling, storage,
handling sample Protocol
Not yet standardize
method
Different target of Gene
RACING TO DEVELOP COVID-19 TESTS
HE tissue Electron microscope Viral Culture NGS RT PCR, LAMP
Protein IsolationSpesific Antibody ELISARapid Lateral FlowChemiluminoscence
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
Predictive,
Risk,
susceptibility
Early
detection &
Screening
Diagnosis,
Confirmatory & Staging
Pharmaco-
genetics &
Targeted
Therapy
Monitoring
Therapy &
Prognostic
Type of Biomarkers
DIFFERENT TYPE OF ANALYTE LABORATORY TESTING RELATED COVID-19
RNA
ORFla/b Gene
N Gene
E Gene
S Gene
Antigen
N Protein
S Protein
Antibody
IgM
IgG
IgA
Host Respons
CBC
CRP
D Dimer
SGOT
Albumin
LDH, etc
Potencial Succebility
ACE2 Gene
HLA Gene
rRTPCR, LAMP, NGS
ELISA, Immuno-chromatography
ELISA, Immuno-chromatography,
Chemiluminoscence immnoassay
Enzymatic, colorimetry,
flowcytometry, impedance
Genotyping microarray, RTPCR,
Sanger Seq, NGS
NUCLEIC ACID TESTING (RNA SARS CORONA 2)
Upper airway specimens
Nasopharyngeal swabs
Nasal swabs
Nasopharyngeal secretions
Lower airway specimens
Sputum
Airway secretion
Bronchoalveolar lavage fluid
Other
Blood
Feces
Urine
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
nasal mid-turbinate (NMT) swab
anterior nares specimen
lower respiratory tract specimens (sputum or BAL)
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 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 ISCURRENTLY BASED ON:
Collection of an upper respiratory specimen
(i.e.,nasopharyngeal AND oropharyngeal swabs)
Analysis of the sample by (real-time) reverse
transcription polymerase chainreaction (rRT-PCR)
https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelinesclinical-specimens.html
First line screening:
E gene
Confirmatory screening:
RdRP gene
Additional confirmatory
screening: N gene
Gene target
for Diagnosis COVID-19
Real-time reverse transcription polymerase
chain reaction (rRT-PCR) is the current gold
standard for diagnosing suspected cases of
COVID-19
Gold standard for Diagnosis COVID-19
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 InfectiousDiseases, Japan
Pancorona and multiple targets, Spike 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
• More Safety & Standardize
• Open system
• Easy & Faster to develop new test
Molecular Based testing
• Rapid immunochromatigraphy
• Faster results, Easy to use
• ELISA or Chemiluminoscence
• More standardize & possible to Quantify
Immunoassay Based testing
DIFFERENT TYPE OF ANALYTE LABORATORY TESTING RELATED COVID-19
RNA
ORFla/b Gene
N Gene
E Gene
S Gene
Antigen
N Protein
S Protein
Antibody
IgM
IgG
IgA
Host Respons
CBC
CRP
D Dimer
SGOT
Albumin
LDH, etc
Potencial Succebility
ACE2 Gene
HLA Gene
rRTPCR, LAMP, NGS
ELISA, Immuno-chromatography
ELISA, Immuno-chromatography,
Chemiluminoscence immnoassay
Enzymatic, colorimetry,
flowcytometry, impedance
Genotyping microarray, RTPCR,
Sanger Seq, NGS
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
R. Patel et al., mBio. 11 (2020), doi:10.1128/mBio.00722-20.
Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19
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
• Lack of identification/misidentification
• Inadequate procedures for specimen (e.g. swab) collection, handling, transport General
• Collection of inappropriate or inadequate material for quality or volume
• Presence of interfering substances
• Manual (pipetting) errorsStorage
• Sample contamination
• Testing in patients receiving antiretroviral therapySpecificG. 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.
Testing carried out outside of the
diagnostic window
Active viral recombination
Use of non-adequately
validated assays
Lack of harmonization of
primers and probes
Instrument malfunctioning
Insufficient or inadequate
material
Non-specific PCR annealing
Misinterpretation of expression
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 be in the early stage of the disease with
a viral load that is too low to be detected.
They may have no major respiratory symptoms, so
there could be little detectable virus in the
patient’s throat and nose.
There may have been a problem with sample
collection, meaning there was very little sample to
test.
There may have been poor handling and
shipping of samples and test materials.
There may have been technical issues inherent
in the test, e.g. virus 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
` 2m
HOW TO PREVENT
SYMPTOMS
FEVER(High Temperature)
COUGH SHORTNESS OF BREATH
BREATHINGDIFFICULTIES
If you have fever
or cough you should stay at
home regardless of your
travel or contact history.
WASHyour hands well and often to avoid contamination
COVERyour mouth and nose with a tissue or sleeve when coughing or sneezing and discard tissue
AVOIDtouching eyes, nose, or mouth with unwashed hands
CLEANand disinfect frequently touched objects and surfaces
STOP shaking hands or hugging when saying hello or greeting other people.
DISTANCE yourself at least 2 meters (6 feet) away from other people, especially those who might be unwell.
Coronavirus COVID-19
EVALUASI PEMBICARA PATELKI
www.bit.ly/kuisionerPNTPNama: Miswar Fattah
Judul: Laboratory testing related covid-19
Nama Acara: WEBINAR COVID-19
Penyelenggara: DPP PATELKI
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