Dr. Miswar Fattah, MSi 1997 : SMAK Depkes Makassar th …

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 [email protected]

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


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.


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


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.


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


pdspatklin. Alur Px Rapid Test Covid-19 PDS PatKLIn. PDSPATKLIN. www.pdspatklin.or.id

RAPID TEST ANTIBODY GUIDELINE


RAPID TEST ANTIGENE GUIDELINE


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


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

Documents

Dr. Miswar Fattah, MSi 1997 : SMAK Depkes Makassar th …