Pengurusan Sample Bagi Kes Jangkitan “Middle East Respiratory

Syndrome- Coronavirus” (Mers-CoV)

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Ref:NIAID

• Background of the Virus

• Samples suitable for testing and WHO Guidelines

• Real time RT-PCR for Mers-CoV

• Main Hospitals and MKAK Sg Buloh and MKA Kota Kinabalu

Overview

Virus classification -RNA viruses

Middle East Respiratory Syndrome-Coronavirus (Mers-CoV)

First reported in June 2012, Saudi Arabia Coronaviridae Family, Genus Betacoronavirus (same as SARS-CoV). Positive sense, single stranded RNA virus About 26-32 Kb with “crown-like” feature

Transmission- Close Contact -aerosol (droplet), further investigation.

(SARS-CoV- “unique pathogenesis” as involved both upper and lower respiratory tract and gastro enteritis)

WHO Guidelines (27 June 2013)

Generally incubation period for cases of strong suspicion is less than 1 week

BUT in at least 1 case, known exposure occurred 9 to 12 days prior to onset of illness

Longer period of observation for contacts of cases

Incubation period may exceed 1 week but is less than 2 weeks

Source of Clinical Specimens

Hospitals

– Inpatients with severe Influenza

NO clinical specimens from outpatients and contacts!

Preferred Sample For Testing (WHO Guidelines, 27 June 2013)

Lower Respiratory Tract Sputum Endotracheal Aspirate Bronchoalveolar Lavage

If pt without signs and symptoms of lower respiratory tract infection and if lower respiratory tract specimen NOT Possible or Clinically Indicated

Both Nasopharyngeal and Oropharyngeal specimens should be collected

If initial testing of Nasopharyngeal swab is NEGATIVE BUT pt is Strongly Suspected of Mers-CoV, pt MUST be RE-TESTED using Lower Respiratory Tract Specimen

Others: tissue from biopsy/autopsy including lung, whole blood (in EDTA), paired serum for serology (4 weeks apart)

When to collect specimen

• As soon as possible after symptoms begin (24-72hrs)

• Best before antiviral medications are administered

Swabs

• Ideal – synthetic tip

• Specimens collected with swabs made of

calcium alginate, cotton or wooden sticks are NOT ACCEPTABLE (inhibit PCR)

Sample collection

Nasopharyngeal swab

Transport media

- Plain sterile bottles for aspirates and sputum

- VTM for swabs

- Plain tubes for paired sera

Viral Transport Media (VTM)

• Place swabs in sterile collection vials containing 1-2 ml of VTM

• Vials can be stored in a freezer at -20 oC until use

• Vials can be stored for short periods of time at 4 – 6oC

Storage and transport of specimens

• Transport to the laboratory as soon as possible

• Store specimens and transport at 4oC

• Store specimens at -70oC beyond 48 hours.

• If a -70°C freezer is not available, specimens should be kept at 4°C, preferably no longer than 4 days.

• Freezing at higher temperatures (e.g., -20°C) can reduce the likelihood of virus detection.

3 layer packaging

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2

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• Shipping clinical specimens:

- Clinical specimens should be shipped in ice (cold chain) in appropriate packaging

- All specimens should be labeled clearly and include information requested .

Transportation of Samples to Testing Facilities

Clinicians/Health care providers advised to wear appropriate PPE during sample taking from patients

All secretions should be placed in sterile bottle and ttransported on ice

All swabs must be placed in sterile tubes with sufficient VTM and transported on ice.

All samples must use “triple packaging” format with request forms before being transported to testing facilities

Issues

Laboratory Testing Methods

1. Real time RT-PCR (molecular lab)

2. Cell Culture

3. RT-PCR & Sequencing

4. Serology (paired sera 4 weeks apart)

Lower Respiratory Tract (Sputum, Endotracheal Aspirate, Bronchoalveolar Lavage)Other respiratory tract samples (Both Nasopharyngeal and oropharyngeal specimens), T/S

IMR will provide laboratory testing for these facilities until 01/08/2013

False Negative Results:

Samples NOT from Lower Respiratory Tract (request for fresh sample from lower respiratory

tract if HIGH disease suspicion index)

Poor quality of specimen/ PCR inhibition

Specimen was collected late or very early in the illness

The specimen was not handled or shipped appropriately

Quality Control of Testing during rRT-PCR

In the event of “positive results”, Samples should be referred to IMR for confirmation (sequencing)- only in INITIAL stage

IMR will provide Quality Assurance Programme for all testing facilities this year onwards for rRT-PCR Mers-CoV.

Briefing

Testing Procedures

List Of Facilities Trained To Perform rRT-PCR for Mers-CoV

1. Makmal Kesihatan Awam Kebangsaan, Sg Buloh2. Makmal Kesihatan Awam Kota Kinabalu3. Hospital Sungai Buloh4. Hospital Kuala Lumpur5. Hospital Umum Sarawak, Kuching6. Hospital Pulau Pinang7. Hospital Sultanah Aminah Johor Bahru8. Hospital Raja Permaisuri Bainun Ipoh9. Hospital HTAA, Kuantan10.Hospital Melaka11.Hospital HSNZ Kuala Trengganu12.Hospital HRPZ II Kota Bharu13.Hospital Sultanah Bahiyah Alor Setar14.Hospital Tuanku Jaafar Seremban

Tentative Start Date for Testing : 01/08/2013