MERS CoV & RESPIRATORY PCR

1. ​​Throat / nasopharyngeal swabs : Use only Dacron / rayon-tipped dry swabs with plastic shafts or flocked swabs. Send dry in the swab sheath or in a dry sterile screw-capped container. Laryngeal swabs will be rejected.
2. Sputum
3. In addition, the following specimens from invasive procedures can be taken:
   • bronchoalveolar lavage
   • endotracheal tube aspirate

These specimens are to be sent in screw-capped sterile containers without adding viral transport media.

For detection of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and multiple respiratory viruses and bacteria from individuals suspected of respiratory tract infections.

​For urgent cases, please contact the laboratory (63266920/65767620). Urgent specimens must be hand-delivered to the Academia Building, Diagnostics Tower. Normal opening hours are from 8.00am to 5.10pm on Monday to Friday and 8.00am to 1.00pm on Saturdays.

All specimens must be transported to the laboratory promptly within a few hours of collection. If a delay in transport is anticipated, specimens should also be kept cold at 4°C, and thereafter delivered within 24 hours of collection.

• Tighten collection containers properly to prevent leakage of specimen
• Laboratory forms and specimens must be completely labelled with patient's name, identification number, date of collection and type of specimen.
• Specimens should be transported in a secondary non-breakable carrier with a tight lid.

Specimen can be transported at 18-25°C to the testing laboratory if the total storage and transport time at 18-25°C does not exceed one hour. Otherwise, specimen should be stored and transported cooled (2-8°C or with ice pack) and to reach the testing laboratory within 48 hours of collection.

BioFire® FilmArray® Respiratory 2.1 plus (RP2.1plus) (BioMerieux)

​Routine: Next working day

Urgent: 3 hours (require discussion with on-call microbiologist)

​Mondays to Saturdays (Routine)

In addition to standard precautions, strict barrier precautions are required in the collection of respiratory samples from patients suspected to be infected with MERS coronavirus. This includes the use of personal protective equipment like gloves, gowns and apron, safety eyewear and powered air purifying respirators (PAPR) or N95 masks.

Note that urgent out-of-hours testing will only be done on inpatients in SGH. These must be ordered by an infectious diseases physician and discussed with Microbiologist-on-call for SGH Molecular Laboratory. Patient samples for urgent/stat testing must be from patients who meet MOH case definition of a suspect case.

Performance Characteristics:

Analytical Sensitivity (Manufacturer's claim):

Viruses

3000 IU/mL for Adenovirus (Species C, Serotype 2 - 100% confidence level)

330 copies/mL for Influenza A H1-2009 (100% confidence level)

21 copies/mL for Influenza A H3 (100% confidence level)

34 copies/mL for Influenza B (100% confidence level)

130 copies/mL for MERS-CoV (100% confidence level)

9 copies/mL for Respiratory Syncytial Virus (100% confidence level)

160 copies/mL for SARS-CoV-2 (100% confidence level)

Bacteria

41 CFU/mL for Bordetella parapertussis (IS1001 - 95% confidence level)

1000 CFU/mL for Bordetella pertussis (ptxP - 100% confidence level)

130 copies/mL for Chlamydia pneumoniae (100% confidence level)

460 copies/mL for Mycoplasma pneumoniae (100% confidence level)

Analytical Specificity (Manufacturer's claim):

No cross reactivity with Acinetobacter calcoaceticus, Bordetella avium, Bordetella bronchiseptica, Bordetella hinzii, Bordetella holmesii, Legionella bozemanii, Legionella dumoffii, Legionella feeleii, Legionella longbeacheae, Legionella micdadei, Legionella pneumophila, Chlamydia trachomatis, Corynebacterium diphtheriae, Enterobacter aerogenes, Escherichia coli, Haemophilus influenzae, Klebsiella oxytoca, Klebsiella pneumoniae, Lactobacillus acidophilus, Lactobacillus plantarum, Moraxella catarrhalis, Mycoplasma genitatlium, Mycoplasma hominis, Mycoplasma orale, Mycobacterium tuberculosis, Neisseria elongata, Neisseria gonorrhoeae, Neisseria meningitidis, Proteus mirabilis, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Staphylococcus epidermis, Stenotrophomonas maltophilia, Streptococcus pneumoniae, Streptococcus agalactiae, Streptococcus pyogenes, Streptococcus salivarius, Ureaplasma urealyticum, BAT SARS-like Coronavirus (recombinant), BAT SARS-like Coronavirus HKU5 (recombinant), Severe Acute Respiratory Syndrome Coronavirus (SARS), Bocavirus, Cytomegalovirus (CMV), Epstein-Barr Virus (EBV), Herpes Simplex Virus 1, Herpes Simplex Virus 2, Human Herpes Virus 6, Human Parechovirus, Influenza C, Measles Virus, Mumps, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus and Aspergillus flavus.

Assay limitations:

1. The Influenza A H1-2009 assay may react with H1 hemagglutinin gene sequences from viruses of swine origin. This assay will report either Influenza A H1 or Influenza A H1-2009, depending on the strain and concentration in the sample. Swine origin Hsw1N1 (A/New Jersey/8/1976 ; ATCC VR-897) was detected as either Influenza A H1 or Influenza A H1-2009 at a concentration of 8.9E+06 CEID 50/mL.

2. Performance characteristics for Influenza A were established when influenza A H1-2009 (H1N1pdm09), A H1, and A H3 were the predominant Influenza A viruses in circulation. Performance of detecting influenza A may vary if other influenza A strains are circulating or a novel influenza A virus emerges.

3. The influenza A subtyping assays target the influenza A hemagglutinin (H) gene only. The assay does not detect or differentiate the influenza A neuraminidase (N) subtypes.

4. The assay may not be able to distinguish between existing viral strains and new variants as they emerge. For example, the assay can detect Influenza A H3N2v (first recognized in August, 2011), but will not be able to distinguish this variant from Influenza A H3N2 seasonal.

5. At a sufficiently high concentration (e.g. >4.5E+07 CFU/mL of Bordetella pertussis), cross reactivity may occur between Bordetella spp. and the Human Rhinovirus/Enterovirus assays. The following results may be seen:

• B.pertussis present: reported as "Bordetella pertussis (ptxP) Detected AND "Human Rhinovirus/Enterovirus Detected"
• B.parapertussis present: reported as "Bordetella parapertussis (IS1001) Detected AND "Human Rhinovirus/Enterovirus Detected"
• B.bronchiseptica (non-IS1001-carrying strains) present: reported (falsely) as only "Human Rhinovirus/Enterovirus Detected"

6. Due to the genetic similarity between Human Rhinovirus and Enterovirus, the assay cannot reliably differentiate them– i.e. will all be reported as 'Rhinovirus/enterovirus'. A "Rhinovirus/Enterovirus" Detected result should be followed-up using an alternate method (e.g.  enterovirus PCR available in SGH Molecular Laboratory if differentiation between the viruses is required.

7. Does not differentiate between RSV A and RSV B – i.e. will all be reported as RSV.

8. Does not target Human Bocavirus.

9. We have found the assay to be less sensitive for the bacterial analytes compared to our current "Pneumonia Multiplex PCR" test and does NOT cover Legionella pneumophila. As such, our Pneumonia Multiplex PCR (which tests for Bordetella parapertussis, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasmoides pneumoniae and Legionella pneumophila) will remain available for separate order, if clinically indicated.

10. Currently does not give cycle threshold (CT) values for SARS-CoV-2.

11. Primers for both SARS-CoV-2 assays share substantial homology with the Bat coronavirus RaTG13 (accession: MN996532) and cross-reactivity with this closely-related viral sequence is predicted. In addition, the SARS-CoV-2 assay may cross-react with Pangolin coronavirus (accession: MT084071) and two other bat SARS-like coronavirus sequences (accession MG772933 and MG772934). It is unlikely that these viruses would be found in a human clinical nasopharyngeal swab; but if present, the cross-reactive product(s) produced by the assay will be detected as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

12. Some strains of B. bronchiseptica (rarely isolated from humans) do carry IS1001 insertion sequences identical to those carried by most strains of B. parapertussis. These sequences will be amplified by the IS1001 assay and reported by the assay as Bordetella parapertussis (IS1001).