Guidance

Desktop Validation Report for Q-POC

Updated 18 February 2022

1. Assay description and intended purpose (from the IFU)

IFU Q2700 June (draft)

Q-POC™ is a portable and battery-operated molecular diagnostic system which offers sample to answer analysis within 30 minutes (one sample in 30 minutes per machine).

The SARS-CoV-2 assay is intended for the qualitative detection of nucleic acid from the SARS-CoV-2 viral RNA in nasopharyngeal swabs from individuals who are suspected of coronavirus (COVID-19) by their healthcare provider.

Of the MSwab UTM sample, 400ul is loaded onto the disposable microfluidic cassette using a fixed volume pipette (provided) and the cap attached. This creates a fully enclosed device, with no air venting, preventing the generation of amplicon contamination. The disposable is put into the Q-POC™, the patient details added, and test started. The device automatically performs the assay.

Sample prep: Rapid lysis is performed via a heat conditioning step on the cassette. The lysate rehydrates lyophilized PCR reagents, and 3 loci of the SARS-CoV-2 genome are amplified by RT-PCR using a shuttle-flow PCR method, where the PCR reaction mix is oscillated between static heat blocks at 2 distinct temperatures. Microfluidics cycle the sample over these heat blocks, for rapid ramping.

Assay detects Orf1, N, S and human gene RnaseP. DNA detection: Sensitive in-line optics observe the generation of fluorescence as the target region is amplified providing a qPCR read-out, for sample to qPCR result.

1.1 Results are for the identification of SARS-CoV-2 RNA

Positive results are indicative of the presence of SARS-CoV-2 RNA; clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status.

Negative results should be treated as presumptive and, if inconsistent with clinical signs and symptoms or necessary for patient management, should be tested with different authorised or cleared molecular tests. Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions.

Negative results should be considered in the context of a patient’s recent exposures, history and the presence of clinical signs and symptoms consistent with COVID-19.

This test is intended for use by medical professionals or trained operators who are proficient in performing tests using the Q-POC™ instrument.

1.2 The assay is a standalone test for use on the Q-POC™ instrument

1.3 There is no viral inactivation report for this assay, and the manufacture makes no claim for viral inactivation

Due to the initial pipetting step loading the Q-POC™ test cassette should be performed in a biological safety cabinet (BSL II).

2. Type of sample to be used in validation

Copan Nasopharyngeal swabs in Copan MSwab were prospectively collected for dual testing via Q-POC™ SARS-CoV-2 assay and the comparator qPCR assay.

Inclusion criteria:

• participants who are suspected of having COVID-19
• nasopharyngeal swab sample collection

TVG followed the IFU for samples collection: Copan Nasopharyngeal swab is the validated swab for use. To collect a nasopharyngeal swab sample, carefully insert the swab into the nostril exhibiting the most visible drainage, or the nostril that is most congested if drainage is not visible. Pass the swab directly backwards without tipping the swab head up or down.

The nasal passage runs parallel to the floor, not parallel to the bridge of the nose. Using gentle rotation, insert the swab into the anterior nare parallel to the palate advancing the swab into the nasopharynx, leave in place for a few seconds, and then slowly rotate the swab as it is being withdrawn.

To ensure proper collection, the swab should be passed a distance that is halfway of that from the nose to the tip of the ear. This is about half the length of the swab.

Do not use force while inserting the swab.

The swab should travel smoothly with minimal resistance; if resistance is encountered, withdraw the swab a little bit without taking it out of the nostril. Then elevate the back of the swab and move it forward into the nasopharynx.

3. Equipment and reagents

3.1 List all the equipment required that is or is not supplied by the manufacturer

Product components supplied:

• Q-POC™ cartridges (require storage at room temperature)
• fixed pipette for delivery of 400μL; provided with the QuantuMDx Q-POC™ Starter
• Copan MSwab® medium + flexible FLOQswab (catalogue number – 6E013N)
• package insert
• quick reference instructions

Product components required but not supplied:

• biological safety cabinet (BSL II)
• QuantuMDx Q-POC™ instrument
• disposable, powder-free gloves (latex or nitrile)
• biohazard bag for tips and tube disposal
• 10% (v/v) freshly made from household bleach solution (0.5% w/v sodium hypochlorite in water)
• 70% ethanol (freshly made)
• dedicated laboratory coats

3.2 List all the reagents required that is not provided by the manufacturer with shelf-life expiry dates and storage conditions

Include positive and negative control materials.

4. Performance characteristics

4.1 Analytical sensitivity and linearity of SARS-CoV-2 targets

4.1.1 Dilution series

Copies/ml	Result on Q-POC™ (Q-PLOT) (for at least 2 replicates)
100,000	Positive
10,000	Positive
7,500	Positive
5,000	Positive
2,500	Positive
1,000	Positive

4.1.2 Linearity and efficiency

The assay gives a qualitative result, so this section is not applicable.

4.1.3 Lowest limits of detection (LLOD)

The LLOD stated by the company is 1,000 copies/ml; the data in table 1 confirms that the LLOD is <1,000copies/ml.

5. Precision and robustness

5.1 Intra-assay precision

The assay gives a qualitative result, so this section is not applicable.

5.2 Inter-assay precision

The assay gives a qualitative result, so this section is not applicable.

5.3 Repeatability

This was not performed.

6. Analytical specificity (Interferences and cross-reactions)

6.1 Cross-reactivity to non-target samples or organisms

A range of samples either direct clinical samples or spiked samples that are known positives for other diseases, both closely related to be tested.

Zeprometrix cross reactivity panel samples	Result with Q-POC
B. pertussis A639	Negative
B. parapertussis A747	Negative
Metapneumovirus 8 (Peru6-2003)	Negative
Coronavirus 229E	Negative
Negative Control	Negative
Coronavirus HKU-1	Negative
Rhinovirus Type 1A	Negative
M. pneumoniae M129	Negative
C. pneumoniae CWL-029	Negative
Coronavirus OC43	Negative
Coronavirus NL63	Negative
Parainfluenza 3	Negative
Parainfluenza 4	Negative
RSV A2	Negative
Adenovirus 1	Negative
Adenovirus 3	Negative
Adenovirus 31	Negative
Influenza AH1 A/NewCal/20/99	Negative
Influenza AH3 A/Brisbane/10/07	Negative
Influenza B B/Florida/02/06	Negative
Parainfluenza 1	Negative
Parainfluenza 2	Negative

7. Diagnostic sensitivity and specificity

Clinical validation with confirmed positives and negatives.

7.1 Diagnostic sensitivity

Table 4. Comparison with reference method (note prevalence of 26%)

		Comparator	Comparator
		Positive	Negative	Total
Q-POC™ (Q-PLOT)	Positive	108	6	114
Q-POC™ (Q-PLOT)	Negative	27	384	411
	Total	135	390	525

Sensitivity = 80.0% (95% CI 72.1-86.2%) this meets the acceptable criteria for sensitivity of the MHRA POC TPP.

It should be noted that there were a high proportion of patients with a CT over 30 which may affect the overall sensitivity.

Table 5. Performance of Q-POC™ (Q-PLOT) at different viral loads, as defined by CT value

CT values were only available for 133/135 samples tested.

Basingstoke
CT	Comparator assay Viasure	Positive match on Q-POC	Sens %
<25	39	39	100
25-30	22	20	90.9
30-35	19	13	68.4
>35	6	0	0
undefined	0
Gibraltar
CT	Comparator assay QuantumDx PCR	Positive match on Q-POC	Sens %
<25	22	21	95.5
25-30	6	5	83.3
30-35	8	5	62.5
>35	6	1	16.7
undefined	0
SGUL
CT	Comparator assay Altona	Positive match on Q-POC	Sens %
<25	3	3	100
25-30	0	0	na
30-35	2	0	0
>35	0	0	na
undefined	0
Total
CT	Comparator assay	Positive match on Q-POC	Sens %
<25	64	63	98.4
25-30	28	25	89.3
30-35	29	18	62.1
>35	12	1	8.3
undefined	0

7.2 Diagnostic specificity

Specificity = 98.5% (95% CI 96.5-99.4%), meets the acceptable criteria for specificity of the MHRA POC TPP.

8. Summary

TVG uses a wide range of sites in order to validate new technologies and tests. These independent sites use a range of RT-qPCR assays against different genomic regions, and it is recognised that for some assay comparisons the sensitivity of RT-qPCR assay(s) may subtly differ from the true sensitivity of the test if compared to the same genomic region.

This assay does meet the acceptable criteria for sensitivity, and the desirable criteria for specificity of the MHRA TPP for POC assays.

The assay has good performance for low CT (<25, high viral load).

9. Extra data tables

Table 6. Failure rate of the Q-POC assay

Total number of samples tested	Number of IC* failures	Percentage of IC failures (%)	Number of technical failures	Percentage of technical failures (%)	Total number of failures	Percentage of total failures (%)
595	22	3.7%	29	4.9%	51	8.6%

*internal process control