Discrepancy between PCR based SARS-CoV-2 tests suggests the need to re-evaluate diagnostic assays

Mushtaq, Muhammad Zain; Shakoor, Sadia; Kanji, Akbar; Shaheen, Najma; Nasir, Asghar; Ansar, Zeeshan; Ahmed, Imran; Mahmood, Syed Faisal; Hasan, Rumina; Hasan, Zahra

doi:10.1186/s13104-021-05722-5

BMC Research Notes

Table 1 Description of COVID-19 patients and their differential diagnostic PCR results

From: Discrepancy between PCR based SARS-CoV-2 tests suggests the need to re-evaluate diagnostic assays

No	Age range^a (years)	Duration of illness at presentation (Days)	Severity	Chest imaging (radiography/ CT scan)	Results—cobas 6800 SARS-Co-V-2 assay (*orf1ab* and E gene targets)	Results for the BIOFIRE Filmarray RP2.1 assay (S and M gene targets)^d	Results for TaqPath 2019-nCoV assay *orf1ab*, S and N gene targets with (CT values)	Explanation for discrepancy with cobas 6800 Roche or BIOFIRE Filmarray assays
1	> 75	7	Non-severe	CT: bilateral ground glass opacities	NEG^b	POS	orf1ab (25.86), S (18.49), and N (27.95) detected	Possible orf1ab and E gene polymorphism
2	65–74	5	Severe	CT: bilateral patchy consolidations	NEG^b	POS^c	orf1ab (30.11) and N (30) detected (SGTF)	Possible orf1ab, E and S gene polymorphism
3	65–74	8	Severe	CT: bilateral ground glass opacities	NEG^b	POS	No targets detected, SGTF	Possible N, E, and orf1ab gene and S gene polymorphism
4	45–54	5	Severe	CT: bilateral ground glass opacities	NEG^b	POS^c	S (30.63) and N (31.14) detected (orf1ab not detected)	Possible E and orf1ab polymorphism
5	65–74	8	Critical	Radiograph: bilateral infiltrates	NEG^b	POS	orf1ab (11.85), S (9.91), and N (19.02) detected	Possible orf1ab and E gene polymorphism
6	65–74	10	Critical	Radiograph: predominant right infiltrates	NEG^b	POS	orf1ab (18.16), S (15.53), and N (18.45) detected	Possible orf1ab and E gene polymorphism
7	65–74	40	Long COVID/Post COVID sequelae	CT: bilateral ground glass opacities	NEG^b	POS	orf1ab (21.15), S (23.85), and N (31.71) detected	Possible orf1ab and E gene polymorphism
8	> 75	8	Critical	Radiograph: bilateral infiltrates	NEG^b	POS	orf1ab (31.2), S (31.41), and N (31.22) detected	Possible orf1ab gene polymorphism
9	65–74	7	Critical	CT: bilateral ground glass opacities	NEG^b	POS	No targets detected, SGTF	Possible N, E, orf1ab and S gene polymorphism
10	35–44	10	Non-severe	CT: bilateral ground glass opacities	NEG^b	POS^c	orf1ab (18.92), S (24.97), and N (20.68) detected	Possible orf1ab and E gene polymorphism

NP not performed, D Detected, NEG Negative, POS Positive, CT Cycle threshold, SGTF S gene target failure
^aPatient ages are given as age ranges to preserve confidentiality and anonymity
^bResults rechecked on a new sample collected within 48 h
^cResults rechecked on same sample
^dResults negative for all other pathogens detected by Filmarray RP2.1 i.e., Adenovirus, influenza A viruses H1, 2009H1, H3 (FluA-H1, FluA-2009H1, FluA-H3), influenza B virus (FluB), parainfluenza virus types 1 to 4 (Para 1–4), coronaviruses 229E, HKU1, OC43, and NL63 (CoV-HKU1, NL63, 229E, OC43), MERS-CoV (MERS coronavirus), human metapneumovirus (hMPV), Respiratory Syncytial Virus (RSV), human rhinovirus/enterovirus (Rhino/Entero), Chlamydia pneumoniae, Mycoplasma pneumoniae, Bordetella pertussis, and Bordetella parapertussis

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ISSN: 1756-0500

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