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J Virol Methods ; 289: 114042, 2021 03.
Article in English | MEDLINE | ID: covidwho-988684


Utilising diverse molecular platforms has formed a solid foundation in New Zealand's COVID-19 response. We evaluated multiple extraction and PCR assays for the detection of SARS-CoV-2. We included 65 positive samples which were run on the Panther Fusion using a laboratory developed test (LDT, E gene target). Where viral RNA was extracted by MagNA Pure (MP) 96 extraction platform or EpMotion 5075/Geneaid extraction kit, SARS-CoV-2 detection was performed on Light Cycler (LC) 480 using a LDT (E gene) or 3 commercial assays; Certest Viasure (Orf1ab, N genes) GenePro (E, RdRp genes) and A* Star Fortitude (proprietary target). Median Cts on LC 480 LDT for specimens (n = 9) extracted on MP 96 (26.6) were lower than on EpMotion (31.6) whereas median Cts for specimens (n = 10) extracted on the Panther Fusion LDT (23.1) were comparable with MP 96 /LC480 LDT (23.6). Specimens tested on Panther Fusion LDT (n = 28), extracted by MP 96, and amplified using commercial assays showed good concordance with a few exceptions; lower median Ct values were seen for 2 targets on GenePro (16.9, 21.5) and Viasure (19.5, 21.1) than for the Panther Fusion LDT (24.2) and A* Star Fortitude (25.6). Specimens tested on MP 96 (n = 18) had comparable results using commercial assays, with lower median Cts for Viasure (22.2, 23.7) compared with the LC 480 LDT (24.7), GenePro (24.7,25.7) and A*Fortitude (25.1) assays. The study provides an early assessment of the performance characteristics of 3 extraction methods for viral RNA and 5 PCR assays for the detection of SARS-CoV-2.

COVID-19 Testing/methods , COVID-19/diagnosis , Polymerase Chain Reaction/methods , RNA, Viral/analysis , SARS-CoV-2/isolation & purification , Disease Outbreaks , Humans , New Zealand/epidemiology , Sensitivity and Specificity , Specimen Handling