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N Z Med J ; 135(1559): 53-58, 2022 08 05.
Article in English | MEDLINE | ID: covidwho-2147482


AIM: To compare detection of SARS-CoV-2 from paired nasopharyngeal swabs (NPS) and saliva using molecular methods in common use for testing swabs in New Zealand. METHOD: Samples from individuals testing positive for SARS-CoV-2 in Auckland, Wellington and Dunedin were tested at the local laboratories using methods previously established for these sample types. RESULTS: One hundred and ninety-six paired samples from unique individuals were tested, with 46 (23%) positive from either sample type, of which 43/46 (93%) tested positive from NPS, and 42/46 (91%) from saliva, indicating no significant difference in performance between sample types (p=0.69). The average Δ Ct between saliva and nasopharyngeal swabs overall across the sample set was 0.22 cycles, indicating excellent concordance; however, the difference between NPS and saliva collected from the same individual was quite variable with up to 19 cycles difference between the sample types. CONCLUSION: We found that saliva is an equivalent sample type to nasopharyngeal swab for the detection of SARS-CoV-2 in our laboratories using multiple assay combinations and is suitable for use as a diagnostic and surveillance test for selected groups of individuals.

COVID-19 , Nucleic Acids , COVID-19/diagnosis , Clinical Laboratory Techniques/methods , Humans , Nasopharynx , New Zealand , SARS-CoV-2/genetics , Saliva , Specimen Handling/methods
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