Alinity m

Nasopharyngeal (NP) swabs in transport media and plasma samples were held at 4°C (or −80°C if > 12 h) prior to testing on the Alinity M SARS CoV-2 Amp kit and/or Cepheid Xpert Xpress SARS-CoV-2 kit. The GeneXpert ®Dx System (Cepheid) and Alinity M (Abbott) performed automated specimen processing and real-time RT-PCR analysis. The Cepheid Xpert Xpress SARS-CoV-2 kit detects N and E genes of the SARS CoV-2 genome; Alinity M SARS CoV-2 Amp kit detects RdRp and N genes.

SARS-CoV-2 infections were diagnosed in individuals who returned an ‘RNA detected’ result by real-time, quantitative reverse-transcriptase PCR (RT-qPCR) on nasopharyngeal swabs, performed on either the Alinity M (Abbott, Abbott Park, IL, USA), Respibio (Serosep, Limerick, Ireland) or GeneXpert (Cepheid, Sunnyvale, CA, USA) diagnostic SARS-CoV-2 platforms. Samples were collected in the context of suspected COVID-19 infection, as part of routine post-admission surveillance testing, or as part of contact tracing efforts during outbreak investigations. Healthcare-associated infections (HCAIs) and community-acquired infections (CAIs) were categorized in accordance with national surveillance definitions [18 ]. ‘Probable’ outbreak cases were defined as those in which a combination of both epidemiological and genomic data provided support for viral transmission, while ‘possible’ outbreak cases were those linked by epidemiological or genomic information alone.

RT-PCR testing of a nasopharyngeal or oropharyngeal swab was done on the Cobas 6800 instrument (Roche diagnostics, Basel, Switzerland) or the Alinity® m instrument (Abbott Laboratories, Chicago, IL, USA) according to the manufacturers’ instructions.
The result was declared borderline positive when only 1 of 2 PCR targets was detected, the E-gene or ORF-1 (open reading frame) (Roche Cobas), or the cycle threshold value (CT-value) was between 38.0 and 40.0 (Abbott Alinity m). For conversion to quantitative test results of the virus concentration, 3 quantitative comparison samples containing 10⁵, 10⁶, and 10⁷ SARS-CoV-2 (BetaCoV/Munich/ChVir984/2020) RNA copies/mL were used. A standard curve was used to calculate the viral RNA copies/mL.

Different SARS-CoV-2 RT-qPCR protocols were used for detection of SARS-CoV-2. In brief, the following methods were used: (i) cobas® SARS-CoV-2 test kit running on the cobas 6800® (Roche Diagnostics, Mannheim, Germany) was used for 385 (55.32%) samples according to the manufacturer's instructions. (ii) SARS-CoV-2 AMP kit on the Alinity m (Abbott, Illinois, USA) was used for 62 (8.91%) samples. (iii) Multiplex RT-qPCR with LightMix® SarbecoV E-gene (TIB Molbiol, Berlin, Germany) running on the Panther Fusion® (Hologic, Wiesbaden, Germany) was used for 2 (0.29%) samples. (iv) For 244 (35.06%) specimens, samples from up to ten asymptomatic employees were pooled and tested for SARS-CoV-2 infection using the methods (i) and (ii). All samples within a negative pool were considered negative. For positive pools all samples were retested individually using the methods (i) and (ii). (v) Xpert® Xpress SARS-CoV-2 (Cepheid, Sunnyvale, USA) test kit was used for 3 (0.43%) samples according to the manufacturer's instructions. To enable comparison of Cycle threshold (Ct) values between different RT-qPCR protocols, Ct values were translated into copies/ml and converted to a cobas 6800®-adjusted Ct value. Detailed descriptions of the RT-qPCR protocols and Ct value conversion can be found in previous publications [10 , 27 ].