Application of digital PCR to determine the reliability of Xpert Xpress SARS-CoV-2 assay with envelope (E) gene negative and nucleocapsid (N2) gene positive results.

This study used digital polymerase chain reaction (dPCR) to determine whether envelope (E) gene-negative and nucleocapsid (N2) gene-positive (E-N+) results obtained with the Cepheid Xpert Xpress SARS-CoV-2 assay are reliable. Using droplet digital PCR results as a reference, 18 of 22 E-N+ samples with a low viral load (81.8%) were identified as true positives.

Spread of SARS-CoV-2 aerosols via two connected drainage stacks in a high-rise housing outbreak of COVID-19.

Vertical transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) along a vertical column of flats has been documented in several outbreaks of coronavirus disease 2019 (COVID-19) in Guangdong and Hong Kong. We describe an outbreak in Luk Chuen House, involving two vertical columns of flats associated with an unusually connected two-stack drainage system, in which nine individuals from seven households were infected. The index case resided in Flat 812 (8th floor, Unit 12), two flats (813, 817) on its opposite side reported one case each (i.e., a horizontal sub-cluster). All other flats with infected residents were vertically associated, forming a vertical sub-cluster. We injected tracer gas (SF6) into drainage stacks via toilet or balcony of Flat 812, monitored gas concentrations in roof vent, toilet, façade, and living room in four of the seven flats with infected residents and four flats with no infected residents. The measured gas concentration distributions agreed with the observed distribution of affected flats. Aerosols leaking into drainage stacks may generate the vertical sub-cluster, whereas airflow across the corridor probably caused the horizontal sub-cluster. Sequencing and phylogenetic analyses also revealed a common point-source. The findings provided additional evidence of probable roles of drainage systems in SARS-CoV-2 transmission.

Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay.

BACKGROUND: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. These non-validated specimen types, however, do have significant diagnostic value. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. METHODS: 162 specimens from 158 patients with suspected COVID-19 disease were tested with Xpert Xpress SARS-CoV-2 assay. These included 120 DTS and 42 LRT specimens i.e. 35 sputum, 6 tracheal aspirate and one bronchoalveolar lavage. Results were compared to those by the TIB-Molbiol LightMix® SarbecoV E-gene assay. RESULTS: Xpert Xpress SARS-CoV-2 assay has satisfactory performance when compared with reference method. The positive percent agreement (PPA) of DTS and LRT specimens were 98.86 % & 100 % respectively while the negative percent agreement (NPA) was 100 % for both DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens.