12Diagnostic testing for COVID-19 is central to controlling the global pandemic. Recently, To and 13 colleagues reported that 20 of 23 (87%) patients who had SARS-CoV-2 detected by reverse-14 transcriptase PCR (RT-PCR) in nasopharyngeal swabs (NPS) or sputum also had SARS-CoV-2 15 detectable in saliva (1). The use of saliva has several advantages compared to collection of NPS. In 16 particular, the close contact involved in swab collection poses a risk to healthcare workers, and 17 collection of saliva may reduce this risk. Further, saliva collection does not require specialised 18 consumables, causes less patient discomfort, and may be a useful sample for self-collection (2). 20We further investigated the feasibility and utility of saliva collection from ambulatory patients 21 presenting to a dedicated COVID-19 screening clinic at the Royal Melbourne Hospital (RMH), 22Melbourne, Australia. Between 25 th March and 1 st April 2020, 622 patients were tested for COVID-23 19 through the screening clinic. All patients had NPS, and 522/622 (83.9%) patients also provided 24 saliva. Patients were asked to pool saliva in their mouth for 1-2 minutes prior to collection, and gently 25 spit 1-2 mL of saliva into a 25mL collection pot. Neat saliva specimens were transported to the 26 laboratory where an approximate 1:1 ratio of liquid Amies media was immediately added. We 27 specifically chose to use liquid Amies media in order to: (i) evaluate the use of an alternative transport 28 media in the face of global shortages of viral transport medium (VTM), and (ii) to preserve VTM in 29 our own laboratory. The median time from sample collection to addition of media was 180 minutes 30 (range 55 -537 minutes). NPS and saliva specimens underwent nucleic acid extraction on the Qiagen 31 EZ1 platform (QIAGEN, Hilden, Germany). An extraction volume of 200uL of the sample was used, 32 with RNA eluted in 60uL. Reverse-transcriptase PCR (RT-PCR) testing was performed using a 33 multiplex RT-PCR test for SARS-CoV-2 and other seasonal coronaviruses (Coronavirus Typing (8-34 well) assay, AusDiagnostics, Mascot, Australia). All positive NPS samples for SARS-CoV-2 35 underwent confirmatory testing at a local reference laboratory (the Victorian Infectious Diseases 36 Reference Laboratory) using previously published primers (3). 38Overall, 39/622 (6.3%; 95% confidence interval [CI] 4.6%-8.5%) patients had PCR-positive NPS, and 39 33/39 patients (84.6%; 95% CI 70.0%-93.1%) had SARS-CoV-2 detected in saliva. The median cycle 40 threshold (Ct) value was significantly lower in NPS than saliva ( Figure 1A), suggestive of higher viral 41 loads in NPS, and in both samples, there was a correlation between Ct value and days from symptom 42 onset ( Figure 1B). To assess specificity, a subset of saliva specimens from 50 patients with PCR-43 negative swabs was also tested. Of note, SARS-CoV-2 was detected in 1/50 (2%; 95% CI 0.1%-44 11.5%) of these saliva samples, which may reflect differing quality of NPS collection. 46To date, studies assessing the utilit...

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Background Robust serological assays are essential for long-term control of the COVID-19 pandemic. Many recently released point-of-care (PoCT) serological assays have been distributed with little premarket validation. Methods Performance characteristics for 5 PoCT lateral flow devices approved for use in Australia were compared to a commercial enzyme immunoassay (ELISA) and a recently described novel surrogate virus neutralization test (sVNT). Results Sensitivities for PoCT ranged from 51.8% (95% confidence interval [CI], 43.1%–60.4%) to 67.9% (95% CI, 59.4%–75.6%), and specificities from 95.6% (95% CI, 89.2%–98.8%) to 100.0% (95% CI, 96.1%–100.0%). ELISA sensitivity for IgA or IgG detection was 67.9% (95% CI, 59.4%–75.6%), increasing to 93.8% (95% CI, 85.0%–98.3%) for samples >14 days post symptom onset. sVNT sensitivity was 60.9% (95% CI, 53.2%–68.4%), rising to 91.2% (95% CI, 81.8%–96.7%) for samples >14 days post symptom onset, with specificity 94.4% (95% CI, 89.2%–97.5%). Conclusions Performance characteristics for COVID-19 serological assays were generally lower than those reported by manufacturers. Timing of specimen collection relative to onset of illness or infection is crucial in reporting of performance characteristics for COVID-19 serological assays. The optimal algorithm for implementing serological testing for COVID-19 remains to be determined, particularly in low-prevalence settings.

Background: Robust serological assays are essential for long-term control of the COVID-19 pandemic. Many recently released point-of-care (PoCT) serological assays have been distributed with little pre-market validation. Methods: Performance characteristics for five PoCT lateral flow devices approved for use in Australia were compared to a commercial enzyme immunoassay (ELISA) and a recently described novel surrogate virus neutralisation test (sVNT). Results: Sensitivities for PoCT ranged from 51.8% (95% CI 43.1 to 60.4%) to 67.9% (95% CI 59.4-75.6%), and specificities from 95.6% (95% CI 89.2-98.8%) to 100.0% (95% CI 96.1-100.0%). Overall ELISA sensitivity for either IgA or IgG detection was 67.9% (95% CI 59.4-75.6), increasing to 93.8% (95% CI 85.0-98.3%) for samples >14 days post symptom onset. Overall, sVNT sensitivity was 60.9% (95% CI 53.2-68.4%), rising to 91.2%% (95% CI 81.8-96.7%) for samples collected >14 days post-symptom onset, with a specificity 94.4% (95% CI 89.2-97.5%), Conclusion: Performance characteristics for COVID-19 serological assays were generally lower than those reported by manufacturers. Timing of specimen collection relative to onset of illness or infection is crucial in the reporting of performance characteristics for COVID-19 serological assays. The optimal algorithm for implementing serological testing for COVID-19 remains to be determined, particularly in low-prevalence settings.

Objective: To describe COVID-19 infections amongst healthcare workers (HCWs) at the Royal Melbourne Hospital from 1st July to 31st August 2020 Design: Prospective observational study Setting: A 550 bed tertiary referral hospital in metropolitan Melbourne Participants: All HCWs identified with COVID-19 infection in the period of interest Results: 262 HCW infections were identified over 9 weeks. 68.3% of infected HCWs were nurses and the most affected locations were the geriatric and rehabilitation wards. Clusters of infection occurred in staff working in wards with patients known to have COVID-19 infection. Staff infections peaked when COVID-19 infected inpatient numbers were highest, and density of patients and certain patient behaviours were noted by staff to be linked to possible transmission events. Three small outbreaks on other wards occurred but all were recognised and brought under control. Availability of rapid turn-around staff testing, and regular review of local data and obtaining feedback from staff helped identify useful interventions which were iteratively implemented. Attention to staff wellbeing was critical to the response and a comprehensive support service was implemented. Conclusion(s): A comprehensive multimodal approach to containment was instituted with iterative refinement based on frontline workers observations and ongoing analysis of local data in real time.

Objectives To design and evaluate 3D‐printed nasal swabs for collection of samples for SARS‐CoV‐2 testing. Design An iterative design process was employed. Laboratory evaluation included in vitro assessment of mock nasopharyngeal samples spiked with two different concentrations of gamma‐irradiated SARS‐CoV‐2. A prospective clinical study compared SARS‐CoV‐2 and human cellular material recovery by 3D‐printed swabs and standard nasopharyngeal swabs. Setting, participants Royal Melbourne Hospital, May 2020. Participants in the clinical evaluation were 50 hospital staff members attending a COVID‐19 screening clinic and two inpatients with laboratory‐confirmed COVID‐19. Intervention In the clinical evaluation, a flocked nasopharyngeal swab sample was collected with the Copan ESwab and a mid‐nasal sample from the other nostril was collected with the 3D‐printed swab. Results In the laboratory evaluation, qualitative agreement with regard to SARS‐CoV‐2 detection in mock samples collected with 3D‐printed swabs and two standard swabs was complete. In the clinical evaluation, qualitative agreement with regard to RNase P detection (a surrogate measure of adequate collection of human cellular material) in samples collected from 50 hospital staff members with standard and 3D‐printed swabs was complete. Qualitative agreement with regard to SARS‐CoV‐2 detection in three pairs of 3D‐printed mid‐nasal and standard swab samples from two inpatients with laboratory‐confirmed SARS‐CoV‐2 was also complete. Conclusions Using 3D‐printed swabs to collect nasal samples for SARS‐CoV‐2 testing is feasible, acceptable to patients and health carers, and convenient.

Saliva has recently been proposed as a suitable specimen for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Use of saliva as a diagnostic specimen may present opportunities for SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) testing in remote and low-resource settings. Determining the stability of SARS-CoV-2 RNA in saliva over time is an important step in determining optimal storage and transport times. We undertook an in vitro study to assess whether SARS-CoV-2 could be detected in contrived saliva samples. The contrived saliva samples comprised 10 ml pooled saliva spiked with gamma-irradiated SARS-CoV-2 to achieve a concentration of 2.58×104 copies ml SARS-CoV-2, which was subsequently divided into 2 ml aliquots comprising: (i) neat saliva; and a 1 : 1 dilution with (ii) normal saline; (iii) viral transport media, and (iv) liquid Amies medium. Contrived samples were made in quadruplicate, with two samples of each stored at either: (i) room temperature or (ii) 4 °C. SARS-CoV-2 was detected in all SARS-CoV-2 spiked samples at time point 0, day 1, 3 and 7 at both storage temperatures using the N gene RT-PCR assay and time point 0, day 1 and day 7 using the Xpert Xpress SARS-CoV-2 (Cepheid, Sunnyvale, USA) RT-PCR assay. The ability to detect SARS-CoV-2 in saliva over a 1 week period is an important finding that presents further opportunities for saliva testing as a diagnostic specimen for the diagnosis of SARS-CoV-2.

Invasive fungal diseases (IFD) are serious infections associated with high mortality, particularly in immunocompromised patients. The prescribing of antifungal agents to prevent and treat IFD is associated with substantial economic burden on the health system, high rates of adverse drug reactions, significant drug-drug interactions and the emergence of antifungal resistance. As the population at risk of IFD continues to grow due to the increased burden of cancer and related factors, the need for hospitals to employ antifungal stewardship (AFS) programmes and measures to monitor and prevent infection has become increasingly important. These guidelines outline the essential components, key interventions and metrics, which can help guide implementation of an AFS programme in order to optimise antifungal prescribing and IFD management. Specific recommendations are provided for quality processes for the prevention of IFD in the setting of outbreaks, during hospital building works, and in the context of Candida auris infection. Recommendations are detailed for the implementation of IFD surveillance to enhance detection of outbreaks, evaluate infection prevention and prophylaxis interventions and to allow benchmarking between hospitals. Areas in which information is still lacking and further research is required are also highlighted.