We present a case of late symptom onset of COVID-19 infection 72 days after initial diagnosis in an immunocompromised 53-year-old man. SARS-CoV-2 was cultured from his sputum sample at this time, and genomic sequencing suggested reinfection was unlikely. After receipt of convalescent plasma, SARS-CoV-2 became undetectable by PCR 111 days after diagnosis, although SARS-CoV-2 antibodies remained not detectable. This case posed difficult public health management issues in a low prevalence COVID-19 setting as the person required extended home isolation given his prolonged SARS-CoV-2 PCR detection.

Background Hepatitis E virus (HEV) is a common cause of acute viral hepatitis with significant morbidity and mortality, particularly in pregnant women. There are four major genotypes which can cause disease in humans. Genotypes 1 and 2 are usually associated with outbreaks and spread via facal/oral route or contaminated water. Genotypes 3 and 4 are zoonotic and usually associated with handling of pigs or consumption of contaminated pork. The strains circulating in Australia have never been characterized. Rationale/Aims The aims for this project are to identify the HEV genotypes found in Australia and link them to possible sources of transmission by phylogenetic analysis. Materials and Methods Between 2015 and 2020, 91 HEV isolates were sequenced and genotyped using an in-house PCR. Sixty-six of these were also sequenced by using the international HEVnet primers. Genotypes were determined using the BLASTn program. Relatedness to other strains in Australia was determined by phylogenetic analyses of the HEVnet sequences. Isolates were also stratified by state of origin, gender, age, predisposing factors and travel history (if known). Results Of the 91 HEV isolates sequenced, 55 (60.4%) were genotype 1. There were 34 (37.4%) genotype 3 strains and two genotype 4 (2.2%). At least 20 of the genotype 1 strains have been linked to travel in India, and another three with Pakistan. Five of the “Indian” strains were closely related and are suspected to have originated in Gujarat. Phylogenetic analysis also showed that 12 genotype 3 strains were genetically related and potentially acquired in/from New South Wales, Australia. The two genotype 4 strains may have originated in China. Discussion This is the first study to describe the HEV isolates identified in Australia. The results infer that HEV may be acquired during overseas travel as well as locally, presumably from consumption of pork or pork-related products. The phylogenetic analyses also reveal clusters of infection originating from India and Pakistan. This study provides some insight into the source and epidemiology of HEV infection in Australia which may be used to guide public health procedure and enable the implementation of measures to deal with potential outbreaks of infection.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has significantly increased demand on laboratory throughput and reagents for nucleic acid extraction and polymerase chain reaction (PCR). Reagent shortages may limit the expansion of testing required to scale back containment measures. The aims of this study were to investigate the viability of sample pooling as a strategy for increasing test throughput and conserving PCR reagents; and to report our early experience with pooling of clinical samples. A pre-implementation study was performed to assess the sensitivity and theoretical efficiency of two, four, and eight-sample pools in a real-time reverse transcription PCR-based workflow. A standard operating procedure was developed and implemented in two laboratories during periods of peak demand, inclusive of over 29,000 clinical samples processed in our laboratory. Sensitivity decreased (mean absolute increase in cycle threshold value of 0.6, 2.3, and 3.0 for pools of two, four, and eight samples, respectively) and efficiency increased as pool size increased. Gains from pooling diminished at high disease prevalence. Our standard operating procedure was successfully implemented across two laboratories. Increased workflow complexity imparts a higher risk of errors, and requires risk mitigation strategies. Turnaround time for individual samples increased, hence urgent samples should not be pooled. Pooling is a viable strategy for high-throughput testing of SARS-CoV-2 in low-prevalence settings.

The unprecedented scale of testing required to effectively control the coronavirus disease (COVID-19) pandemic has necessitated urgent implementation of rapid testing in clinical microbiology laboratories. To date, there are limited data available on the analytical performance of emerging commercially available assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and integration of these assays into laboratory workflows. Here, we performed a prospective validation study of a commercially available assay, the AusDiagnostics Coronavirus Typing (8-well) assay. Respiratory tract samples for SARS-CoV-2 testing were collected between 1 March and 25 March 2020. All positive samples and a random subset of negative samples were sent to a reference laboratory for confirmation. In total, 2673 samples were analysed using the Coronavirus Typing assay. The predominant sample type was a combined nasopharyngeal/throat swab (2640/2673; 98.8%). Fifty-four patients were positive for SARS-CoV-2 (2.0%) using the Coronavirus Typing assay; 53/54 (98.1%) positive results and 621/621 (100%) negative results were concordant with the reference laboratory. Compared to the reference laboratory gold standard, sensitivity of the Coronavirus Typing assay for SARS-CoV2 was 100% (95% CI 93.2-100%), specificity 99.8% (95% CI 99.1-100%), positive predictive value 98.1% (95% CI 90.2-99.7%) and negative predictive value 100% (95% CI 99.4-100%). In many countries, standard regulatory requirements for the introduction of new assays have been replaced by emergency authorisations and it is critical that laboratories share their post-market validation experiences, as the consequences of widespread introduction of a suboptimal assay for SARS-CoV-2 are profound. Here, we share our in-field experience, and encourage other laboratories to follow suit.

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.

Introduction: The BioFire FilmArray Meningitis/Encephalitis PCR panel targets 14 pathogens with minimal staff processing and rapid result availability. BioFire was compared to established laboratory testing for accuracy and turnaround time (TAT).

Abstract Background Pyogenic vertebral osteomyelitis (PVO) is rising in incidence, but optimal methods of investigation and duration of antibiotic therapy remain controversial. Methods We conducted a single-center retrospective cohort study of PVO at an Australian teaching hospital. We included all adults with a first episode of PVO between 2006 and 2015. PVO was defined based on the presence of prespecified clinical and radiological criteria. The main exposures of interest were investigation strategy and antibiotic treatment. The main outcome measures were duration of hospital admission, mortality during index admission, symptom resolution during index admission, and attributable readmission within 2 years. Results Of 129 included patients, 101 (78%) had a causative organism identified. Patients with an identified pathogen were more likely to be febrile (75% compared with 29%, P < .001) and had a higher mean admission C-reactive protein (207 vs 54, P < .001) compared with patients without an identified pathogen. However, they were less likely to experience an adverse outcome (death or attributable readmission within 2 years; adjusted odds ratio, 0.36; 95% confidence interval, 0.13–0.99; P = .04). Open biopsy of vertebral tissue had a higher diagnostic yield (70%) than fine needle aspirate (41%) or core biopsy (30%). Despite receiving a median of 6 weeks of intravenous antibiotics, only 15% of patients had a full recovery on discharge from index admission. Conclusions Clinical outcomes for patients with PVO were poor. Obtaining a microbiological diagnosis is associated with a better outcome. However, prospective and randomized studies are essential to establishing optimal investigation and treatment pathways.

Whipple’s disease is a rare infective condition, classically presenting with gastrointestinal manifestations. It is increasingly recognized as an important cause of culture-negative endocarditis. We present a case of Whipple’s endocarditis presenting with heart failure. A literature review identified 44 publications documenting 169 patients with Whipple’s endocarditis. The average age was 57.1 years. There is a clear sex predominance, with 85% of cases being male. Presenting symptoms were primarily articular involvement (52%) and heart failure (41%). In the majority of cases, the diagnosis was made on examination of valvular tissue. Preexisting valvular abnormalities were reported in 21%. The aortic valve was most commonly involved, and multiple valves were involved in 64% and 23% of cases, respectively. Antibiotic therapy was widely varied and included a ceftriaxone, trimethoprim, and sulfamethoxazole combination. The average follow-up was 20 months, and mortality was approximately 24%. Physician awareness is paramount in the diagnosis and management of this rare condition.