Non-SARS-CoV-2 respiratory viral detection and whole genome sequencing from COVID-19 rapid antigen test devices: a laboratory evaluation study.

BACKGROUND: There has been high uptake of rapid antigen test device use for point-of-care COVID-19 diagnosis. Individuals who are symptomatic but test negative on COVID-19 rapid antigen test devices might have a different respiratory viral infection. We aimed to detect and sequence non-SARS-CoV-2 respiratory viruses from rapid antigen test devices, which could assist in the characterisation and surveillance of circulating respiratory viruses in the community. METHODS: We applied archival clinical nose and throat swabs collected between Jan 1, 2015, and Dec 31, 2022, that previously tested positive for a common respiratory virus (adenovirus, influenza, metapneumovirus, parainfluenza, rhinovirus, respiratory syncytial virus [RSV], or seasonal coronavirus; 132 swabs and 140 viral targets) on PCR to two commercially available COVID-19 rapid antigen test devices, the Panbio COVID-19 Ag Rapid Test Device and Roche SARS-CoV-2 Antigen Self-Test. In addition, we collected 31 COVID-19 rapid antigen test devices used to test patients who were symptomatic at The Royal Melbourne Hospital emergency department in Melbourne, Australia. We extracted total nucleic acid from the device paper test strips and assessed viral recovery using multiplex real-time PCR (rtPCR) and capture-based whole genome sequencing. Sequence and genome data were analysed through custom computational pipelines, including subtyping. FINDINGS: Of the 140 respiratory viral targets from archival samples, 89 (64%) and 88 (63%) were positive on rtPCR for the relevant taxa following extraction from Panbio or Roche rapid antigen test devices, respectively. Recovery was variable across taxa: we detected influenza A in nine of 18 samples from Panbio and seven of 18 from Roche devices; parainfluenza in 11 of 20 samples from Panbio and 12 of 20 from Roche devices; human metapneumovirus in 11 of 16 from Panbio and 14 of 16 from Roche devices; seasonal coronavirus in eight of 19 from Panbio and two of 19 from Roche devices; rhinovirus in 24 of 28 from Panbio and 27 of 28 from Roche devices; influenza B in four of 15 in both devices; and RSV in 16 of 18 in both devices. Of the 31 COVID-19 devices collected from The Royal Melbourne Hospital emergency department, 11 tested positive for a respiratory virus on rtPCR, including one device positive for influenza A virus, one positive for RSV, four positive for rhinovirus, and five positive for SARS-CoV-2. Sequences of target respiratory viruses from archival samples were detected in 55 (98·2%) of 56 samples from Panbio and 48 (85·7%) of 56 from Roche rapid antigen test devices. 98 (87·5%) of 112 viral genomes were completely assembled from these data, enabling subtyping for RSV and influenza viruses. All 11 samples collected from the emergency department had viral sequences detected, with near-complete genomes assembled for influenza A and RSV. INTERPRETATION: Non-SARS-CoV-2 respiratory viruses can be detected and sequenced from COVID-19 rapid antigen devices. Recovery of near full-length viral sequences from these devices provides a valuable opportunity to expand genomic surveillance programmes for public health monitoring of circulating respiratory viruses. FUNDING: Australian Government Medical Research Future Fund and Australian National Health and Medical Research Council.

An integrated public health response to an outbreak of Murray Valley encephalitis virus infection during the 2022-2023 mosquito season in Victoria.

Introduction: Murray Valley encephalitis virus (MVEV) is a mosquito-borne flavivirus known to cause infrequent yet substantial human outbreaks around the Murray Valley region of south-eastern Australia, resulting in significant mortality. Methods: The public health response to MVEV in Victoria in 2022-2023 included a climate informed pre-season risk assessment, and vector surveillance with mosquito trapping and laboratory testing for MVEV. Human cases were investigated to collect enhanced surveillance data, and human clinical samples were subject to serological and molecular testing algorithms to assess for co-circulating flaviviruses. Equine surveillance was carried out via enhanced investigation of cases of encephalitic illness. Integrated mosquito management and active health promotion were implemented throughout the season and in response to surveillance signals. Findings: Mosquito surveillance included a total of 3,186 individual trapping events between 1 July 2022 and 20 June 2023. MVEV was detected in mosquitoes on 48 occasions. From 2 January 2023 to 23 April 2023, 580 samples (sera and CSF) were tested for flaviviruses. Human surveillance detected 6 confirmed cases of MVEV infection and 2 cases of "flavivirus-unspecified." From 1 September 2022 to 30 May 2023, 88 horses with clinical signs consistent with flavivirus infection were tested, finding one probable and no confirmed cases of MVE. Discussion: The expanded, climate-informed vector surveillance system in Victoria detected MVEV in mosquitoes in advance of human cases, acting as an effective early warning system. This informed a one-health oriented public health response including enhanced human, vector and animal surveillance, integrated mosquito management, and health promotion.

Reducing unnecessary testing on sputum specimens from patients with cystic fibrosis: pathology stewardship in microbiology.

Chronic respiratory tract infection by Pseudomonas aeruginosa is the hallmark of established lung disease in patients with cystic fibrosis (CF). Antibiotic therapy can usually only suppress but not eradicate infection. In recent years, pulmonary infection with non-tuberculous Mycobacteria (NTM) species has also been increasing. These patients are often colonised with multiple isolates and determination of clinical significance of each isolate is difficult. The clinical value of frequent routine susceptibility testing of individual isolates is unproven, particularly since a delay in susceptibility testing is inevitable when purification of multiple cultured isolates is required to test each isolate separately. From August 2019 until December 2020 we ceased routine susceptibility testing on P. aeruginosa respiratory tract isolates from patients with CF if a previous isolate from the patient had susceptibility testing performed. We found that the proportion of P. aeruginosa isolates that had susceptibility testing performed dropped from 97% to 11% as a result of this change in laboratory process. During this time, we also ceased routine culture for acid-fast bacilli if this had been performed within the previous 6 months. We present the cost and resource savings for these changes in laboratory process and assess for clinical impact measured as hospital admissions, length of stay in hospital and mortality.

Congenital asplenia study: clinical and laboratory characterisation of adults with congenital asplenia.

Congenital asplenia is a rare disorder commonly associated with other visceral and cardiac congenital anomalies. Isolated congenital asplenia is even less common than syndromic forms. The risk of severe bacterial infections associated with asplenia is the most concerning clinical implication and carries a significant mortality risk. Prophylactic measures against the clinical syndrome known as overwhelming postsplenectomy infections (OPSI) include vaccination, prophylactic and emergency antibiotics and health education including fever management and travel advice. This case series describes fourteen adults with congenital asplenia and polysplenia syndrome, most of whom were diagnosed incidentally as adults, and outlines the nature of their diagnosis, clinical phenotype, family history and key pathology findings.

Corynebacterium macginleyi in the era of MALDI-TOF MS: epidemiology, susceptibility patterns and prevalence of co-infection.

Corynebacterium macginleyi has long been associated with ocular infections and has more recently been rarely implicated in systemic infections. There is a paucity of literature regarding the rate of C. macginleyi co-infection with other bacterial and viral pathogens and regarding the incidence of C. macginleyi infection in the paediatric population. In this study, we report 30 isolates of C. macginleyi of ocular origin from 26 patients, identified using matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS). The rates of co-isolation with bacterial and viral pathogens were 62% (n=16/26) and 39% (n=5/13), respectively, in this study. Of these, 13 patients had molecular testing performed as requested by treating clinicians for either the Chlamydia trachomatis/Neisseria gonorrhoeae PCR or herpes/enterovirus/adenovirus multiplex PCR. All isolates tested susceptible to linezolid, vancomycin and ciprofloxacin, with variable resistance to tetracycline, clindamycin and penicillin using EUCAST breakpoints.

Celebrating the career and contributions of Dr Henry T. Lynch (1928-2019).

This article celebrates the career of Dr Henry Lynch and his contributions to cancer genetics through his extensive research, clinical practice and his passion for personalising care by using a patient's genetic profile to determine management and treatment. Dr Lynch's contributions were momentous and continue to have relevance to medical practice, in particular in the fields of clinical genetics, medical oncology and gastroenterology.

Analysis of patient reports on the referral process to two NSW cancer genetic services.

To evaluate trends and associations surrounding patient referral to cancer genetics services in NSW. The specific aims of the questionnaire used to collect information were to: (1) quantify the types of cancers being referred, (2) identify the source of referral for the patients, (3) categorise the referral as being either sought by the patient or suggested by the doctor, (4) quantify how often family history was asked, (5) determine who first raised the topic of family history, (6) identify any discouragement faced by patients, (7) clarify the cancer status of patients referred. A comparative patient-reported study was carried out using a questionnaire as the data collection tool in structured short interviews. The questions were aimed at eliciting the patient's understanding of why they were referred to the clinic, whether family history was discussed at the time of referral and who raised the issue via a series of YES/NO and open response questions. Data were collected from March 2012 to August 2012 from two different clinics, St Vincent's Hereditary Cancer Clinic, Sydney and the Hunter Family Cancer Service, Newcastle-both in New South Wales, Australia. Written consent was obtained. The study found that specialists were responsible for the majority of the 150 referrals and were more likely to be proactive in referring, as opposed to GPs (Phi and Cramer's V test). Patients reported that at the time of referral their family history was not asked in 13.5 % of cases, despite being significant. In the 131 cases where family history was discussed, it was the patient on approximately 2 in 5 occasions that brought up the topic. The most common types of cancer seen were breast cancer and colorectal. At both services GP referrals were more common then specialist referrals. On three occasions patients sought referral after being notified that the bloods they had collected by their GP for genetic testing were held by the laboratory due to failure to follow protocol. Six patients reported being discouraged to attend when seeking a referral. At the time of referral 58.7 % of patients were considered to be without cancer. Overall, 20 % of patients requested their referral to the cancer genetics clinics. The discussion of family history in the context of familial cancer is key to accurate risk assessment and management advice. Further education of doctors is required as evidenced by the number of patients where family history was not asked and in those patients who had bloods collected by their GP without counselling.