Diagnostic testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone significant changes over the duration of the pandemic. In early 2020, SARS-CoV-2 specific nucleic acid testing (NAT) protocols were predominantly in-house assays developed based on protocols published in peer reviewed journals. As the pandemic has progressed, there has been an increase in the choice of testing platforms. A proficiency testing program for the detection of SARS-CoV-2 by NAT was provided to assist laboratories in assessing and improving test capabilities in the early stages of the pandemic. This was vital in quality assuring initial in-house assays, later commercially produced assays, and informing the public health response. The Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) offered three rounds of proficiency testing for SARS-CoV-2 to Australian and New Zealand public and private laboratories in March, May, and November 2020. Each round included a panel of five specimens, consisting of positive (low, medium or high viral loads), inconclusive (technical specimen of selected SARS-CoV-2 specific genes) and negative specimens. Results were received for round 1 from 16, round 2 from 97 and round 3 from 101 participating laboratories. Improvement in the accuracy over time was shown, with the concordance of results in round 1 being 75.0%, in round 2 above 95.0% for all samples except one, and for round 3 above 95.0%. Overall, participants demonstrated high capabilities in detecting SARS-CoV-2, even in samples of low viral load, indicating excellent testing accuracy and therefore providing confidence in Australian and New Zealand public and private laboratories test results.

The adoption of whole genome sequencing (WGS) data over the past decade for pathogen surveillance, and decision-making for infectious diseases has rapidly transformed the landscape of clinical microbiology and public health. However, for successful transition to routine use of these techniques, it is crucial to ensure the WGS data generated meet defined quality standards for pathogen identification, typing, antimicrobial resistance detection and surveillance. Further, the ongoing development of these standards will ensure that the bioinformatic processes are capable of accurately identifying and characterising organisms of interest, and thereby facilitate the integration of WGS into routine clinical and public health laboratory setting. A pilot proficiency testing (PT) program for WGS of infectious agents was developed to facilitate widely applicable standardisation and benchmarking standards for WGS across a range of laboratories. The PT participating laboratories were required to generate WGS data from two bacterial isolates, and submit the raw data for independent bioinformatics analysis, as well as analyse the data with their own processes and answer relevant questions about the data. Overall, laboratories used a diverse range of bioinformatics tools and could generate and analyse high-quality data, either meeting or exceeding the minimum requirements. This pilot has provided valuable insight into the current state of genomics in clinical microbiology and public health laboratories across Australia. It will provide a baseline guide for the standardisation of WGS and enable the development of a PT program that allows an ongoing performance benchmark for accreditation of WGS-based test processes.

Biosecurity is a term broadly applied to the protection, control and accountability of biological agents and toxins to minimise the risk of their introduction through natural, unintentional (accidents) or deliberate processes. Biosecurity protection involves the engagement of all stakeholders including government, public health networks, industry, and scientific community. While the Commonwealth Government primarily manages biosecurity, it is also a shared responsibility with State and Territory governments. Rapid, accurate diagnosis is essential to informing all levels of response to biosecurity threats. External quality assurance (EQA) through proficiency testing (PT) is an indispensable tool to allow assessment of laboratory performance. This ensures laboratory capability and capacity are in a constant state of readiness to effectively detect biological threats and reduce the impact and transmission of disease. Since 2009, the Royal College of Pathologists Australasia Quality Assurance Program (RCPAQAP) has been contracted by the Australian Government Department of Health to establish a proficiency testing program (PTP) for the detection of biological threat agents. Starting out as a PTP for the detection of Bacillus anthracis, RCPAQAP Biosecurity has undergone significant transformation, thereby building and enhancing laboratory preparedness. Alterations in the program have been in line with the changing landscape of biosecurity and other emerging infectious diseases across Australia, and worldwide.

I hope that this Vertical Transmission finds you and your families safe and well.At the time of writing, some of you are in parts of Australia with few or no COVID-19 infections, while those of you in Victoria are in Stage 4 lockdown and dealing with the confusion, anxiety and uncertainty of this pandemic.What is clear isthat the work of our dedicated epidemiologists, microbiologists, medical scientists, nurses, GPs, hospital clinicians and researchers improves the lives and health of our community, and that approaching a complicated issue from many angles will enable us to find the solutions to carry us through this situation.On behalf of the ASM, I extend our sincere gratitude to all of you.

Bioterrorism is the deliberate misuse of a pathogen (virus, bacterium or other disease-causing microorganisms) or biotoxin (poisonous substance produced by an organism) to cause illness and death amongst the population. Bioterrorism and biological warfare (biowarfare) are terms often used interchangeably. However, bioterrorism is typically attributed to the politically motivated use of biological weapons by a rogue state, terrorist organisation or rogue individual whereas biological warfare refers to a country's use of bioweapons. Although rare, bioterrorism is a rapidly evolving threat to global security due to significant advancements in biotechnology in recent years and the severity of agents that could be exploited. The pursuit of publicity plays a vital role in bioterrorism. The success of a biological attack is often calculated by the extent of terror resulting from the event, psychological disruption of society and political breakdown, rather than the lethal effects of the agent used.

The current public health emergency surrounding the COVID-19 pandemic, that is the illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in thousands of cases in Australia since 25 January 2020 when the first case was diagnosed. This emerging virus presents particular hazards to researchers and laboratory staff in a clinical setting, highlighted by rapid and widespread global transmission. Based on the epidemiological and clinical data that have become available in mid-2020, we propose the interim classification of SARS-CoV-2 as a Risk Group 3 organism is reasonable, and discuss establishing Biosafety Level 3 (BSL-3) regulations accordingly. Despite its global spread, the reported mortality rate of SARS-CoV-2 ranging from 0.13% to 6.22% is considerably less than that of other Risk Group 4 agents including Ebola and Marburg viruses with fatality rates as high as 90%. In addition, studies have demonstrated that approximately 86% of patients presenting with severe courses of the disease are aged 70 years or above, with the presence of comorbid conditions such as cardiovascular and respiratory system diseases in the majority of all fatal cases. In contrary to recent discussions surrounding the protective and administrative measures needed in a laboratory, the emerging evidence surrounding mortality rate, distinct demographics of severe infections, and the presence of underlying diseases does not justify the categorisation of SARS-CoV-2 as a Risk Group 4 organism. This article summarises biosafety precautions, control measures and appropriate physical containment facilities required to minimise the risk of laboratory-acquired infections with SARS-CoV-2.

The Royal College of Pathologists (RCPA) and then RCPA Quality Assurance Programs Pty Ltd (RCPAQAP), a company independent from but aligned with the RCPA, have been producing proficiency testing programs (PTP) for infectious diseases for 52 years. This involves sending infectious disease material in surveys to over 80 countries worldwide throughout any year. The PTP panels are developed depending on the prevalence of diseases, which requires flexible panel composition and dynamic enrolments. The Defence Trade Controls Act was introduced in 2012 as part of a wider international regulatory counter-proliferation framework. In 2017, the inclusion of inactivated infectious diseases as controlled microorganisms in the Defence Strategic Goods List (DSGL) had the potential to completely disrupt the RCPAQAP business model in the provision of infectious disease PTP. Some strategies for mitigating this risk are discussed in this paper.

The first reported case of Middle East respiratory syndrome coronavirus (MERS‐CoV) infection was identified in Saudi Arabia in September 2012, since which time there have been over 2000 laboratory‐confirmed cases, including 750 deaths in 27 countries. Nucleic acid testing (NAT) is the preferred method for the detection of MERS‐CoV. A single round of a Proficiency Testing Program (PTP) was used to assess the capability of laboratories globally to accurately detect the presence of MERS‐CoV using NAT. A panel of eleven lyophilized specimens containing different viral loads of MERS‐CoV, common coronaviruses, and in vitro RNA transcripts was distributed to laboratories in all six World Health Organization regions. A total of 96 laboratories from 79 countries participating in the PTP, with 76 of 96 (79.2%) reporting correct MERS‐CoV results for all nine scored specimens. A further 10 laboratories (10.4%) scored correctly in eight of nine specimens of the PTP. The majority of laboratories demonstrated satisfactory performance in detecting the presence of MERS‐CoV using NAT. However, some laboratories require improved assay sensitivity, reduced cross contamination of samples, and improved speciation of coronavirus subtypes for potentially complex clinical specimens. Further PTP and enhanced links with expert laboratories globally may improve the laboratory performance.

ABSTRACT The unprecedented 2015 Ebolavirus (EBOV) outbreak in West Africa was declared a public health emergency, making diagnosis and quality of testing a global issue. The accuracy of laboratory diagnostic capacity for EBOV was assessed in 2014 to 2016 using a proficiency testing (PT) strategy developed by the Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) in Biosecurity. Following a literature search, EBOV-specific gene targets were ranked according to the frequency of their use in published methods. The most commonly used gene regions (nucleoprotein [NP], glycoprotein [GP], and RNA-dependent RNA polymerase [L]) were selected for the design of in vitro RNA transcripts to be included in the simulated EBOV specimens used for EBOV detection with PCR-based assays. Specimens were tested for stability and found to be stable on long-term storage (1 year) at −80°C and on shorter-term storage in lyophilized form (1 week at ambient temperature and a subsequent week at −80°C). These specimens were used in three EBOV PTs offered from April 2014 to March 2016. In the first and third PTs, all laboratories (3/3 and 9/9, respectively) correctly identified specimens containing EBOV RNA transcripts, while in the second PT, all but one laboratory (5/6) correctly confirmed the presence of EBOV. The EBOV PT panel was useful for ensuring the competency of laboratories in detecting EBOV in the absence of readily available clinical samples. The simulated EBOV specimen was safe, stable, and reliable and can be used in lyophilized form for future EBOV PT programs, allowing simplicity of transport.