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O'Toole, A.; Hill, V.; Pybus, O. G.; Watts, A.; Bogoch, II, Khan, K.; Messina, J. P.; consortium, Covid- Genomics UK, Network for Genomic Surveillance in South, Africa, Brazil, U. K. Cadde Genomic Network, Tegally, H.; Lessells, R. R.; Giandhari, J.; Pillay, S.; Tumedi, K. A.; Nyepetsi, G.; Kebabonye, M.; Matsheka, M.; Mine, M.; Tokajian, S.; Hassan, H.; Salloum, T.; Merhi, G.; Koweyes, J.; Geoghegan, J. L.; de Ligt, J.; Ren, X.; Storey, M.; Freed, N. E.; Pattabiraman, C.; Prasad, P.; Desai, A. S.; Vasanthapuram, R.; Schulz, T. F.; Steinbruck, L.; Stadler, T.; Swiss Viollier Sequencing, Consortium, Parisi, A.; Bianco, A.; Garcia de Viedma, D.; Buenestado-Serrano, S.; Borges, V.; Isidro, J.; Duarte, S.; Gomes, J. P.; Zuckerman, N. S.; Mandelboim, M.; Mor, O.; Seemann, T.; Arnott, A.; Draper, J.; Gall, M.; Rawlinson, W.; Deveson, I.; Schlebusch, S.; McMahon, J.; Leong, L.; Lim, C. K.; Chironna, M.; Loconsole, D.; Bal, A.; Josset, L.; Holmes, E.; St George, K.; Lasek-Nesselquist, E.; Sikkema, R. S.; Oude Munnink, B.; Koopmans, M.; Brytting, M.; Sudha Rani, V.; Pavani, S.; Smura, T.; Heim, A.; Kurkela, S.; Umair, M.; Salman, M.; Bartolini, B.; Rueca, M.; Drosten, C.; Wolff, T.; Silander, O.; Eggink, D.; Reusken, C.; Vennema, H.; Park, A.; Carrington, C.; Sahadeo, N.; Carr, M.; Gonzalez, G.; Diego, Search Alliance San, National Virus Reference, Laboratory, Seq, Covid Spain, Danish Covid-19 Genome, Consortium, Communicable Diseases Genomic, Network, Dutch National, Sars-CoV-surveillance program, Division of Emerging Infectious, Diseases, de Oliveira, T.; Faria, N.; Rambaut, A.; Kraemer, M. U. G..
Wellcome Open Research ; 6:121, 2021.
Article in English | MEDLINE | ID: covidwho-1259748


Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website ( which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

Microbiology Australia ; 42(1):3, 2021.
Article in English | EMBASE | ID: covidwho-1223134
Pathology ; 52(7): 745-753, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-1042213


The first laboratory confirmed case of Coronavirus disease 2019 (COVID-19) in Australia was in Victoria on 25 January 2020 in a man returning from Wuhan city, Hubei province, the People's Republic of China. This was followed by three cases in New South Wales the following day. The Australian Government activated the Australian Health Sector Emergency Response Plan for Novel Coronavirus on 27 February 2020 in anticipation of a pandemic. Subsequently, the World Health Organization declared COVID-19 to be a Public Health Emergency of International Concern followed by a pandemic on 30 January 2020 and 11 March 2020, respectively. Laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is key in identifying infected persons to guide timely public health actions of contact tracing and patient isolation to limit transmission of infection. This article aims to provide a comprehensive overview of current laboratory diagnostic methods for SARS-CoV-2, including nucleic acid testing, serology, rapid antigen detection and antibody tests, virus isolation and whole genome sequencing. The relative advantages and disadvantages of the different diagnostic tests are presented, as well as their value in different clinical, infection control and public health contexts. We also describe the challenges in the provision of SARS-CoV-2 diagnostics in Australia, a country with a relatively low COVID-19 incidence in the first pandemic wave but in which prevalence could rapidly change.

COVID-19 Testing/methods , COVID-19/diagnosis , SARS-CoV-2/isolation & purification , Australia , Clinical Laboratory Techniques/methods , Humans
Microbiology Australia ; 41(3):145-149, 2020.
Article in English | EMBASE | ID: covidwho-944038


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.

Microbiology Australia ; 41(3):115, 2020.
Article in English | EMBASE | ID: covidwho-944037
Pathology ; 52 (Supplement 1):S52, 2020.
Article in English | EMBASE | ID: covidwho-830394


Background: Quality assurance (QA) of testing is important for our ability to be certain results we provide to patients are accurate and definitive. Testing agents of biosecurity concern includes Security Sensitive Biological Agents (SSBA) such as Tier 1 agents (anthrax, Ebolavirus, influenza, HPAI, SARS, smallpox, plague) and Tier 2 agents (swine fever, botulism, Tularaemia, yellow fever, etc). Test QA is limited by need for containment at BSL3 and BSL4 level, difficulties accessing reagents due to serious public health consequences of organism release, and increasing regulation. Methods in providing QA: The Biosecurity Quality Assurance Program (BSQAP) was formed after 2008 when the SSBA Regulatory Scheme for control of select agents was established. The program addresses the unique problems of SSBA by utilising novel methods for QA, including subgenomic non-infectious molecular targets, online e-learning, and recently whole genome sequencing (WGS) programs assessing new technologies. Discussion(s): Emerging technologies (multiplex Biofire systems, WGS) and continuing emergence of novel threats (Ebolavirus, HPAI) mean laboratories need rapid, accurate QA support. Tests introduced nationally by reference laboratories in response to emergent threats often lack prior QA, experience, and appropriate reagents. Addressing these systematically through regulatory preparedness (the 'PHLN' module, early governmental engagement), novel methodologies (above), high level engagement (Commonwealth, WHO, AFP) and expertise has assisted successful public health responses. Acknowledgements: BSQAP program members Joanna Gray, Torsten Theis, Katherine Lau, Peter Santosa, RCPQAP Tony Badrick, Commonwealth Government. References 1. Lau KA, Theis T, Gray J, et al. Ebola preparedness: diagnosis improvement using rapid approaches for proficiency testing. J Clin Microbiol 2016;55: 783-90. 2. Theis T, Lau KA, Gray J, et al. Proficiency testing for the detection of Middle East respiratory syndrome-coronavirus demonstrates global capacity to detect MERS-CoV. J Med Virol 2018;90: 1827-33. Copyright © 2020