Decentralised COVID-19 molecular point-of-care testing: lessons from implementing a primary care-based network in remote Australian communities

Abstract

First Nations people experience high levels of chronic disease, resulting from a history of colonisation, institutional racism and policies that have disempowered participation in practices that would otherwise support health and wellbeing.^{1, 2} In addition, First Nations people living in remote areas have limited access to primary and specialist care, hospital and pathology services and reduced infrastructure.^{3, 4} These factors contribute to infectious diseases having a disproportionately greater impact on First Nations people living in remote areas compared with urban settings.^{4, 5} Funded by the Australian Government and with First Nations-led governance, the Aboriginal and Torres Strait Islander COVID-19 Point-of-Care Testing Program (hereafter referred to as the program) was implemented in early 2020. Testing was conducted by primary care clinicians using the GeneXpert assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; Xpert Xpress SARS-CoV-2, Cepheid) enabling increased access to molecular-based testing, and therefore quicker results. The program rapidly became the world's largest decentralised SARS-CoV-2 molecular point-of-care (POC) testing network.⁶ The program was delivered across three distinct epidemiological phases of the coronavirus disease 2019 (COVID-19) epidemic in Australia, each with associated public health responses (Box 1).

To inform future infectious disease pandemic preparedness and responses, we used an adapted POC testing framework,⁶ based on the World Health Organization health system building blocks⁷ to systematically review program documents, including standard operating procedures, internal team communications, and formal program updates to partners. The review process identified, collated and documented key recommendations. Box 2 shows the updated framework, which now includes workforce and training, results support, and reflects an enhanced focus on the community as central to program effectiveness.

The success of the COVID-19 response in First Nations communities in Australia is attributed to engagement and leadership by First Nations people.^{8, 9} The program was overseen by the National Aboriginal and Torres Strait Islander Health Protection subcommittee (formerly the Aboriginal and Torres Strait Islander Advisory Group on COVID-19) of the Australian Health Protection Committee.¹⁰ This group was made up of representatives from Aboriginal community-controlled health services, other First Nations experts and government; and was responsible for the co-design and oversight of the program, and final approval of protocols, expansions and allocation of testing resources. Consistent with National Pathology Accreditation Advisory Council (NPAAC) guidelines on POC testing,¹¹ the program ensured a model of clinical governance through a clinical advisory group with expertise in virology, infectious diseases, and First Nations remote clinical practice. The expertise of this group proved invaluable in ensuring the POC testing systems were tailored appropriately to First Nations-led health services. The governance model was later modified, retaining the First Nations governance with a dedicated First Nations leaders group, complemented with a formal clinical POC testing governance model led by a virologist. A multidisciplinary operational team consisting of medical laboratory scientists, public health epidemiologists, information technology specialists, logisticians, clinicians, POC testing experts and Aboriginal and Torres Strait Islander health workers ensured a responsive and adaptable program network.

Maintaining the patient and community as central to the program framework was fundamental to its effectiveness and is a key difference compared with other frameworks in infectious disease diagnostic testing.^{12, 13} Each health service integrated molecular POC testing in ways that met community needs and staff capacity. Approaches included regular testing of clinical staff to minimise furloughing, thereby keeping the service open during peak community outbreaks and having a dedicated POC operator during high demand periods. Health services led communications regarding the availability of the molecular POC testing in their community.

From April 2020 to August 2022, health services conducted 72 624 SARS-CoV-2 patient POC tests (average of 596 tests per week).¹⁴ Most tests (67.1%) were conducted in First Nations peoples,¹⁵ with limited testing conducted in non-Indigenous people (clinical staff or other frontline workers). This proportion of testing in First Nations peoples increased from 65.3% in Phase 1 to 75.3% in Phase 3, suggesting more targeted testing once community transmission was established.¹⁴ Program data facilitated support to services to ensure targeted testing occurred, particularly during periods of limited testing resources. The test positivity rate per 100 tests, by jurisdiction, has been described elsewhere.¹⁵

Molecular POC testing detected the first positive cases in most communities (Box 3), leading to rapid responses from health service staff in partnership with visiting public health teams within 0–1 day following case detection (unpublished data from public health departments and Aboriginal community-controlled health organisations across three jurisdictions with the highest number of participating services).

As of 31 August 2022, 105 clinics (government-managed or community-controlled) were enrolled in the program.¹⁵ Most clinics were in very remote (66%) and remote areas (12%) (Box 4) across six jurisdictions. Communities ranged in size from 80 to over 9000 First Nations people. The initial site selection criteria⁶ evolved with each epidemiological phase, with greater demand for additional clinic enrolment where existing laboratory capacity was exceeded. Hub and spoke models, with molecular POC testing at a larger clinic and the ability to provide test results to nearby smaller communities, were effective only in a limited number of settings as the increased demand on staff time for transportation of samples became unfeasible.

The median aerial distance from participating health services to the nearest laboratory that offered molecular SARS-CoV-2 testing was 569 km (interquartile range [IQR], 351–1128 km), with the average driving time about 8 hours. Some services endured additional accessibility challenges, such as services on remote islands or where road travel was disrupted by monsoonal conditions. Most (90%) services were in areas considered to be among the most disadvantaged nationally (based on the Socio-Economic Indexes for Areas deciles 1–3).¹⁶ Three services withdrew from the program (up to August 2022) indicating workforce constraints and/or waning perceived benefit as pandemic risk abated.

Across all phases, the program ensured that operating procedures were consistent with relevant national laboratory guidelines, and regulatory frameworks for POC testing.^{11, 17, 18} Following the availability of rapid antigen tests (RATs) (November 2021), the program (in consultation with the clinical advisory group and jurisdictional partners) provided guidance on appropriate use of molecular POC testing (Box 5). Considering the lower sensitivity and thus higher false-negative result rate with RATs compared with molecular POC tests (particularly in early or asymptomatic infection),^{19, 20} solely relying on RATs to detect the first cases in a community would have led to substantial delays in individual and public health responses.

The program team participated in intensive stakeholder engagement to target support and identify high risk community events, including COVID-19 cases detected in other communities with known community links, and wastewater surveillance detections. This approach enabled the program to respond quickly to changing demand, identify optimal transport routes, coordinate local consumable surge supply storage, and deploy additional or new testing equipment to locations where outbreaks were expected (Box 6).

Program engagement with pathology providers ensured complementary and equitable testing coverage, enhanced capacity where needed, and identified appropriate referral testing pathways. The program became an important source of bidirectional communication to alert health services, public health, reference laboratories and government regarding first cases in remote communities. Following the first outbreak in a remote area, the program disseminated key lessons learnt with stakeholders across the network that were yet to experience an outbreak to assist community preparation.

The program's risk and quality management framework was developed in accordance with the NPAAC requirements for POC testing in Australia and included risk assessment and mitigation, POC operator training and competency assessment, quality control and external quality assurance.⁶ This framework was continuously enhanced in response to the changing epidemiology (Box 7).

As of the end of August 2022, 908 clinic staff (nurse, Aboriginal health practitioner or doctor) had completed theoretical training and practical competency assessments.¹⁵ Following the increase in COVID-19 cases (Phases 2 and 3), additional focus was placed on potential risk for contamination, waste disposal, infection prevention and control during the testing process, including environmental monitoring and decontamination procedures and device/equipment maintenance.

Existing constrained staff capacity in remote health services was further exacerbated by the pandemic travel restrictions.²³ Staff capacity was often identified as a key factor for testing errors, highlighting the need for a dedicated, sustainably funded, POC test operator workforce model and scientific support services going forward. During peaks in testing demand (Phases 2 and 3), the program (in consultation with the clinical advisory group) provided evidence-based, epidemiologically guided support to staff to prioritise molecular POC testing to balance workload demands, community expectations and maintain test quality.

The program connectivity system^{6, 24} was optimised to strengthen the reliability and timeliness of results delivery, including automated email alerts and middleware upgrades to enable more streamlined identification and rectification of connectivity disruptions and support changes to testing guidelines, results management and compatibility with co-implemented proprietary testing software (GxDx, Cepheid).

The median transmission time for test results to end-user databases (calculated from the start of test to receipt by recipient, inclusive of test run time of 45 minutes) was 1.4 hours (IQR, 0.95–2.4 hours) in 2021.²⁴ Considering the receipt of a centralised pathology result for samples collected in remote communities routinely takes 4–6 days (longer in outbreak periods), the 72 624 patient tests conducted at the POC testing sites equated to 17 564 days saved in receiving positive SARS-CoV-2 test results (calculation based on 4391 positive test results¹⁵ and the four-day minimum result turnaround time from centralised laboratories within the study period).

All six jurisdictions were supplied with test results in a manner that satisfied mandatory case notification requirements for public health surveillance, representing the first large decentralised POC testing network of its kind in Australia to satisfy this requirement.

Procurement and access to test cartridges was coordinated nationally by the Australian Government. The program received a third of all cartridges available nationally each week — above the population proportional allocation — accounting for the specific risks associated with higher levels of chronic disease and lack of timely testing alternatives in remote communities. Despite this, demand exceeded supply during Phases 1 and 2, until RATs became available during Phase 3.

The program used an agile supply management system to ensure adequate stocks across the network, particularly in locations often cut off from regular supply routes due to COVID-19 border closures or seasonal weather. Key adaptations to enhance the system included: (i) the establishment of an electronic alert system to identify low clinic stock; (ii) engagement with services to pre-empt increased test demand; (iii) collaboration with pathology providers to ensure adequate testing coverage; and (iv) stock expiry management.

There was an early and justifiable recognition in Australia that COVID-19 public health responses needed to prioritise and tailor strategies for remote areas to ensure equitable access to health and other support services for First Nations peoples. In Australia, this translated to significant action through the implementation of service-led, decentralised COVID-19 molecular POC testing, which became part of a comprehensive, responsive and integrated public health response.

Decentralised molecular POC testing embedded into primary health services was an integral component of Australia's COVID-19 outbreak response in First Nations communities and if sustained, will provide key preparedness infrastructure to respond to future pandemics.

Fundamental recommendations are summarised in Box 8. We acknowledge the limitations of these recommendations as they were generated through the lens of program staff, and therefore may contain some biases. However, as these staff were involved in the implementation of this program over the entirety of the pandemic response, this perspective provides a unique insight that warrants reporting.

The established relationships, First Nations people-led governance, decentralised asset network and infrastructure provide the opportunity to evaluate, implement and scale up POC testing for other priority infections in these communities (including influenza, respiratory syncytial virus, sexually transmitted infections, hepatitis C, human papillomavirus and group A Streptococcus), and serves as a model for future emergency responses for infectious diseases with epidemic potential. Going forward, establishing sustainable funding models to support all facets of the program (Box 2) will be critical to the wider adoption of decentralised molecular testing in Australia and other settings.

Open access publishing facilitated by University of New South Wales, as part of the Wiley - University of New South Wales agreement via the Council of Australian University Librarians.

Cepheid has contributed in-kind study equipment (cartridges, machines) to the project Scaling up Infectious Disease Point-of-care Testing for Indigenous People (RARUR000080) funded by the Medical Research Future Fund (MRFF) Rapid Applied Research Translation (RART) grant.

Not commissioned; externally peer reviewed.