Table 3.

Sub-themes inductively developed in thematic analysis of LHS responses to pandemics

Theme	n	Example text from article	Refs
Subtheme
Definition
Science and Informatics
Heath information systems   Centralizing electronic data processing, storage, linking, and prediction (eHR/eMR, clinical prediction/decision, routine data collection, machine learning/AI)	26	“The technology team programmed automated eHR alerts which prompt clinicians to complete the form when a SARS-CoV-2 test is ordered, a COVID positive isolation flag is entered, or a COVID order set is initiated, to capture basic data for surveillance reporting to public health authorities. Clinicians can suppress the form if they do not consider their patient to have active COVID-19.” [64]	[31, 36–38, 40–47, 49–52, 54–58, 60, 61, 63–65]
Data-driven research and knowledge translation   Using data to automate or drive decision making and practice change (dashboard, policy, report, publication, meeting agenda based on evidence/data)	21	“…The dashboard was generated from the database and offered a snapshot of number of questions, their status (search in progress, review in progress, completed, update in progress, updated review, cancelled, review delayed).” [2]	[2, 37–42, 44–47, 49–52, 55–57, 59, 61, 65]
Digital healthcare services   Using information and communication technologies to capture and monitor patient data (remote consultation programs, the utilization of mobile apps, software, websites, smart devices)	16	“Some of the key COVID-19 Yorkshire Rehabilitation Scale questions have been embedded into a bespoke digital platform which monitors general health, The patient completes the questionnaire on a smartphone application and the clinicians access the results on a web portal.” [36]	[2, 36, 39, 41, 43, 47, 49, 51, 53, 55, 57, 58, 62–65]
Health data management   Managing the lifecycle of health data (data warehouse, repositories, database, registry, data linkage)	15	“… the RRTF decided to develop and actively maintain a registry for COVID-19 surveillance and intrahospital outcomes as a key tangible output of its research-acceleration function.” [47]	[2, 44, 45, 47, 50–52, 54, 56–58, 60, 61, 64, 65]
Patient–Clinician Partnerships
Dissemination   Communicating with the public, Improving patient health literacy	14	“The trial team also works closely with a team of communications experts to share patient stories, engage with local media to raise awareness, and create patient-facing educational materials.” [45]	[38–41, 43–45, 50, 51, 56, 57, 61, 63, 65]
Engagement   Co-design of programs, Stakeholder consultation	9	“…the LHS invested in elevating patient voices through focus groups, interviews, and surveys.” [38]	[31, 36, 38, 40, 44, 45, 49, 50, 61]
Inclusiveness   Equitable access to care	5	“However, the proliferation of telehealth also requires a deliberate focus on health equity.” [39]	[36, 39, 45, 49, 65]
Other   Exclusion of patients   Implementation theories	3	"Lay members of the public were not involved when CEST was being developed due to time and financial constraints." [2] “To this end, the growing field of implementation science will be invaluable to the continued maturation and application of clinical prediction rules to patient care.” [50]	[2, 50, 57]
Incentives
Financing   Program financial support for the development/maintenance of the LHS   Staff financial support for staff training, capacity building,   Rewards and incentives, such as   funding for participation	15	"The KPWA LHS receives programmatic funding from the health system and external funding through research-care delivery partnerships.” [38] “The CoP may also provide learning and growth opportunities, such as clinical or VHA operational fellowships and research grants.” [31] "Best practices in patient engagement, including financial compensation for participation, were incorporated" [44]	[31, 37–40, 44, 46, 49, 53, 55, 57, 58, 62, 65]
Transparency   Information available about decision-making, outcomes, processes, and costs	8	"To achieve this acceptance, trustworthiness, trust, and transparency regarding rules and ownership for this traceability platform will be mandatory." [54]	[31, 38, 45, 48, 50, 54, 59, 64]
Policies aligned for value   Policies promote measurement and evaluation of programs and improvement of processes	5	“We measure this by monitoring average time from publication of high quality evidence (e.g., Cochrane reviews, meta-analyses) to publication of an organizational guideline for a practice, and average time from release of an internal evidence-based practice (EBP) guideline to uptake among a percentage of the organization's care teams.” [38]	[38, 46, 48, 54, 55]
Program sustainability   Long term viability of the LHS	2	“… the CEST initiative experienced financial restrictions which affected its accessibility and sustainability.” [2]	[2, 62]
Continuous Learning Culture
Workforce   Experience and training   Facilitating knowledge and skill development in the LHS workforce	20	"Training programs were rapidly deployed to healthcare professionals to face this new disease, such as for patient transportation, clinical protocol, and personal protective equipment" [41] “To maintain trial awareness, we continuously reach out to hospitals across the system to promote the trial, identify local champions, and address questions" [64] "CoP members and leadership facilitate communication and set up formal collaborations with other non-VHA health care systems to create an intersystem network of collaboration for long COVID care" [31] "…dedicated time to meet to solve problems and support continuous learning" [38]	[2, 31, 37, 38, 40, 41, 43–49, 53, 55, 57, 60, 62, 64, 65]
Empowerment   Championing workforce members to become integral to the LHS
Leadership   Formal or informal leadership teams that facilitate a culture of change and learning
Capacity   Dedicated time, capacity-building or institutional support in the LHS workforce
Continuous refinement and learning   Using feedback and review to inform cycles of quality improvement	19	“…Once the data are validated, data scientists create report summaries and the evidence is presented to the initiators of the request to inform clinical guideline creation. As a clinical need evolves over time, this process can undergo further iterative cycles to refine guidelines to adapt to a changing environment."[58]	[2, 31, 40, 43–47, 50, 53–55, 57–60, 62, 64, 65]
Communication pathways   Facilitating communication via meetings, newsletters, dashboards, or resources	13	“The distribution of health education resources and the supporting of online training was facilitated by an online webinar for managers and facility trainers, as well as through the establishment of a training support WhatsApp group.” [37]	[2, 31, 36, 37, 44, 47, 48, 53, 55, 57, 58, 60, 64]
Learning collaborations   Learning via collaborations between stakeholders or a multidisciplinary team	12	"Working groups established within each regional health authority inclusive of patients, clinicians, professional services, and researchers." [44]	[2, 31, 36, 37, 44, 47, 52, 55, 57–59, 64]
Structure and Governance
Leveraging committees   Creating or using established committees to structure pandemic response	18	To provide rapid responses while preserving research integrity, two system-wide subcommittees were established…..” [47]	[2, 36–38, 40, 44–47, 49, 51, 55, 57, 59–61, 64, 65]
Leveraging supportive collaborations   Formalising collaborations with external organizations to structure the pandemic response	14	“to enhance coordination and learning as regards public health emergencies, the NCDC collaborated with state governments to set up Public Health Emergency Operations Centres (PHEOCs)." [55]	[2, 40, 44, 49, 52–55, 57, 59–61, 64, 65]
Leveraging state/national policy   Using, modifying, or creating state or national policy in the pandemic response	12	“Data access for researchers is governed by the policies and procedures dictated by the academic institutions and Ministry of Health.” [44]	[36, 40, 44–47, 50, 54, 55, 61, 64, 65]
Leveraging local policy   Using, modifying, or creating LHS-specific l policies in the pandemic response	9	“[We] assessed the quality of evidence of new programs and policies submitted as VHA legislative and budget proposals using a novel strength of evidence checklist." [40]	[38–40, 45, 51, 52, 54, 57, 61]
Setting strategic goals and planning   Creation of formal goals or plans for the pandemic response	6	“We intentionally align[ed] learning activities and opportunities with strategic and operational goals across organizational levels.” [38]	[37, 38, 40, 47, 55, 57]
Funding   Financial investment in research and staff   Provision of funding for staff specific to pandemic response	3	“Research scholars and analytic staff have been hired to support a robust set of outputs to inform care and identify research questions.” [44]	[44, 45, 51]

n number of studies. Acronyms within table: AI artificial intelligence, CEST COVID-19 evidence support team, COP community of practice, eHR electronic health records, eMR electronic medical records, KPWA Kaiser Permanente Washington, NCDC Nigeria Centre for Disease Control, RRTF retrospective research task force, VHA US Veterans Health Administration