​Fall 2022

​Emerging amid the spread of yet another variant of SARS-CoV-2, the monkeypox outbreak feels a bit like a test of how well public health agencies have learned the lessons of the COVID-19 pandemic. Well into the third year of the pandemic and staring down an uncertain autumn, the timing is right to build on the momentum of support for public health laboratories to further strengthen laboratory systems and their place in ongoing global surveillance efforts.

Hands of different skin tones surrounding and protecting a globe picturing Africa and Asia

by Jill Sakai, PhD, writer

In May, a small cluster of monkeypox cases was identified in the United Kingdom. Global public health agencies acted quickly, monitoring the outbreak from its earliest days and gearing up for possible wider testing needs.

Emerging amid the spread of yet another variant of SARS-CoV-2, the monkeypox outbreak feels a bit like a test of how well public health agencies have learned the lessons of the COVID-19 pandemic. The past few years have made clear that global collaboration and communication are critical for identifying and managing public health risks, and that a strong system of public health laboratories—in the US and abroad—is central to these surveillance efforts.

That global perspective is a critical foundation for successful public health efforts domestically.

"We have to care about what’s going on outside our borders. Monkeypox didn’t originate here, yet here we are,” said Lucy Maryogo-Robinson, MPH, APHL director of Global Health. “Surveillance is really the best tool we have.”

Well into the third year of the COVID-19 pandemic and staring down an uncertain autumn, the timing is right to build on the momentum of support for public health laboratories, to further strengthen laboratory systems and their place in ongoing global surveillance efforts.

“I think that we are at a turning point now,” said Sébastien Cognat, PharmD, MSc, head of the Public Health Laboratory Strengthening unit of the World Health Organization (WHO). “We need to think of how to make sure that all the investments, the momentum, the recognition of the role of laboratories is sustained, … that laboratories are not seen only as a tool to support patient care or as a tool to support surveillance, but truly as a key element.” At the same time, there is an opportunity to harness that progress to integrate efforts across multiple health sectors toward a more unified, One Health approach that is ready and able to detect future threats.

Centering Surveillance

Even as more testing is now shifting out of the laboratory to clinic and at-home testing, public health laboratories still have a key role to play. Ongoing COVID-19 monitoring—as well as experiences with Ebola and, increasingly, monkeypox—shows that laboratory data can be a useful real-time tool for surveillance.

Many laboratory systems are now leveraging the substantial pandemic-driven investments in infrastructure and capacity to bolster ongoing surveillance efforts. In Africa, for example, when COVID-19 was declared a public health emergency of international concern, only two national laboratories on the continent had validated testing protocols for SARS-CoV-2—in South Africa and Senegal. Over the following months and years, Africa CDC spearheaded an effort to build laboratory capacity across the continent.  The team trained laboratorians from more than 40 countries and coordinated partnerships with governments, companies and national and international organizations to mobilize support and supplies. They provided laboratories with guidelines, technical assistance and quality assessment.

At the same time, Africa CDC built capacity for next-generation sequencing (NGS), mobilizing funding and manufacturers to enable molecular surveillance at a network of laboratories across the continent. In 2019, just seven national public health institutes had sequencing capabilities; now 37 countries can do in-country sequencing and the rest can access sequencing support through regional hubs.

In addition to representing an enormous step for the region, this network lays key groundwork for future preparedness efforts, said Yenew Kebede Tebeje, MD, MPH, MSc, head of the Division of Laboratory Systems and acting head for the Division of Surveillance and Disease Intelligence at Africa CDC. “The next step for us will be how to sustain this program, which means applying these technologies beyond COVID-19.”  Similarly, laboratorians in Southeast Asia are thinking about how significant investments in NGS infrastructure and expertise can now be used to support genomic surveillance for multiple pathogens and disease threats, including acute febrile illness, antimicrobial resistance and priority zoonotic diseases such as influenza, rabies, nipah virus and more. Disease-agnostic approaches are an important strategy to improve efficiencies and integrate a One Health focus that spans sectors to simultaneously support human, animal, food and environmental health.

“Right now, we have really good opportunities to develop infrastructure [and] human resources that will last to help with other diseases,” said Ong-orn Prasarnphanich, DVM, MPH, DACVPM, chief of US Centers for Disease Control & Prevention (CDC) Thailand’s One Health Branch. One example in the region is wastewater-based SARS-CoV-2 surveillance, which is being expanded beyond humans to monitor the environment in Thailand, wildlife in Vietnam, and both bats and the animal-human interface in Indonesia.

An Environmental View

Wastewater-based surveillance is an important focus in Africa as well, part of the Global Fund’s project STELLAR to scale up testing for long-term strengthening of laboratory systems. Environmental surveillance offers a powerful opportunity to span disease pillars, said Toni Whistler, PhD, a US CDC detailee to the Global Fund. Up to now, she noted, most programs have had a singular focus: HIV, for example, or tuberculosis, or malaria.

“One thing this pandemic has shown us over and over and over again is that, from a laboratory systems point of view, that really doesn’t work when you want preparedness.” Environmental surveillance programs are already used to monitor polio and other agents in parts of Africa.

“Wastewater is a valuable, complex sample that has a host of molecular and NGS applications, including polio, monkeypox, antimicrobial resistance markers, pan-respiratory disease agents and emerging infectious diseases,” said Noah Hull, PhD, MPH, APHL laboratory technical manager for Global Health.

“It is also independent of healthcare-seeking behaviors. This is really where NGS and wastewater-based surveillance can intersect and provide valuable—and actionable—public health intelligence.”

Newer initiatives in South Africa and Botswana (as well as in the US) have shown the utility of wastewater for COVID-19 monitoring as well.

“Through use of [waste]water-based surveillance systems, countries or public health institutions were able to identify potential new hotspots for COVID-19 before actual cases were realized,” said Osborn Otieno, STELLAR project manager and advisor for the Global Fund’s Integrated Laboratory Systems Strengthening and Health Security team. That makes the approach “a very critical tool as an early warning indicator before an outbreak or a spike can be reported within any community setting.”

Earlier this year, thanks to support from the Global Fund, APHL started wastewater-based surveillance pilots for SARS-CoV-2 in Kenya, Uganda, Ethiopia and Mozambique. The APHL team has conducted in-country needs assessments and is providing technical assistance to develop detailed protocols for implementation, drawing on protocols that have been used successfully in the US and working with the Ministries of Health and National Institutes of Health to adapt them to local contexts. Sampling and molecular analysis were scheduled to roll out in late summer, alongside efforts to develop local dashboards that would allow national public health institutes to access data in real time.

The project partners work with each country to model the implementation through a bottom-up process. It takes time, Otieno said, “but the beauty of it is that the countries have been able to come up with a scientific protocol that is country-owned and jointly developed through stakeholder participation at country level.”

That ownership is key for the sustainability of these projects. It is also critical when thinking about data management, because considerations and sensitivities around data and information vary from country to country.

Some countries are open, while others have a lot of rules and regulations on how to manage public health information,” Otieno said. In Kenya, with input from stakeholders across multiple ministries, they have been able to develop a laboratory information system interface to automate data collection and transmit it to a national repository to guide decision making, while ensuring data integrity and de-identification.

Importantly, these “environmental surveillance pilots are being implemented at a time where there’s a massive decline in testing,” Whistler said. In this context, environmental surveillance for enteric pathogens provides a critical window into the course of the pandemic, including tracking the emergence of new variants.

“It’s the first time, really, that we’ve had tools available to us that would allow low-middle income countries or countries with lesser surveillance capacity to … have a very useful tool at their fingertips for surveillance,” she said

A Laboratory Ecosystem

To be truly successful, such laboratory strengthening efforts need to occur within the framework of a broader laboratory ecosystem that can streamline disease-agnostic financing, procurement, workforce development and, ultimately, delivery of services.

“The last mile, as we say, is extremely difficult,” Cognat said. “If you have done all the steps from research, development, delivery [and] regulations, but then your diagnostics are in laboratories that are not available for most of the population”—due to geographic, financial or information barriers, for example—”the efforts and investments made upstream are totally useless.”

Currently, various aspects of that ecosystem fall under purview of a wide range of agencies, ministries and departments. In this fragmented environment, laboratory systems need to have strong leaders who can convey the importance and value of laboratory services to non-experts, including policymakers, Cognat said. Too often, “laboratories are seen as a cost, not as an investment,” he noted.

“We need to change this mindset. We need to be able to articulate a new vision, we need to be able to convince decision makers.”

This is where the Global Laboratory Leadership Programme (GLLP) comes in, to foster a new generation of laboratory leaders who can articulate the value of laboratories and advocate for laboratory needs. This program, developed in partnership by the APHL, US CDC, European Centre for Disease Prevention and Control, Food and Agriculture Organization of the United Nations, World Organization for Animal Health and WHO, includes a comprehensive framework of core competencies for building resilient, responsive laboratory systems and is now in the pilot phase.

One focus is to make the GLLP a true One Health program, engaging individuals from multiple sectors to work on joint projects that address the needs and strengths of each sector toward a better overall outcome. The goal is not just to know each other, but to know how to work together, Cognat said.

Spanning Silos

Such partnerships are at the heart of many COVID-19 success stories, as the scope, scale and urgency of the pandemic pushed a wide range of groups toward a shared focus. Powerful—and sometimes unexpected—collaborations emerged during the pandemic.

“We did not think that we can really get so many stakeholders together before,” Prasarnphanich said. But forging those connections is critical. Kebede attributes much of the success of Africa CDC’s programs to the authority and buy-in given to the agency by the member states, noting that they were able to convene heads of state 13 times in the last two years in a joint continental effort for pandemic response.

Integration across sectors also holds several advantages for surveillance efforts specifically. One is that, especially in the case of zoonotic disease, early signs of outbreaks can often be detected in animals long before people. Another is the potential cost savings when sectors share costly facilities and equipment, such as sequencing platforms or high-containment laboratories. And in many cases, a richer data set can be obtained by combining inputs from multiple sectors. Signs of antimicrobial resistance, for example, can be detected in animals, people, food products and the environment, such as in sewage, water or soil.

"It’s of mutual benefit,” Cognat said. “It’s not only the animal and environmental sector contributing to human health, it’s also the other way around.”

Within that, it is critical to remember that each organization at a table has its own agenda, priorities, mandates and regulations.

“We cannot really force them to see the same picture,” Prasarnphanich said. “But I think we can frame the big picture together—find a common goal.”

COVID-19 is a perfect example: essentially, everyone would like the pandemic to be over. But how each agency and organization can contribute to—and benefit from—that goal will be different. Some organizations might be able to provide training and technical expertise, while others might provide access to new regions to expand surveillance reach. Still others might be best able to contribute financially. “We cannot expect all organizations to have the same level of funding, the same level of human resources or the same level of expertise to offer,” Prasarnphanich said.

Likewise, different health sectors work in different contexts, and supporting them may require different approaches and investments. Thinking about surveillance in Thailand, for example, the public health sector already has established platforms to store health data but could benefit from help to utilize their data most effectively and efficiently. The animal health sector may have access to information but lacks a central data management system. And none of these mechanisms may be relevant for the wildlife health sector, where rangers need to be able to collect data in the field.

True multi-sector partnerships must be built on mutual understanding and trust that each sector will contribute as it is best able to meet the collective need. For a true One Health approach, all sectors need to have equally strong seats at the table, said Beth Skaggs, PhD, laboratory team lead of US CDC’s Division of Global Health Protection Thailand office. That can be a challenge when the sectors do not have the same capabilities and resources, setting up inequities that must constantly be addressed. Continuity of funding is a constant challenge. In the absence of a threat like the pandemic, funding for surveillance gets cut, Skaggs said.

“We end up having to do patchwork approaches to sustain surveillance when things are calm—which is unfortunate, but that’s the reality,” she said. Continuous, reliable funding for sustained surveillance efforts would go a long way toward easing imbalances. So would an established data system compatible across sectors and data-sharing agreements that allow real-time analysis for decision making.

Data Modernization

Despite clear benefits to the global population when countries share surveillance data, such as through the GISAID platform, data sharing is an ongoing challenge. Country-specific laws and concerns about data privacy and security can create barriers to transparency and openness, and there are often delays. For avian influenza surveillance work in Thailand, Prasarnphanich said, it took six months to a year to get the needed representatives from both public health and animal health sectors on board, then establish a platform for sharing information. That investment is key to building the foundational relationships, Prasarnphanich said. “Once that platform [and] the trust is established, I think it’s easier to continue that kind of communication among different sectors.”

It’s well known, though, that infrastructure to support public health data collection—whether in support of surveillance, response or even research—is in dire need of updating and expansion. Those needs have been exacerbated by the demands of COVID-19, said Xenophon Santas, associate director of Informatics at US CDC’s Center for Global Health. After years of advocacy work by the APHL and other partners, CDC’s Data Modernization Initiative received a large infusion of funding through the CARES Act and the American Rescue Plan to update public health data infrastructure and processes throughout the US. In recognition that other countries face similar challenges, the American Rescue Plan included $140 million over three years for a project that will expand similar efforts globally.

Now, Santas said, there is an opportunity to assist global partners to modernize and strengthen their data infrastructure and data governance to better enable data collection and sharing. “The world benefits by having better ways of sharing data in order to be able to detect [and] respond to emerging health threats.”

The CDC-led and APHL-supported project adopts a two-pronged strategy: focus on solutions that can demonstrate immediate impact and serve as proof-of-concept for one or more countries, while simultaneously working on longer-term governance initiatives to ensure sustained and continued use of modernized systems and approaches. Multiple components will address data automation to streamline electronic capture of laboratory results internally within a testing laboratory and external reporting from a testing laboratory to relevant public health systems and stakeholders, electronic laboratory reporting, and data analytics for rapid and informed decision making.

APHL will help each host country government define a locally appropriate system architecture for consolidating data and systems. Importantly, the project will also draw on lessons learned from the US Data Modernization Initiative to address concerns around cloud hosting of laboratory data. These issues include the use of cloud infrastructure and shared services, required governance, and legal and policy development to protect data ownership, storage and sharing. Additional components will target workforce strengthening and coordination and communication, with efforts made to adapt progress from the US Data Modernization Initiative. These efforts are underway in 10 countries: three in Asia, four in Africa and three in Latin America.

“Data infrastructure needs to be thought of as a consolidated activity, not a one-off, so that we’re not reinventing the wheel every time we have a new public health threat,” Santas said. An effective information management system should be in place before it’s needed. “Prior to the current modernization efforts, it could take longer to design and stand up a system than it would for an outbreak to mature and peak and be finished.”

Preparing for the Future

Ultimately, the global community is interconnected, and now is the time to build strong structures and partnerships to sustain that community through whatever is coming next. “You cannot spend much time building your capacity during wartime. During war, you go with whatever tools that you have,” Kebede said. “We need to do a lot of investment during normal time.”

That also means shaping preparedness efforts around the priorities that should be reflected during active outbreaks. Prasarnphanich’s vision is to formalize One Health within the structure of organizations and integrate interagency coordination as part of the routine work of each: “To make One Health not just an approach, but more of the culture,” she said.

Asked what a successful surveillance program would look like, Cognat emphasized real-time information sharing in support of decision making, with mutual trust across sectors. It’s also essential, he said, to ensure that the people and systems who are providing the data receive equitable benefit from the vaccines, therapeutics and knowledge that emerge from that data.

"At the moment, we can’t tell what will come next. Robust surveillance activities will be a key tool to identify potential future pandemics and elicit public health response in very good time,” Otieno said. “There have been a lot of lessons learned from COVID-19, and we should not make a repeat of those same mistakes.”