Potential Benefits of Implementing High-Throughput Sequencing (HTS) Technologies for Pandemic Pathogen Detection in Latin America and the Caribbean

This project was carried out as part of the “Carreras con Impacto” program during the 14- week mentorship phase. You can find more information about the program in this entry.

Overview

The world has seen a significant rise in catastrophic global risks, with pandemics being among the most prominent. The COVID-19 pandemic exemplifies this global risk, having devastating consequences on regional security, public health, and socio-economic stability. The high population density, accelerated urbanization, and inequalities in healthcare access have exacerbated the impact of epidemics in this region.

This post explores the potential benefits of implementing high-throughput sequencing (HTS) technologies to enhance pathogen detection and prevention in Latin America and the Caribbean (LAC). By leveraging advanced genomic tools, the region can improve its ability to detect, monitor, and respond to emerging health threats.

References

• Soon, W. W., Hariharan, M., & Snyder, M. P. (2013). High‐throughput sequencing for biology and medicine. Molecular Systems Biology, 9(1), 640. https://doi.org/10.1038/msb.2012.61
• Talia Kustin, Kustin, T., Adi Stern, & Stern, A. (2020). Biased mutation and selection in RNA viruses. Molecular Biology and Evolution, 38(2), 575–588. https://doi.org/10.1093/molbev/msaa247
• Wang, Y., Zhao, Y., Bollas, A., Wang, Y., & Au, K. F. (2021). Nanopore sequencing technology, bioinformatics and applications. Nature Biotechnology, 39(11), 1348–1365. https://doi.org/10.1038/s41587-021-01108-x
• World Health Organization. (2021). Medidas decisivas de preparación, disposición a la acción y respuesta frente a la COVID-19. WHO/2019-nCoV/Community_Actions/2021.1

Motivation and strategy
Motivation

In a rapidly changing world with significant technological advances, diagnostic methods must evolve in tandem with these changes. It is not feasible to rely on traditional techniques to protect us from catastrophic events, much like insisting on doing mathematical calculations by hand instead of using a computer—it sounds crazy, right? This is why the primary motivation for this document is the urgent need to improve the detection and prevention of pandemic pathogens in Latin America and the Caribbean (LAC). Pandemic prevention and preparedness has often been a neglected area globally, yet we must be prepared for rapid responses and effective actions. The COVID-19 pandemic could have had a much lower mortality rate if the world had been better prepared in prevention and diagnosis. However, instead of viewing this pandemic as a loss or something negative, it is proposed to see it as a time for experience and learning. Now, with the rapid development of high-throughput sequencing (HTS) technologies, there is a timely opportunity to leverage these advancements to enhance pathogen detection and epidemiological surveillance. Additionally, Latin America and the Caribbean are areas of interest due to their high genetic diversity and varied levels of public health infrastructure, making regional collaboration and capacity building crucial.

Figure 1: Theory of Change - This diagram outlines the inputs, outputs, outcomes, and goals associated with implementing sequencing techniques in Latin America and the Caribbean to enhance pandemic preparedness and public health surveillance.

Strategy

  Comprehensive Literature Review: To establish a solid evidence base on current epidemiological surveillance and the applications of HTS technology.

  Case Studies and Examples: To illustrate the effectiveness of HTS technologies, the document presents case studies or examples from other regions or countries that have successfully implemented these tools.

  Advocacy and Policy Integration: The strategy includes advocating for policy changes and increased investment in HTS technologies. This involves highlighting the long-term benefits of improved pathogen detection and pandemic preparedness for public health and economic stability.

Methodology
Firstly, data analysis played a crucial role in identifying trends, patterns, and gaps in current pathogen detection capabilities. The development of recommendations was based on the insights gained from data analysis and stakeholder engagement. It is proposed that experts in the field formulate viable options for policy changes. These recommendations increased investment in HTS technologies, and the enhancement of infrastructure and capacity building. The goal was to ensure that the implementation of HTS technologies would address identified gaps and improve the overall effectiveness of pathogen detection and pandemic preparedness in Latin America and the Caribbean.

Table 1. Pathogen Scoring Based on Evaluation Criteria

Note: A: Epidemiology, B: Transmissibility, C: Prevention and Control, D: Pathogen Characteristics, E: Impact and Response

Table 2: Comparative Results of Traditional Detection and Diagnostic Methods vs. Sequencing Methods

Results and discussion 

In the realm of pathogen detection and pandemic preparedness, categorizing pathogens was a critical first step. Pathogens were systematically categorized according to their potential to cause pandemics in Latin America and the Caribbean. This list considered factors such as transmissibility, morbidity, mortality, and the ability to cause widespread outbreaks. Based on this, prioritization criteria such as infection rate, disease severity, vaccine development potential, and public health impact were defined, and each was assigned a scoring system to classify pathogens and ensure a methodical evaluation that highlights those requiring immediate attention and resources.

The Coronavirus SARS-CoV-2 received the highest score of 81.5 points due to its high airborne transmissibility, extensive global spread, and significant impact on public health and the economy. The constant emergence of new variants increased its pandemic potential. The Coronavirus SARS-CoV and Influenza A viruses H2N2, H3N2, and H1N1 also received high scores, ranging between 77.25 and 77.5 points. These viruses shared a high transmission capacity and a history of causing significant pandemic outbreaks. Influenza A, known for its mutability, represented a continuous threat due to its rapid spread and pandemic potential.

It was interesting to note that despite the extreme danger of the Ebola virus, its transmission capacity limited to direct contact with bodily fluids reduced its potential to cause global pandemics compared to respiratory viruses. The ease of propagation of respiratory viruses, combined with the high incidence of asymptomatic or mild cases, presents a significant challenge for control and response. Additionally, the high mutation rate of RNA viruses, such as coronaviruses and influenza viruses, facilitates their rapid adaptation to new hosts or conditions, increasing their virulence and ability to evade the host immune response.

In pathogen detection, an exhaustive categorization of diagnostic methods was carried out. Information was collected on the most used methods in Latin America and the Caribbean for the surveillance, control, diagnosis, and detection of priority, emerging, and re-emerging pathogens. Several sequencing methods were also selected based on their technical characteristics to compare their features and results in different areas. To define prioritization criteria and scoring levels, several technical, economic, and social factors were established. Technical criteria, covering 60 points, included sensitivity, specificity, reproducibility, accuracy, response time, availability of reagents, storage and stability of reagents, detection limit, robustness, result stability, dynamic range, interferences, and compatibility with automation. Economic criteria, covering 12 points, considered cost, infrastructure, and equipment requirements. Human talent criteria, also with 12 points, included training needs, ease of use, and safety. Finally, social and political management criteria were considered, such as adaptability and scalability, applicability in various contexts, impact on patient management, accessibility, acceptability, regulation and approval, government and political support, and sustainability.

Detection methods were classified into traditional and sequencing methods. PCR was highly valued for its sensitivity and specificity relative to its cost-benefit ratio, making it particularly attractive for diagnosing complex or high-risk diseases. Despite being a more expensive technique, PCR was considered the gold standard in many diagnostics in both health and research fields. However, traditional detection and diagnostic techniques, such as urine and blood tests, remain the most used due to their low cost and ease of implementation.

Sequencing technologies, on the other hand, scored higher due to their greater sensitivity, robustness, and dynamic range. Sanger sequencing, although known for its precision, was limited by its slowness and high cost. Illumina technology, despite its high accuracy, presented complications in sample preparation. Ion Torrent technology, although fast and accurate, had issues with errors in homopolymers. The PacBio Sequel sequencer, using SMRT technology, stood out for its high precision and ability to generate extremely long reads. Oxford Nanopore's nanopore sequencing technology also stood out for its ability to generate real-time data and ultra-long reads without the need for DNA amplification.

The MinION from Oxford Nanopore Technologies (ONT) emerges as an outstanding option for diagnostic methods due to its ability to sequence long DNA and RNA reads in real-time. Unlike traditional techniques such as PCR and ELISA, which require amplification and are limited in the length of sequences they can analyze, the MinION allows for direct sequencing without the need for amplification, thereby reducing the risk of errors associated with these additional steps. This is especially advantageous in identifying pathogens with complex or highly mutable genomes, as it provides a more comprehensive and accurate view of their genetic composition. Additionally, the ability to generate real-time data allows for faster detection and response in critical situations, which is essential for outbreak control and pandemic prevention.

Compared to other sequencing technologies like Illumina and PacBio, the MinION offers several significant advantages. While technologies like Illumina require complex and lengthy sample preparation procedures, the MinION simplifies this process by allowing direct sequencing, which is crucial in resource-limited settings. Furthermore, the MinION is portable and can be used in the field, something not possible with larger and less mobile platforms like PacBio Sequel or Illumina systems. This portability allows its use in remote areas or emergency situations, facilitating the acquisition of crucial data on-site without the need to transport samples to centralized laboratories. The MinION's ability to generate extremely long reads also surpasses many traditional technologies and other sequencing techniques, providing more comprehensive genome coverage and facilitating the identification of critical genetic variations.

From an economic standpoint, the MinION offers a very attractive cost-effectiveness balance. Despite the initial costs of acquiring the device, operational costs are considerably lower compared to larger sequencing platforms. The consumables and reagents required for the MinION are more accessible and require less maintenance, which is ideal for developing countries or institutions with limited budgets. Additionally, creating a collaborative database from data generated by the MinION can transform the landscape of epidemiological surveillance. The ability to share and compare pathogen genetic data globally facilitates rapid identification and tracking of outbreaks, promoting a more coordinated and effective response to public health emergencies. This global collaboration is essential to facing future pandemics more efficiently and reducing the impact on public health and the economy.

Implementation

The implementation of HTS technologies faces several challenges:

• Resource Availability: LAC may struggle to implement HTS techniques due to insufficient funding allocated to biotechnology research and development.
• Prioritization of Pathogens: Properly identifying and prioritizing pathogens of global importance requires a deep understanding of global and local epidemiology.
• Monitoring Techniques: Current monitoring and sequencing techniques may not meet the required standards, necessitating significant improvements.
• Comparison of Technologies: Evaluating the effectiveness and utility of HTS in the local context may be difficult due to a lack of comparative data.
• Infrastructure and Training: Establishing the necessary infrastructure and training personnel in bioinformatics and genomic analysis will require substantial investments.
• Ethical and Legal Considerations: Addressing the ethical and legal challenges related to the collection, storage, and use of genomic data is crucial for gaining public trust and ensuring proper handling of genetic information.
• Political and Governmental Support: Gaining the necessary political and governmental support is essential for the successful and sustainable implementation of HTS technologies.

Conclusion

Future perspectives in the field of pandemic and epidemic intelligence focus on the innovation of diagnostic methods and the improvement of data supervision and regulation. Developing innovative, cost-effective, and multipathogen laboratory diagnostic methods is essential to improve pathogen detection at the point of care. These rapid and precise diagnostics can significantly reduce the time between disease exposure, diagnosis, and the initiation of treatment, in addition to being accessible and easy to use. Incorporating genomic data and accessing a diversified global genomic database can strengthen the capacity to monitor multiple pathogens, ensuring adequate representation of diverse populations and geographical areas. Additionally, the supervision, standardization, and regulation of data are essential to ensure consistency and quality in data generation, supporting the validation and optimization of modeling and real-time prediction tools to improve outbreak preparedness and response.

Call to Action

Stakeholders, including governments, international organizations, and the scientific community, must collaborate to support the implementation of HTS technologies in LAC. By investing in advanced genomic tools and building regional capacities, we can create a more resilient and prepared health infrastructure to face future pandemics.

Future Perspectives

The use of artificial intelligence (AI) also stands out as a powerful tool to support complex decision-making during health emergencies, integrating data from different sources and dynamically adjusting risk assessments. Validating data obtained through AI is crucial to ensure its accuracy and relevance, avoiding misinformation, and improving public trust. Additionally, social science approaches for data sharing, the use of federated systems, and the investigation of data value chains can facilitate more efficient and secure information exchange, promoting a more coordinated and effective public health response. Evaluating and improving data governance models and infrastructures is essential to meet surveillance requirements and generate robust and sustainable pandemic and epidemic intelligence.