Phylodynamic analysis in the understanding of the current COVID-19 pandemic and its utility in vaccine and antiviral design and assessment

Abstract

Over the last decades, the use of phylogenetic methods in the study of emerging infectious diseases has gained considerable traction in public health. Particularly, the integration of phylogenetic analyses with the understanding of the pathogen dynamics at the population level has provided powerful tools for epidemiological surveillance systems. In the same way, the development of statistical methods and theory, as well as improvement of computational efficiency for evolutionary analysis, has expanded the use of these tools for vaccine and antiviral development. Today with the Coronavirus Disease 2019 (COVID-19), this seems to be critical. In this article, we discuss how the application of phylodynamic analysis can improve the understanding of current pandemic dynamics as well as the design, selection, and evaluation of vaccine candidates and antivirals.

Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance

“…Benefits of genomic data sharing include more efficient public health surveillance (enabling better targeted and nuanced interventions or "precision public health"), the ability to examine local data in the global context in real time, and opportunities for research and development from data re-use (4,12,132,133). The risks of data sharing are largely of concern to data donors and relate to patient privacy, confidentiality, and data protection and security.…”

“…As such, availability of WGS capacity for pathogen surveillance is integral to recommendations on future pandemic preparedness (2). Motivated by this progress, an acceleration of a decade-long paradigm shift from traditional sector-specific epidemiological surveillance based on case notification to realtime, genomic-enhanced surveillance systems that span across sectors for the prevention and control of infectious diseases is occurring (4,9,10). These new systems integrate the epidemiological context with pathogen sequence data in a One Health framework to provide more precise risk assessment.…”

“…These new systems integrate the epidemiological context with pathogen sequence data in a One Health framework to provide more precise risk assessment. In turn, this informs the design and evaluation of adaptive responses as pathogens emerge, spread, and evolve in terms of their host range, pathogenicity, drug resistance, or capacity to escape vaccines (4,11,12). However, health inequalities and public health system vulnerabilities need to be addressed to ensure global access to WGS-based methods to enhance infectious disease surveillance and provide timely epidemic alerts and responses.…”

The Constant Threat of Zoonotic and Vector-Borne Emerging Tropical Diseases: Living on the Edge

“…Many tools have been deployed to counteract emerging infectious diseases. Amongst these are active surveillance (some supported by artificial intelligence) (140)(141)(142), leading to the rapid identification of novel pathogens by genome sequencing and phylogenetic tracing studies (36,105,107,(143)(144)(145)(146) based on computing methods to predict possible interspecies barriers spillover between humans and animals (147). Coupling biotechnological approaches with social sciences-the holistic understanding of humans and their interactions in the disease ecosystems-is also a critical element needed when studying emerging infectious diseases (148,149).…”

Vacunas para COVID-19 - ¿Podemos evitar volver a vivir en un pueblo fantasma?

“…Por todo ello, desde el inicio de la pandemia, hace más de un año, se comprendió la urgente necesidad de tratamientos y vacunas eficaces y efectivas (9,10). Afortunadamente, en este camino de piedra, el rápido desarrollo de una gran cantidad de candidatos a vacunas COVID-19 allanó el camino para las esperanzas de control de la pandemia (11).…”