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28/09/2023

Vall d'Hebron researchers publish the first methodological guide for the study of viral quasispecies

Josep Quer, Francisco Rodríguez-Frías i Josep Gregori

The doctors Josep Quer, Josep Gregori i Francisco Rodríguez-Frías

Llibre Quasiespecies

El llibre Viral Quasispecies diversities and evolution

28/09/2023

The book is the culmination of the last ten years of research by Dr Gregori, Dr Quer and Dr Rodríguez-Frías in the Viral Hepatitis laboratory

Three researchers from the Liver Diseases research group at Vall d'Hebron Institute of Research (VHIR) have edited the first book that compiles the main methodological tools to study viral quasispecies. Quasispecies are structures within a population of viruses that contain a multitude of genomes each having small genetic variations between them and which are subject to a continuous process of mutation, competition, and selection. "Understanding them is key to predicting the evolution of viruses, such as the development of an antiviral resistance," says Dr Quer.

Doctors Josep Gregori, Francisco Rodríguez-Frías and Josep Quer conceived the book as a means to synthesise and highlight the developments and discoveries of the Viral Hepatitis research laboratory within the Liver Diseases research group. For more than thirty years, the laboratory has been pioneering the study of viral quasispecies, including being the first group in the world to investigate this feature of viral complexity in a human infectious agent: the hepatitis C virus. For more than ten years, it has been providing experimental and computational methodological solutions in this field through the application of Next Generation Sequencing (NGS) techniques. The ultimate goal of the book is to create "a useful tool for new generations of researchers who wish to study this field, placing the different methods in their historical context from a scientific and technological point of view," explains Dr. Gregori.

An exponential evolution of information, from 20 sequences to more than 100,000.

One of the aspects that the book aims to reflect is the evolution that the field has undergone in terms of the data available for researchers to analyse. Until 2010, the most widely used technique was cloning, which provided between 10 and 50 sequences. A totally insufficient number, considering that the quantity of viral particles in the body of a patient with an acute hepatitis infection may be greater than that of the world's population today.

This problem was solved with NGS tools, first in 2010 with the 454 GS FLX instrument that allowed a minimum target of 10,000 sequences per Amplicon to be set, and in 2016 with MiSeq, which efficiently produces around 100,000 sequences per Amplicon. This large amount of data has required researchers to design computer programmes that allow the information obtained to be processed, ordered and understood so that it can be used reliably and reproducibly. Dr. Rodríguez-Frías considers that "for a technician to use the tools created appropriately, they must not only know what purpose these tools serve, but they must also understand what their limitations and history are".

An intentionally didactic structure


The book can be divided into three main parts to facilitate its didactic function. The first part, consisting of the Foreword, Preface, Introduction and Background, places the reader in the context in which the different techniques were developed, explaining their purpose and usefulness. The central part of the book is made up of six mainly methodological papers that have been contextualised with comments and notes linking them together. The first three papers delve into the use, interpretation, and usefulness of biodiversity indices, some specific to genetic populations and others imported from the field of ecology. The last three highlight some limitations of these indices and address the development of integrative tools that provide a more direct interpretation in biological and clinical terms. The last part has two sections, one on the observations and conclusions of the book as a whole, and a section reflecting on the limitations of studying complex and dynamic systems such as viral quasispecies.

L'objectiu final del llibre és crear una eina útil per les noves generacions d'investigadors

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