Introduction to “Viral quasispecies complexity measures”

Read the full article on ScienceDirect.

Text by Michael Emerman (Editor-in-Chief, Virology)


Viruses exist as collections of mutants. The high error rate of viral replication, especially for RNA viruses, magnifies this effect since each round of virus growth leads to more mutations.   Because of interactions between different members of this mutant “swarm”, the population can have properties that are just the sum of the individual mutants. This phenomenon is called the ‘viral quasispecies’ and was reviewed recently in the 60th Anniversary Issue of Virology. However, while the advent of new sequencing technology has increased the power to document the distribution of mutations within a virus population, the ability to understand the data has somewhat lagged.

A new manuscript, recently published in Virology titled “Viral quasispecies complexity measures” reviews the different ways that the distribution of mutations within the viral quasispecies can be described using concepts originally developed in ecology. The authors also provide recommendations for analysis of this richness of virus sequence data.



Figure legend

Schematic representation of the sequences (reads) obtained from a NGS experiment. Viral genomes are represented as horizontal lines and mutations as different colored symbols on the lines. The sequences are clustered by haplotypes (Hpl). The information obtained from the sequence alignment can be divided into a haplotype alignment (each different sequence is counted once), and a vector of frequencies (shows the frequency of different haplotypes).

About the research

Viral quasispecies complexity measures

Josep Gregori, Celia Perales, Francisco Rodriguez-Frias, Juan I. Esteban, Josep Quer, Esteban Domingo

Virology, Volume 493, June 2016, Pages 227–237