Quasispecies complexity measures

A decade after transitioning from clonal sequencing to next-generation sequencing (NGS) for quasispecies analysis, we have gained a comprehensive perspective on viral quasispecies structure and diversity. While traditional diversity indices (e.g.,Shannon entropy, Simpson index) remain valuable, they can yield identical values for quasispecies with distinct haplotype distributions, highlighting the limitations of entropy-based measures alone. Similar effects may be observed with genetic diversity indices (e.g., mutation frequency, nucleotide diversity). Through studies of HEV quasispecies with exceptional diversity yet high functionality, we developed novel indicators (such as quasispecies maturity and synonymity) that reveal the complex interplay between genetic diversity and functional stability. These concepts provide insights into flat-like quasispecies, characterized by dynamic, low-dominance haplotype distributions. We propose an expanded analytical framework using these indicators, which offer more intuitive, structure-focused interpretations than classical diversity indices. This approach aligns closely with quasispecies fitness and may have substantial implications for clinical applications, enhancing our understanding of viral population dynamics, disease progression, and therapeutic interventions.