In-host flat-like quasispecies, methods and clinical implications (Respiratory viruses VHIR 62)

The repeated observation of treatment failures to chronically infected patients with hepatitis virus, hepatitis E virus (HEV) and hepatitis C virus (HCV), with no resistance-associated substitutions (RAS) at sensible abundances, and in particular as response to long treatments with mutagenic agents of HEV, show that the quasispecies structure may play an important role beyond single point mutations. In this work, using very high next-generation sequencing (NGS) depth analysis, we confront data from anti-HCV and anti-HEV treatment failures with data from acute infectious respiratory viruses (betacoronaviruses, enterovirus, respiratory syncytial viruses, and metapneumovirus). The results provide evidence of flat-like quasispecies structure in the case of treatment failure to HEV and HCV chronic infected patients with no RAS, consisting in the presence of a very high number of different haplotypes, all at very low frequencies, with no significantly dominant haplotype, and spanning a high number of substitution multiplicities relative to the master hap-lotype, with a high level of synonymity which translates to a much lower diversity at the phenotypic level. Currently, we lack any clinical approach to deal with flat quasispecies. Here we propose methods to identify them, as a step for the investigation of alternative treatment protocols.