In-Host Flat-like Quasispecies: Characterization Methods and Clinical Implications

Abstract

Cuasiespecies; Mutágenos; Mutaciones

Quasispecies; Mutagens; Mutations

Quasiespècie; Mutàgens; Mutacions

The repeated failure to treat patients chronically infected with hepatitis E (HEV) and C (HCV) viruses, despite the absence of resistance-associated substitutions (RAS), particularly in response to prolonged treatments with the mutagenic agents of HEV, suggests that quasispecies structure may play a crucial role beyond single point mutations. Quasispecies structured in a flat-like manner (referred to as flat-like) are considered to possess high average fitness, occupy a significant fraction of the functional genetic space of the virus, and exhibit a high capacity to evade specific or mutagenic treatments. In this paper, we studied HEV and HCV samples using high-depth next-generation sequencing (NGS), with indices scoring the different properties describing flat-like quasispecies. The significance of these indices was demonstrated by comparing the values obtained from these samples with those from acute infections caused by respiratory viruses (betacoronaviruses, enterovirus, respiratory syncytial viruses, and metapneumovirus). Our results revealed that flat-like quasispecies in HEV and HCV chronic infections without RAS are characterized by numerous low-frequency haplotypes with no dominant one. Surprisingly, these low-frequency haplotypes (at the nucleotide level) exhibited a high level of synonymity, resulting in much lower diversity at the phenotypic level. Currently, clinical approaches for managing flat-like quasispecies are lacking. Here, we propose methods to identifying flat-like quasispecies, which represents an essential initial step towards exploring alternative treatment protocols for viruses resistant to conventional therapies.

This study was partially supported by Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business, grant number IDI-20200297; Grant PID2021-126447OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by ERDF A way of making Europe; Fondo de Investigación Sanitaria, Ministerio Español de Economía y Competitividad (grants FIS PI19/00301, PI22/00258, PI22/00023 and PI23/01065); CIBER—Consorcio Centro de Investigación Biomédica en Red—(CIBERINFEC, ISCIII—CIBER de Enfermedades Infecciosas & CIBEREHD, ISCIII. CIBER de Enfermedades Hepáticas y Digestivas), Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación and Unión Europea—NextGenerationEU; S.C.-C received support from the Spanish Ministry of Education grant FPU21/04150. M.I.-L. received the support of a fellowship from ”La Caixa” Foundation (ID 100010434), whose code is “LCF/BQ/DR23/12000020”. C.C. has received a fellowship from VHIR.