Attenuated dengue viruses are genetically more diverse than their respective wild-type parents

Abstract

Dengue poses a significant burden of individual health, health systems and the economy in dengue endemic regions. As such, dengue vaccine development has been an active area of research. Previous studies selected attenuated vaccine candidates based on plaque size. However, these candidates led to mixed safety outcome in clinical trials, suggesting it is insufficiently informative as an indicator of dengue virus (DENV) attenuation. In this study, we examined the genome diversity of wild-type DENVs and their attenuated derivatives developed by Mahidol University and tested in phase 1 clinical trials. We found that the attenuated DENVs, in particular the strain under clinical development by Takeda Vaccines, DENV2 PDK53, showed significantly higher genome diversity than its wild-type parent, DENV2 16681. The determinant of genomic diversity was intrinsic to the PDK53 genome as infectious clone of PDK53 showed greater genomic diversity after a single in vitro passage compared to 16681 infectious clone. Similar trends were observed with attenuated DENV1 and DENV4, both of which were shown to be attenuated clinically, but not DENV3 that was not adequately attenuated clinically. Taken together, evidence presented here suggests that genome diversity could be developed into a marker of DENV attenuation.

Intra-Host Diversity of Dengue Virus in Mosquito Vectors

“…Moreover, while the conventional sample pooling strategy adopted to achieve sufficient starting materials for sequencing has proved fruitful in identifying common variants, it may obscure low-frequency variants due to the averaging effect of combining individuals. Despite that, advances in next generation sequencing capabilities, specifically the ability to call low frequency variants (Wilm et al, 2012;Bifani DENV quasispecies diversity key questions…”

“…Likewise, for DENV and other closely related arboviruses, an optimal level of diversity in a quasispecies is required to maintain viral fitness ( Vignuzzi et al., 2006 ; Beck et al., 2014 ; Rozen-Gagnon et al., 2014 ; Beck et al., 2018 ). Studies have demonstrated that strains that have a significantly elevated or reduced level of quasispecies diversity compared to wildtype tend to be less fit ( Vignuzzi et al., 2008 ; Bifani et al., 2021 ). In DENV, clinically-tested successful attenuated vaccine candidate strains harbored a greater level of quasispecies diversity than their virulent parental strains ( Bifani et al., 2021 ).…”

“…Studies have demonstrated that strains that have a significantly elevated or reduced level of quasispecies diversity compared to wildtype tend to be less fit ( Vignuzzi et al., 2008 ; Bifani et al., 2021 ). In DENV, clinically-tested successful attenuated vaccine candidate strains harbored a greater level of quasispecies diversity than their virulent parental strains ( Bifani et al., 2021 ).…”

“…Previous studies have clearly demonstrated that quasispecies diversity has the ability to shape viral fitness and pathogenesis ( Vignuzzi et al., 2006 ). Arbovirus strains that have significantly more or less population diversity than wildtype stains have been associated with diminished fitness ( Coffey et al., 2011 ; Beck et al., 2014 ; Rozen-Gagnon et al., 2014 ; Beck et al., 2018 ; Bifani et al., 2021 ). However, alternating between a mammalian host and a mosquito vector imposes restrictions on diversity of the DENV genome which are lost when DENV is exclusively passaged in either mammalian or mosquito cells ( Dolan et al., 2021 ).…”

Current Development and Challenges of Tetravalent Live-Attenuated Dengue Vaccines

“…DENV-2 PDK-53 was derived from the wild-type DENV-2 16681 virus strain through serial passage in primary dog kidney cells ( 45 ). The attenuated DENV2 PDK-53 virus exhibits distinct features that differ from its parental strain, such as temperature sensitivity, less effective replication, attenuated neurovirulence, and greater genetic diversity, which affected the fitness of DENV2 PDK-53 ( 46 ). These features are mainly attributed to 5’-NCR-57 C-to-T, NS1-53 Gly-to-Asp, and NS3-250 Glu-to-Val mutations ( 45 ).…”