Dengue virus genomic variation associated with mosquito adaptation defines the pattern of viral non-coding RNAs and fitness in human cells

Abstract

The Flavivirus genus includes a large number of medically relevant pathogens that cycle between humans and arthropods. This host alternation imposes a selective pressure on the viral population. Here, we found that dengue virus, the most important viral human pathogen transmitted by insects, evolved a mechanism to differentially regulate the production of viral non-coding RNAs in mosquitos and humans, with a significant impact on viral fitness in each host. Flavivirus infections accumulate non-coding RNAs derived from the viral 3’UTRs (known as sfRNAs), relevant in viral pathogenesis and immune evasion. We found that dengue virus host adaptation leads to the accumulation of different species of sfRNAs in vertebrate and invertebrate cells. This process does not depend on differences in the host machinery; but it was found to be dependent on the selection of specific mutations in the viral 3’UTR. Dissecting the viral population and studying phenotypes of cloned variants, the molecular determinants for the switch in the sfRNA pattern during host change were mapped to a single RNA structure. Point mutations selected in mosquito cells were sufficient to change the pattern of sfRNAs, induce higher type I interferon responses and reduce viral fitness in human cells, explaining the rapid clearance of certain viral variants after host change. In addition, using epidemic and pre-epidemic Zika viruses, similar patterns of sfRNAs were observed in mosquito and human infected cells, but they were different from those observed during dengue virus infections, indicating that distinct selective pressures act on the 3’UTR of these closely related viruses. In summary, we present a novel mechanism by which dengue virus evolved an RNA structure that is under strong selective pressure in the two hosts, as regulator of non-coding RNA accumulation and viral fitness. This work provides new ideas about the impact of host adaptation on the variability and evolution of flavivirus 3’UTRs with possible implications in virulence and viral transmission.

Antagonism of type I interferon by flaviviruses

“…However, it remains to be determined whether an impaired sfRNA-TRIM25 interaction is contributing to this phenotype. Interestingly, ZIKV did not present this change on sfRNA patterns between hosts, neither between epidemic and pre-epidemic strains, indicating that the two viruses evolved under different selective pressures [89]. More research is needed to fully elucidate the mechanisms by which sfRNAs regulate the strength of the immune response and viral fitness in different hosts.…”

Genomic variations in the 3′‐termini of Rice stripe virus in the rotation between vector insect and host plant

“…The mutations in the 3′‐untranslated region are beneficial for viral replication in mosquito cells, whereas they are detrimental in mammalian cells (Villordo et al ., 2015). Some specific mutations in the 3′‐untranslated region of dengue virus produce different species of subgenomic flavivirus RNAs that play key roles in immune responses in vertebrate and invertebrate cells after viral infection (Filomatori et al ., 2017). …”

Biochemistry and Molecular Biology of Flaviviruses

“…107–109 These dumbbell structures are predicted to form pseudoknot structures (PK3 and PK4) that are essential for their role in translation and may also function as additional Xrn1-stalling sites in a species-specific manner (see section 5). 104,107,110–113 …”

“…It should be noted that ZIKV adapted to either human or mosquito cells produced the same sfRNA species. 113 …”

“…106,110,113,485,491 It was recently demonstrated that sfRNA could increase mosquito transmission. 492,493 WNV mutants that were depleted of the longer species of sfRNAs produced a lower infection rate of mosquito saliva, a proxy for transmission.…”