OmniVira

Duplication of specialized cis-acting elements SLI and SLIII in the viral RNA 3'UTR enables mosquito-borne orthoflavivirus adaptation to avian hosts.

Li Mao1 Yu He1,2,3,4,5 Tao Wang1,2,3,5 Zhen Wu1,2,3,4,5 Andres Merits6 Mingshu Wang1,2,3,5 Renyong Jia1,2,3,5 Dekang Zhu1,2,3,5 Mafeng Liu1,2,3,5 Xinxin Zhao1,2,3,5 Qiao Yang1,2,3,5 Ying Wu1,2,3,5 Shaqiu Zhang1,2,3,5 Juan Huang1,2,3,5 Xumin Ou1,2,3,4,5 Di Sun1,2,3,5 Bin Tian1,2,3,4 Anchun Cheng1,2,3,5,7 Shun Chen1,2,3,4,5
Affiliations 7 institutions
  1. Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
  2. Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
  3. Agricultural Animal Diseases and Veterinary Public Health Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
  4. Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
  5. Engineering Research Center of Southwest Animal Disease Prevention and Control Technology for Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
  6. Institute of Bioengineering, University of Tartu, Tartu, Estonia.
  7. Institute of Veterinary Immunology and Green Drugs, Veterinary Department in College of Animal Science, State Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China.
PMID42578371 DOI10.1093/nar/gkag791 Year2026 Journal Nucleic acids research Nucleic Acids Res Languageeng Statusppublish

Abstract

Cross-species transmission of mosquito-borne orthoflaviviruses (MBFVs) relies on multi-host switching and adaptation, yet the underlying mechanisms remain incompletely understood. Domain I of the 3'-untranslated region (UTR) is highly structured and shaped by host-driven selection. Mammalian MBFVs usually have two functional stem-loops (SLs), while avian MBFVs possess two extra SLs (SLI and SLIII), whose functions remain unclear. Using Tembusu virus (TMUV) and Japanese encephalitis virus (JEV), we mutated Domain I and characterized recombinant viruses. TMUV mutants with only one SL showed attenuated replication, with efficiency dependent on SL identity. Duplicating SLII boosted TMUV replication in mammalian and avian cells but not in mosquito cells, indicating that repeated SLs contribute to host-specific proliferation. Deleting SLI and/or SLIII impaired TMUV replication in avian cells but not mammalian cells, and dual deletion significantly reduced virulence in ducklings but had limited impact in mice. Replacement of JEV SLI/SLIII with homologous elements derived from a duck-associated strain improved its proliferation in avian cells. Mechanistically, SLI/SLIII regulate TMUV replication in avian cells by interacting with the host factor CELF2, which specifically facilitates viral replication in avian cells. Collectively, SLI and SLIII are important determinants of avian host proliferation in MBFVs, improving understanding of their multi-host ecology and transmission.

Supporting text Virus Host Location
3' Untranslated Regions 3 Flavivirus 16 RNA, Viral 193 Animals 1948 Cell Line 158 Culicidae 22 Ducks 81 Encephalitis Virus, Japanese 8 Mice 253 Mosquito-Borne Diseases 2 Virulence 108 Virus Replication 191 Tembusu virus 6

Evidence records

5 total
Functional Mechanism
5 records · 1 evidence types
Evidence type Molecular Adaptation
5 records
OVE11983 Molecular Adaptation
Key finding

Deletion of 3'UTR SLI and/or SLIII in TMUV impairs replication in avian cells but not mammalian cells, and dual deletion reduces virulence in ducklings with limited impact in mice.

Virus
Tembusu virus
Host
Not specified
Location
Not specified
Supporting text

Deleting SLI and/or SLIII impaired TMUV replication in avian cells but not mammalian cells, and dual deletion significantly reduced virulence in ducklings but had limited impact in mice.

Genes or proteins
3'-UTR Domain I | SLI | SLIII
Mutations
deletion of SLI | deletion of SLIII | dual deletion of SLI/SLIII
Mechanism types
replication adaptation | virulence adaptation | host-range expansion
OVE11986 Molecular Adaptation
Key finding

TMUV 3'UTR SLI/SLIII promote replication in avian cells via interaction with the host factor CELF2.

Virus
Tembusu virus
Host
Not specified
Location
Not specified
Supporting text

Mechanistically, SLI/SLIII regulate TMUV replication in avian cells by interacting with the host factor CELF2, which specifically facilitates viral replication in avian cells.

Genes or proteins
3'-UTR Domain I | SLI | SLIII
Host factors
CELF2
Mechanism types
replication adaptation | host-range expansion
OVE11984 Molecular Adaptation
Key finding

Duplication of SLII in the TMUV 3'UTR enhances replication in mammalian and avian cells but not mosquito cells, indicating host-specific proliferation effects.

Virus
Tembusu virus
Host
Not specified
Location
Not specified
Supporting text

Duplicating SLII boosted TMUV replication in mammalian and avian cells but not in mosquito cells, indicating that repeated SLs contribute to host-specific proliferation.

Genes or proteins
3'-UTR Domain I | SLII
Mutations
duplication of SLII
Mechanism types
replication adaptation | host-range expansion
OVE11985 Molecular Adaptation
Key finding

Replacing JEV SLI/SLIII with homologous elements from a duck-associated strain increases JEV proliferation in avian cells.

Virus
Japanese encephalitis virus
Host
Not specified
Location
Not specified
Supporting text

Replacement of JEV SLI/SLIII with homologous elements derived from a duck-associated strain improved its proliferation in avian cells.

Genes or proteins
3'-UTR Domain I | SLI | SLIII
Mutations
replacement of SLI/SLIII with duck-associated homologous elements
Mechanism types
replication adaptation | host-range expansion
OVE11987 Molecular Adaptation
Key finding

TMUV mutants retaining only one 3'UTR stem-loop are replication-attenuated, with efficiency dependent on which SL is retained.

Virus
Tembusu virus
Host
Not specified
Location
Not specified
Supporting text

TMUV mutants with only one SL showed attenuated replication, with efficiency dependent on SL identity.

Genes or proteins
3'-UTR Domain I | SLI | SLII | SLIII
Mutations
single-SL mutants
Mechanism types
replication adaptation