Analysis of SalHV-1 Genes by Structure Prediction and Comparison Shows an Expanded Core Gene Set of the Order Herpesvirales

Richard J. Roller; Joan Martí-Carreras; Piet Maes

doi:10.3390/v18030372

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Analysis of SalHV-1 Genes by Structure Prediction and Comparison Shows an Expanded Core Gene Set of the Order Herpesvirales

Journal article

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Analysis of SalHV-1 Genes by Structure Prediction and Comparison Shows an Expanded Core Gene Set of the Order Herpesvirales

Richard J. Roller, Joan Martí-Carreras and Piet Maes

Viruses, Vol.18(3), 372

03/17/2026

DOI: 10.3390/v18030372

PMCID: PMC13030845

PMID: 41902279

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Abstract

The order Herpesvirales contains three families, Orthoherpesviridae, Alloherpesviridae, and Malacoherpesviridae. The time since divergence of families from the common ancestor makes protein primary sequence comparison an insensitive tool for identifying common genes. Comparison of three-dimensional protein structures can reveal similarities that are not evident in primary sequences. Salmonid herpesvirus 1 (SalHV-1) is an alloherpesvirus. Complete sequencing of SalHV-1 VR-868 strain Winthrop by a combination of short- and long-read methods revealed 120 putative open reading frames (ORFs). BLAST search for similar protein sequences discovered five ORFs that encoded proteins with homologs in the orthoherpesviruses, including the major capsid protein, capsid triplex subunit 2, the catalytic subunit of the DNA polymerase, the helicase subunit of the helicase/primase complex, and the terminase ATPase subunit. An annotation of the ORFs of SalHV-1 was performed in which ORFs of SalHV-1 were modeled using AlphaFold3, and the models were used as prompts for structural similarity search using DALI and FoldSeek. Completion of this search strategy for the entire genome expanded the set of genes shared among the Herpesvirales to include additional proteins related to DNA replication and genome integrity, capsid assembly and genome packaging, and capsid nuclear egress. No homologs for any tegument proteins or proteins of the conserved entry apparatus of the Herpesviridae (gB, gH or gL) were discovered.

herpesviruses

virus evolution

structural modeling and similarity search

alloherpesviruses

Details

Title: Subtitle: Analysis of SalHV-1 Genes by Structure Prediction and Comparison Shows an Expanded Core Gene Set of the Order Herpesvirales
Creators: Richard J. Roller - University of Iowa
Joan Martí-Carreras - Rega Institute for Medical Research
Piet Maes - Rega Institute for Medical Research
Resource Type: Journal article
Publication Details: Viruses, Vol.18(3), 372
DOI: 10.3390/v18030372
PMID: 41902279
PMCID: PMC13030845
NLM abbreviation: Viruses
ISSN: 1999-4915
eISSN: 1999-4915
Publisher: MDPI
Grant note: Department of Microbiology and Immunology at the University of Iowa (RJR)National Institutes of Health: R01 AI150718 HONOURs Marie-Sklodowska-Curie training network: 721367
This work was supported by National Institutes of Health grant R01 AI150718 and the Department of Microbiology and Immunology at the University of Iowa (RJR), and JMC was funded by HONOURs Marie-Sklodowska-Curie training network (grant number 721367).
Language: English
Date published: 03/17/2026
Academic Unit: Microbiology and Immunology
Record Identifier: 9985147076502771

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