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Updated: Jun 8, 2026
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
Transcriptome analysis of rainbow trout infected with high and low virulence strains of infectious hematopoietic
Maureen K Purcell1, Inderjit Singh Marjara, William Batts
1Western Fisheries Research Center, US Geological Survey, 6505 NE 65th Street, Seattle, WA 98115, USA. mpurcell@usgs.gov
Abstract:
There are three main genetic lineages or genogroups of Infectious hematopoietic necrosis virus (IHNV) in N. America. Strains representing the M genogroup are more virulent in rainbow trout relative to the U genogroup. In this study, we used microarray analysis to evaluate potential mechanisms responsible for host-specific virulence in rainbow trout that were given intraperitoneal injections of buffer or a representative M or U type virus strain. Reverse transcriptase quantitative PCR (RT-qPCR) was used to assess viral load and gene expression of select immune genes. Viral load was significantly higher in trout infected with the M virus starting at 24h post-infection (p.i.) and continuing until 72 h p.i. Microarray analysis of the 48 h time point revealed 153 up-regulated and 248 down-regulated features in response to M virus infection but only 62 up-regulated and 49 down-regulated features following U virus infection. Translation and transcription features were among the most frequent down-regulated features in response to M virus infection and may be associated with the host cell shutoff phenomenon. A greater host cell shutoff response by the M virus may facilitate subversion of the host cell transcriptional machinery and enhance viral replication, suggesting the M virus may be better optimized to manipulate the rainbow trout transcriptional and translational machinery. Anti-viral associated features were the most commonly up-regulated features. A common set of features were up-regulated in both the M and U infection groups, but were induced to a higher magnitude in the M infection group. Gene expression of the anti-viral genes Mx-1 and Vig-1 was correlated but not entirely dependent on viral load in the anterior kidney. Slower replication of the U virus may allow the host more time to induce protective anti-viral immune mechanisms.
Insights
Infectious hematopoietic necrosis virus (IHNV) M genogroup strains are more virulent in rainbow trout. The M strain causes higher viral loads and greater host cell shutoff, enhancing replication compared to the U strain.
Area of Science:
- Virology
- Immunology
- Aquatic Animal Health
Background:
- Infectious hematopoietic necrosis virus (IHNV) has distinct genetic lineages (genogroups) in North America.
- The M genogroup of IHNV exhibits higher virulence in rainbow trout compared to the U genogroup.
Purpose of the Study:
- To investigate the molecular mechanisms underlying host-specific virulence of IHNV M and U genogroups in rainbow trout.
- To compare viral load and host gene expression profiles following infection with M and U IHNV strains.
Main Methods:
- Rainbow trout were infected with buffer, M strain IHNV, or U strain IHNV.
- Viral load was quantified using reverse transcriptase quantitative PCR (RT-qPCR).
- Host gene expression was analyzed using microarray analysis and RT-qPCR at 48 hours post-infection.
Main Results:
- The M strain IHNV resulted in significantly higher viral loads from 24 to 72 hours post-infection compared to the U strain.
- Microarray analysis revealed more extensive gene expression changes (up- and down-regulated features) in trout infected with the M strain.
- Down-regulated features in M strain infection included translation and transcription, suggesting a host cell shutoff phenomenon, potentially enhancing viral replication.
- Up-regulated features were predominantly anti-viral, with higher magnitude induction in the M strain group.
Conclusions:
- The M IHNV strain appears better adapted to manipulate rainbow trout's transcriptional and translational machinery, leading to greater virulence.
- Host cell shutoff by the M strain may facilitate viral replication and immune evasion.
- While both strains induce anti-viral responses, the U strain's slower replication may allow for more effective host immune induction.
