Species-specific transcriptomic changes upon respiratory syncytial virus infection in cotton rats

Abstract

The cotton rat (Sigmodon) is the gold standard pre-clinical small animal model for respiratory viral pathogens, especially for respiratory syncytial virus (RSV). However, without a reference genome or a published transcriptome, studies requiring gene expression analysis in cotton rats are severely limited. The aims of this study were to generate a comprehensive transcriptome from multiple tissues of two species of cotton rats that are commonly used as animal models (Sigmodon fulviventer and Sigmodon hispidus), and to compare and contrast gene expression changes and immune responses to RSV infection between the two species. Transcriptomes were assembled from lung, spleen, kidney, heart, and intestines for each species with a contig N50 > 1600. Annotation of contigs generated nearly 120,000 gene annotations for each species. The transcriptomes of S. fulviventer and S. hispidus were then used to assess immune response to RSV infection. We identified 238 unique genes that are significantly differentially expressed, including several genes implicated in RSV infection (e.g., Mx2, I27L2, LY6E, Viperin, Keratin 6A, ISG15, CXCL10, CXCL11, IRF9) as well as novel genes that have not previously described in RSV research (LG3BP, SYWC, ABEC1, IIGP1, CREB1). This study presents two comprehensive transcriptome references as resources for future gene expression analysis studies in the cotton rat model, as well as provides gene sequences for mechanistic characterization of molecular pathways. Overall, our results provide generalizable insights into the effect of host genetics on host-virus interactions, as well as identify new host therapeutic targets for RSV treatment and prevention.

A chromosome-level genome assembly of the Hispid cotton rat (Sigmodon hispidus), a model for human pathogenic virus infections

“…2, 1 and 16, respectively. These data were confirmed further by alignment of independent RNA-seq libraries generated from cotton rat individuals exposed to RSV infection (Strickland et al 2022).…”

“…For comparisons with RNA-seq data generated independently (Strickland et al 2022), Illumina raw reads were downloaded from SRA database (https://www.ncbi.nlm.nih.gov/sra/?term=%20SRR23104992). Alignments against our cotton rat genome assembly were performed using STAR 2.79a with command lines: STAR --genomeDir ../Star2.79a -- readFilesIn <(zcat SRR23104982_1.fastq.gz) <(zcat SRR23104982_2.fastq.gz) --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix Inf1 --sjdbOverhang 99 –sjdbGTFfile ../mSigHis_REL_1907.gff3 --runThreadN 16.…”

“…However, the lack of a cotton rat reference genome has limited such experiments. In recent studies, immune responses of RSV-infected cotton rats were evaluated by comparing RNA expression patterns in infected versus uninfected lungs (Rajagopala et al 2018) (Strickland et al 2022). As in humans, numerous immune genes related to defense against viral infections were upregulated, while others were downregulated late during infection.…”

SARS-CoV-2 infection augments species- and age-specific predispositions in cotton rats

“…Most of the work has been performed in SH, however, there are multiple cotton rat species. For example, Sigmodon fulviventer (SF) is a less frequently used species of cotton rats, but it shows differences compared to SH in responses to human parainfluenza virus 21 and respiratory syncytial virus (RSV) infections 22 , has a different microbiome community structure 23 , and appears to be more susceptible to infection with HCoV-229E (ongoing studies). These species-level differences may provide an opportunity to study the heterogeneity of the COVID-19 pathogenesis.…”