Characterization of viral RNA splicing using whole-transcriptome datasets from host species

An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule

Virus circular RNAs (circRNA) have been reported to be extensively expressed and play important roles in viral infections. Previously we build the first database of virus circRNAs named VirusCircBase which has been widely used in the field. This study significantly improved the database on both the data quantity and database functionality: the number of virus circRNAs, virus species, host organisms was increased from 46440, 23, 9 to 60859, 43, 22, respectively, and 1902 full-length virus circRNAs were newly added; new functions were added such as visualization of the expression level of virus circRNAs and visualization of virus circRNAs in the Genome Browser. Analysis of the expression of virus circRNAs showed that they had low expression levels in most cells or tissues and showed strong expression heterogeneity. Analysis of the splicing of virus circRNAs showed that they used a much higher proportion of non-canonical back-splicing signals compared to those in animals and plants, and mainly used the A5SS (alternative 5' splice site) in alternative-splicing. Most virus circRNAs have no more than two isoforms. Finally, human genes associated with the virus circRNA production were investigated and more than 1000 human genes exhibited moderate correlations with the expression of virus circRNAs. Most of them showed negative correlations including 42 genes encoding RNA-binding proteins. They were significantly enriched in biological processes related to cell cycle and RNA processing. Overall, the study provides a valuable resource for further studies of virus circRNAs and also provides new insights into the biogenesis mechanisms of virus circRNAs.

Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease

Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have potential normalization and assay platform stability advantages over gene expression for diagnosis. Here, we present a computational framework for developing AS diagnostic biomarkers. Leveraging a large prospective cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and whole-blood RNA sequencing (RNA-seq) data, we identify a major functional AS program switch upon viral infection. Using an independent cohort, we demonstrate the improved accuracy of AS biomarkers for SARS-CoV-2 diagnosis compared with six reported transcriptome signatures. We then optimize a subset of AS-based biomarkers to develop microfluidic PCR diagnostic assays. This assay achieves nearly perfect test accuracy (61/62 = 98.4%) using a naive principal component classifier, significantly more accurate than a gene expression PCR assay in the same cohort. Therefore, our RNA splicing computational framework enables a promising avenue for host-response diagnosis of infection.

Identification of a Novel Densovirus in Aphid, and Uncovering the Possible Antiviral Process During Its Infection

Densoviruses (DVs) are single-stranded DNA viruses and exclusively happen in invertebrates. Most of DVs reported in insects are pathogenic to their native hosts, however, no pathogenic effect of them has been examined in vertebrates. Hence, DVs are the potential agents used in pest managements. Aphids are the primary vectors of plant viruses. In this study, we identified a novel DV in Chinese Sitobion miscanthi population, provisionally named “Sitobion miscanthi densovirus” (SmDV). Taxonomically, SmDV belongs to genus Hemiambidensovirus. In S. miscanthi, SmDV is hosted in diverse cells and can be horizontally transmitted via wheat feeding. Subject to SmDV, aphids activate their intrinsic antiviral autophagy pathway. Grouped with ascorbate and aldarate metabolism, chlorophyll metabolism, p450 related drug metabolism, and retinoid metabolism, aphids form a complex immune network response to the infection of SmDV. Obviously, it works as elder aphids still alive even they contain the highest examined concentration of SmDV. This study provides a foundation for the identifications of novel DVs, and further improves the understanding of the molecular interactions between insects and DVs.

Selective ablation of 3' RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts

Alternative splicing (AS) is necessary for viral proliferation in host cells and a critical regulatory component of viral gene expression. Conventional RNA-seq approaches provide incomplete coverage of AS due to their short read lengths and are susceptible to biases and artifacts introduced in prevailing library preparation methodologies. Moreover, viral splicing studies are often conducted separately from host cell transcriptome analysis, precluding an assessment of the viral manipulation of host splicing machinery. To address current limitations, we developed a quantitative full-length direct cDNA sequencing strategy to simultaneously profile viral and host cell transcripts. This nanopore-based approach couples processive reverse transcriptases with a novel one-step chemical ablation of 3' RNA ends (termed CASPR), which decreases ribosomal RNA reads and enriches polyadenylated coding sequences. We extensively validate our approach using synthetic reference transcripts and show that CASPR doubles the breadth of coverage per transcript and increases detection of long transcripts (>4 kb), while being functionally equivalent to PolyA+ selection for transcript quantification. We used our approach to interrogate host cell and HIV-1 transcript dynamics during viral reactivation and identified novel putative HIV-1 host factors containing exon skipping or novel intron retentions and delineated the HIV-1 transcriptional state associated with these differentially regulated host factors.

Principal component analysis of coronaviruses reveals their diversity and seasonal and pandemic potential

Coronaviruses and influenza viruses have similarities and differences. In order to comprehensively compare them, their genome sequencing data were examined by principal component analysis. Coronaviruses had fewer variations than a subclass of influenza viruses. In addition, differences among coronaviruses that infect a variety of hosts were also small. These characteristics may have facilitated the infection of different hosts. Although many of the coronaviruses were conservative, those repeatedly found among humans showed annual changes. If SARS-CoV-2 changes its genome like the Influenza H type, it will repeatedly spread every few years. In addition, the coronavirus family has many other candidates for new pandemics.

Reference gene and small RNA data from multiple tissues of Davidia involucrata Baill

Davidia involucrata Baill. is a rare plant endemic to China. Its exclusive evolutionary position and specific floral organs endow it with a high research value. However, a lack of genomic resources has constrained the study of D. involucrata functional genomics. Here, we report D. involucrata transcriptome reads from different floral tissues pooled from six individuals at two developmental stages using Illumina HiSeq technology and the construction of a high-quality reference gene set containing a total of 104,463 unigenes with an N50 of 1,693 bp and 48,529 high-quality coding sequences. The transcriptome data exhibited 89.24% full-length completeness with respect to the benchmarking universal single-copy (BUSCO) dataset and a PLAZA CoreGF weighted score of 98.85%. In total, 65,534 (62.73%) unigenes were functionally annotated, including 58 transcription factor families and 44,327 simple sequence repeats (SSRs). In addition, 96 known and 112 novel miRNAs were identified in the parallel small RNA sequencing of each sample. All these high-quality data could provide a valuable annotated gene set for subsequent studies of D. involucrata.