Serratus Examplars

A curated collection of papers which make effective use of the Serratus data. These are great hands-on tutorials which you can follow along with.

Virus Discovery

1. Diversification of mammalian deltaviruses by host shifting. PNAS. Bergner et al., 2021 (link)

Serratus pilot analysis was used to identify SRA libraries containing novel Deltaviruses which greatly expanded the host-species diversity and phylogenetic history of these viruses. Initial SRA-wide analysis was performed to geo-localize SRA data globally and measure virus enrichment across continents.

2. Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus Evolution. Mifsud et al., 2022 (link)

A comprehensive search for Flaviviridae viruses across the SRA which expands the known host range for these viruses. Good example of mining out a complete family of viruses with 32 novel viruses characterized

3. Two novel bornaviruses identified in colubrid and viperid snakes Archives of Virology. *Pfaff and Rubbenstroth. (link)

Quick serratus.io web-search yields two new bornaviruses. How to write a paper on a lazy friday afternoon.

4. The Expanding Menagerie of Prunus-Infecting Luteoviruses Khalili et al., 2023 (link)

Effective use of SRA-Explorer to identify libraries containing a novel Luteovirus related to the viruses found in their study.

5. Accumulated metagenomic studies reveal recent migration, whole genome evolution, and undiscovered diversity of orthomyxoviruses. Dudas and Batson. 2022 (link)

Effective use of Serratus to localize SRA datasets containing novel orthomyxoviruses for assembly and characterization. Quite streamlined and a good tutorial.

Virus Ecology/Tropism

1. Latent human herpesvirus 6 is reactivated in chimeric antigen receptor T cells. Nature. Lareau et al., 2023 (link)

Used the Serratus nucleotide RefSeq genome search to identify human SRA libraries showing expression of latent DNA viruses. Included a systematic analysis of tissue-of-origin across the SRA which allowed the identification of an unexpected re-activation and tropism for HHV6.

2. Diversity and pathobiology of an ilarvirus unexpectedly detected in diverse host plants and in global sequencing data. Phytopathology. Rivarez et al., 2022. (link)

Great use of SRA data to extend the phylogeography of ilarviruses.

3. An Unwanted Association: The Threat to Papaya Crops by a Novel Potexvirus in Northwest Argentina. Mederos et al., 2022 (link)

Technical Papers

1. Ribovirus classification by a polymerase barcode sequence. Babaian and Edgar. 2022 (link)

Technical paper describing the palmprint sub-sequence of RdRp, which forms the backbone of the Serratus databases. Description of palmID search tool as a proof of concept.

2. RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data. Charon et al., 2022. (link)

Use of Serratus and palmDB sequences in the construction of sets RdRp-specific HMM for virus classification.

Other

1. Expansion of viral genomes with viral protein genome linked copies. Warsaba et al., 2022 (link)

Mining of the Serratus assembled transcriptomes to localize novel dicistroviruses, and describe genetic variation in their VPg.