VIRAL SURVEY OF THREE AMAZONIAN BAT SPECIES USING A LARGE COLLECTION OF TAXONOMICALLY SPECIFIC PROFILE HIDDEN MARKOV MODELS

Nayara Almeida Amed; Liliane Santana; Mariana Costa Dias; Leonardo Trevelin; Santelmo Vasconcelos; Guilherme Oliveira; Desconhecido766

Paper Title

Authors

Nayara Almeida Amed
Liliane Santana
Mariana Costa Dias
Leonardo Trevelin
Santelmo Vasconcelos
Guilherme Oliveira
Desconhecido766

Modality

Xpress presentation

Subject area

Omics

Publishing Date

26/04/2022

Country of Publishing

Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeetingxp2021/419274-viral-survey-of-three-amazonian-bat-species-using-a-large-collection-of-taxonomically-specific-profile-hidden-mar

ISBN

978-65-5941-645-5

Keywords

Viral metagenomics, profile HMM, viral discovery, Amazonian bat

Summary

Our group has recently developed TABAJARA, a program for the rational design of profile HMMs that may detect and differentiate specific taxonomic groups. A collection of thousands of models is now publicly available on the Viral Minion Database (http://www.bioinfovir.icb.usp.br/minion_db/) and can be used to screen metagenomic data for the detection and classification of known and novel viruses. Here, we report a viral survey using RNAseq data derived from three species of Amazonian bats from Carajás (State of Pará): Natalus macrourus, Furipterus horrens and Lonchorhina aurita. A set of 10,527 taxonomically specific profile HMMs of eukaryotic viruses was used to interrogate datasets composed of sequences previously assembled with Trinity program. All these models were tested and validated by TABAJARA against viral sister groups. Since this survey represents the first large scale application of such models for viral detection, we used it as case study to standardize the methodology. Dataset screening was performed with HMM-Prospector, a tool that automatically performs 6-frame translation of nucleotide sequences and invokes hmmsearch (HMMER package) to run similarity searches using cutoff scores pre-defined by TABAJARA for each model. We observed that the profile HMMs did not show cross-detection of viral families and genera, as expected. However, models derived from some particular viruses (e.g. Phycodnaviridae, Mimiviridae and Baculoviridae, among others) detected host sequences with bitscores much higher than the established cutoff scores. We performed a manual curation and realized that these models were all derived from protein sequences that present highly conserved orthologs in a broad extent of taxonomic levels, from viruses to vertebrates. With such a high conservation level, it is unfeasible to determine cutoff scores that can reliably discriminate viral from host sequences. Thus, we created a dataset of protein sequences from a variety of representatives of the major eukaryotic taxonomic groups, including unicellular and multicellular organisms. Using this dataset, we identified models that show cross-detection and discarded them for downstream use. Finally, we were able to specifically detect viral sequences belonging to families Astroviridae, Papillomaviridae and Herpesviridae in N. macrourus, Astroviridae and Picornaviridae in F. horrens, and Iflaviridae, Paramyxoviridae and Parvoviridae in L. aurita. We are now standardizing the use of short-length profile HMMs (Minions) against assembled and unassembled sequence data. The methodology developed in this work is generic and may be applied to any other biological domain where a set of sequences must be specifically detected or differentiated from other sets of sequences.

Title of the Event: X-Meeting XPerience 2021
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

AMED, Nayara Almeida et al.. VIRAL SURVEY OF THREE AMAZONIAN BAT SPECIES USING A LARGE COLLECTION OF TAXONOMICALLY SPECIFIC PROFILE HIDDEN MARKOV MODELS.. In: X-Meeting presentations. Anais...São Paulo(SP) AB3C, 2021. Available in: https//www.even3.com.br/anais/xmeetingxp2021/419274-VIRAL-SURVEY-OF-THREE-AMAZONIAN-BAT-SPECIES-USING-A-LARGE-COLLECTION-OF-TAXONOMICALLY-SPECIFIC-PROFILE-HIDDEN-MAR. Access in: 30/04/2025