xploring Virome Diversity in Public Data in South America as an Approach for Detecting Viral Sources From Potentially Emerging Viruse

Autor(es)

Mazur, Fernando G. ^[1] ; Morinisi, Leandro M. ^[1] ; Martins, Junior Olimpio ^[1] ; Guerra, Pedro Pontes Bueno ^[1] ; Freire, Caio C. M. ^[1]

Afiliação do(s) autor(es)

^[1] UFSCar Fed Univ Sao Carlos, Dept Genet & Evolut, Sao Carlos - Brazil

• Tipo de documento: Artigo Científico
• Fonte: FRONTIERS IN GENETICS; v. 12, JAN 21 2022.
• Citações Web of Science: 0

Resumo

The South American continent presents a great diversity of biomes, whose ecosystems are constantly threatened by the expansion of human activity. The emergence and re-emergence of viral populations with impact on the human population and ecosystem have shown increases in the last decades. In deference to the growing accumulation of genomic data, we explore the potential of South American-related public databases to detect signals that contribute to virosphere research. Therefore, our study aims to investigate public databases with emphasis on the surveillance of viruses with medical and ecological relevance. Herein, we profiled 120 ``sequence read archives{''} metagenomes from 19 independent projects from the last decade. In a coarse view, our analyses identified only 0.38% of the total number of sequences from viruses, showing a higher proportion of RNA viruses. The metagenomes with the most important viral sequences in the analyzed environmental models were 1) aquatic samples from the Amazon River, 2) sewage from Brasilia, and 3) soil from the state of Sao Paulo, while the models of animal transmission were detected in mosquitoes from Rio Janeiro and Bats from Amazonia. Also, the classification of viral signals into operational taxonomic units (OTUs) (family) allowed us to infer from metadata a probable host range in the virome detected in each sample analyzed. Further, several motifs and viral sequences are related to specific viruses with emergence potential from Togaviridae, Arenaviridae, and Flaviviridae families. In this context, the exploration of public databases allowed us to evaluate the scope and informative capacity of sequences from third-party public databases and to detect signals related to viruses of clinical or environmental importance, which allowed us to infer traits associated with probable transmission routes or signals of ecological disequilibrium. The evaluation of our results showed that in most cases the size and type of the reference database, the percentage of guanine-cytosine (GC), and the length of the query sequences greatly influence the taxonomic classification of the sequences. In sum, our findings describe how the exploration of public genomic data can be exploited as an approach for epidemiological surveillance and the understanding of the virosphere. (AU)

• Processo FAPESP: 14/17766-9 - Abordagem sistêmica no estudo da permissividade do Anticarsia gemmatalis múltiplo nucleopoliedrovírus (AgMNPV)
• Beneficiário: Paolo Marinho de Andrade Zanotto
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 14/06090-4 - Estimativa da diversidade intra e inter populacional gênica e genética do baculovírus Anticarsia gemmatalis múltiplo nucleopoliedrovírus (AgMNPV) em isolados de campo na América do Sul
• Beneficiário: Caio César de Melo Freire
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado