Characterization of RNA and DNA viromes in sewage samples collected from Buenos Aires, Argentina

ZAMBRANA MONTAÑO R; BLANCO FERNÁNDEZ MD; TORRES C

Congreso; XIII Argentine Congress of Bioinformatics and Computational Biology (XIII CAB2C); 2023

BACKGROUND. The utilization of next-generation sequencing (NGS) techniques on environmental samples plays a crucial role in public health to identify the presence of viral species that are responsible for a wide variety of human diseases. The aim of this work was to conduct an initial approach into the RNA and DNA virome of two sewage samples collected in Buenos Aires province (Argentina) during two seasons, Summer (February) and Spring (October) 2022.RESULTS. A virus concentration method based on prefiltering a 2L sample using 0.45 and 0.22 μm filters, followed by ultrafiltration (50 kDa) and PEG precipitation was used. RNA and DNA extraction was carried out separately using commercial kits. To facilitate viral detection in NGS, sequence-independent single-primer-amplification (SISPA) was implemented on RNA and DNA samples. Paired-end sequences were obtained from the Illumina platform (2x150). Adaptors and primers were removed, short reads were trimmed (< 75 bp) and reads with low-quality score (Phred score below 30) were eliminated using Trim Galore. Then, the taxonomic classification of reads was performed using Kraken2 and Bracken against the NCBI RefSeq viral database.RNA sample obtained in Summer was composed of viral (30.3%), bacterial (20.6%) and unclassified sequences (48.8%), whereas that obtained in Spring showed viral (24.8%), bacterial (48.3%) and unclassified (26.1%) sequences. Among the viruses, despite the overrepresentation of Virgaviridae (94.8-99.3%), our analysis revealed species from more than 30 other families, including Astroviridae, and detected reads corresponding to the Picornaviridae family in Summer and Caliciviridae in Spring viromes.DNA samples resulted in a low recovery of viral sequences (< 10% of total reads). Most of the viruses found belonged to the Duplodnaviria domain (91.4%-97.7%), dominated by dsDNA phages of the order Caudovirales. In both Summer and Spring samples, a low abundance of Herpesviridae, Circoviridae, Parvoviridae, Poxviridae, and Adenoviridae families was found, among others. Besides, the Summer samples also had reads classified as belonging to Papillomaviridae and Polyomaviridae families.CONCLUSIONS. The strategy implemented in this work allowed the detection of several viral families from different host species in sewage samples in Argentina. Subsequent analyzes will allow a deep characterization of viral species and their diversity.