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

ZAMBRANA MONTAÑO R; BLANCO FERNÁNDEZ MD; TORRES C

Congreso; VI INTERNATIONAL CONGRESS IN TRANSLATIONAL MEDICINE; 2023

BACKGROUND AND AIMS. The study of viral species present in environmental samples has been shown to be a valuable strategy for detecting a wide variety of human, animal, and plant infections. The next-generation sequencing (NGS) techniques allow these detections to be untargeted and cheaper than some years ago, complementing traditional strategies of monitoring.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.METHODS. Samples (2L) were concentrated by ultrafiltration and PEG precipitation. 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). Bioinformatic processing of raw data included the removal of low-quality reads (Phred score below 30), trimming of adaptors, primers and short reads. The taxonomic classification of remaining reads was performed using Kraken2 and Bracken against the NCBI RefSeq viral database.RESULTS. 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.