key: cord-351197-xv6ymc4l authors: Cibulski, Samuel; Alves de Lima, Diane; Fernandes dos Santos, Helton; Teixeira, Thais Fumaco; Tochetto, Caroline; Mayer, Fabiana Quoos; Roehe, Paulo Michel title: A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil date: 2020-09-28 journal: Virology DOI: 10.1016/j.virol.2020.09.005 sha: doc_id: 351197 cord_uid: xv6ymc4l A viral metagenomics study was conducted in beef, pork, and chicken sold in supermarkets from Southern Brazil. From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. From pork, genomes of numerous anelloviruses, porcine parvovirus 5 (PPV5) and 6 (PPV6), two new genomoviruses and two new CRESS-DNA viruses were found. Finally, two new CRESS-DNA genomes were recovered from beef. Although none of these viruses have history of transmission to humans, the findings reported here reveal that such agents are inevitably consumed in diets that include these types of meat. Meat and meat products are the source of numerous bacteria (e.g. Salmonella 33 enterica), protozoa (e.g. Toxoplasma gondii) and worms (e.g. Trichinella spiralis) that 34 may cause significant illness in humans. Therefore, it has been rising the overall 35 concern of viral transmission by food products, especially the ones causes by meat and 36 meat-derived. Meats have been pointed in charge, once is well-known that food-source 2009; Morse et al., 2012) . Today, emerging viruses are a major concern, since 44 devastating, occasionally life-threatening epidemics -e.g., COVID-19 and pandemic 45 influenza -are caused by viruses which originally spilled over from animals to humans. 46 In 2014, an interesting study identified a series of viral genome sequences in 47 Approximately 531,000 high-quality reads were generated by metagenomic 131 sequencing. After assembly, a total of 2,370 contigs were generated; 50.3% were viral 132 contigs. From these, 0.75% were assigned to eukaryotic viruses and 99.25% to 133 bacteriophages. However, despite the relatively small number of contigs associated with 134 viral genomes previously known to infect Eukarya, ~20% of the reads were mapped 135 back to these contigs, indicating a high sequence coverage. A detailed taxonomic 136 classification, including the numbers of reads for each Eukarya-related viral contig 137 recovered is this study, is provided in Supplementary gives them the ability to persist and spread in the environment. Chicken meat has been 149 reported to carry numerous gyroviruses, including the highly prevalent CAV, the 150 worldwide distributed, and recognized pathogen of chicken. Over the last decade, 151 twelve new putative Gyrovirus species were described, most of these recovered from This fragment shares low nt and aa identity with previously reported GyV3 isolates 163 (~72% of nt and ~75% at amino acid level), and probably represents another genome 164 variant, since the degree of VP1 identity between other GyV3 is greater than 70%. 165 Another interesting remark is that, to date, GyV3 has only been identified in feces from 166 mammalian hosts (human and cat). Therefore, it seems very likely that GyV3 may, in Sequences described in this study are marked in red. 206 The last two genomes recovered were CRESS-DNA viruses that could not be 207 allocated to any previously described viral family. CRESS 53F (5,532) exhibited four 208 ORFs encoding Rep, Cap and two hypothetical proteins (with homologues in other 209 CRESS-DNA viruses) ( Figure 3A ). The N-terminus of Cap presented a R-rich region, 210 whereas the Rep showed motifs implicated in RCR (Supplementary Table 2 Approximately 465,000 high-quality reads were produced by metagenomic 241 sequencing of pork sample. After assembly, a total of 2,922 contigs were generated; 242 55% of these were representative of viral sequences. From these, 1.4% were assigned to 243 eukaryotic viruses, whilst the remaining sequences were representatives of 244 bacteriophages. A detailed taxonomic classification, including the numbers of 245 J o u r n a l P r e -p r o o f sequenced reads of each Eukarya-related viral contig recovered in this study, is 246 provided in Supplementary Table 1 . 247 In the same way that gyroviruses were found in large amounts in chicken meat, 248 Anelloviridae contigs (Torque teno sus Gascuel, 2003). Sequences described in this study are marked in red. 328 J o u r n a l P r e -p r o o f Approximately 523,000 high-quality reads were obtained at metagenomic 330 sequencing. After assembly, a total of 1,739 contigs were generated; 51.6% were viral 331 contigs. From these, 0.5% were assigned to eukaryotic viruses, whereas remaining 332 contigs corresponded to bacteriophage sequences. A detailed taxonomic classification, 333 including numbers of sequenced reads of each Eukarya-related viral contig recovered in 334 this study, is provided in Supplementary Table 1 . 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