Affiliation:
1. Golestan University of Medical Sciences
2. Iran University of Medical Sciences
Abstract
AbstractMetagenomics is a promising approach to discovering viral sequences in environmental samples. We used recently published RNA-Seq data ofSolanum tuberosum(S. tuberosum) from China for a metavirome study. Several environmentally related non-intact viruses read from forest animals, moths, bacteria, and amoeba were detected. Further investigation resulted in non-indigenous sequences of SARS-CoV-2 genomes of lineage B with novel substitutions. Three substitutions, including A22D and A36V in the envelope protein and Q498H in the spike glycoprotein that were recently reported from a laboratory strain virus with enhanced virulence, were detected in all samples. Further substitutions at ORF1ab were also uncovered. These were L1457V, D4553N, W6538S, I1525T, D1585Y, D6928G, N3414K, T3432S. Two unexpected frameshifts, ORF1a:2338–4401 and ORF1a:3681–4401, were noticed within the ORF1ab. The genomic evidence and geographical evidence of lab leaks are also provided. The findings of the presented study highlight the threats of the emerged potentially severe genotypes bearing substitutions that are not yet clinically reported. More studies are warranted to uncover the role of the novel substitutions in the severity of SARS-coV-2
Publisher
Research Square Platform LLC
Reference31 articles.
1. Using Metagenomics to Characterize an Expanding Virosphere;Zhang YZ;Cell,2018
2. Going to extremes - a metagenomic journey into the dark matter of life;Aevarsson A;FEMS Microbiol. Lett.,2021
3. "Metagenomic Analysis of Marigold: Mixed Infection… Google Scholar. Available at: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=%22Metagenomic+Analysis+of+Marigold%3A+Mixed+Infection+Including+Two+New+Viruses%22&btnG=. (Accessed: 15th January 2023)
4. Metagenomic identification of novel viruses of maize and teosinte in North America;Lappe RR;BMC Genomics,2022
5. Damian, D., Berg, M., Johansson Wensman, J., Maghembe, R. & Damas, M. Application of viral metagenomics for study of emerging and reemerging tick-borne viruses. liebertpub.com 20, 557–565 (2020).