Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

Jurasz, Henryk; Pawłowski, Tomasz; Perlejewski, Karol

doi:10.3389/fmicb.2021.745076

Cited by 36 publications

(34 citation statements)

References 160 publications

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“…Regardless of potential contamination issues that are common in viral metagenomics (Jurasz et al, 2021), this result is not surprising for FAC-sorted MVs, as the size fraction of sorted particles includes that of small bacteria.…”

Section: Metagenomic Sequencing Data and Biodiversity Of Putative Dna...mentioning

confidence: 84%

“Quasigenus” amongPhycodnaviridae: A diversity of chlorophyte-infecting viruses in response to a dense algal culture in a high-rate algal pond

Chase

Pitot

Bouchard

et al. 2022

Preprint

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This study approaches a high rate algal pond (HRAP) culture by metagenomic sequencing of the viral DNA fraction, this includes the so-called giant virus fraction (phylumNucleocytoviricota), with the goal of revealing viruses coexisting within an intensified algal culture. A wealth of interesting novel viruses is revealed, including members ofNucleocytoviricota,Lavidaviridae, and polinton-like viruses, which are taxa containing previously characterized algal viruses. Our sequencing results are coupled with a virus targeted qPCR study and 18S rDNA metabarcoding to elucidate potential virus-host interactions. Several species of green algae are identified (Chlorophyta), likely representing the alternating dominant populations during the year of study. Finally, we observe a bloom of viral diversity within the familyPhycodnaviridae(Nucleocytoviricota), including highly related but non-identical genotypes, appearing in the HRAP in September and October 2018. This bloom is most likely the cause of a mass mortality event of the cultured algae that occurred during these same months. We hypothesize that these relatedPhycodnaviridaelineages selectively infect different strains of the same algal species of the GenusPicochlorumthat have been identified in the HRAP by metabarcoding and coined this phenomenon a "quasigenus" by analogy to the RNA virus quasispecies concept.

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Section: Metagenomic Sequencing Data and Biodiversity Of Putative Dna...mentioning

confidence: 84%

“Quasigenus” amongPhycodnaviridae: A diversity of chlorophyte-infecting viruses in response to a dense algal culture in a high-rate algal pond

Chase

Pitot

Bouchard

et al. 2022

Preprint

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“…We built this data set primarily for virome-based virus detection. However, the HTS-based viral metagenome is prone to be contaminated by LCD viral sequences and vector-derived viral functional cassettes ( 11 , 12 , 16 , 37 ), which are also recorded in GenBank. This issue cannot be addressed by removing them from the reference database because those sequences would still be annotated by their genetically close relatives.…”

Section: Resultsmentioning

confidence: 99%

Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis

et al. 2022

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High-throughput sequencing-based viromics highly depends on reference databases, but foreign contamination is widespread in public databases and often leads to confusing and even wrong conclusions in genomic analysis and viromic profiling. To address this issue, we systematically detected and identified the contamination in the largest viral sequence collections of GenBank and UniProt based on a stringent scrutiny pipeline.

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“…With default Unicycler settings, only strain L15762 was successfully circularized, while 10 contigs and one non-circular contig were generated for strains F9160 and L15527, respectively. A small contig of 5,386 bp was also generated for strains L15762 and L15527 that corresponded to the PhiX174 E. coli phage used for quality and calibration assessment of Illumina sequencing and was therefore removed from the final data [ 19 ].…”

Section: Resultsmentioning

confidence: 99%

Genomic features of Mycoplasma bovis subtypes currently circulating in France

et al. 2022

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Background Mycoplasma (M.) bovis is a major etiological agent of bovine respiratory disease, which is the most economically costly disease of cattle worldwide. Cattle disease surveillance on M. bovis is increasingly using gene-based techniques, such as multilocus sequence typing (MLST), or genome-based techniques such as core genome MLST that both require only partial genomic data. However, accurate up-to-date surveillance also demands complete, circular genomes that can be used as reference to track the evolution of the different lineages. Yet, in France, two of the main subtypes currently circulating still have no representing genome in public databases. Here, to address this gap, we provide and compare three new complete M. bovis genomes obtained from recent clinical isolates that represent major subtypes circulating in France and Europe. Results Genomes were obtained using a hybrid assembly strategy (Illumina and Nanopore) with fine-tuning of settings and inputs used in the Unicycler assembly pipeline, such as size selection of reads and quality trimming of the FASTQ files. The main characteristics and synteny of the genomes were compared. The three genomes mainly differed by their content in terms of mobile genetic elements, i.e. integrative conjugative elements (ICE) and insertion sequences (IS), a feature that impacts their structure. For instance, strain L15527, representing subtype3 (st3), harbours an exceptionally high number of ICEs, which results in a bigger-sized genome than all those previously described and could be associated with the propensity of st3 to gain and fix mutations through chromosomal transfer mechanisms. In contrast, strain F9160, of st1, is very close to the PG45 type strain isolated in 1961 in the USA, and harbours a huge number of IS. These features may be associated with an evolution towards a host-restricted state or in a “closed” host or environment reservoir until a recent re-emergence. Conclusions Whole-genome comparison of the three French M. bovis subtypes provides valuable resources for future studies combining epidemiology, phylogenetic data, and phylodynamic methods.

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Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

Cited by 36 publications

References 160 publications

“Quasigenus” amongPhycodnaviridae: A diversity of chlorophyte-infecting viruses in response to a dense algal culture in a high-rate algal pond

“Quasigenus” amongPhycodnaviridae: A diversity of chlorophyte-infecting viruses in response to a dense algal culture in a high-rate algal pond

Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis

Genomic features of Mycoplasma bovis subtypes currently circulating in France

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