SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data

Laubscher, Florian; Kaiser, Laurent; Cordey, Samuel

doi:10.3390/v15071575

Cited by 5 publications

(4 citation statements)

References 22 publications

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“…Sequencing resulted in an average of 3.77 × 10 6 paired reads per sample (range 2.5 × 10 6 to 4.42 × 10 6 ) ( Table S4 ). The reads were mapped to the SCANellome database (version 19 April 2023), a database containing the ORF1 reference sequences of 3636 representatives of human-infecting anelloviruses [ 27 ]. We used a cutoff of 75% read coverage against a SCANellome representative to determine lineage abundance.…”

Section: Resultsmentioning

confidence: 99%

“…Anelloviruses are extremely diverse and individuals can be infected with many lineages [ 3 ]. Even though the SCANellome database we used as reference contains 3636 different human anellovirus references [ 27 ], it is possible that not all lineages present in our individuals have a representative in the SCANellome database. On the other hand, the genus-specific PCR primers, designed on the most conserved region of the genome, may also have missed certain variants.…”

Section: Discussionmentioning

confidence: 99%

“…Raw Illumina reads (fastq format) were trimmed using Trimmomatic (version 0.39) on GITbash (version v2.35.2) and quality-checked using FastQC [3]. The trimmed reads were aligned to the SCANellome database (version 19 April 2023), which is an anellovirus database that contains 3636 human anellovirus ORF1 reference genomes (408 TTV, 1855 TTMV, 1373 TTMDV) [27]. Alignments were performed using Bowtie2 (version 2.2.5) with the "very sensitive" setting and the end-to-end mode on the Snellius cluster computer (https://www.…”

Section: Scanellome-prevalence Of Anellovirusesmentioning

confidence: 99%

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The Impact of First-Time SARS-CoV-2 Infection on Human Anelloviruses

Timmerman,

Commandeur,

Deijs

et al. 2024

Viruses

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Members of the Anelloviridae family dominate the blood virome, emerging early in life. The anellome, representing the variety of anelloviruses within an individual, stabilizes by adulthood. Despite their supposedly commensal nature, elevated anellovirus concentrations under immunosuppressive treatment indicate an equilibrium controlled by immunity. Here, we investigated whether anelloviruses are sensitive to the immune activation that accompanies a secondary infection. As a model, we investigated 19 health care workers (HCWs) with initial SARS-CoV-2 infection, with blood sampling performed pre and post infection every 4 weeks in a 3-month-follow-up during the early 2020 COVID-19 pandemic. A concurrently followed control group (n = 27) remained SARS-CoV-2-negative. Serum anellovirus loads were measured using qPCR. A significant decrease in anellovirus load was found in the first weeks after SARS-CoV-2 infection, whereas anellovirus concentrations remained stable in the uninfected control group. A restored anellovirus load was seen approximately 10 weeks after SARS-CoV-2 infection. For five subjects, an in-time anellome analysis via Illumina sequencing could be performed. In three of the five HCWs, the anellome visibly changed during SARS-CoV-2 infection and returned to baseline in two of these cases. In conclusion, anellovirus loads in blood can temporarily decrease upon an acute secondary infection.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Scanellome-prevalence Of Anellovirusesmentioning

confidence: 99%

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The Impact of First-Time SARS-CoV-2 Infection on Human Anelloviruses

Timmerman,

Commandeur,

Deijs

et al. 2024

Viruses

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“…This is a significant improvement, considering the limitations of current metagenomic methods when dealing with low viral loads of non-linear viruses. Laubscher et al at the University of Geneva introduced SCANellome, a user-friendly tool to investigate the primate anellome composition at the genus, species, and genotype levels of samples from metagenomics data generated by the Illumina and Nanopore platforms [ 3 ]. Finally, in Argentina, Reyes et al determined TTV species diversity and variability in 27 renal transplant recipients, finding that the median number of TTV species per sample was five, with TTV3 and TTV13 in 75% of cases.…”

mentioning

confidence: 99%

The Emerging Tool of the Human Anellovirome

Focosi,

Spezia,

Maggi

2024

Viruses

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Novel lineage of anelloviruses with large genomes identified in dolphins

De Koch,

Krupovic,

Fielding

et al. 2024

J Virol

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Anellovirus infections are ubiquitous in mammals but lack any clear disease association, suggesting a commensal virus-host relationship. Although anelloviruses have been identified in numerous mammalian hosts, their presence in members of the family Delphinidae has yet to be reported. Here, using a metagenomic approach, we characterize complete anellovirus genomes ( n = 69) from four Delphinidae host species: short-finned pilot whale ( Globicephala macrorhynchus , n = 19), killer whale ( Orcinus orca , n = 9), false killer whale ( Pseudorca crassidens , n = 6), and pantropical spotted dolphin ( Steno attenuatus , n = 1). Sequence comparison of the open reading frame 1 (ORF1) encoding the capsid protein, the only conserved gene shared by all anelloviruses, shows that the Delphinidae anelloviruses form a novel genus-level clade that encompasses 22 unique species-level groupings. We provide evidence that different Delphinidae species can be co-infected by multiple anelloviruses belonging to distinct species groupings. Notably, the ORF1 protein of the Delphinidae anelloviruses is considerably larger than those encoded by all previously described anelloviruses from other hosts (spanning 14 vertebrate orders and including 27 families). Comprehensive analysis of the ORF1 sequences and predicted protein structures showed that the increased size of these proteins results from divergent elaborations within the capsid-distal P2 subdomain and elongation of the C-terminal domain of ORF1. Comparative structural and phylogenetic analyses suggest that acquisition of the P2 subdomain and its diversification occurred convergently in the anelloviruses associated with primate and Delphinidae hosts. Collectively, our results further the appreciation of diversity and evolution of the ubiquitous and enigmatic viruses in the family Anelloviridae . IMPORTANCE Anelloviruses are ubiquitous in mammals, but their infection has not yet been linked to any disease, suggesting a commensal virus-host relationship. Here, we describe the first anelloviruses associated with diverse species of dolphins. The dolphinid anelloviruses represent a new genus (tentatively named “Qoptorquevirus”) and encode open reading frame 1 (ORF1) (capsid) proteins that are considerably larger than those encoded by previously described anelloviruses from other hosts. Comprehensive analysis of the ORF1 sequences and predicted protein structures revealed the underlying structural basis for such an extravagant ORF1 size and suggested that ORF1 size increased convergently in the anelloviruses associated with primate and Delphinidae hosts, respectively. Collectively, our results provide insights into the diversity and evolution of Anelloviridae . Further exploration of the anellovirus diversity, especially in the host species that have not yet been sampled, is expected to further clarify their evolutionary trajectory and explain the unusual virus-host commensal relationship.

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SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data

Cited by 5 publications

References 22 publications

The Impact of First-Time SARS-CoV-2 Infection on Human Anelloviruses

The Impact of First-Time SARS-CoV-2 Infection on Human Anelloviruses

The Emerging Tool of the Human Anellovirome

Novel lineage of anelloviruses with large genomes identified in dolphins

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