# Metagenome-assembled complete genome of Bohxovirus , a virulent bacteriophage involved in the prediction of hospital-acquired pneumonia in intubated critically ill patients

Hussein Anani, Grégory Destras, Hadrien Regue, Simon Bulteau, Céline

Bressollette-Bodin, Antoine Roquilly, Laurence Josset

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Hussein Anani, Grégory Destras, Hadrien Regue, Simon Bulteau, Céline Bressollette-Bodin, et al. Metagenome-assembled complete genome of Bohxovirus , a virulent bacteriophage involved in the prediction of hospital-acquired pneumonia in intubated critically ill patients. Microbiology Resource Announcements, 2025, 14 (12), pp.e0059225. 10.1128/mra.00592-25 . inserm-05444283

HAL Id: inserm-05444283

https://inserm.hal.science/inserm-05444283v1

Submitted on 6 Jan 2026

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<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons CC BY 4.0 - Attribution - International License
<figure><img src="image_2.png" /><figcaption>FIG 1 Genomic and comparative analysis of the vcOTU56. (A) A graphical circular map of the vcOTU56 genome. From the outside to the center: viral protein-coding genes. G + C skew and G + C content. (B) Maximum-likelihood phylogenetic tree showing the position of vcOTU56 (in red) relative to other closely related viral taxa. Sequences were aligned using MAFFT v7.508 (13) and trimmed with trimAl v1.4.1 (14), and the tree was constructed with IQ-TREE2 v2.2.2.3 using 1,000 rapid bootstrap replicates (15). Node bootstrap values are highlighted in blue. (C) Matrix showing the average nucleotide identity (ANI) values between vcOTU56 and other closely related taxa.</figcaption></figure>

gene-level annotation and clustering by comparing viral proteins against the most recent International Committee on Taxonomy of Viruses database release to assign taxonomic information. vcOTU56 was annotated as a *BohxoVirus*, classified within the *Suoliviridae* family, has a virulent lifestyle, and infects *Prevotella jejuni*, a bacterium that inhabits the human oral and gut microbiomes (10).
<table><caption>TABLE 1 Genome features of vcOTU56 closely relative sequences</caption><thead><tr><th>Closest relative sequence by BLASTn</th><th>Phabox2 classification</th><th>Phabox2 confidence</th><th>CheckV quality</th><th>Max score</th><th>Total score</th><th>Query cover</th><th>E value</th><th>Identity (%)</th><th>Length (bp)</th><th>Accession</th></tr></thead><tbody><tr><td>MAG TPA_asm: Caudoviricetes sp. isolate ctRU85</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>29,990</td><td>1.37E + 05</td><td>95%</td><td>0</td><td>92.7</td><td>99,611</td><td>BK019655.1</td></tr><tr><td>MAG TPA_asm: Podoviridae sp. ctZkC8</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>28,692</td><td>97,088</td><td>70%</td><td>0</td><td>91.94</td><td>93,668</td><td>BK016062.1</td></tr><tr><td>MAG TPA_asm: Bacteriophage sp. isolate ctxN72</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>27,366</td><td>1.32E + 05</td><td>95%</td><td>0</td><td>93.46</td><td>97,813</td><td>BK028985.1</td></tr><tr><td>Uncultured phage cr61_1</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>23,893</td><td>61,579</td><td>59%</td><td>0</td><td>87.72</td><td>98,573</td><td>NC_067209.1</td></tr><tr><td>MAG TPA_asm: Caudoviricetes sp. isolate ctss16</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>23,889</td><td>1.04E + 05</td><td>71%</td><td>0</td><td>92.6</td><td>100,941</td><td>BK046077.1</td></tr><tr><td>MAG TPA_asm: Caudoviricetes sp. isolate ctnLP2</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>20,825</td><td>1.23E + 05</td><td>94%</td><td>0</td><td>89.64</td><td>102,343</td><td>BK039644.1</td></tr><tr><td>MAG TPA_asm: Caudoviricetes sp. isolate ctTb212</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>20,040</td><td>31,089</td><td>21%</td><td>0</td><td>93.72</td><td>26,228</td><td>BK039806.1</td></tr><tr><td>MAG TPA_asm: Caudoviricetes sp. isolate ctJxl8</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>18,454</td><td>69,215</td><td>45%</td><td>0</td><td>93.72</td><td>58,045</td><td>BK058154.1</td></tr><tr><td>MAG TPA_asm: Caudoviricetes sp. isolate ctR5o17</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>17,998</td><td>46,892</td><td>34%</td><td>0</td><td>93.08</td><td>38,277</td><td>BK057929.1</td></tr><tr><td>MAG TPA_asm: Caudoviricetes sp. isolate ctdNw4</td><td>Bohхovirus</td><td>High confidence</td><td>Complete</td><td>17,860</td><td>1.02E + 05</td><td>86%</td><td>0</td><td>87.51</td><td>99,284</td><td>BK038595.1</td></tr></tbody></table>

vcOTU56, present in 29% of samples, with reads remapping (mean relative abundance of 0.05%), has a complete circular genome of 98,381 bp with a sequencing depth of 2,372x and GC content of 33.06% (100% completeness and 0% contamination). Genome annotation using Prokka v1.14.6 (11) with the --kingdom Viruses parameter predicts 168 viral genes and 5 tRNA genes. vcOTU56 genome was visualized using PhageScope (12) (Fig. 1A). Phylogenetic analysis of vcOTU56 and the 10 closest BLASTn-identified sequences from nucleotide-NCBI database showed that vcOTU56 formed a separate group (Fig. 1B). Interestingly, all closest sequences, like vcOTU56, were predicted to belong to *Bohхovirus* (Table 1).

vcOTU56 exhibits a 92.70% ANI with its closest sequence (*Caudoviricetes_sp_isolate_ctRU85*, Fig. 1C). In accordance with the 95% species demarcation threshold, these data suggest that vcOTU56 is a new species of the genus *Bohхovirus*, which warrants further investigation.

## ACKNOWLEDGMENTS

The study was funded by the European Union's Horizon 2020 research and innovation program under the grant agreement number 847782 (HAP2 project). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

## AUTHOR AFFILIATIONS

<footnote n="1">¹GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France</footnote>

<footnote n="2">²CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France</footnote>

<footnote n="3">³Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France</footnote>
⁴Nantes Université, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France

⁵Nantes Université, CHU Nantes, Service de virologie, Nantes, France

⁶Nantes Université, CHU Nantes, Service d'anesthésie réanimation, Nantes, France

⁷Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia

## AUTHOR ORCIDs

Hussein Anani https://orcid.org/0000-0003-4047-2013

Grégory Destras https://orcid.org/0000-0001-6817-7118

Laurence Josset https://orcid.org/0000-0002-7158-1186

## FUNDING

<table><thead><tr><td>Funder</td><td>Grant(s)</td><td>Author(s)</td></tr></thead><tbody><tr><td>Horizon 2020 Framework Programme</td><td>847782</td><td>Hussein Anani</td></tr></tbody></table>

## AUTHOR CONTRIBUTIONS

Hussein Anani, Conceptualization, Data curation, Formal analysis, Validation, Visualization, Writing – original draft, Writing – review and editing | Grégory Destras, Validation, Writing – original draft, Writing – review and editing | Hadrien Regue, Data curation | Simon Bulteau, Data curation | Céline Bressollette-Bodin, Writing – review and editing | Antoine Roquilly, Writing – review and editing | Laurence Josset, Funding acquisition, Supervision, Writing – original draft, Writing – review and editing

## DATA AVAILABILITY

The complete sequence of vcOTU56 has been deposited in GenBank under the accession number PV686213, and raw reads are available under the BioProject number PRJNA1132989.

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