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Genome Sequences
human-microbiomeHuman MicrobiomeGenome sequences of human anelloviruses in the Lamedtorquevirus, Memtorquevirus, and Samektorquevirus genera identified from the female genital tract
Do Eric D. 1 Data curation Formal analysis Writing – original draft
https://orcid.org/0000-0003-0649-3611
Holland Steven C. 2 Formal analysis Writing – original draft Writing – review and editing
Kaelin Emily A. 1 2 Data curation
Mitchell Caroline 3 Resources
https://orcid.org/0000-0002-5863-0502
Soria Jaime 4 Resources
La Rosa Alberto 5 6 Resources
Ticona Eduardo 7 Resources
Coombs Robert W. 8 Funding acquisition Resources
https://orcid.org/0000-0001-9566-8959
Frenkel Lisa M. 8 9 10 Funding acquisition Resources
Bull Marta E. 9 10 Resources
https://orcid.org/0000-0002-3397-9310
Lim Efrem S. 1 2 Conceptualization Funding acquisition Supervision Writing – original draft Writing – review and editing Efrem.Lim@asu.edu

1 School of Life Sciences, Arizona State University , Tempe, Arizona, USA
2 Center for Fundamental and Applied Microbiomics, the Biodesign Institute , Tempe, Arizona, USA
3 Department of Obstretrics and Gynecology, University of Washington , Seattle, Washington, USA
4 Infectious Diseases Departmento, Hospital Nacional Dos de Mayo, Universidad de San Marcos , Lima, Peru
5 Asociaciòn Civil Impacta Salud y Educación , Lima, Peru
6 MSD Peru , Lima, Peru
7 Infectious Diseases Departamento, Hospital Nacional Dos de Mayo, Asociaciòn Civil Impacta Salud y Educación, Universidad de San Marcos , Lima, Peru
8 Departments of Medicine; Laboratory Medicine and Pathology, University of Washington , Seattle, Washington, USA
9 Seattle Children’s Research Institute , Seattle, Washington, USA
10 Department of Pediatrics, University of Washington , Seattle, Washington, USA
Editor Roux Simon DOE Joint Genome Institute , Berkeley, California, USA

Address correspondence to Efrem S. Lim, Efrem.Lim@asu.edu
Present address: Vincent Center for Reproductive Biology, Massachusetts General Hospital, Harvard University, Boston, Massachusetts, USA

Present address: University of Kentucky, Lexington, Kentucky, USA

Present address: Professor Emeritus, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA

Present address: VIR Biotechnology, San Francisco, California, USA

Eric D. Do and Steven C. Holland contributed equally to this article. The author order was determined alphabetically.

The authors declare no conflict of interest.

9 2024
05 8 2024
05 8 2024
13 9 e00582-2431 5 2024
19 7 2024
Copyright © 2024 Do et al.
2024
Do et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

We identified and characterized seven anellovirus genome sequences in the female genital tract through virome metagenomic sequencing of cervicovaginal lavage specimens from women living with HIV in Peru. Phylogenetic and genomic analyses indicate that they belong to three newly proposed Lamedtorquevirus, Memtorquevirus, and Samektorquevirus genera in the Anelloviridae family.

KEYWORDS

Anelloviridae
female genital tract
cover-dateSeptember 2024
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pmcANNOUNCEMENT

Anelloviruses (family Anelloviridae) are small, nonenveloped viruses with a circular negative sense, single-stranded DNA genomes typically ranging between 1.6 and 3.9 kb in length (1). In humans, anelloviruses can be found in a broad range of body sites including blood, stool, and the female genital tract (2–4). While anelloviruses are not known to be associated with disease, changes in anellovirus load have been implicated in host immune competency such as organ transplant immunosuppression (5).

As part of ongoing efforts to characterize the human virome, we conducted virome metagenomic sequencing of 31 women living with HIV over a 2-year period (125 cervicovaginal specimens) in Lima, Peru who were on long-term antiretroviral therapy (6, 7). Cervicovaginal lavage specimens were subjected to virus-like particle enrichment (filtered through 0.2 µm pore filter, digestion of non-encapsidated nucleic acids with benzonase and Baseline-ZERO DNase), and total nucleic acid extraction (bioMérieux eMAG). Viral DNA was amplified using multiple displacement amplification (GenomiPhi V2), used for library preparation (Illumina DNA Prep library kit), followed by next-generation sequencing (Illumina NextSeq 2000 2 × 150 bp paired-end reads). Sequencing reads were trimmed to remove adapter sequences [Cutadapt v.4.0 (8)], quality filtered (trimq = 30, min length = 75, min avg quality = 20), PhiX and human host read removed, and deduplicated (BBTools). Contigs were assembled with metaSPAdes [V. 3.15.4 (9)] and queried against viral protein sequences from NCBI RefSeq and viral neighbor genome sequences (downloaded on January 2023) (10) using blastx (e-value 1 × 10−3). All tools were run with default parameters unless specified. We identified seven contig sequences collected from six individuals from September 2007 through September 2008 that had limited identity to alphatorquevirus, betatorquevirus, and gammatorquevirus sequences that are typically the most prevalent human anelloviruses. Based on terminal redundancy, four sequences were circular, full-length, complete genomes, and three were near-complete genomes (Fig. 1A).

Fig 1 (A) Summary details of genome sequences. (B) Phylogeny of anellovirus ORF1 amino acid sequences. Sequences identified in this study are in boldface, with complete genomes denoted by an asterisk. Genbank accession numbers and virus species names are indicated. Bootstrap support values are labeled at tree nodes.

The International Committee on Taxonomy of Viruses and community guidelines for genus demarcation criteria are based on the ORF1 amino acid sequences (1, 11). We performed a phylogenetic analysis on the ORF1 amino acid sequence alignment using MAFFT v. 7.505 (12), trimmed with trimAl (v.1.4.rev15) using the -gt 0.2 gappyout option (13) of our seven genome sequences and 23 reference sequences from the Samektorquevirus, Memtorquevirus, Lamedtorquevirus, Alphatorquevirus, Betatorquevirus, Gammatorquevirus, Hetorquevirus, Omegatorquevirus, Yodtorquevirus, Epsilontorquevirus, and Zetatorquevirus genera. The maximum likelihood phylogeny was constructed with IQ-TREE (v. 2.0.3) with the model VT + F + G and 1,000 bootstrap replicates (14) and visualized in FigTree (v. 1.4.4) (15). The seven new sequences grouped with members of the newly proposed Lamedtorquevirus, Memtorquevirus, and Samektorquevirus genera (16), designated as Lamedtorquevirus hominid11 (GenBank accession number PP728778), Memtorquevirus hominid13 (PP728777), Memtorquevirus hominid14 (PP728782), Samektorquevirus hominid16 (PP728776), Samektorquevirus hominid17 (PP728779, PP728780), and Samektorquevirus hominid18 (PP728781) (Fig. 1B).

These findings highlight the understudied nature of the female genital tract virome and demonstrate the inclusion of human anelloviruses in the Lamedtorquevirus, Memtorquevirus, and Samektorquevirus genera within the Anelloviridae family.

All study participants provided informed consent. This study was approved by the Institutional Review Boards of the Hospital Dos de Mayo (Lima, Peru), Seattle Children’s Hospital (Seattle, Washington, USA), and Arizona State University (Tempe, Arizona, USA).

ACKNOWLEDGMENTS

This work was supported by the National Institute of Allergy and Infectious Disease at the National Institutes of Health. R01 AI071212 and R01 AI091550 awarded to L.M.F.; UM1-AI-106701 awarded to R.W.C.; UW/FHCRC CFAR P30-AI-027757; and R00DK107923 awarded to E.S.L.

DATA AVAILABILITY

The sequences of the seven genomes of anellovirus identified in this study have been deposited into the NCBI GenBank database under accession numbers: PP728776–PP728782. Raw sequencing reads have been deposited into the NCBI SRA under project number PRJNA1077994.
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