Human Anelloviruses: Influence of Demographic Factors, Recombination, and Worldwide Diversity

Abstract

Anelloviruses represent the major and most diverse component of the healthy human virome, referred to as the anellome. In this study, we determined the anellome of 50 blood donors, forming two sex- and age-matched groups. Anelloviruses were detected in 86% of the donors. The number of detected anelloviruses increased with age and was approximately twice as high in men as in women. A total of 349 complete or nearly complete genomes were classified as belonging to torque teno virus (TTV), torque teno mini virus (TTMV), and torque teno midi virus (TTMDV) anellovirus genera (197, 88, and 64 sequences, respectively). Most donors had intergenus (69.8%) or intragenus (72.1%) coinfections. Despite the limited number of sequences, intradonor recombination analysis showed 6 intragenus recombination events in ORF1. As thousands of anellovirus sequences have been described recently, we finally analyzed the global diversity of human anelloviruses. Species richness and diversity were close to saturation in each anellovirus genus. Recombination was found to be the main factor promoting diversity, although its effect was significantly lower in TTV than in TTMV and TTMDV. Overall, our results suggest that differences in diversity between genera may be caused by variations in the relative contribution of recombination. IMPORTANCE Anelloviruses are the most common human infectious viruses and are considered essentially harmless. Compared to other human viruses, they are characterized by enormous diversity, and recombination is suggested to play an important role in their diversification and evolution. Here, by analyzing the composition of the plasma anellome of 50 blood donors, we find that recombination is also a determinant of viral evolution at the intradonor level. On a larger scale, analysis of anellovirus sequences currently available in databases shows that their diversity is close to saturation and differs among the three human anellovirus genera and that recombination is the main factor explaining this intergenus variability. Global characterization of anellovirus diversity could provide clues about possible associations between certain virus variants and pathologies, as well as facilitate the implementation of unbiased PCR-based detection protocols, which may be relevant for using anelloviruses as endogenous markers of immune status.

Keywords: anellovirus; blood anellome; metagenomics; recombination; virome.

FIG 1

Influence of demographic factors on expected anellovirus. The number of anelloviruses per individual was estimated using a generalized linear model in which the response variable was anellovirus contig count (modeled using a Tweedie distribution) and the explanatory factors were age, sex, and their interaction.

FIG 2

Distribution of anellovirus contigs generated for female (A) and male (B) samples. For each sample, the proportion of sequences belonging to the TTV, TTMV, and TTMDV genera is shown in blue, green, and red, respectively.

FIG 3

Schematic representation of the recombination events detected. The six recombination events finally detected are plotted on the reference genome of each genus. The red line indicates the location of ORF1, which is the region used in recombination analyses, for each reference genome.

FIG 4

Sample-size-based interpolation (rarefaction) and extrapolation curves for species richness (A) and Shannon diversity (B) of each anellovirus genus. Solid lines represent interpolation (rarefaction), dashed lines represent extrapolation, solid shapes indicate observed values, and shaded areas show 95% confidence intervals. Species richness and diversity analyses were performed with the iNEXT package in R (58).