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

Abstract

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.

Keywords: SARS-CoV-2; TTMDV; TTMV; TTV; anellome; virome.

Figure 1

Anellovirus load in blood following SARS-CoV-2 infection. Anellovirus load (copies/mL), either TTV, TTMV or TTMDV, was determined in health care workers (HCWs) followed for three months (T0-12 weeks). The anellovirus load of each individual HCW (left) and mean with standard deviation (right) is shown. The anellovirus load was log transformed. Each color of the lines represents one health care worker (HCW). (A) SARS-CoV-2 seroconverters group. (B) SARS-CoV-2 negative group. Dashed line corresponds to the detection limit (DL). * = p ≤ 0.05, *** = p ≤ 0.001.

Figure 2

Anellovirus load after symptom initiation of SARS-CoV-2 infection. Anellovirus load (copies/mL) was determined in the SARS-CoV-2 seroconverter group during a follow-up of three months. Severity of symptoms and date of symptom onset were collected using surveys. Colors represent unique HCWs and symbols represent anellovirus genera: TTV (circle), TTMV (square) and TTMDV (triangle). Dashed line corresponds to the detection limit (DL).

Figure 3

Anellovirus concentration and SARS-CoV-2 antibodies in blood following SARS-CoV-2 infection. (A–H). Anellovirus load (copies/mL; left Y-axis), either TTV (orange), TTMV (green) or TTMDV (grey), was determined in health care workers (HCWs—S3-02, S3-05, S3-06, S3-08, S3-11, S3-13, S3-15 and S3-16) followed for three months (T0-12 weeks). Antibodies targeting Spike (light green dotted line), Receptor Binding Domain (dark blue dotted line), and Nucleocapsid proteins (light blue dotted line) of SARS-CoV-2 are shown as median fluorescent intensity (MFI) on the right Y-axis. Dashed line corresponds to the qPCR detection limit (DL).

Figure 4

Blood anellome of individuals following SARS-CoV-2 infection. Heat maps of various anellovirus lineages and their abundance in health care workers (HCWs) followed for three months (T0, 4 weeks, 8 weeks and 12 weeks). The intensity of the green color refers to the relative abundance and the white color represents absence of a lineage in the sample. Dark grey squares indicate the sample was not included for next-generation sequencing due to absence of anelloviruses measured by qPCR. The colors of the reference genomes refer to different genera: TTV (orange), TTMV (cyan) and TTMDV (grey). (A) Individual S3-02, (B) individual S3-06, (C) individual S3-08, (D) individual S3-11, (E) individual S3-15. * indicates APOBEC3 editing.