Associations Between Salivary Bacteriome Diversity and Salivary Human Herpesvirus Detection in Early Childhood: A Prospective Cohort Study

Abstract

Background: The bacteriome is associated with susceptibility to some eukaryotic viruses, but no study has examined associations between the salivary bacteriome and human herpesviruses (HHVs). We provide new prevalence and incidence estimates for salivary herpesviruses detection and estimate associations with bacteriome diversity in young children.

Methods: Salivary samples collected at ages ~2, 8, 12, and 24 months from 153 children participating in the Center for Oral Health Research in Appalachia cohort 2 (COHRA2) were screened for HHVs using the Fast-Track Neuro9 multiplex PCR assay, and for the bacteriome using 16S rRNA amplicon sequencing. We used Cox proportional hazard models to test for associations between the salivary bacteriome and hazards of cytomegalovirus (CMV) and human herpesvirus-6 (HHV6).

Results: CMV, HHV6, and Epstein-Barr virus (EBV) were detected at all visits. Human herpesvirus-7 (HHV7) was first detected at the 8-month visit and herpes simplex virus 1 (HSV1) was only detected at the 12-month visit. Varicella-zoster virus, herpes simplex virus 2, and human herpesvirus-8 were never detected. HHV6 (24-month cumulative incidence: 73.8%) and CMV (24-month cumulative incidence: 32.3%) were detected most frequently. Increasing salivary bacteriome diversity was associated with longer survival to first detection of CMV (hazard ratio [95% CI]: 0.24 [0.12, 0.49]) and HHV6 (hazard ratio [95% CI]: 0.24 [0.13, 0.44]).

Conclusion: CMV, HHV6, EBV, HHV7, and HSV1 were detected in the saliva during the first 2 years of life. Time to first detection of CMV and HHV6 was associated with salivary bacteriome diversity, suggesting a possible interaction between HHVs and the salivary bacteriome.

Keywords: CMV; HHV6; early childhood; human herpesviruses; prospective cohort; salivary bacteriome.

Figure 1.

Cumulative incidence (lines) and prevalence (bars) estimates for the 4 most commonly detected herpesviruses in a sample of 153 children from the Pennsylvania site of the Center for Oral Health Research in Appalachia 2 study: HHV6, CMV, HHV7, and EBV. HSV1 was only detected in 2 samples from the 12-month time point, data not shown. No HSV2, VZV, or Kaposi’s sarcoma herpesvirus was detected. Inset graph shows cumulative incidence and prevalence data for the 65 individuals for whom 24-month salivary samples were available; otherwise, data are for all 153 individuals for whom salivary samples up to and including the 12-month visit were available. Abbreviations: CMV, cytomegalovirus; EBV, Epstein-Barr virus; HHV6, human herpesvirus-6; HHV7, human herpesvirus-7; HSV1, herpes simplex virus 1; HSV2, herpes simplex virus 1; VZV, varicella-zoster virus.

Figure 2.

(A) Relative abundance plots of bacteriome salivary composition over time (facets correspond to visits). Each bar is a sample, and the colors correspond to taxonomic classifications displayed in the legend, colors are stacked from the top down in the order they appear in the legend. Highly abundant species are displayed in darker hues of the genus color. Genera with a mean relative abundance of 1% (ie, <0.01) were collapsed to an “Other” category—displayed in gray. (B) Violin plots with captive box plots showing the distribution of Shannon index from both rarefied and non-rarefied samples over time (facets correspond to visits).