# Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants

## TL;DR

This study explores how the gut bacteria and viruses in mothers and infants change before and after SARS-CoV-2 infection, with a focus on those living with HIV.

## Contribution

The study reveals that SARS-CoV-2 infection disrupts the gut microbiome diversity trajectory in women, independent of HIV status.

## Key findings

- Maternal gut microbiome diversity increased before SARS-CoV-2 infection but decreased afterward.
- Infant gut microbiome and virome changes were primarily driven by development, not SARS-CoV-2.
- No significant interactions between HIV and SARS-CoV-2 were found in gut microbiome or virome dynamics.

## Abstract

Microbiome perturbations can have long-term effects on health. The dynamics of the gut microbiome and virome in women living with HIV (WLHIV) and their newborn infants is poorly understood. Here, we performed metagenomic sequencing analyses on longitudinal stool samples including 23 mothers (13 WLHIV, 10 HIV-negative) and 12 infants that experienced SARS-CoV-2 infection with mild disease, as well as 40 mothers (18 WLHIV, 22 HIV-negative) and 60 infants that remained SARS-CoV-2 seronegative throughout the study follow-up. Regardless of HIV or SARS-CoV-2 status, maternal bacterial and viral profiles were distinct from infants. Using linear mixed effects models, we showed that while the microbiome alpha diversity trajectory was not significantly different between SARS-CoV-2 seropositive and seronegative women. However, seropositive women’s positive trajectory while uninfected was abruptly reversed after SARS-CoV-2 infection (p = 0.015). However, gut virome signatures of women were not associated with SARS-CoV-2. Alterations in infant microbiome and virome diversities were generally not impacted by SARS-CoV-2 but were rather driven by development. We did not find statistically significant interactions between HIV and SARS-CoV-2 on the gut microbiome and virome. Overall, our study provides insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status.