Nasopharyngeal microbiome in SARS-CoV-2 infected women and infants

SARS-CoV-2, the etiological agent of the Coronavirus Disease 2019, has had broad impacts on health. However, the impact of SARS-CoV-2 on the nasopharyngeal microbiome is not fully characterized, with many disagreements between studies. Furthermore, the interplay between SARS-CoV-2 and other viral diseases such as HIV is not well characterized. The purpose of this study is to analyze the relationship between the nasopharyngeal microbiome and SARS-CoV-2 in women living with HIV and their HIV-exposed unaffected (HEU) infants, as well as HIV-uninfected women and their HIV-unexposed unaffected women (HUU). We performed metagenomic sequencing of the bacterial microbiome in nasopharyngeal specimens collected longitudinally from Mathare, Kenya over a 8 month period. Characterizing the nasopharyngeal microbiome during SARS-CoV-2 infected and mediated HIV infection may identify bacteria implicated in SARS-CoV-2 dysbiosis or protection of the microbiome upon viral infection.