Nasopharyngeal Microbiota Profiling of Pregnant Women with SARS-CoV-2 Infection

Background: We aimed to characterize the role of the nasopharyngeal microbiota in pregnant women with and without SARS-CoV-2 infection.Methods: Pregnant women from a multicenter prospective population-based cohort (March-June 2020 in Barcelona, Spain) in which the status of SARS-CoV-2 infection was known by nasopharyngeal RT-PCR and antibodies in peripheral blood. DNA was extracted from nasopharyngeal swab samples, and the V3-V4 region of the 16S rRNA of bacteria was amplified using regions’ specific primers. Differential abundance of taxa was tested, alpha/beta diversity were evaluated.Findings: Among 76 women, 38 were classified as positive and 38 as negative for SARS-CoV-2 infection. All positive women were diagnosed by antibodies and 14 (37%) had also a positive RT-PCR. SARS-CoV-2 infection altered the overall composition of the nasopharyngeal microbiota (p=0.001) with higher relative abundance of Tenericutes and Bacteroidetes phylum, higher abundance of Prevotellaceae family. Infected women presented a different pattern of microbiota profiling due to beta diversity, and higher richness (Observed ASV<0.001) and evenness (Shannon index<0.001) at alpha diversity. These changes persisted after the acute infection revealed by a negative RT-PCR but positive antibodies, suggesting a long-lasting effect of SARS-CoV-2 in the nasopharyngeal microbiota. No significant differences were reported in mild vs. severe cases, suggesting a role of the SARS-CoV-2 infection itself but not on its severity.Interpretations: This is the first study on nasopharyngeal microbiota during pregnancy. SARS-CoV-2 infection altered the overall structure and diversity of the nasopharyngeal microbiota profiling and this effect seems to persist after the acute moment of the infection.Funding: This study was partially funded by the KidsCorona Child and Mother COVID- 19 OpenData and Biobank Initiative from Hospital Sant Joan de Déu (Stavros Niarchos Foundation, Santander Foundation and others), “LaCaixa” Foundation, Sant Pau Research Institute, ISGlobal and Fundació Privada Daniel Bravo Andreu, Barcelona, Spain. All funders had no role in the study design, data collection, data analysis, data interpretation and writing the manuscript.Declaration of Interest: Dr. Gratacós reports grants from Stavros Niarchos Foundation, Santander Foundation, and “La Caixa” Foundation, during the conduct of the study. Dr. Carmen Muñoz-Almagro reports grants and personal fees as speaker from Roche, Qiagen and Pfizer outside the submitted manuscript. The remaining authors had no conflicts of interest to be declared.Ethical Approval: The study was approved by the Review Board at each institution and informed written consent was obtained in all women (HCB/2020/0434, PIC-56-20).