Žuštra Ayla, Leonard Victoria R, Holland LaRinda A, Hu James C, Mu Tianchen, Holland Steven C, Wu Lily I, Begnel Emily R, Ojee Ednah, Chohan Bhavna H, Richardson Barbra A, Kinuthia John, Wamalwa Dalton, Slyker Jennifer, Lehman Dara A, Gantt Soren, Lim Efrem S
Arizona State University.
University of Washington.
Res Sq. 2024 Apr 17:rs.3.rs-4257641. doi: 10.21203/rs.3.rs-4257641/v1.
The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest and of clinical relevance. The impact of SARS-CoV-2, the etiological agent of the Coronavirus Disease 2019 (COVID-19) pandemic, on the nasopharyngeal microbiome, particularly among individuals living with HIV, is not fully characterized. Here we describe the nasopharyngeal microbiome before, during and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their infants (18 HIV-exposed, uninfected and 18 HIV-unexposed, uninfected), followed between September 2021 through March 2022. We show using genomic epidemiology that mother and infant dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. Additionally, we used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and infants infected with SARS-CoV-2, 6 infants negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint matched SARS-CoV-2 negative mothers and infants. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- and long-term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and infants had significantly different microbiome composition and bacterial load (p-values <.0001). However, in both mothers and infants, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV-exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.
鼻咽部及其微生物群与呼吸健康和疾病有关。病毒感染与鼻咽微生物群之间的相互作用是一个越来越受关注且具有临床相关性的领域。2019年冠状病毒病（COVID-19）大流行的病原体严重急性呼吸综合征冠状病毒2（SARS-CoV-2）对鼻咽微生物群的影响，尤其是在艾滋病毒感染者中，尚未完全明确。在此，我们描述了2021年9月至2022年3月期间对肯尼亚女性（21名艾滋病毒感染者和14名未感染艾滋病毒者）及其婴儿（18名暴露于艾滋病毒但未感染、18名未暴露于艾滋病毒且未感染）进行纵向队列研究中，SARS-CoV-2感染前、感染期间和感染后的鼻咽微生物群情况。我们通过基因组流行病学研究表明，母婴二元组感染了在肯尼亚迅速传播的同一株SARS-CoV-2奥密克戎变异株。此外，我们使用宏基因组测序对20名感染SARS-CoV-2的女性和婴儿、6名SARS-CoV-2检测阴性但有呼吸道症状的婴儿以及34名时间点匹配的SARS-CoV-2阴性的母亲和婴儿的鼻咽微生物群进行了特征分析。由于个体在SARS-CoV-2感染前后进行了纵向采样，我们能够确定SARS-CoV-2感染对鼻咽微生物群的短期和长期影响。我们发现母亲和婴儿的微生物群组成和细菌载量存在显著差异（p值<.0001）。然而，在母亲和婴儿中，无论艾滋病毒暴露状态如何，SARS-CoV-2感染前后鼻咽微生物群均无差异。我们的结果表明，鼻咽微生物群对SARS-CoV-2感染具有弹性，且未受到艾滋病毒的显著影响。
