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
School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
mSystems. 2025 May 20;10(5):e0156824. doi: 10.1128/msystems.01568-24. Epub 2025 Apr 22.
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. The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 pandemic, on the nasopharyngeal microbiome 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 children (18 HIV-exposed, uninfected and 7 HIV-unexposed, uninfected) between September 2021 and March 2022. We show using genomic epidemiology that mother and child dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. We used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and children infected with SARS-CoV-2, six children negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint-matched SARS-CoV-2-negative mothers and children. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- (within a week of infection) and longer- (average of 38 days post-infection) term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and children had significantly different microbiome composition and bacterial load (-values < 0.0001). In both mothers and children, 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.
The nasopharyngeal microbiome plays an important role in human health. The degree of impact that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has on the nasopharyngeal microbiome varies among studies and may be influenced by diverse SARS-CoV-2 variants and variations in the microbiome between individuals. Our results show that the nasopharyngeal microbiome was not altered substantially by SARS-CoV-2 infection nor by HIV infection in mothers or HIV exposure in children. Our findings highlight the resilience of the nasopharyngeal microbiome after SARS-CoV-2 infection. These findings advance our understanding of the nasopharyngeal microbiome and its interactions with viral infections.
鼻咽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的领域。2019冠状病毒病大流行的病原体严重急性呼吸综合征冠状病毒2（SARS-CoV-2）对艾滋病毒感染者鼻咽微生物群的影响尚未完全明确。在此，我们描述了2021年9月至2022年3月期间，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）及其子女（18名暴露于艾滋病毒但未感染、7名未暴露于艾滋病毒且未感染）的纵向队列中，SARS-CoV-2感染前、感染期间和感染后的鼻咽微生物群。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。我们使用宏基因组测序来表征20名感染SARS-CoV-2的妇女和儿童、6名SARS-CoV-2检测阴性但有呼吸道症状的儿童以及34名时间点匹配的SARS-CoV-2阴性母亲和儿童的鼻咽微生物群。由于个体在SARS-CoV-2感染前后进行了纵向采样，我们能够表征SARS-CoV-2感染对鼻咽微生物群的短期（感染后一周内）和长期（感染后平均38天）影响。我们发现母亲和儿童的微生物群组成和细菌载量存在显著差异（P值<0.0001）。在母亲和儿童中，无论艾滋病毒暴露状况如何，SARS-CoV-2感染前后的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改变。
鼻咽微生物群在人类健康中起着重要作用。严重急性呼吸综合征冠状病毒2（SARS-CoV-2）感染对鼻咽微生物群的影响程度在不同研究中有所不同，可能受到多种SARS-CoV-2变异株以及个体间微生物群差异的影响。我们的结果表明，SARS-CoV-2感染、母亲的艾滋病毒感染或儿童的艾滋病毒暴露均未使鼻咽微生物群发生实质性改变。我们的研究结果突出了SARS-CoV-2感染后鼻咽微生物群的弹性。这些发现增进了我们对鼻咽微生物群及其与病毒感染相互作用的理解。
