1 Alterations of the upper respiratory microbiome among children living with HIV infection in Botswana Sweta M. Patel, MD 1,2* , John Farirai, MBBCh 3 , Mohamed Z. Patel, MBBCh, FCPaed 4 , Sefelani Boiditswe, BNSc 5 , Leabaneng Tawe, PhD 6 , Shimane Lekalake 3 , Mogomotsi Matshaba, MBBCh 3,7 , Andrew P. Steenhoff, MBBCh, FCPaed, 5,8 Tonya Arscott-Mills, MD 5 Kristen A. Feemster, MD 8 , Samir S. Shah, MD 9 Nathan Thielman, MD 2,10 , Coleen K. Cunningham, MD 11,12 , Lawrence A. David, PhD 13 , David Murdoch, MD 1 , Matthew S. Kelly, MD 2,5,14 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University, Durham, NC, USA; 2 Duke Global Health Institute, Duke University, Durham, NC, USA; 3 Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; 4 Department of Paediatric and Adolescent Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana; 5 Botswana - University of Pennsylvania Partnership, Gaborone, Botswana; 6 Office of Research and Graduate Studies, Faculty of Medicine, University of Botswana, Gaborone, Botswana; 7 Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; 8 Division of Pediatric Infectious Diseases and Global Health Center, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA; 9 Divisions of Hospital Medicine and Infectious Diseases, Cincinnati Children's Medical Center, Cincinnati, OH, USA; 10 Division of Infectious Diseases, Duke University, Durham, NC, USA; 11 Department of Pediatrics, University of California, Irvine, Irvine, CA, USA; 12 Department of Pediatrics, Children’s Hospital of Orange County, Orange, CA, USA; 13 Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA; 14 Division of Pediatric Infectious Diseases, Duke University, Durham, NC, USA . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted December 20, 2022. ; https://doi.org/10.1101/2022.12.19.22283664 doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.