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SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome.
J Allergy Clin Immunol. 2021 04; 147(4):1226-1233.e2.JA

Abstract

BACKGROUND

Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, and the upper respiratory tract (URT) microbiome.

OBJECTIVE

We sought to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults and to examine the association of SARS-CoV-2 viral load with the URT microbiome during COVID-19.

METHODS

We characterized the URT microbiome using 16S ribosomal RNA sequencing in 59 adults (38 with confirmed, symptomatic, mild to moderate COVID-19 and 21 asymptomatic, uninfected controls). In those with COVID-19, we measured SARS-CoV-2 viral load using quantitative reverse transcription PCR. We then examined the association of SARS-CoV-2 infection status and its viral load with the ⍺-diversity, β-diversity, and abundance of bacterial taxa of the URT microbiome. Our main models were all adjusted for age and sex.

RESULTS

The observed species index was significantly higher in SARS-CoV-2-infected than in -uninfected adults (β linear regression coefficient = 7.53; 95% CI, 0.17-14.89; P = .045). In differential abundance testing, 9 amplicon sequence variants were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified amplicon sequence variant being more abundant in those with SARS-CoV-2 infection and in those with high viral load during COVID-19, whereas Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 Corynebacterium_1 unclassified amplicon sequence variants were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19.

CONCLUSIONS

Our findings suggest complex associations between SARS-CoV-2 and the URT microbiome in adults. Future studies are needed to examine how these viral-bacterial interactions can impact the clinical progression, severity, and recovery of COVID-19.

Authors+Show Affiliations

Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn.Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tenn.Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn.Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tenn.Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tenn.Vanderbilt University School of Medicine, Nashville, Tenn.Vanderbilt University School of Medicine, Nashville, Tenn.Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn.Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn.Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tenn. Electronic address: justin.h.turner@vumc.org.Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tenn; Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn. Electronic address: suman.r.das@vumc.org.

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural

Language

eng

PubMed ID

33577896

Citation

Rosas-Salazar, Christian, et al. "SARS-CoV-2 Infection and Viral Load Are Associated With the Upper Respiratory Tract Microbiome." The Journal of Allergy and Clinical Immunology, vol. 147, no. 4, 2021, pp. 1226-1233.e2.
Rosas-Salazar C, Kimura KS, Shilts MH, et al. SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome. J Allergy Clin Immunol. 2021;147(4):1226-1233.e2.
Rosas-Salazar, C., Kimura, K. S., Shilts, M. H., Strickland, B. A., Freeman, M. H., Wessinger, B. C., Gupta, V., Brown, H. M., Rajagopala, S. V., Turner, J. H., & Das, S. R. (2021). SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome. The Journal of Allergy and Clinical Immunology, 147(4), 1226-e2. https://doi.org/10.1016/j.jaci.2021.02.001
Rosas-Salazar C, et al. SARS-CoV-2 Infection and Viral Load Are Associated With the Upper Respiratory Tract Microbiome. J Allergy Clin Immunol. 2021;147(4):1226-1233.e2. PubMed PMID: 33577896.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome. AU - Rosas-Salazar,Christian, AU - Kimura,Kyle S, AU - Shilts,Meghan H, AU - Strickland,Britton A, AU - Freeman,Michael H, AU - Wessinger,Bronson C, AU - Gupta,Veerain, AU - Brown,Hunter M, AU - Rajagopala,Seesandra V, AU - Turner,Justin H, AU - Das,Suman R, Y1 - 2021/02/09/ PY - 2020/10/09/received PY - 2020/12/20/revised PY - 2021/02/03/accepted PY - 2021/2/13/pubmed PY - 2021/4/16/medline PY - 2021/2/12/entrez KW - 16S rRNA sequencing KW - COVID-19 KW - SARS-CoV-2 KW - coronavirus KW - microbiome KW - nasal KW - nasopharynx KW - respiratory SP - 1226 EP - 1233.e2 JF - The Journal of allergy and clinical immunology JO - J Allergy Clin Immunol VL - 147 IS - 4 N2 - BACKGROUND: Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, and the upper respiratory tract (URT) microbiome. OBJECTIVE: We sought to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults and to examine the association of SARS-CoV-2 viral load with the URT microbiome during COVID-19. METHODS: We characterized the URT microbiome using 16S ribosomal RNA sequencing in 59 adults (38 with confirmed, symptomatic, mild to moderate COVID-19 and 21 asymptomatic, uninfected controls). In those with COVID-19, we measured SARS-CoV-2 viral load using quantitative reverse transcription PCR. We then examined the association of SARS-CoV-2 infection status and its viral load with the ⍺-diversity, β-diversity, and abundance of bacterial taxa of the URT microbiome. Our main models were all adjusted for age and sex. RESULTS: The observed species index was significantly higher in SARS-CoV-2-infected than in -uninfected adults (β linear regression coefficient = 7.53; 95% CI, 0.17-14.89; P = .045). In differential abundance testing, 9 amplicon sequence variants were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified amplicon sequence variant being more abundant in those with SARS-CoV-2 infection and in those with high viral load during COVID-19, whereas Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 Corynebacterium_1 unclassified amplicon sequence variants were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19. CONCLUSIONS: Our findings suggest complex associations between SARS-CoV-2 and the URT microbiome in adults. Future studies are needed to examine how these viral-bacterial interactions can impact the clinical progression, severity, and recovery of COVID-19. SN - 1097-6825 UR - https://www.unboundmedicine.com/medline/citation/33577896/SARS_CoV_2_infection_and_viral_load_are_associated_with_the_upper_respiratory_tract_microbiome_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0091-6749(21)00177-9 DB - PRIME DP - Unbound Medicine ER -