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SARS-CoV-2 infection and viral load are associated with the upper respiratory tract microbiome.
Rosas-Salazar, Christian; Kimura, Kyle S; Shilts, Meghan H; Strickland, Britton A; Freeman, Michael H; Wessinger, Bronson C; Gupta, Veerain; Brown, Hunter M; Rajagopala, Seesandra V; Turner, Justin H; Das, Suman R.
  • Rosas-Salazar C; Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn.
  • Kimura KS; Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tenn.
  • Shilts MH; Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn.
  • Strickland BA; 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.
  • Freeman MH; Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tenn.
  • Wessinger BC; Vanderbilt University School of Medicine, Nashville, Tenn.
  • Gupta V; Vanderbilt University School of Medicine, Nashville, Tenn.
  • Brown HM; Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn.
  • Rajagopala SV; Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn.
  • Turner JH; Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tenn. Electronic address: justin.h.turner@vumc.org.
  • Das SR; 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.
J Allergy Clin Immunol ; 147(4): 1226-1233.e2, 2021 04.
Article in English | MEDLINE | ID: covidwho-1071535
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, ß-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 adultslinear 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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Respiratory System / Viral Load / Microbiota / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Adult / Female / Humans / Male / Middle aged Language: English Journal: J Allergy Clin Immunol Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Respiratory System / Viral Load / Microbiota / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Adult / Female / Humans / Male / Middle aged Language: English Journal: J Allergy Clin Immunol Year: 2021 Document Type: Article