key: cord-0725261-yustkoy3
authors: 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.
title: SARS-CoV-2 Infection and Viral Load are Associated with the Upper Respiratory Tract Microbiome
date: 2021-02-09
journal: J Allergy Clin Immunol
DOI: 10.1016/j.jaci.2021.02.001
sha: 940189f877567a1aab666a0032ee52762253bf54
doc_id: 725261
cord_uid: yustkoy3

Background Little is known about the relationships between SARS-CoV-2, the respiratory virus responsible for the ongoing COVID-19 pandemic, and the upper respiratory tract (URT) microbiome. Objective Our objectives were 1) to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults, and 2) 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=0.045). In differential abundance testing, 9 amplicon sequence variants (ASVs) were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified ASV 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 ASVs were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19. Conclusion 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.

The body of research suggests that interactions between common respiratory viruses and the 124 upper respiratory tract (URT) microbiome can impact respiratory health. 1 In this context, we and 125 others have shown that viral-bacterial interactions can influence viral load, 2 host transcriptome 126 patterns, 3, 4 acute severity, 3, 4 and even long-term outcomes of common respiratory viruses (such 127 as respiratory syncytial virus), 5 as well as the acute immune response to these infectious agents. Their baseline characteristics are shown in Table 1 . The median (interquartile range [IQR]) age 142 was 30 (27-45) years. None of the participants had used antibiotics in the prior 2 weeks or were 143 using intranasal mediations at the time of sampling. There were no significant differences in 144 baseline characteristics between those with and without SARS-CoV-2 infection, although those 145 infected were more likely to have at least one other comorbidity (Table 1) In the adults with COVID-19, there were no significant associations between high vs. low SARS-178

CoV-2 viral load with any of the ⍺-diversity or β-diversity metrics of the URT microbiome 179 (p>0.05 for all comparisons). In differential abundance testing using DESeq2, 21 ASVs were 180 significantly different between groups ( Figure 4A) and Prevotella ASVs) in those with high viral load when compared to those with low viral load 184 ( Figure 4B ). The abundance of 14 of these 21 ASVs was significantly different and had a 185 consistent direction of association using a similar definition of high viral load but based on N2 186

CT values by RT-qPCR ( Figure 4B) . Furthermore, the abundance of 9 of these 21 ASVs was 187 also significantly different and had a consistent direction of association between adults with and 188 without SARS-CoV-2 infection, with Peptoniphilus lacrimalis, Campylobacter hominis,

Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 192

Corynebacterium_1 unclassified ASVs were more abundant in those without SARS-CoV-2 193 infection and in those with low viral loads during COVID-19 (Figure 3 and Figure 4B) . none of which overlapped with the ones we found to be differentially abundant in adults with and 205 without SARS-CoV-2 in our study. 17 In addition to the methodological differences between these 206 studies and ours, neither of them included a group of asymptomatic, uninfected controls, as the 207 comparisons group for both of these studies included adults with other acute respiratory 208 infections. In one study using metatranscriptomics that did include a group of uninfected, 209 asymptomatic controls, 18 Shen et al found differences in the β-diversity of the LRT microbiome 210 between adults with and without SARS-CoV-2 infection, but no ⍺-diversity or differential 211 abundance analyses were performed and this study was smaller than ours (including only 8 potential confounders in their statistical analyses, which can also explain the discrepant results, 214 as all of our statistical analyses included age and sex as covariates. To prevent overfitting and 215 maximize sample size, we did not include other covariates in our main models. However, we 216 obtained similar results in sensitivity analyses including other potential confounders. Interestingly, one prior report found a high abundance of Brevundimonas spp. in the lungs of 20 224 deceased adults with COVID-19 and one case report described a SARS-CoV-2 + Granulicatella 225 adiacens co-infection, both of which were differentially abundant between SARS-CoV-2-226 infected and -uninfected adults in our study and are overall rare taxa of the upper or LRT 227 microbiome in the general population. 20, 21 Furthermore, we found multiple taxa to be associated 228 not only with SARS-CoV-2-infection status, but also with a higher viral load during COVID-19 229 (such as Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an 230

Anaerococcus unclassified ASV). Taken together, these findings suggest that SARS-CoV-2 can 231 directly impact the abundance of certain URT taxa. Within a given genus, associations appeared 232 to be taxon-specific, as SARS-CoV-2 infection and high viral load during COVID-19 was 233 associated with an increase of certain Corynebacterium ASVs but with a decrease of others. Our 

Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients

Metatranscriptomic 326 Characterization of COVID-19 Identified A Host Transcriptional Classifier Associated 327

With Immune Signaling

Acute Respiratory Syndrome-Coronavirus 2 in Patients With Coronavirus Disease

Co-infections in people with COVID-19: a 332 systematic review and meta-analysis

The lung tissue microbiota features 334 of 20 deceased patients with COVID-19

COVID-19 Complicates an Already Difficult Presentation of Infective 336

Contagion Live

Alterations of the Gut Microbiota in 338 Patients with COVID-19 or H1N1 Influenza

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection 341

With Human Rhinovirus and Respiratory Syncytial Virus in Infancy

Rates of Co-infection Between