SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp

Abstract

Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions and to test whether our past observations linking SARS-CoV-2 abundance to Rothia sp. in hospitals also hold in a residential setting, we performed a detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences (to assess the bacterial community at each location), and to the Cq value of the contemporaneous clinical test. Our results showed that the highest SARS-CoV-2 load in this setting is on touched surfaces, such as light switches and faucets, but a detectable signal was present in many untouched surfaces (e.g., floors) that may be more relevant in settings, such as schools where mask-wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g., touching a light switch) or indirectly (e.g., by droplets or aerosols settling). We found the highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g., in schools, where students did not touch the light switches and also wore masks such that they had no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.

Keywords: COVID-19; RT-qPCR; Rothia; SARS-CoV-2; built-environment; environmental monitoring; isolation; quarantine; surface sampling; swab.

FIG 1

Distribution of SARS-CoV-2 viral load in isolation dorm apartments. (A to C) Floor plans for each apartment highlighted where SARS-CoV-2 RNA signatures were detected. (Inset) 3D rendering of the kitchen in apartment C showing SARS-CoV-2 viral load in genomic equivalents (GEs) mapped to features in that room.

FIG 2

(A) Area under the precision-recall curve showing the overall prediction performance of the random forest classifiers when trained on the features from two apartments and cross-validated on the remaining apartment. (B) Confusion matrix showing per-room type classifiers’ performances (AURPC) when cross-applied to the remaining room types. The diagonal represents self-validation. (C) Phylogenetic tree visualization (EMPress) where the differentially abundant features between SARS-CoV-2 status groups identified by multinomial regression (Songbird) are plotted on the inner ring (red: positive fold change in SARS-CoV-2 positive group; blue: negative fold change in SARS-CoV-2 positive group) and the ranked sOTUs (top 32) identified as important by the random forest classifier are indicated on the outer ring. Leaves of the phylogenetic tree represent sOTUs relevant to the microbiome diversity and differential abundance analyses (number of sOTUs = 1047). The taxonomic classification (p_:phylum) of the sOTUs is indicated as colored branches in the phylogenetic tree.