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SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp.
Cantú, Victor J; Salido, Rodolfo A; Huang, Shi; Rahman, Gibraan; Tsai, Rebecca; Valentine, Holly; Magallanes, Celestine G; Aigner, Stefan; Baer, Nathan A; Barber, Tom; Belda-Ferre, Pedro; Betty, Maryann; Bryant, MacKenzie; Casas Maya, Martín; Castro-Martínez, Anelizze; Chacón, Marisol; Cheung, Willi; Crescini, Evelyn S; De Hoff, Peter; Eisner, Emily; Farmer, Sawyer; Hakim, Abbas; Kohn, Laura; Lastrella, Alma L; Lawrence, Elijah S; Morgan, Sydney C; Ngo, Toan T; Nouri, Alhakam; Plascencia, Ashley; Ruiz, Christopher A; Sathe, Shashank; Seaver, Phoebe; Shwartz, Tara; Smoot, Elizabeth W; Ostrander, R Tyler; Valles, Thomas; Yeo, Gene W; Laurent, Louise C; Fielding-Miller, Rebecca; Knight, Rob.
  • Cantú VJ; Department of Bioengineering, University of California San Diegogrid.266100.3, La Jolla, CA, USA.
  • Salido RA; Department of Bioengineering, University of California San Diegogrid.266100.3, La Jolla, CA, USA.
  • Huang S; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Rahman G; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Tsai R; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
  • Valentine H; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Magallanes CG; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
  • Aigner S; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
  • Baer NA; Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.
  • Barber T; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Belda-Ferre P; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
  • Betty M; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Bryant M; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Casas Maya M; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Castro-Martínez A; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Chacón M; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Cheung W; Rady Children's Hospital, San Diego, CA, USA.
  • Crescini ES; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • De Hoff P; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Eisner E; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Farmer S; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Hakim A; Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.
  • Kohn L; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Lastrella AL; San Diego State University, San Diego, CA, USA.
  • Lawrence ES; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Morgan SC; Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.
  • Ngo TT; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Nouri A; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
  • Plascencia A; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Ruiz CA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Sathe S; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Seaver P; Herbert Wertheim School of Public Health, University of California San Diegogrid.266100.3, La Jolla, CA, USA.
  • Shwartz T; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Smoot EW; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Ostrander RT; Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.
  • Valles T; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Yeo GW; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Laurent LC; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Fielding-Miller R; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Knight R; Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.
mSystems ; 7(3): e0141121, 2022 Jun 28.
Article in English | MEDLINE | ID: covidwho-1846330
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.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Observational study / Prognostic study Language: English Journal: MSystems Year: 2022 Document Type: Article Affiliation country: Msystems.01411-21

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Observational study / Prognostic study Language: English Journal: MSystems Year: 2022 Document Type: Article Affiliation country: Msystems.01411-21