SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis.
<h4>Rationale</h4>There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear.<h4>Objectives</h4>We aime...
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Public Library of Science (PLoS)
2021
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oai:doaj.org-article:e8e489eea1df45e5aa006cfc7c4a97c22021-12-02T20:05:17ZSARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis.1932-620310.1371/journal.pone.0253578https://doaj.org/article/e8e489eea1df45e5aa006cfc7c4a97c22021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0253578https://doaj.org/toc/1932-6203<h4>Rationale</h4>There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear.<h4>Objectives</h4>We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis.<h4>Methods</h4>Samples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing.<h4>Measurements and main results</h4>Improved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing.<h4>Conclusions</h4>This study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs.David A CoilTimothy AlbertsonShefali BanerjeeGreg BrennanA J CampbellStuart H CohenSatya DandekarSamuel L Díaz-MuñozJonathan A EisenTracey GoldsteinIvy R JoseMaya JuarezBrandt A RobinsonStefan RothenburgChristian SandrockAna M M StoianDaniel G TompkinsAlexandre Tremeau-BravardAngela HaczkuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 6, p e0253578 (2021) |
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Medicine R Science Q David A Coil Timothy Albertson Shefali Banerjee Greg Brennan A J Campbell Stuart H Cohen Satya Dandekar Samuel L Díaz-Muñoz Jonathan A Eisen Tracey Goldstein Ivy R Jose Maya Juarez Brandt A Robinson Stefan Rothenburg Christian Sandrock Ana M M Stoian Daniel G Tompkins Alexandre Tremeau-Bravard Angela Haczku SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis. |
| description |
<h4>Rationale</h4>There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear.<h4>Objectives</h4>We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis.<h4>Methods</h4>Samples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing.<h4>Measurements and main results</h4>Improved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing.<h4>Conclusions</h4>This study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs. |
| format |
article |
| author |
David A Coil Timothy Albertson Shefali Banerjee Greg Brennan A J Campbell Stuart H Cohen Satya Dandekar Samuel L Díaz-Muñoz Jonathan A Eisen Tracey Goldstein Ivy R Jose Maya Juarez Brandt A Robinson Stefan Rothenburg Christian Sandrock Ana M M Stoian Daniel G Tompkins Alexandre Tremeau-Bravard Angela Haczku |
| author_facet |
David A Coil Timothy Albertson Shefali Banerjee Greg Brennan A J Campbell Stuart H Cohen Satya Dandekar Samuel L Díaz-Muñoz Jonathan A Eisen Tracey Goldstein Ivy R Jose Maya Juarez Brandt A Robinson Stefan Rothenburg Christian Sandrock Ana M M Stoian Daniel G Tompkins Alexandre Tremeau-Bravard Angela Haczku |
| author_sort |
David A Coil |
| title |
SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis. |
| title_short |
SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis. |
| title_full |
SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis. |
| title_fullStr |
SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis. |
| title_full_unstemmed |
SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis. |
| title_sort |
sars-cov-2 detection and genomic sequencing from hospital surface samples collected at uc davis. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2021 |
| url |
https://doaj.org/article/e8e489eea1df45e5aa006cfc7c4a97c2 |
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