SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

• Published in: PloS one 2021-06, Vol.16 (6), p.e0253578
• Main Authors: Coil, David A, Albertson, Timothy, Banerjee, Shefali, Brennan, Greg, Campbell, A J, Cohen, Stuart H, Dandekar, Satya, Díaz-Muñoz, Samuel L, Eisen, Jonathan A, Goldstein, Tracey, Jose, Ivy R, Juarez, Maya, Robinson, Brandt A, Rothenburg, Stefan, Sandrock, Christian, Stoian, Ana M M, Tompkins, Daniel G, Tremeau-Bravard, Alexandre, Haczku, Angela
• Format: Article
• Language: English
• Subjects: Analysis; Animals; Biology and life sciences; Chlorocebus aethiops; Contamination; Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 - genetics; COVID-19 - transmission; Critical care; Disease transmission; DNA sequencing; Fomites; Funding; Gene sequencing; Genome, Viral; Genomes; Genomics; Health care facilities; Hospitals; Hospitals, Teaching; Humans; HVAC; Immunology; Infectivity; Internal medicine; Laboratories; Medicine; Medicine and health sciences; Nucleic acids; Nucleotide sequence; Nucleotide sequencing; Pandemics; Patients; Phylogeny; Research and Analysis Methods; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Sequence Analysis, RNA; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Sleep; Software; Supervision; Vero Cells; Viral diseases; Virions; Viruses; Whole genome sequencing
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0253578

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. We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis. 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. 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. 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.