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

Coil, David A.; Albertson, Timothy E; Banerjee, Shefali; Brennan, Greg; Campbell, Alexandra 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; Tremeau‐Bravard, Alexandre; Haczku, Angela Franciska

doi:10.1371/journal.pone.0253578

Cited by 40 publications

(31 citation statements)

References 39 publications

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“…In environmental samples collected from hospital surfaces in the University of California - Davis, the majority of the samples depicted a coverage below 15% (2.19-14.78%). Our results were comparable with this study [ 44 ]. Low viral load, matrix interference and integrity damage are known and pose a significant challenge for the detection of viruses in environmental samples [ 45 , 46 ].…”

Section: Discussionsupporting

confidence: 93%

SARS-CoV-2 in hospital air as revealed by comprehensive respiratory viral panel sequencing

Habibi

Uddin

Behbehani

et al. 2022

Infection Prevention in Practice

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Background Nosocomially acquired severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection has become the most significant pandemic of our lifetime. Though its transmission was essentially attributed to droplets from an infected person, with recent advancements in knowledge, aerosol transmission seems to be a viable pathway, as well. Because of the lower biological load in ambient aerosol, detection of SARS-CoV-2 is challenging. A few recent attempts of sampling large aerosol volumes and using next-generation sequencing (NGS) to detect the presence of SARS-CoV-2 in the air at very low levels gave positive results. These results suggest the potential of using this technique to detect the presence of SARS-CoV-2 and use it as an early warning signal for possible outbreak or recurrence of coronavirus disease 2019 (COVID-19). Aim To assess efficacy of comprehensive respiratory viral panel (CRVP) sequencing and RT-PCR for low-level identification of SARS-CoV-2 and other respiratory viruses in indoor air. Methods A large volume of indoor aerosol samples from three major hospitals involved in COVID-19 care in Kuwait was collected. Viral RNA was isolated and subjected to comprehensive respiratory viral panel sequencing (CRVP) as per the standard protocol to detect the SARS-CoV-2 and other respiratory viruses in the hospital aerosol and monitor variations within the sequences. RT-PCR was also employed to estimate the viral load of SARS-CoV-2. Findings 13 of 15 (86.7%) samples exhibited SARS-CoV-2 with a relative abundance of 0.2 to 33.3%. The co-occurrence of human adenoviruses (type C1, C2, C5, C4), respiratory syncytial virus (RSV), influenza B, and non-SARS-CoV-229E were also recorded. Alignment of SARS-CoV-2 sequences against the reference strain of Wuhan China revealed variations in the form of single nucleotide polymorphisms (SNPs-17), insertions and deletions (indels-1). These variations were predicted to create missense (16), synonymous (15), frameshift (1) and stop-gained (1) mutations with a high (2), low (15), and moderate (16) impact. Conclusions Our results suggest that using CRVP on a large volume aerosol sample was a valuable tool for detecting SARS-CoV-2 in indoor aerosols of health care settings. Owing to its higher sensitivity, it can be employed as a surveillance strategy in the post COVID times to act as an early warning system to possibly control future outbreaks.

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Section: Discussionsupporting

confidence: 93%

SARS-CoV-2 in hospital air as revealed by comprehensive respiratory viral panel sequencing

Habibi

Uddin

Behbehani

et al. 2022

Infection Prevention in Practice

View full text Add to dashboard Cite

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“…In addition, the fact that dust was obtained at heights >60 cm over the top of the cages further signifies the magnitude of virus transmission via infected respiratory bio-aerosols. The contamination of surfaces by SARS-CoV-2 genetic material has been previously demonstrated at various settings [35][36][37]. Mink-to-mink transmission in farms occurs through contaminated dust from the excretions of the infected animals, including fecal matter.…”

Section: Plos Pathogensmentioning

confidence: 99%

Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination

Chaintoutis

Thomou²,

Mouchtaropoulou

et al. 2021

PLoS Pathog

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SARS-CoV-2 infection outbreaks in minks have serious implications associated with animal health and welfare, and public health. In two naturally infected mink farms (A and B) located in Greece, we investigated the outbreaks and assessed parameters associated with virus transmission, immunity, pathology, and environmental contamination. Symptoms ranged from anorexia and mild depression to respiratory signs of varying intensity. Although the farms were at different breeding stages, mortality was similarly high (8.4% and 10.0%). The viral strains belonged to lineages B.1.1.218 and B.1.1.305, possessing the mink-specific S-Y453F substitution. Lung histopathology identified necrosis of smooth muscle and connective tissue elements of vascular walls, and vasculitis as the main early key events of the acute SARS-CoV-2-induced broncho-interstitial pneumonia. Molecular investigation in two dead minks indicated a consistently higher (0.3–1.3 log10 RNA copies/g) viral load in organs of the male mink compared to the female. In farm A, the infected farmers were responsible for the significant initial infection of 229 out of 1,000 handled minks, suggesting a very efficient human-to-mink transmission. Subsequent infections across the sheds wherein animals were being housed occurred due to airborne transmission. Based on a R0 of 2.90 and a growth rate equal to 0.293, the generation time was estimated to be 3.6 days, indicative of the massive SARS-CoV-2 dispersal among minks. After the end of the outbreaks, a similar percentage of animals were immune in the two farms (93.0% and 93.3%), preventing further virus transmission whereas, viral RNA was detected in samples collected from shed surfaces and air. Consequently, strict biosecurity is imperative during the occurrence of clinical signs. Environmental viral load monitoring, in conjunction with NGS should be adopted in mink farm surveillance. The minimum proportion of minks that need to be immunized to avoid outbreaks in farms was calculated at 65.5%, which is important for future vaccination campaigns.

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“…S1F). PCR analysis using the CDC method [29] confirmed the presence of SARS-CoV-2 RNA in the three cases that had frozen brain tissues (Fig. 1I).…”

Section: Resultsmentioning

confidence: 98%

SARS-CoV-2 invades cognitive centers of the brain and induces Alzheimer’s-like neuropathology

Shen

Logue

Yang

et al. 2022

Preprint

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Major cell entry factors of SARS-CoV-2 are present in neurons; however, the neurotropism of SARS-CoV-2 and the phenotypes of infected neurons are still unclear. Acute neurological disorders occur in many patients, and one-third of COVID-19 survivors suffer from brain diseases. Here, we show that SARS-CoV-2 invades the brains of five patients with COVID-19 and Alzheimers, autism, frontotemporal dementia or no underlying condition by infecting neurons and other cells in the cortex. SARS-CoV-2 induces or enhances Alzheimers-like neuropathology with manifestations of beta-amyloid aggregation and plaque formation, tauopathy, neuroinflammation and cell death. SARS-CoV-2 infects mature but not immature neurons derived from inducible pluripotent stem cells from healthy and Alzheimers individuals through its receptor ACE2 and facilitator neuropilin-1. SARS-CoV-2 triggers Alzheimers-like gene programs in healthy neurons and exacerbates Alzheimers neuropathology. A gene signature defined as an Alzheimers infectious etiology is identified through SARS-CoV-2 infection, and silencing the top three downregulated genes in human primary neurons recapitulates the neurodegenerative phenotypes of SARS-CoV-2. Thus, SARS-CoV-2 invades the brain and activates an Alzheimers-like program.

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

Cited by 40 publications

References 39 publications

SARS-CoV-2 in hospital air as revealed by comprehensive respiratory viral panel sequencing

SARS-CoV-2 in hospital air as revealed by comprehensive respiratory viral panel sequencing

Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination

SARS-CoV-2 invades cognitive centers of the brain and induces Alzheimer’s-like neuropathology

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