Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SARS-CoV-2 spillover into hospital outdoor environments.

ABSTRACT: Facing the ongoing coronavirus infectious disease-2019 (COVID-19) pandemic, many studies focus on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in indoor environment, on solid surface or in wastewater. It remains unclear whether SARS-CoV-2 can spill over into outdoor environments and impose transmission risks to surrounding people and communities. In this study, we investigated the presence of SARS-CoV-2 by measuring viral RNA in 118 samples from outdoor environment of three hospitals in Wuhan. We detected SARS-CoV-2 in soils (205-550 copies/g), aerosols (285-1,130 copies/m³) and wastewaters (255-18,744 copies/L) in locations close to hospital departments receiving COVID-19 patients or in wastewater treatment sectors. These findings revealed a significant viral spillover in hospital outdoor environments that was possibly caused by respiratory droplets from patients or aerosolized particles from wastewater containing SARS-CoV-2. In contrast, SARS-CoV-2 was not detected in other areas or on surfaces with regular implemented disinfection. Soils may behave as viral warehouse through deposition and serve as a secondary source spreading SARS-CoV-2 for a prolonged time. For the first time, our findings demonstrate that there are high-risk areas out of expectation in hospital outdoor environments to spread SARS-CoV-2, calling for sealing of wastewater treatment unit and complete sanitation to prevent COVID-19 transmission risks.

SUBMITTER: Zhang D

PROVIDER: S-EPMC8132549 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

SARS-CoV-2 detection in hospital indoor environments, NW Iran.

Project description:This study aimed to investigate the potential contamination of SARS-CoV-2 in indoor settled dust and surfaces of Amir Al-Muminin hospital in Maragheh, Iran. Samples were taken from surfaces and settled dust using a passive approach and particulate matter (PM) using an active approach from different hospital wards. SARS-CoV-2 was detected in 15% of settled dust samples (N = 4/26) and 10% of surface samples (3/30). SARS-CoV-2 has been detected in 13.8% and 9.1% of the dust samples collected at a distance of fewer than 1 m and more than 3 m from the patient bed, respectively. SARS-CoV-2 was found in 11% of surface samples from low-touch surfaces and 8% from high touch surfaces. The relationship between PM2.5, PM10, humidity, temperature, and positive samples of SARS-CoV-2 was investigated. A positive correlation was observed between relative humidity, PM2.5, and positive SARS-CoV-2 samples. Principal component analysis (PCA) suggested positive correlation between positive SARS-CoV-2 samples, relative humidity, and PM2.5. Risk assessment results indicated that the annual mean infection risk of SARS-CoV-2 for hospital staff with illness and death was 2.6 × 10-2 and 7.7 × 10-4 per person per year. Current findings will help reduce the permanence of viral particles in the COVID 19 tragedy and future similar pandemics e.g., novel influenza viruses.

| S-EPMC9301582 | biostudies-literature

SARS-CoV-2 in hospital indoor environments is predominantly non-infectious.

Project description:BackgroundThe ongoing SARS-CoV-2 pandemic has spread rapidly worldwide and disease prevention is more important than ever. In the absence of a vaccine, knowledge of the transmission routes and risk areas of infection remain the most important existing tools to prevent further spread.MethodsHere we investigated the presence of the SARS-CoV-2 virus in the hospital environment at the Uppsala University Hospital Infectious Disease ward by RT-qPCR and determined the infectivity of the detected virus in vitro on Vero E6 cells.ResultsSARS-CoV-2 RNA was detected in several areas, although attempts to infect Vero E6 cells with positive samples were unsuccessful. However, RNase A treatment of positive samples prior to RNA extraction did not degrade viral RNA, indicating the presence of SARS-CoV-2 nucleocapsids or complete virus particles protecting the RNA as opposed to free viral RNA.ConclusionOur results show that even in places where a moderate concentration (Ct values between 30 and 38) of SARS-CoV-2 RNA was found; no infectious virus could be detected. This suggests that the SARS-CoV-2 virus in the hospital environment subsides in two states; as infectious and as non-infectious. Future work should investigate the reasons for the non-infectivity of SARS-CoV-2 virions.

| S-EPMC8170062 | biostudies-literature

SARS-CoV-2 spillover transmission due to recombination event.

Project description:In late 2019, a novel Coronavirus emerged in China. Perceiving the modulating factors of cross-species virus transmission is critical to elucidate the nature of virus emergence. Using bioinformatics tools, we analyzed the mapping of the SARS-CoV-2 genome, modeling of protein structure, and analyze the evolutionary origin of SARS-CoV-2, as well as potential recombination events. Phylogenetic tree analysis shows that SARS-CoV-2 has the closest evolutionary relationship with Bat-SL-CoV-2 (RaTG13) at the scale of the complete virus genome, and less similarity to Pangolin-CoV. However, the Receptor Binding Domain (RBD) of SARS-CoV-2 is almost identical to Pangolin-CoV at the aa level, suggesting that spillover transmission probably occurred directly from pangolins, but not bats. Further recombination analysis revealed the pathway for spillover transmission from Bat-SL-CoV-2 and Pangolin-CoV. Here, we provide evidence for recombination event between Bat-SL-CoV-2 and Pangolin-CoV that resulted in the emergence of SARS-CoV-2. Nevertheless, the role of mutations should be noted as another influencing factor in the continuing evolution and resurgence of novel SARS-CoV-2 variants.

| S-EPMC7884226 | biostudies-literature

Structures from "Engineering Neutralizing SARS-CoV Antibodies to Bind SARS-CoV-2"

Project description: Not available

| S-BSST379 | biostudies-other

Airborne SARS-CoV-2 in home and hospital environments investigated with a high-powered air sampler.

Project description:BackgroundThe initial aim was to study the effects of face masks worn by recently infected individuals on the airborne spread of SARS-CoV-2, but findings motivated us to proceed with comparing the presence of SARS-CoV-2 in air samples near infected individuals at home with those near infected intensive care unit (ICU) patients.AimTo assess the presence of SARS-CoV-2 in the air of homes of infected individuals and in ICU rooms of critically ill patients with COVID-19 who were undergoing different forms of potential aerosol-generating medical procedures.MethodsA high-volume air sampler method was developed that used a household vacuum cleaner with surgical face masks serving as sample filters. SARS-CoV-2 RNA was harvested from these filters and analysed by polymerase chain reaction. Fog experiments were performed to visualize the airflow around the air sampler. Air samples were acquired in close proximity of infected individuals, with or without wearing face masks, in their homes. Environmental air samples remote from these infected individuals were also obtained, plus samples near patients in the ICU undergoing potential aerosol-generating medical procedures.FindingsWearing a face mask resulted in a delayed and reduced flow of the fog into the air sampler. Face masks worn by infected individuals were found to contain SARS-CoV-2 RNA in 71% of cases. SARS-CoV-2 was detected in air samples regardless of mask experiments. The proportion of positive air samples was higher in the homes (29/41; 70.7%) than in the ICU (4/17; 23.5%) (P < 0.01).ConclusionSARS-CoV-2 RNA could be detected in air samples by using a vacuum cleaner based air sampler method. Air samples in the home environment of recently infected individuals contained SARS-CoV-2 RNA nearly three times more frequently by comparison with those obtained in ICU rooms during potential aerosol-generating medical procedures.

| S-EPMC8572039 | biostudies-literature

Citizen volunteers detect SARS-CoV-2 RNA from outdoor urban fomites

Project description:In COVID-19 pandemics ordinary citizens are overwhelmed by the often contradictory information about transmission of SARS-CoV-2 through surfaces, especially outdoors. Citizen volunteers (N = 39) and researchers, working together for the first time on SARS-CoV-2 detection, searched this virus' RNA on outdoors urban furniture of Mieres (Asturias, Spain) during the summer of 2020. RNA extraction and RT-PCR were conducted using point-of-care technology. A wooden slide and a sanitizer dispenser gave positive amplification of Spike gene. Contrary to expectations of higher virus survival in cold humid conditions, positivity rate was significantly higher in sunny sampling days, perhaps reflecting a higher frequentation of public outdoors spaces. All the participants considered the experience totally satisfactory and declared to have acquired new useful knowledge to face the pandemic. Significant increases of self-declared knowledge about virus transmission and protection measures, and confidence in hands hygiene for COVID-19 prevention, were found in the citizen volunteers following this experience. Results suggest the need for more control of playgrounds and public sanitizer dispensers. They also show how citizen volunteers can help to detect potential environmental reservoirs of disease agents from RNA analysis. Finally, ordinary citizens involved in COVID-19 research in small groups, following adequate training and safety protocols, feel empowered while valuably co-creating knowledge with researchers. Graphical abstract Unlabelled Image

| S-EPMC8117540 | biostudies-literature

Viral, host and environmental factors that favor anthropozoonotic spillover of coronaviruses: An opinionated review, focusing on SARS-CoV, MERS-CoV and SARS-CoV-2.

Project description:Environmental factors play a key role in the zoonotic transmission of emerging pathogenic viruses as mankind is constantly disturbing wildlife's ecosystems usually by cutting down forests to build human settlements or by catching wild animals for food, which deprives the viruses of their natural hosts and gives them opportunity to infect humans. In December 2019, a new coronavirus emerged from bats and was named SARS-CoV-2 by the International Committee for Taxonomy of Viruses, and the disease it causes named COVID-19 by the World Health Organization. Disease outbreaks such as SARS in 2002-2003, MERS in 2012 and the current COVID-19 pandemic are the result of higher mutation rates of coronaviruses and their unique capacity for genetic recombination, resulting in adaptations that make them more suitable to cross the species barriers and infect other species. This ability for host switching and interspecies infection is often attributed to the great diversity of these viruses, which is a result of viral and host factors such as the low fidelity of their RNA-dependent RNA polymerase, the high frequency of their homologous RNA recombination, and the adaptation of the S protein to bind host receptors like the angiotensin converting enzyme 2 (ACE2) in the case of SARS-CoV and SARS-CoV-2, and dipeptidyl peptidase 4 (DDP4) in MERS-CoV. This review presents an overview of the zoonotic transmission of SARS, MERS and COVID-19, focusing on the viral, host and environmental factors that favor the spillover of these viruses into humans, as well as the biological and ecological factors that make bats the perfect animal reservoir of infection for these viruses.

| S-EPMC7405882 | biostudies-literature

SARS-CoV-2 surveillance in indoor and outdoor size-segregated aerosol samples.

Project description:We aimed to determine the presence of SARS-CoV-2 RNA in indoor and outdoor size-segregated aerosol samples (PM10-2.5, PM2.5). Five outdoor daily samples were collected between November and December 2020 in an urban/industrial area with relatively high PM10 levels (Maliaño, Santander, Spain) by using a PM impactor (air flowrate of 30 L/min). In a non-hospital indoor sampling surveillance context, 8 samples in classrooms and 6 samples in the central library-Paraninfo of the University of Cantabria (UC) were collected between April and June 2021 by using personal PM samplers (air flowrate of 3 L/min). Lastly, 8 samples in the pediatric nasopharyngeal testing room at Liencres Hospital, 6 samples from different single occupancy rooms of positive patients, and 2 samples in clinical areas of the COVID plant of the University Hospital Marqués de Valdecilla (HUMV) were collected between January and May 2021. N1, N2 genes were used to test the presence of SARS-CoV-2 RNA by RT-qPCR. SARS-CoV-2 positive detection was only obtained from one fine fraction (PM2.5) sample, corresponding to one occupancy room, where a patient with positive PCR and cough was present. Negative results found in other sampling areas such as the pediatric nasopharyngeal testing rooms should be interpreted in terms of air sampling volume limitation and good ventilation.

| S-EPMC9023038 | biostudies-literature

Control of complement-induced inflammatory responses to SARS-CoV-2 infection by anti-SARS-CoV-2 antibodies

Project description:Dysregulated immune responses contribute to the excessive and uncontrolled inflammation observed in severe COVID-19. However, how immunity to SARS-CoV-2 is induced and regulated remains unclear. Here we uncover a role of the complement system in the induction of innate and adaptive immunity to SARS-CoV-2. Complement rapidly opsonizes SARS-CoV-2 particles via the lectin pathway. Complement-opsonized SARS-CoV-2 efficiently induces type-I interferon and pro-inflammatory cytokine responses via activation of dendritic cells, which are inhibited by antibodies against the complement receptors (CR) 3 and 4. Serum from COVID-19 patients, or monoclonal antibodies against SARS-CoV-2, attenuate innate and adaptive immunity induced by complement-opsonized SARS-CoV-2. Blocking of CD32, the FcγRII antibody receptor of dendritic cells, restores complement-induced immunity. These results suggest that opsonization of SARS-CoV-2 by complement is involved in the induction of innate and adaptive immunity to SARS-CoV-2 in the acute phase of infection. Subsequent antibody responses limit inflammation and restore immune homeostasis. These findings suggest that dysregulation of the complement system and FcγRII signaling may contribute to severe COVID-19.

| S-SCDT-10_1038-S44318-024-00061-0 | biostudies-other

Comparative phylogenetic analysis of SARS-CoV-2 spike protein-possibility effect on virus spillover.

Project description:Coronavirus disease 2019 has developed into a dramatic pandemic with tremendous global impact. The receptor-binding motif (RBM) region of the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to host angiotensin-converting enzyme 2 (ACE2) receptors for infection. As ACE2 receptors are highly conserved within vertebrate species, SARS-CoV-2 can infect significant animal species as well as human populations. An analysis of SARS-CoV-2 genotypes isolated from human and significant animal species was conducted to compare and identify mutation and adaptation patterns across different animal species. The phylogenetic data revealed seven distinct phylogenetic clades with no significant relationship between the clades and geographical locations. A high rate of variation within SARS-CoV-2 mink isolates implies that mink populations were infected before human populations. Positions of most single-nucleotide polymorphisms (SNPs) within the spike (S) protein of SARS-CoV-2 genotypes from the different hosts are mostly accumulated in the RBM region and highlight the pronounced accumulation of variants with mutations in the RBM region in comparison with other variants. These SNPs play a crucial role in viral transmission and pathogenicity and are keys in identifying other animal species as potential intermediate hosts of SARS-CoV-2. The possible roles in the emergence of new viral strains and the possible implications of these changes, in compromising vaccine effectiveness, deserve urgent considerations.

| S-EPMC8083239 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data