Monitoring COVID-19 transmission risks by RT-PCR tracing of droplets in hospital and living environments

SARS-CoV-2 environmental contamination occurs through droplets and biological fluids released in the surroundings from patients or asymptomatic carriers. Surfaces and objects contaminated by saliva or nose secretions represent a risk for indirect transmission of COVID-19. We assayed surfaces from hospital and living spaces to identify the presence of viral RNA and the spread of fomites in the environment. Anthropic contamination by droplets and biological fluids was monitored by detecting the microbiota signature using multiplex RT-PCR on selected species and massive sequencing on 16S-amplicons. A total of 92 samples (flocked swab) were collected from critical areas during the pandemic, including indoor (3 hospitals and 3 public buildings) and outdoor surfaces exposed to anthropic contamination (handles and handrails, playgrounds). Traces of biological fluids were frequently detected in spaces open to the public and on objects that are touched with the hands (>80%). However, viral RNA was not detected in hospital wards or other indoor and outdoor surfaces either in the air system of a COVID-hospital, but only in the surroundings of an infected patient, in consistent association with droplets traces and fomites. Handled objects accumulated the highest level of multiple contaminations by saliva, nose secretions and faecal traces, further supporting the priority role of handwashing in prevention. In conclusion, anthropic contamination by droplets and biological fluids is widespread in spaces open to the public and can be traced by RT-PCR. Monitoring fomites can support evaluation of indirect transmission risks for Coronavirus or other flu-like viruses in the environment. Importance Several studies searched for SARS-CoV-2 in the environment because saliva and nasopharyngeal droplets can land on objects and surfaces creating fomites. However, the ideal indicator would be the detection of the biofluid. This approach was not yet considered, but follows a traditional principle in hygiene, using indicators rather than pathogens. We searched for viral RNA but also for droplets on surfaces at risk. For the first time, we propose to monitor droplets thorugh their microbiota, by RT-PCR or NGS. Even if performed during the pandemic, SARS-CoV-2 wasn’t largely spread on surfaces, unless in proximity of an infectious patient. However, anthropic contamination was frequently at high level, suggesting a putative marker for indirect transmission and risk assessment. Moreover, all SARS-CoV-2-contaminated surfaces showed the droplets’ microbiota. Fomites detection may have an impact on public health, supporting prevention of indirect transmission also for other communicable diseases such as Flu and Flu-like infections. ![Figure][1] GRAPHICAL ABSTRACT ### Competing Interest Statement The authors have declared no competing interest. ### Clinical Trial No clinical trial ### Funding Statement No external founding ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: It is not a clinical trial. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data are reported in the manuscript. additional data can be required to the corresponding. [1]: pending:yes