ABSTRACT
The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including <80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, the reconstructed ancestral scenario suggests a central role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.
ABSTRACT
The aim of this study was the reconstruction of SARS-CoV-2 evolutionary dynamics in time and space in Italy and Europe between February and June 2020. The cluster analysis showed that pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 entered Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, the reconstructed ancestral scenario suggests a central role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.
ABSTRACT
Background: Interleukin 6 (IL-6) is a proinflammatory cytokine that is secreted by cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and it is widely recognized as a negative prognostic factor. The purpose of this study was to analyze the correlations between the olfactory scores determined by psychophysical tests and the serum levels of IL-6 in patients affected by coronavirus disease 2019 (COVID-19)Methods: Patients underwent psychophysical olfactory assessment with Connecticut Chemosensory Clinical Research Center test and IL-6 plasma level determination within 10 days of the clinical onset of COVID-19. Results: Seventy-four COVID-19 patients were included in this study. COVID-19 staged as mild in 34 patients, moderate in 26 and severe in 14 cases. There were no significant differences in olfactory scores across the different COVID-19 severity groups In the patient series, the median plasma level of IL-6 was 7.7 pg/mL (IQR 3.7 – 18.8). The concentration of IL-6 was found to be significantly correlated with the severity of COVID-19 with a directly proportional relationship. The correlation between IL-6 plasma concentrations and olfactory scores was weak (rs=0.182) and not significant (p=0.12).Conclusions: In COVID-19 patients, psychophysical olfactory scores did not show significant correlations with the plasma levels of a well-recognized negative prognostic factor such as IL-6. This observation casts some shadows on the positive prognostic value of olfactory dysfunctions
Subject(s)
COVID-19ABSTRACT
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. ImportanceSeveral 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 wasnt 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. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/20179754v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@b15c11org.highwire.dtl.DTLVardef@1398ddorg.highwire.dtl.DTLVardef@98f501org.highwire.dtl.DTLVardef@1fd5282_HPS_FORMAT_FIGEXP M_FIG C_FIG