Evidence of SARS-CoV-2 RNA in an Oropharyngeal Swab Specimen, Milan, Italy, Early December 2019.
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ABSTRACT:
SUBMITTER: Amendola A
PROVIDER: S-EPMC7853584 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease COVID-19, a public health emergency worldwide, and Italy is among the most severely affected countries. The first autochthonous Italian case of COVID-19 was documented on February 21, 2020. We investigated the possibility that SARS-CoV-2 emerged in Italy earlier than that date, by analysing 40 composite influent wastewater samples collected - in the framework of other wastewater-based epidemiology projects - between October 2019 and February 2020 from five wastewater treatment plants (WWTPs) in three cities and regions in northern Italy (Milan/Lombardy, Turin/Piedmont and Bologna/Emilia Romagna). Twenty-four additional samples collected in the same WWTPs between September 2018 and June 2019 (i.e. long before the onset of the epidemic) were included as 'blank' samples. Viral concentration was performed according to the standard World Health Organization procedure for poliovirus sewage surveillance, with modifications. Molecular analysis was undertaken with both nested RT-PCR and real-rime RT-PCR assays. A total of 15 positive samples were confirmed by both methods. The earliest dates back to 18 December 2019 in Milan and Turin and 29 January 2020 in Bologna. Virus concentration in the samples ranged from below the limit of detection (LOD) to 5.6 × 104 genome copies (g.c.)/L, and most of the samples (23 out of 26) were below the limit of quantification of PCR. Our results demonstrate that SARS-CoV-2 was already circulating in northern Italy at the end of 2019. Moreover, it was circulating in different geographic regions simultaneously, which changes our previous understanding of the geographical circulation of the virus in Italy. Our study highlights the importance of environmental surveillance as an early warning system, to monitor the levels of virus circulating in the population and identify outbreaks even before cases are notified to the healthcare system.
| S-EPMC7428442 | biostudies-literature
Project description:BACKGROUND:To show how to safely perform nasopharyngeal and/or oropharyngeal swabs for 2019-novel coronavirus. METHODS:The video describes in detail the dressing and undressing procedures of health personnel, with the appropriate personal protective equipment. Technical notes for the execution of the nasopharyngeal and oropharyngeal swab are also provided to avoid sampling errors. RESULTS:The undressing phase is the procedure with the highest risk of self-contamination for the health worker. Following the various steps as shown in the video, there were no cases of contagion among the otolaryngology team appointed to perform the swabs for SARS-CoV-2 testing. CONCLUSIONS:This study demonstrates the technical feasibility of safely performing nasopharyngeal and/or oropharyngeal swabs for identification of SARS-CoV-2 viral RNA.
| S-EPMC7267608 | biostudies-literature
Project description:IntroductionDiagnostic confirmation of SARS-CoV-2 by self-collection of specimens is a reliable method compared with healthcare worker collected samples. Citizens' preferences for collection methods are unknown, but at-home collection could have several advantages.MethodsThis study investigated the preference for guided at-home self-collection versus at-hospital specimen collection by healthcare workers.ResultsAmong the 3709 participants, at-home swab collection was the preferred setting for 2362 (63.7%) compared with 1347 (36.3%) reporting a preference for an at-hospital swabbing procedure.ConclusionA high preference for guided at-home self-collection of oropharyngeal/nasal SARS-CoV-2 specimens exists and could be a future norm beyond COVID-19.
| S-EPMC8245307 | biostudies-literature
Project description:The COVID-19 epidemic is believed to have started in late January 2020 in France. Here we report a case of a patient hospitalised in December 2019 in an intensive care unit in a hospital in the north of Paris for haemoptysis with no aetiological diagnosis. RT-PCR was performed retrospectively on the stored respiratory sample and confirmed the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Based on this result, it appears that the COVID-19 epidemic started much earlier in France.
| S-EPMC7196402 | biostudies-literature
Project description:ObjectiveThis study aimed to investigate coronavirus disease (COVID-19) epidemiology in Alberta, British Columbia, and Ontario, Canada.MethodsUsing data through December 1, 2020, we estimated time-varying reproduction number, Rt, using EpiEstim package in R, and calculated incidence rate ratios (IRR) across the 3 provinces.ResultsIn Ontario, 76% (92 745/121 745) of cases were in Toronto, Peel, York, Ottawa, and Durham; in Alberta, 82% (49 878/61 169) in Calgary and Edmonton; in British Columbia, 90% (31 142/34 699) in Fraser and Vancouver Coastal. Across 3 provinces, Rt dropped to ≤ 1 after April. In Ontario, Rt would remain < 1 in April if congregate-setting-associated cases were excluded. Over summer, Rt maintained < 1 in Ontario, ~1 in British Columbia, and ~1 in Alberta, except early July when Rt was > 1. In all 3 provinces, Rt was > 1, reflecting surges in case count from September through November. Compared with British Columbia (684.2 cases per 100 000), Alberta (IRR = 2.0; 1399.3 cases per 100 000) and Ontario (IRR = 1.2; 835.8 cases per 100 000) had a higher cumulative case count per 100 000 population.ConclusionsAlberta and Ontario had a higher incidence rate than British Columbia, but Rt trajectories were similar across all 3 provinces.
| S-EPMC8134904 | biostudies-literature
Project description:BACKGROUND:Tocilizumab, a humanized monoclonal antibody, targets IL-6 receptors blocking downstream pro-inflammatory effects of IL-6. In preliminary reports it was suggested to be beneficial in patients with severe COVID-19. METHODS:In this open-label prospective study we describe clinical characteristics and outcome of 51 patients hospitalized with confirmed and severe COVID-19 pneumonia treated with tocilizumab intravenously. All patients had elevated IL-6 plasma level (>40 pg/mL) and oxygen saturation <93% in ambient air. Clinical outcomes, oxygen support, laboratory data and adverse events were collected over a follow-up of 30 days. RESULTS:Forty-five patients (88%) were on high-flow oxygen supplementation, six of whom with invasive ventilation. From baseline to day 7 after tocilizumab we observed a dramatic drop of body temperature and CRP value with a significant increase in lymphocyte count (p<0.001). Over a median follow-up time of 34 days from tocilizumab, 34 patients (67%) showed an improvement in their clinical severity class; 31 were discharged; 17 (33%) showed a worsening of their clinical status, of these 14 died (27%). The mortality rate was significantly associated with mechanical ventilation at baseline (83.3% vs 20% of patients on non-invasive oxygen support; p=0.0001). The most frequent side effects were an increase of hepatic enzymes (29%), thrombocytopenia (14%), and serious bacterial and fungal infections (27%). CONCLUSION:Tocilizumab exerts a rapidly beneficial effect on fever and inflammatory markers, although no significant impact on the clinical outcome can be inferred by our results. Critically ill patients seem to have a high risk of serious infections with this drug.
| S-EPMC7241995 | biostudies-literature
Project description:Monitoring the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) community-wide transmission with a suitable and effective sampling method would be of great support for public health response to the spreading due to asymptomatic subjects in the community.Here, we describe how using saliva samples for SARS-CoV-2 detection has allowed for a weekly surveillance of a small business company and the early detection of coronavirus disease 2019 cases.As on 23rd March, two cases were detected and investigated, and control measures were rapidly applied.
| S-EPMC8365045 | biostudies-literature
Project description:In 2017, Italy experienced a large measles epidemic with 5408 cases and four deaths. As Subnational Reference Laboratory of the Measles and Rubella surveillance NETwork (MoRoNET), the EpiSoMI (Epidemiology and Molecular Surveillance of Infections) Laboratory (University of Milan) set up rapid and active surveillance for the complete characterisation of the Measles virus (Mv) responsible for the large measles outbreak in Milan and surrounding areas (Lombardy, Northern Italy). The aims of this study were to describe the genetic profile of circulating viruses and to track the pathway of measles transmission. Molecular analysis was performed by sequencing the highly variable 450 nucleotides region of the N gene (N-450) of Mv genome. Two-hundred and ninety-nine strains of Mv were analysed. The phylogenetic analysis showed five different variants, two not previously described in the studied area, belonging to D8 and B3 genotypes. Three events of continuous transmission of autochthonous variants (D8-Osaka, D8-London and B3-Milan variants) and two events of continuous transmission of imported variants (B3-Dublin and D8-Hulu Langat) tracked five different transmission pathways. These pathways outlined two epidemic peaks: the first in April and the second in July 2017. The correlation between Mv variant and the epidemiological data may enable us to identify the sources of virus importation and recognise long-lasting virus transmission pathways.
| S-EPMC6518568 | biostudies-literature
Project description:Given the global shortage of nasopharyngeal (NP) swabs typically used for respiratory virus detection, alternative collection methods were evaluated during the COVID-19 pandemic. This study showed that a combined oropharyngeal/nares swab is a suitable alternative to NP swabs for the detection of SARS-CoV-2, with sensitivities of 91.7% and 94.4%, respectively.
| S-EPMC7228872 | biostudies-literature
Project description:A detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and individuals infected with SARS-CoV-2 involving high throughput quantitative (iTRAQ) proteomics analysis.
2022-12-22 | PXD032150 | Pride