Early phylogenetic estimate of the effective reproduction number of SARS-CoV-2

To reconstruct the evolutionary dynamics of the 2019 novel-coronavirus recently causing an outbreak in Wuhan, China, 52 SARS-CoV-2 genomes available on 4 February 2020 at Global Initiative on Sharing All Influenza Data were analyzed. The two models used to estimate the reproduction number (coalescent-based exponential growth and a birth-death skyline method) indicated an estimated mean evolutionary rate of 7.8 7 10 124 subs/site/year (range, 1.1 7 10 124-15 7 10 124) and a mean tMRCA of the tree root of 73 days. The estimated R value was 2.6 (range, 2.1-5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days. This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing

Definition and classification for adverse events following spinal and peripheral joint manipulation and mobilization: A scoping review

INTRODUCTION Spinal and peripheral joint manipulation and mobilization are interventions used by many healthcare providers to manage musculoskeletal conditions. Although there are many reports of adverse events (or undesirable outcomes) following such interventions, there is no common definition for an adverse event or clarity on any severity classification. This impedes advances of patient safety initiatives and practice. This scoping review mapped the evidence of adverse event definitions and classification systems following spinal and peripheral joint manipulation and mobilization for musculoskeletal conditions in adults. METHODS An electronic search of the following databases was performed from inception to February 2021: MEDLINE, EMBASE, CINAHL, Scopus, AMED, ICL, PEDro, Cochrane Library, Open Grey and Open Theses and Dissertations. Studies including adults (18 to 65 years old) with a musculoskeletal condition receiving spinal or peripheral joint manipulation or mobilization and providing an adverse event definition and/or classification were included. All study designs of peer-reviewed publications were considered. Data from included studies were charted using a standardized data extraction form and synthesised using narrative analysis. RESULTS From 8248 identified studies, 98 were included in the final synthesis. A direct definition for an adverse event and/or classification system was provided in 69 studies, while 29 provided an indirect definition and/or classification system. The most common descriptors to define an adverse event were causality, symptom severity, onset and duration. Twenty-three studies that provided a classification system described only the end anchors (e.g., mild/minor and/or serious) of the classification while 26 described multiple categories (e.g., moderate, severe). CONCLUSION A vast array of terms, definition and classification systems were identified. There is no one common definition or classification for adverse events following spinal and peripheral joint manipulation and mobilization. Findings support the urgent need for consensus on the terms, definition and classification system for adverse events related to these interventions

Contribution of transgender sex workers to the complexity of the HIV-1 epidemic in the metropolitan area of Milan

Objectives: Transgender people are disproportionately affected by the HIV-1 epidemic. We evaluated the origin of HIV-1 variants carried by South American transgenders living in Milan by combining accurate phylogenetic methods and epidemiological data. Methods: We collected 156 HIV-1 pol sequences obtained from transgender patients engaged in sex work (TSWs) followed between 1999 and 2015 at L. Sacco Hospital, Milan, Italy. Phylogenetic analyses were conducted by HIV-TRACE, MrBayes, MacClade and Beast programs. Reference sequences were retrieved from Los Alamos and local databases. Last negative testing or proxy data from clinical records of infected individuals were used to investigate the country of infection. Results: Among South American TSWs, the most represented HIV-1 subtypes were B (70.5%), F1 (12.8%) and C (4.4%). Gene flow migrations of B subtype indicated significant fluxes from TSWs to Italians (21.3%) belonging to all risk groups (26.4% to heterosexuals (HEs), 18.9% to men who have sex with men (MSM), 15.1% to injecting drug users). The largest proportion of bidirectional fluxes were observed between Italians and TSWs (24.6%). For F1 subtype, bidirectional viral fluxes involved TSWs and Italians (7.1% and 14.3%), and a similar proportion of fluxes linked TSWs and Italian HEs or MSM (both 15.8%). Significant fluxes were detected from Italians to TSWs for subtype C involving both MSM (30%) and HEs (40%). Country of HIV-1 acquisition was identified for 72 subjects; overall, the largest proportion of patients with B subtype (73.5%) acquired HIV-1 infection in South America. Conclusions: Our results indicated that South American transgenders largely contribute to the heterogeneity of HIV-1 variants in our country. The high number of clusters based on all subtypes indicated numerous transmission chains in which TSWs were constantly intermixed with HEs and MSM. Our results strongly advocate interventions to facilitate prevention, diagnosis and HIV-1 care continuum among transgender people

International overview of somatic dysfunction assessment and treatment in osteopathic research: A scoping review

Background: Osteopathic manipulative treatment (OMT) is a patient-centred, whole-body intervention aimed at enhance the person’s self-regulation. OMT interventions are focused on somatic dysfunctions (SD) that can be defined as an altered regulative function associated with inflammatory signs palpable in the body framework in different body regions. The conceptual model that sustains SD, as well as its usefulness for the osteopathic profession, is still being discussed by the osteopathic community. Understanding the role and the application of SD is the aim of this scoping review. Methods: A literature search was carried out through the main biomedical databases: Pubmed (Medline), Cochrane, Central (Cochrane), Embase, PEDro and Scopus. Grey literature was considered via Google Scholar and the Osteopathic Research Web. The review was prepared by referring to the “Preferred Reporting Items for Systematic reviews and Meta-Analysis extension for Scoping Reviews” (PRISMA-ScR). Results: A total of 37,279 records were identified through database searching and other sources. After the duplicates were removed, 27,023 titles and abstracts were screened. A total of 1495 full-text articles were assessed for eligibility. The qualitative synthesis included 280 studies. Conclusions: Treating SD is an important part of osteopathic practice that varies from country to country. SD should be considered as a clinical value that assists in the clinical assessment and guides the decision-making process of osteopathic practitioners. Further studies should be designed to better understand why and how to choose the different assessment and intervention modalities to approach SD and to evaluate new osteopathic models

Human‐to‐cat sars‐cov‐2 transmission: Case report and full‐genome sequencing from an infected pet and its owner in Northern Italy

There have been previous reports of the human‐to‐cat transmission of SARS‐CoV‐2, but there are only a few molecular studies that have compared the whole genome of the virus in cats and their owners. We here describe a case of domestic SARS‐CoV‐2 transmission from a healthcare worker to his cat for which nasopharyngeal swabs of both the cat and its owner were used for full-genome analysis. The results indicate that quarantine measures should be extended to pets living in SARS‐CoV‐2‐infected households

Local epidemics gone viral: Evolution and diffusion of the Italian HIV-1 recombinant form CRF60_BC

The molecular epidemiology of HIV-1 in Italy is becoming increasingly complex, mainly due to the spread of non-B subtypes and the emergence of new recombinant forms. We previously characterized the outbreak of the first Italian circulating recombinant form (CRF60_BC), occurring among young MSM living in Apulia between the years 2009 and 2011. Here we show a 5-year follow-up surveillance to trace the evolution of CRF60_BC and to investigate its further spread in Italy. We collected additional sequences and clinical data from patients harboring CRF60_BC, enrolled at the Infectious Diseases Clinic of the University of Bari. In addition to the 24 previously identified sequences, we retrieved 27 CRF60_BC sequences from patients residing in Apulia, whose epidemiological and clinical features did not differ from those of the initial outbreak, i.e., the Italian origin, young age at HIV diagnosis (median: 24 years; range: 18-37), MSM risk factor (23/25, 92%) and recent infection (from 2008 to 2017). Sequence analysis revealed a growing overall nucleotide diversity, with few nucleotide changes that were fixed over time. Twenty-seven additional sequences were detected across Italy, spanning multiple distant regions. Using a BLAST search, we also identified a CRF60_BC sequence isolated in United Kingdom in 2013. Three patients harbored a unique second generation recombinant form in which CRF60_BC was one of the parental strains. Our data show that CRF60_BC gained epidemic importance, spreading among young MSM in multiple Italian regions and increasing its population size in few years, as the number of sequences identified so far has triplicated since our first report. The observed further divergence of CRF60_BC is likely due to evolutionary bottlenecks and host adaptation during transmission chains. Of note, we detected three second-generation recombinants, further supporting a widespread circulation of CRF60_BC and the increasing complexity of the HIV-1 epidemic in Italy

The human-associated bacterium Propionibacterium acnes as a grapevine endophyte

Animals and plants have established a long-lasting cohabitation with a variety of microbes, including pathogens, commensals and beneficials. Studies investigating such associations documented numerous cases of bacterial host switches (usually from domestic animals to humans). The exchange of microbial symbionts between humans and plants is much less investigated. We reported a surprising example of horizontal interkingdom transfer of the human opportunistic pathogen (P. acnes) to grapevine (Vitis vinifera L.). P. acnes was interestingly most common inside the plant's pith tissue. Phylogenetic and population analyses place that the establishment of the grapevine-associated P. acnes likely during the Neolithic, when grapevine was domesticated. The endophytic subspecies of P. acnes was named P. Zappae. An analysis of Propionibacteria in the grapevine endosphere showed that P. Zappae is far from being the only species present in this plant as an endophyt

Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020

: 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 (20B) most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 (20D) 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, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important 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

Open access simulation toolbox for the grid connection of offshore wind farms using multi-terminal HVDC networks

Decarbonisation of the European electricity system can become dauntingly costly due to transmission and distribution network issues arising from the integration of intermittent renewable generation sources. It is expected that wind energy will be the principal renewable source by 2050 and, as such, a number of initiatives in the academia and in the industry are being carried out to propose solutions to best accommodate the wind resource. This paper presents work carried out by DEMO 1 partners within the EU FP7 project BEST PATHS. A MATLAB/Simulink toolbox consisting of the necessary building blocks for the simulation and integration of offshore wind farms using enabling technologies such as multiterminal high-voltage direct-current grids is presented. To illustrate the toolbox capabilities, a number of system topologies is studied. System performance is assessed and measured against a set of key performance indicators. To ensure knowledge dissemination, the toolbox has been made available as open access in the BEST PATHS project website

Real-Life Clinical Data of Cabozantinib for Unresectable Hepatocellular Carcinoma

Introduction: Cabozantinib has been approved by the European Medicine Agency (EMA) for hepatocellular carcinoma (HCC) previously treated with sorafenib. Cabozantinib is also being tested in combination with immune checkpoint inhibitors in the frontline setting. Real-life clinical data of cabozantinib for HCC are still lacking. Moreover, the prognostic factors for HCC treated with cabozantinib have not been investigated. Methods: We evaluated clinical data and outcome of HCC patients who received cabozantinib in the legal context of named patient use in Italy. Results: Ninety-six patients from 15 centres received cabozantinib. All patients had preserved liver function (Child-Pugh A), mostly with an advanced HCC (77.1%) in a third-line setting (75.0%). The prevalence of performance status (PS) > 0, macrovascular invasion (MVI), extrahepatic spread, and alpha-fetoprotein (AFP) >400 ng/mL was 50.0, 30.2, 67.7, and 44.8%, respectively. Median overall survival (OS) and progression-free survival were 12.1 (95% confidence interval 9.4-14.8) and 5.1 (3.3-6.9) months, respectively. Most common treatment-related adverse events (AEs) were fatigue (67.7%), diarrhoea (54.2%), anorexia (45.8%), HFSR (43.8%), weight loss (24.0%), and hypertension (24.0%). Most common treatment-related Grade 3-4 AEs were fatigue (6.3%), HFSR (6.3%), and increased aminotransferases (6.3%). MVI, ECOG-PS > 0, and AFP >400 ng/mL predicted a worse OS. Discontinuation for intolerance and no new extrahepatic lesions at the progression were associated with better outcomes. Conclusions: In a real-life Western scenario (mostly in a third-line setting), cabozantinib efficacy and safety data were comparable with those reported in its registration trial. Data regarding the prognostic factors might help in patient selection and design of clinical trials