Summary of the available molecular methods for detection of SARS-CoV-2 during the ongoing pandemic

Since early 2020, the COVID-19 pandemic has caused an excess in morbidity and mortality rates worldwide. Containment strategies rely firstly on rapid and sensitive laboratory diagnosis, with molecular detection of the viral genome in respiratory samples being the gold standard. The reliability of diagnostic protocols could be affected by SARS-CoV-2 genetic variability. In fact, mutations occurring during SARS-CoV-2 genomic evolution can involve the regions targeted by the diagnostic probes. Following a review of the literature and an in silico analysis of the most recently described virus variants (including the UK B 1.1.7 and the South Africa 501Y.V2 variants), we conclude that the described genetic variability should have minimal or no effect on the sensitivity of existing diagnostic protocols for SARS-CoV-2 genome detection. However, given the continuous emergence of new variants, the situation should be monitored in the future, and protocols including multiple targets should be preferred

Molecular characterization of ‘Candidatus Phytoplasma prunorum’ in Cacopsilla pruni insect vector

Recent investigations on molecular characterization of the ‘Candidatus Phytoplasma prunorum’ (16SrX-B subgroup), causal agent of the European Stone Fruit Yellows (ESFY) syndrome, on the non ribosomal tuf gene resulted in the finding of two groups of isolates, named ‘type a’ and ‘type b’, both with a distinctive geographical distribution in Italian stone fruit growing areas (Ferretti et al., 2007 and 2008). Considering the role of Cacopsylla pruni (Scopoli) in the epidemiological cycle of the disease, the presence of the two groups of isolates has also been investigated in infected psyllid individuals from different Italian areas. Both types have been identified in C. pruni specimens collected on apricot, plum and wild Prunus species, confirming the geographical distribution and the percentages of spread of the two isolates.Keywords: ESFY, phytoplasma, characterization, tuf gene, insect vecto

Pseudomonas aeruginosa infection in cystic fibrosis caused by an epidemic metallo-β-lactamase-producing clone with a heterogeneous carbapenem resistance phenotype

AbstractAn epidemic IMP-13 metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa clone, causing infections and even large outbreaks in Italian critical care settings, was detected in a young cystic fibrosis patient. In this patient, the chronic infection was sustained by distinct clonal sub-populations of the MBL-producing P. aeruginosa clone, either susceptible or resistant to carbapenems. These findings underscore the importance of infection prevention practices in cystic fibrosis settings and pose an important diagnostic and therapeutic challenge

Identification of a novel plasmid lineage associated with the dissemination of metallo-β-lactamase genes among pseudomonads

Acquisition of metallo-\u3b2-lactamases (MBLs) represents one of most relevant resistance mechanisms to all \u3b2-lactams, including carbapenems, ceftolozane and available \u3b2-lactamase inhibitors, in Pseudomonas spp. VIM-type enzymes are the most common acquired MBLs in Pseudomonas aeruginosa and, to a lesser extent, in other Pseudomonas species. Little is known about the acquisition dynamics of these determinants, that are usually carried on integrons embedded into chromosomal mobile genetic elements. To date, few MBL-encoding plasmids have been described in Pseudomonas spp., and their diversity and role in the dissemination of these MBLs remains largely unknown. Here we report on the genetic features of the VIM-1encoding plasmid pMOS94 from P. mosselii AM/94, the earliest known VIM-1-producing strain, and of related elements involved in dissemination of MBL. Results of plasmid DNA sequencing showed that pMOS94 had a modular organization, consisting of backbone modules associated with replication, transfer and antibiotic resistance. Plasmid pMOS94, although not typable according to the PBRT scheme, was classifiable either in MOBF11 or MPFT plasmid families. The resistance region included the class I integron In70, carrying blaVIM-1, in turn embedded in a defective Tn402-like transposon. Comparison with pMOS94-like elements led to the identification of a defined plasmid lineage circulating in different Pseudomonas spp. of clinical and environmental origin and spreading different MBL-encoding genes, including blaIMP-63, blaBIM, and blaVIM-type determinants. Genetic analysis revealed that this plasmid lineage likely shared a common ancestor and had evolved through the acquisition and recombination of different mobile elements, including the MBL-encoding transposons. Our findings provide new insights about the genetic diversity of MBL-encoding plasmids circulating among Pseudomonas spp., potentially useful for molecular epidemiology purposes, and revealed the existence and persistence of a successful plasmid lineage over a wide spatio-temporal interval, spanning over five different countries among two continents and over 20-years

Cryptic diversity of the jewel beetles Agrilus viridis (Coleoptera: Buprestidae) hosted on hazelnut

The genus Agrilus (Coleoptera: Buprestidae) represents a taxonomic puzzle, since the boundaries between species, subspecies and morphotypes tied to different host plants are sometimes difficult to establish on morphological characteristics alone. Some Agrilus species can cause severe agricultural damage; this makes correct distinctions of the taxon and knowing whether the insects switch from one host plant to another important. This study of mtDNA examined the genetic characteristics of lineages of A. viridis, a jewel beetle recently found causing damage to the hazelnut Corylus avellana in NW Italy. Three mitochondrial markers (a portion of the 12S rDNA and a DNA-fragment including partial NADH dehydrogenase subunit I gene, the tRNA Leucine gene and partial 16S rDNA, and partial  Cytochrome c oxidase) were compared between individuals collected on birch Betula sp., beech Fagus sp., willow Salix sp., alder Alnus sp. and hazelnut. We found a high genetic distance between A. viridis sampled on different host plants, while individuals sampled on the same host plant were similar despite a considerable geographic gap between sampled areas. Our study supports the general pattern for strong ecological separation between populations living on different host plants

Aging and memory phenomena in magnetic and transport properties of vortex matter: a brief review

There is mounting experimental evidence that strong off-equilibrium phenomena, such as ``memory'' or ``aging'' effects, play a crucial role in the physics of vortices in type II superconductors. We give a short review, based on a recently introduced schematic vortex model, of current progresses in understanding out of equilibrium vortex behaviours. We develop a unified description of ``memory'' phenomena in magnetic and transport properties, such as magnetisation loops and their ``anomalous'' 2nd peak, logarithmic creep, ``anomalous'' finite creep rate in the limit of vanishing temperature, ``memory'' and ``irreversibility'' in I-V characteristics, time dependent critical currents, ``rejuvenation'' and ``aging'' of the system response.Comment: updated versio

Red Blood Cell Transfusion Need for Elective Primary Posterior Lumbar Fusion in A High-Volume Center for Spine Surgery

(1) Background: This study evaluated the perioperative red blood cell (RBC) transfusion need and determined predictors for transfusion in patients undergoing elective primary lumbar posterior spine fusion in a high-volume center for spine surgery. (2) Methods: Data from all patients undergoing spine surgery between 1 January 2014 and 31 December 2016 were reviewed. Patients' demographics and comorbidities, perioperative laboratory results, and operative time were analyzed in relation to RBC transfusion. Multivariate logistic regression analysis was performed to identify the predictors of transfusion. (3) Results: A total of 874 elective surgeries for primary spine fusion were performed over the three years. Only 54 cases (6%) required RBC transfusion. Compared to the non-transfused patients, transfused patients were mainly female (p = 0.0008), significantly older, with a higher ASA grade (p = 0.0002), and with lower pre-surgery hemoglobin (HB) level and hematocrit (p < 0.0001). In the multivariate logistic regression, a lower pre-surgery HB (OR (95% CI) 2.84 (2.11-3.82)), a higher ASA class (1.77 (1.03-3.05)) and a longer operative time (1.02 (1.01-1.02)) were independently associated with RBC transfusion. (4) Conclusions: In the instance of elective surgery for primary posterior lumbar fusion in a high-volume center for spine surgery, the need for RBC transfusion is low. Factors anticipating transfusion should be taken into consideration in the patient's pre-surgery preparation

C9orf72 ALS/FTD dipeptide repeat protein levels are reduced by small molecules that inhibit PKA or enhance protein degradation

Intronic GGGGCC (G4C2) hexanucleotide repeat expansion within the human C9orf72 gene represents the most common cause of familial forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (C9ALS/FTD). Repeat-associated non-AUG (RAN) translation of repeat-containing C9orf72 RNA results in the production of neurotoxic dipeptide-repeat proteins (DPRs). Here, we developed a high-throughput drug screen for the identification of positive and negative modulators of DPR levels. We found that HSP90 inhibitor geldanamycin and aldosterone antagonist spironolactone reduced DPR levels by promoting protein degradation via the proteasome and autophagy pathways respectively. Surprisingly, cAMP-elevating compounds boosting protein kinase A (PKA) activity increased DPR levels. Inhibition of PKA activity, by both pharmacological and genetic approaches, reduced DPR levels in cells and rescued pathological phenotypes in a Drosophila model of C9ALS/FTD. Moreover, knockdown of PKA-catalytic subunits correlated with reduced translation efficiency of DPRs, while the PKA inhibitor H89 reduced endogenous DPR levels in C9ALS/FTD patient-derived iPSC motor neurons. Together, our results suggest new and druggable pathways modulating DPR levels in C9ALS/FTD

Cochrane rehabilitation: 2020 Annual report

during its fourth year of existence, cochrane rehabilitation went on to promote evidence-informed health decision-making in rehabilitation. in 2020, the outbreak of the coVid-19 pandemic has made it necessary to alter priorities. in these challenging times, cochrane rehabilitation has firstly changed its internal organisation and established a new relevant project in line with pandemic needs: the REH-COVER (Rehabilitation – coVid-19 evidence-based response) action. the aim was to focus on the timely collection, review and dissemination of summarised and synthesised evidence relating to COVID-19 and rehabilitation. Cochrane Rehabilitation REH-COVER action has included in 2020 five main initiatives: 1) rapid living systematic reviews on rehabilitation and coVid-19; 2) interactive living evidence map on rehabilitation and coVid-19; 3) definition of the research topics on “rehabilitation and COVID-19” in collaboration with the World Health Organization (WHO) rehabilitation programme; 4) Cochrane Library special collection on Coronavirus (COVID-19) rehabilitation; and 5) collaboration with COVID-END for the topics “rehabilitation” and “disability.” Furthermore, we are still carrying on five different special projects: Be4rehab; RCTRACK; definition of rehabilitation for research purposes; ebook project; and a prioritization exercise for Cochrane Reviews production. The Review Working Area continued to identify and “tag” the rehabilitation-relevant reviews published in the cochrane library; the publication Working area went on to publish Cochrane Corners, working more closely with the Cochrane Review Groups (CRGs) and Cochrane Networks, particularly with Cochrane Musculoskeletal, oral, skin and sensory Network; the Education Working area, the most damaged in 2020, tried to continue performing educational activities such as workshops in different online meetings; the Methodology Working area organized the third and fourth cochrane Rehabilitation Methodological (CRM) meetings respectively in Milan and Orlando; the Communication Working Area spread rehabilitation evidences through different channels and translated the contents in different languages

Formative Assessment of ARM-U: A Modular Intervention for Decreasing Risk Behaviors Among HIV-Positive and HIV-Negative Methamphetamine-Using MSM

BACKGROUND: Methamphetamine is a major contributor to HIV transmission among men who have sex with men (MSM). Recent studies show that up to one-third of methamphetamine-using MSM (MUMSM) inject the drug. We developed a behavioral intervention for MUMSM to decrease unprotected anal intercourse and increase awareness of parenteral HIV transmission risk. This 6-session (3 in-person, 3 by telephone) modular intervention was designed to be tailored to participants' HIV (+/-) and injection drug user ([IDU] yes/no) status. We present results of formative research used to evaluate the content and to assess feasibility and acceptability of this individual-level HIV risk-reduction intervention. SETTING: HIV research clinic in a high MSM and methamphetamine prevalence neighborhood. PROJECT: Avoiding Risks from Methamphetamine-Use (ARM-U) is a brief toolbox intervention that allows counselors to select modules that suit a client's individual risk profile and intervention needs employing motivational interviewing and cognitive behavioral theory. We evaluated the format and content of the intervention through focus groups and pre-testing of the entire intervention using volunteers from the target population stratified into four groups (HIV+/IDU, HIV-/IDU, HIV+/non-IDU, HIV-/non-IDU). Four individuals in each stratum were recruited to undergo the intervention and complete a satisfaction survey at the end of each in-person session. RESULTS: In total, 25 MUMSM attended one of five focus groups. Participants thought all proposed intervention topics were important and could aid in reducing sexual risk behaviors among MUMSM. However, the neurocognitive effects of methamphetamine were reported to be a barrier to practicing safer sex, condom use negotiation or HIV status disclosure. Fifteen (94%) of 16 participants completed all 6 sessions and the satisfaction survey. On average, participants felt the intervention was useful for MUMSM, made them contemplate and move toward behavior change, and would recommend the program to their peers. LESSONS LEARNED: Based on our formative research, we revised the ARM-U intervention to emphasize pre-planning to avoid combining methamphetamine use and sex or develop strategies to avoid sex risk following methamphetamine use. We also increased emphasis on referrals for care and other requested services. Future efficacy trials are needed to evaluate the intervention's ability to reduce HIV-associated risk behaviors