title: How Large Was the Mortality Increase Directly and Indirectly Caused by the COVID-19 Epidemic? An Analysis on All-Causes Mortality Data in Italy

text: Objective: Overall mortality is a relevant indicator of the population burden during an epidemic. It informs on both undiagnosed cases and on the effects of health system disruption. Methods: We aimed at evaluating the extent of the total death excess during the COVID-19 epidemic in Italy. Data from 4433 municipalities providing mortality reports until April 15th, 2020 were included for a total of 34.5 million residents from all Italian regions. Data were analyzed by region, sex and age, and compared to expected from 2015–2019. Results: In both genders, overall mortality was stable until February 2020 and abruptly increased from March 1st onwards. Within the municipalities studied, 77,339 deaths were observed in the period between March 1st to April 15th, 2020, in contrast to the 50,822.6 expected. The rate ratio was 1.11 before age 60 and 1.55 afterwards. Both sexes were affected. The excess was greater in the regions most affected by COVID-19 but always exceeded the deaths attributed to COVID-19. The extrapolation to the total Italian population suggests an excess of 45,033 deaths in the study period, while the number of COVID–19 deaths was 21,046. Conclusion: Our paper shows a large death excess during the COVID-19 epidemic in Italy; greater than the number attributed to it. Possible causes included both the undetected cases and the disruption of the Health Service organization. Timely monitoring of overall mortality based on unbiased nationwide data is an essential tool for epidemic control.


title: Formation of protein complexes in crowded environments – From in vitro to in vivo

text: Abstract Traditionally, biochemical studies are performed in dilute homogenous solutions, which are very different from the dense mixture of molecules found in cells. Thus, the physiological relevance of these studies is in question. This recognition motivated scientists to formulate the effect of crowded solutions in general, and excluded volume in particular, on biochemical processes. Using polymers or proteins as crowders, it was shown that while crowding tends to significantly enhance the formation of complexes containing many subunits, dimerizations are only mildly affected. Computer simulations, together with experimental evidence, indicate soft interactions and diffusion as critical factors that operate in a concerted manner with excluded volume to modulate protein binding. Yet, these approaches do not truly mimic the cellular environment. In vivo studies may overcome this shortfall. The few studies conducted thus far suggest that in cells, binding and folding occur at rates close to those determined in dilute solutions. Obtaining quantitative biochemical information on reactions inside living cells is currently a main challenge of the field, as the complexity of the intracellular milieu was what motivated crowding research to begin with.


title: A PubMed-Wide Associational Study of Infectious Diseases

text: BACKGROUND: Computational discovery is playing an ever-greater role in supporting the processes of knowledge synthesis. A significant proportion of the more than 18 million manuscripts indexed in the PubMed database describe infectious disease syndromes and various infectious agents. This study is the first attempt to integrate online repositories of text-based publications and microbial genome databases in order to explore the dynamics of relationships between pathogens and infectious diseases. METHODOLOGY/PRINCIPAL FINDINGS: Herein we demonstrate how the knowledge space of infectious diseases can be computationally represented and quantified, and tracked over time. The knowledge space is explored by mapping of the infectious disease literature, looking at dynamics of literature deposition, zooming in from pathogen to genome level and searching for new associations. Syndromic signatures for different pathogens can be created to enable a new and clinically focussed reclassification of the microbial world. Examples of syndrome and pathogen networks illustrate how multilevel network representations of the relationships between infectious syndromes, pathogens and pathogen genomes can illuminate unexpected biological similarities in disease pathogenesis and epidemiology. CONCLUSIONS/SIGNIFICANCE: This new approach based on text and data mining can support the discovery of previously hidden associations between diseases and microbial pathogens, clinically relevant reclassification of pathogenic microorganisms and accelerate the translational research enterprise.


title: Comparison of the fecal microbiota of domestic commercial meat, laboratory, companion, and shelter rabbits (Oryctolagus cuniculi)

text: BACKGROUND: Rabbits are cecotrophic, hindgut-fermenters that rely heavily on their gastrointestinal microbiota for optimal digestion of plant-based diets. Dysbiosis, caused by disruption of the gastrointestinal microbiota, is known to predispose rabbits to rabbit enteritis complex (REC), a major cause of morbidity and mortality. The objectives of this study were to describe the fecal microbiota of domestic rabbits from a variety of settings (commercial meat, companion, laboratory, and shelter) and to identify how factors such as age, season, and routine antimicrobial use affect the fecal microbiota composition. RESULTS: A total of 86 pooled commercial meat, 54 companion, 14 pooled laboratory, and 14 shelter rabbit fecal samples were evaluated using 16S rRNA gene sequencing of the V4 region. In all sample types, the predominant bacterial phylum was Firmicutes. Other commonly identified phyla (composing ≥ 1% of the total microbiota composition) were Verrucomicrobia, Proteobacteria, and Bacteroidetes. Significant differences in composition were noted between commercial, companion, laboratory, and shelter rabbit samples for proportions of Verrucomicrobia (P < 0.01), Proteobacteria (P < 0.01), and Lentisphaerae (P = 0.01) within the total microbiota. Within the commercial meat rabbit samples, significant differences between the microbiota composition of growers (n = 42) and does (n = 44) were limited to one unclassified Firmicutes (P = 0.03) and no differences were identified at the phylum level. Significant differences were present between fecal samples taken from rabbits during the summer (n = 44) compared to the winter (n = 42), with Firmicutes (P = 0.04), Verrucomicrobia (P = 0.03), Proteobacteria (P = 0.02), Deinococcus-Thermus (P = 0.04), Armatimonadates (P = 0.003), and Actinobacteria (P = 0.03) forming significantly different proportions of the microbiota. The only significant difference in composition between those farms that routinely reported antimicrobial use and those that did not was in one unclassified Bacteroidetes (P < 0.05) and no differences were identified at the phylum level. CONCLUSIONS: Rabbit husbandry and diet, in addition to season, significantly influence the fecal microbiota composition of domestic rabbits, while age of the rabbit post-weaning has minimal impact. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12917-018-1464-6) contains supplementary material, which is available to authorized users.


title: Immune modulation in COVID-19: Strategic considerations for personalized therapeutic intervention

text: We are learning that the host response to SARS-CoV-2 infection is complex and highly dynamic. Effective initial host defense in the lung is associated with mild symptoms and disease resolution. Viral evasion of the immune response can lead to refractory alveolar damage, ineffective lung repair mechanisms, and systemic inflammation with associated organ dysfunction. The immune response in these patients is highly variable and can include moderate to severe systemic inflammation and/or marked systemic immune suppression. There is unlikely to be a “one size fits all” approach to immunomodulation in patients with COVID-19. We believe that a personalized, immunophenotype-driven approach to immunomodulation that may include anti-cytokine therapy in carefully selected patients and immunostimulatory therapies in others is the shortest path to success in the study and treatment of patients with critical illness due to COVID-19.


title: Nottingham Trent University and Makerere University School of Public Health partnership: experiences of co-learning and supporting the healthcare system in Uganda

text: Partnerships between developed and developing country institutions are increasingly becoming important in addressing contemporary global health challenges faced by health systems. Inter-university health collaboration such as the Nottingham Trent University (UK) and Makerere University School of Public Health (Uganda) partnership provide opportunities for working together in training, research and service delivery while strengthening health systems. This paper shares the experiences, achievements and opportunities of this partnership in co-learning and supporting the health system in Uganda. This includes a project being implemented to strengthen the training, supervision and motivation of community health workers in rural Uganda. Training and research are a key focus of the partnership and have involved both staff and students of both institutions including guest lectures, seminars and conference presentations. The partnership’s collaboration with stakeholders such as the Ministry of Health (Uganda) and local health authorities has ensured participation necessary in supporting implementation of sustainable interventions. The partnership uses several channels such as email, telephone, Skype, Dropbox and WhatsApp which have been useful in maintaining constant and effective communication. The challenges faced by the partnership include lack of funding to support student mobility, and varying academic schedules of the two institutions. The experiences and prospects of this growing partnership can inform other collaborations in similar settings.


A novel bunyavirus causing fever and thrombocytopenia: More questions than answers


title: Identification and analysis of the gag-pol ribosomal frameshift site of feline immunodeficiency virus

text: Abstract The pol genes of retroviruses are translated as gag-pol fusion proteins by ribosomal frameshifting within the gag-pol overlap region. During the ribosomal frameshift event, the gag open reading frame is shifted -1 nt to allow in-phase reading of the pol open reading frame. A consensus frameshift signal sequence of GGGAAAC within the gag-pol overlap region of feline immunodeficiency virus (FIV) has been identified followed by a sequence that has the potential for a pseudoknot tertiary structure. Using recombinant baculoviruses in which the frameshift occurs efficiently, the consensus sequence has been shown to be the site of the frameshift event. A mutation creating a termination codon just downstream of the putative frameshift signal sequence but upstream of the potential pseudoknot structure made a shorter gag product, but did not affect the efficiency of frameshifting. A mutation creating a termination codon just upstream of the putative frameshift signal made a shorter product and essentially abrogated frameshifting. Mutations in the first stem or the second stem in the potential pseudoknot structure severely reduced the frameshifting efficiency. Mutations which altered the length between the frameshift signal and the pseudoknot structure (the so-called spacer region) also reduced the frameshift efficiency. The insertion of a palindromic sequence, which could form a hairpin structure just upstream of the frameshift signal sequence, also affected the frameshifting. These results support the view that the ribosomal frameshift event in the FIV gag-pol region involves the identified signal sequence and appears to require the precisely positioned downstream sequence and indicated pseudoknot structure for efficient frameshifting.


title: Influence of viral infection on the relationships between airway cytokines and lung function in asthmatic children

text: BACKGROUND: Few longitudinal studies examine inflammation and lung function in asthma. We sought to determine the cytokines that reduce airflow, and the influence of respiratory viral infections on these relationships. METHODS: Children underwent home collections of nasal lavage during scheduled surveillance periods and self-reported respiratory illnesses. We studied 53 children for one year, analyzing 392 surveillance samples and 203 samples from 85 respiratory illnesses. Generalized estimated equations were used to evaluate associations between nasal lavage biomarkers (7 mRNAs, 10 proteins), lung function and viral infection. RESULTS: As anticipated, viral infection was associated with increased cytokines and reduced FVC and FEV(1). However, we found frequent and strong interactions between biomarkers and virus on lung function. For example, in the absence of viral infection, CXCL10 mRNA, MDA5 mRNA, CXCL10, IL-4, IL-13, CCL4, CCL5, CCL20 and CCL24 were negatively associated with FVC. In contrast, during infection, the opposite relationship was frequently found, with IL-4, IL-13, CCL5, CCL20 and CCL24 levels associated with less severe reductions in both FVC and FEV(1). CONCLUSIONS: In asthmatic children, airflow obstruction is driven by specific pro-inflammatory cytokines. In the absence of viral infection, higher cytokine levels are associated with decreasing lung function. However, with infection, there is a reversal in this relationship, with cytokine abundance associated with reduced lung function decline. While nasal samples may not reflect lower airway responses, these data suggest that some aspects of the inflammatory response may be protective against viral infection. This study may have ramifications for the treatment of viral-induced asthma exacerbations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12931-018-0922-9) contains supplementary material, which is available to authorized users.


title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference

text: Vaccinia virus (VACV) is a large, cytoplasmic, double-stranded DNA virus that requires complex interactions with host proteins in order to replicate. To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. The experimental design incorporated a low multiplicity of infection, thereby enhancing detection of cellular proteins involved in cell-to-cell spread of VACV. The screen revealed 153 pro- and 149 anti-viral HFs that strongly influenced VACV replication. These HFs were investigated further by comparisons with transcriptional profiling data sets and HFs identified in RNAi screens of other viruses. In addition, functional and pathway analysis of the entire screen was carried out to highlight cellular mechanisms involved in VACV replication. This revealed, as anticipated, that many pro-viral HFs are involved in translation of mRNA and, unexpectedly, suggested that a range of proteins involved in cellular transcriptional processes and several DNA repair pathways possess anti-viral activity. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. This advancement in our understanding of the VACV life cycle provides a reliable knowledge base for the improvement of poxvirus-based vaccine vectors and development of anti-viral theraputics.


title: Association between Severity of MERS-CoV Infection and Incubation Period

text: We analyzed data for 170 patients in South Korea who had laboratory-confirmed infection with Middle East respiratory syndrome coronavirus. A longer incubation period was associated with a reduction in the risk for death (adjusted odds ratio/1-day increase in incubation period 0.83, 95% credibility interval 0.68–1.03).


title: Influenza Surveillance Among Children With Pneumonia Admitted to a District Hospital in Coastal Kenya, 2007–2010

text: Background. Influenza data gaps in sub-Saharan Africa include incidence, case fatality, seasonal patterns, and associations with prevalent disorders. Methods. Nasopharyngeal samples from children aged <12 years who were admitted to Kilifi District Hospital during 2007–2010 with severe or very severe pneumonia and resided in the local demographic surveillance system were screened for influenza A, B, and C viruses by molecular methods. Outpatient children provided comparative data. Results. Of 2002 admissions, influenza A virus infection was diagnosed in 3.5% (71), influenza B virus infection, in 0.9% (19); and influenza C virus infection, in 0.8% (11 of 1404 tested). Four patients with influenza died. Among outpatients, 13 of 331 (3.9%) with acute respiratory infection and 1 of 196 without acute respiratory infection were influenza positive. The annual incidence of severe or very severe pneumonia, of influenza (any type), and of influenza A, was 1321, 60, and 43 cases per 100 000 <5 years of age, respectively. Peak occurrence was in quarters 3–4 each year, and approximately 50% of cases involved infants: temporal association with bacteremia was absent. Hypoxia was more frequent among pneumonia cases involving influenza (odds ratio, 1.78; 95% confidence interval, 1.04–1.96). Influenza A virus subtypes were seasonal H3N2 (57%), seasonal H1N1 (12%), and 2009 pandemic H1N1 (7%). Conclusions. The burden of influenza was small during 2007–2010 in this pediatric hospital in Kenya. Influenza A virus subtype H3N2 predominated, and 2009 pandemic influenza A virus subtype H1N1 had little impact.


title: Correction to: Rapid guide to the management of cardiac patients during the COVID-19 pandemic in Egypt: “a position statement of the Egyptian Society of Cardiology”

text: An amendment to this paper has been published and can be accessed via the original article.


docid: oneovsiu

title: Dermatological insights from Google Trends: what does the public think is important during COVID‐19 lockdown?

text: In the United Kingdom, Google is often the search engine used to explore information relating to many aspects of people’s lives, including dermatological advice and information. The frequency of searching for particular terms could indicate the relative importance that the public assigns to various conditions and is dynamic, fluctuating in different societal contexts, such as during a pandemic.


title: The feline acute phase reaction

text: Abstract The acute phase reaction (APR) is a response to potentially pathogenic stimuli. It begins with the release of interleukin (IL)-1, IL-6 and tumour necrosis factor (TNF)-α from inflammatory cells. These cytokines induce fever, leucocytosis and release of serum acute phase proteins (APPs). In this review, the characteristics of the feline APR are described. In cats with inflammatory conditions, fever is a common finding, with leucocytosis due to the release of cells from the marginal pool, followed by activation of myelopoiesis. Because excitement frequently causes leucocytosis in cats, a diagnosis of inflammation should therefore be supported by additional findings such as the presence of toxic neutrophils. The major APPs are serum amyloid A and α1-acid glycoprotein (AGP), which both increase a few hours after the inflammatory stimulus and remain elevated for as long as the inflammation persists. AGP plays an important role in the diagnosis of feline infectious peritonitis (FIP) and may also be useful also in studies of FIP pathogenesis.


title: The Footprint of Genome Architecture in the Largest Genome Expansion in RNA Viruses

text: The small size of RNA virus genomes (2-to-32 kb) has been attributed to high mutation rates during replication, which is thought to lack proof-reading. This paradigm is being revisited owing to the discovery of a 3′-to-5′ exoribonuclease (ExoN) in nidoviruses, a monophyletic group of positive-stranded RNA viruses with a conserved genome architecture. ExoN, a homolog of canonical DNA proof-reading enzymes, is exclusively encoded by nidoviruses with genomes larger than 20 kb. All other known non-segmented RNA viruses have smaller genomes. Here we use evolutionary analyses to show that the two- to three-fold expansion of the nidovirus genome was accompanied by a large number of replacements in conserved proteins at a scale comparable to that in the Tree of Life. To unravel common evolutionary patterns in such genetically diverse viruses, we established the relation between genomic regions in nidoviruses in a sequence alignment-free manner. We exploited the conservation of the genome architecture to partition each genome into five non-overlapping regions: 5′ untranslated region (UTR), open reading frame (ORF) 1a, ORF1b, 3′ORFs (encompassing the 3′-proximal ORFs), and 3′ UTR. Each region was analyzed for its contribution to genome size change under different models. The non-linear model statistically outperformed the linear one and captured >92% of data variation. Accordingly, nidovirus genomes were concluded to have reached different points on an expansion trajectory dominated by consecutive increases of ORF1b, ORF1a, and 3′ORFs. Our findings indicate a unidirectional hierarchical relation between these genome regions, which are distinguished by their expression mechanism. In contrast, these regions cooperate bi-directionally on a functional level in the virus life cycle, in which they predominantly control genome replication, genome expression, and virus dissemination, respectively. Collectively, our findings suggest that genome architecture and the associated region-specific division of labor leave a footprint on genome expansion and may limit RNA genome size.


title: Design, Synthesis, and Biological Evaluation of Novel C5-Modified Pyrimidine Ribofuranonucleosides as Potential Antitumor or/and Antiviral Agents.

text: BACKGROUND Nucleoside analogues are well known antitumor, antiviral, and chemotherapeutic agents. Alterations on both their sugar and the heterocyclic parts may lead to significant changes in the spectrum of their biological action and the degree of selective toxicity, as well as in their physicochemical properties. METHOD C5-arylalkynyl-β-D-ribofuranonucleosides 3-6, 3΄-deoxy 12-15, 3΄-deoxy-3΄-C-methyl-β-D-ribofurananucleosides 18-21 and 2΄-deoxy-β-D-ribofuranonucleosides 23-26 of uracil, were synthesized using a one-step Sonogashira reaction under microwave irradiation and subsequent deprotection. RESULTS All newly synthesized nucleosides were tested for their antitumor or antiviral activity. Moderate cytostatic activity against cervix carcinoma (HeLa), murine leukemia (L1210) and human lymphocyte (CEM) tumor cell lines was displayed by the protected 3΄-deoxy derivatives 12b, 12c, 12d, and the 3΄-deoxy-3΄-methyl 18a, 18b, 18c. Antiviral evaluation revealed appreciable activity against Coxsackie virus B4, Respiratory syncytial virus, Yellow Fever Virus and Human Coronavirus (229E) for the 3΄-deoxy compounds 12b, 14, and the 3΄-deoxy-3΄-methyl 18a, 18c, 18d, accompanied by low cytotoxicity. CONCLUSION This report describes the total and facile synthesis of modified furanononucleosides of uracil, with alterations on both the sugar and the heterocyclic portions. Compounds 12b, 14 and 18a,c,d showed noticeable antiviral activity against a series of RNA viruses and merit further biological and structural optimization investigations.


title: Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA

text: BACKGROUND: The use of sequence independent methods combined with next generation sequencing for identification purposes in clinical samples appears promising and exciting results have been achieved to understand unexplained infections. One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. METHODS: VIDISCA is normally combined with next generation sequencing, however, we set up a simplified VIDISCA which can be used in case next generation sequencing is not possible. Stool samples of 10 patients with unexplained acute flaccid paralysis showing cytopathic effect in rhabdomyosarcoma cells and/or mouse cells were used to test the efficiency of this method. To further characterize the viruses, VIDISCA-positive samples were amplified and sequenced with gene specific primers. RESULTS: Simplified VIDISCA detected seven viruses (70%) and the proportion of eukaryotic viral sequences from each sample ranged from 8.3 to 45.8%. Human enterovirus EV-B97, EV-B100, echovirus-9 and echovirus-21, human parechovirus type-3, human astrovirus probably a type-3/5 recombinant, and tetnovirus-1 were identified. Phylogenetic analysis based on the VP1 region demonstrated that the human enteroviruses are more divergent isolates circulating in the community. CONCLUSION: Our data support that a simplified VIDISCA protocol can efficiently identify unrecognized viruses grown in cell culture with low cost, limited time without need of advanced technical expertise. Also complex data interpretation is avoided thus the method can be used as a powerful diagnostic tool in limited resources. Redesigning the routine diagnostics might lead to additional detection of previously undiagnosed viruses in clinical samples of patients. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1743-422X-11-146) contains supplementary material, which is available to authorized users.


title: Toward an integrative molecular approach to wildlife disease

text: Pathogens pose serious threats to human health, agricultural investment, and biodiversity conservation through the emergence of zoonoses, spillover to domestic livestock, and epizootic outbreaks. As such, wildlife managers are often tasked with mitigating the negative effects of disease. Yet, parasites form a major component of biodiversity that often persist. This is due to logistical challenges of implementing management strategies and to insufficient understanding of host–parasite dynamics. We advocate for an inclusive understanding of molecular diversity in driving parasite infection and variable host disease states in wildlife systems. More specifically, we examine the roles of genetic, epigenetic, and commensal microbial variation in disease pathogenesis. These include mechanisms underlying parasite virulence and host resistance and tolerance, and the development, regulation, and parasite subversion of immune pathways, among other processes. Case studies of devil facial tumor disease in Tasmanian devils (Sarcophilus harrisii) and chytridiomycosis in globally distributed amphibians exemplify the broad range of questions that can be addressed by examining different facets of molecular diversity. For particularly complex systems, integrative molecular analyses present a promising frontier that can provide critical insights necessary to elucidate disease dynamics operating across scales. These insights enable more accurate risk assessment, reconstruction of transmission pathways, discernment of optimal intervention strategies, and development of more effective and ecologically sound treatments that minimize damage to the host population and environment. Such measures are crucial when mitigating threats posed by wildlife disease to humans, domestic animals, and species of conservation concern.


title: Characteristics of Emergency Department Patients With COVID‐19 at a Single Site in Northern California: Clinical Observations and Public Health Implications

text: In December 2019, a novel coronavirus disease (COVID-19) emerged in Wuhan, China and spread globally, resulting in the first World Health Organization (WHO) classified pandemic in over a decade.1 As of April 2020, the United States (US) has the most confirmed COVID-19 cases worldwide, but public health interventions and testing availability have varied across the country. 2.


docid: kkzpqbry

title: Telerehabilitation during COVID 19: Shoulder rehabilitation


docid: kxtmvfup

title: Toward the Development of an Infectious cDNA Clone of a Human Enteric Coronavirus


title: Vaccine Effectiveness against Medically Attended Laboratory-Confirmed Influenza in Japan, 2011–2012 Season

text: The objective of this study was to estimate influenza vaccine effectiveness (VE) against medically attended, laboratory-confirmed influenza during the 2011–2012 season in Japan using a test-negative case-control study design. The effect of co-circulating non-influenza respiratory viruses (NIRVs) on VE estimates was also explored. Nasopharyngeal swab samples were collected from outpatients with influenza-like illnesses (ILIs) in a community hospital in Nagasaki, Japan. Thirteen respiratory viruses (RVs), including influenza A and B, were identified from the samples using a multiplex polymerase chain reaction. The difference in VE point estimates was assessed using three different controls: ILI patients that tested negative for influenza, those that tested negative for all RVs, and those that tested positive for NIRVs. The adjusted VE against medically attended, laboratory-confirmed influenza using all influenza-negative controls was 5.3% (95% confidence interval [CI], −60.5 to 44.1). The adjusted VEs using RV-negative and NIRV-positive controls were −1.5% (95% CI, −74.7 to 41) and 50% (95% CI, −43.2 to 82.5), respectively. Influenza VE was limited in Japan during the 2011–2012 season. Although the evidence is not conclusive, co-circulating NIRVs may affect influenza VE estimates in test-negative case-control studies.


Anticipated Negative Responses by Students to Possible Ebola Virus Outbreak, Guangzhou, China


title: Evaluation of yield of currently available diagnostics by sample type to optimize detection of respiratory pathogens in patients with a community‐acquired pneumonia

text: BACKGROUND: For the detection of respiratory pathogens, the sampling strategy may influence the diagnostic yield. Ideally, samples from the lower respiratory tract are collected, but they are difficult to obtain. OBJECTIVES: In this study, we compared the diagnostic yield in sputum and oropharyngeal samples (OPS) for the detection of respiratory pathogens in patients with community‐acquired pneumonia (CAP), with the objective to optimize our diagnostic testing algorithm. METHODS: Matched sputum samples, OPS, blood cultures, serum, and urine samples were taken from patients (>18 years) with CAP and tested for the presence of possible respiratory pathogens using bacterial cultures, PCR for 17 viruses and five bacteria and urinary antigen testing. RESULTS: When using only conventional methods, that is, blood cultures, sputum culture, urinary antigen tests, a pathogen was detected in 49·6% of patients (n = 57). Adding molecular detection assays increased the yield to 80%. A pathogen was detected in 77 of the 115 patients in OPS or sputum samples by PCR. The sensitivity of the OPS was lower than that of the sputum samples (57% versus 74%). In particular, bacterial pathogens were more often detected in sputum samples. The sensitivity of OPS for the detection of most viruses was higher than in sputum samples (72% versus 66%), except for human rhinovirus and respiratory syncytial virus. CONCLUSION: Addition of PCR on both OPS and sputum samples significantly increased the diagnostic yield. For molecular detection of bacterial pathogens, a sputum sample is imperative, but for detection of most viral pathogens, an OPS is sufficient.


title: Houttuynia cordata blocks HSV infection through inhibition of NF-κB activation

text: Abstract Houttuynia cordata Thunb. is a medicinal plant widely used in folk medicine in several Asian countries. It has been reported that a water extract of H. cordata exhibits activity against herpes simplex virus (HSV) and the virus of severe acute respiratory syndrome (SARS), although the mechanisms are not fully understood yet. Previous studies have demonstrated absolute requirement of NF-κB activation for efficient replication of HSV-1 and HSV-2 and inhibition of NF-κB activation has been shown to suppress HSV infection. Here we show that a hot water extract of H. cordata (HCWE) inhibits HSV-2 infection through inhibition of NF-κB activation. The IC50 was estimated at 50μg/ml of lyophilized HCWE powder. At 150 and 450μg/ml, HCWE blocked infectious HSV-2 production by more than 3 and 4 logs, respectively. The inhibitory activity was concomitant with an inhibition of NF-κB activation by HSV-2 infection. Although activation of NF-κB and Erk MAPK has been implicated for HSV replication and growth, HCWE showed no effect on HSV-2-induced Erk activation. Furthermore, we show that treatment with quercetin, quercitrin or isoquercitrin, major water extractable flavonoids from H. cordata, significantly blocked HSV-2 infection. These results together demonstrated that H. cordata blocks HSV-2 infection through inhibition of NF-κB activation.


title: Digital solutions to combat Covid-19

text: Albert Cho, vice president and general manager at Xylem, discusses how utilities are responding to Covid-19, the digital technologies that are assisting operational continuity and what the pandemic means for the future of utility management.


title: Heat shock protein 70 in lung and kidney of specific-pathogen-free chickens is a receptor-associated protein that interacts with the binding domain of the spike protein of infectious bronchitis virus

text: Avian infectious bronchitis virus (IBV) is a member of the family Coronaviridae. A binding domain that mediates the attachment of the virus to its receptor has been identified in the S1 protein of prototype IBV strain M41. In this study, we identified this binding domain in a different strain, as well as the cellular proteins that interact with it. First, we expressed the S1(N) proteins (residues 19-270) of M41 and another isolate, SCZJ3, and compared the binding capacities of recombinant S1(N)-M41 and S1(N)-SCZJ3 to host tissues. Protein histochemistry showed that both S1(N)-M41 and S1(N)-SCZJ3 could bind to lung and kidney, and that recombinant S1(N)-SCZJ3 displayed a distinctive staining pattern in the proventriculus. Recombinant S1(N)-SCZJ3 was then employed to purify binding-associated proteins in lung, kidney, and proventriculus. Using an affinity chromatography assay, two common bands of about 60 kDa and 70 kDa were obtained from the total tissue proteins. These protein bands were identified by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) as protein disulfide isomerase (PDI) and heat shock protein 70 (HSP70). Finally, infection of chicken embryo kidney (CEK) cells by SCZJ3 was found to be inhibited by anti-HSP70 but not anti-PDI polyclonal antibody. These data indicate that HSP70 is part of the receptor complex of IBV and might help to understand the mechanism of S-mediated cell entry of IBV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-017-3280-x) contains supplementary material, which is available to authorized users.


title: Chinese herbal Huo-Gu formula for the treatment of steroid-associated osteonecrosis of femoral head: A 14-year follow-up of convalescent SARS patients

text: Summary Purpose The coronavirus disease 2019 (COVID-19) reminds us of the severe acute respiratory syndrome (SARS) outbreak in 2003, and up to date, corticosteroid is commonly administrated to severe patients with COVID-19. Osteonecrosis of the femoral head (ONFH) is a common disabling complication among convalescent SARS patients who received corticosteroid therapy. In China, a considerable number of convalescent SARS patients with steroid-associated ONFH had undergone conservative treatment by traditional Chinese medicine, and this study aims to evaluate the long-term results of a spleen-invigorating Huo-Gu formula (HGF) therapy in these patients. Participants and methods A total of 33 convalescent SARS patients (9 males and 24 females) with bilateral steroid-associated ONFH (66 hips) were enrolled in this study. All patients received oral HGF therapy for 6 months when they were confirmed the diagnosis of steroid-associated ONFH. They had been regularly followed up at an interval of 1 year. Harris hip score and medical imaging modalities, including plain radiography, computed tomography and magnetic resonance imaging, were performed to evaluate the outcomes. Results Based on average 14 years of follow-up of HGF therapy (ranging from 6 to 16 years), 38 hips (57%) among the 66 hips developed definite osteoarthritis, and 14 hips (26%) in 53 precollapse hips (Association Research Circulation Osseous [ARCO] Stage I or II) progressed to femoral head collapse (ARCO Stage III or IV). Only five patients (also 5 hips) underwent total hip arthroplasty, and the mean hip survival time was over 15 years by the Kaplan–Meier analysis. We observed a mean Harris hip score of 63 points, which represented the reserve of 55% in pain score and 70% in physical function score. The severity of groin pain was not correlated to the severity of osteoarthritis. Conclusion Chinese herbal HGF therapy demonstrates beneficial effects on preventing femoral head collapse, delaying total hip arthroplasty, and maintaining physical function in the treatment of steroid-associated ONFH. HGF therapy might be therefore a good alternative for the treatment of steroid-associated ONFH secondary to rheumatologic and infection diseases.


title: Hospitalization for Ambulatory-care-sensitive Conditions in Taiwan Following the SARS Outbreak: A Population-based Interrupted Time Series Study

text: Background/Purpose In 2003, the severe acute respiratory syndrome (SARS) outbreak resulted in 8096 probable cases and 774 deaths in 26 countries. The purpose of this study was to explore the effect of the SARS outbreak on hospitalization for chronic ambulatory-care-sensitive conditions (ACSCs) in Taiwan. Methods We applied a population-based interrupted time series study design and used the time series auto-regressive integrated moving-average model to compare the actual and predicted admission rates of seven selected chronic ACSCs. The analyses were based on National Health Insurance hospital inpatient claims data from 1997 to 2003. Results The impact of SARS on ACSCs after the outbreak varied among seven selected chronic conditions. Hospitalization for respiratory conditions was significantly lower than the predicted values, whereas hospitalization for diabetes was significantly higher than the predicted values after the outbreak. Conclusion Admission rates for most ACSCs, except for diabetes, did not change in the post-SARS period. The reductions in outpatient utilization during the SARS outbreak did not appear to affect adversely admissions for most ACSCs.


title: Human infection with avian influenza A H6N1 virus: an epidemiological analysis

text: Summary Background Avian influenza A H6N1 virus is one of the most common viruses isolated from wild and domestic avian species, but human infection with this virus has not been previously reported. We report the clinical presentation, contact, and environmental investigations of a patient infected with this virus, and assess the origin and genetic characteristics of the isolated virus. Methods A 20-year-old woman with an influenza-like illness presented to a hospital with shortness of breath in May, 2013. An unsubtyped influenza A virus was isolated from her throat-swab specimen and was transferred to the Taiwan Centres for Disease Control (CDC) for identification. The medical records were reviewed to assess the clinical presentation. We did a contact and environmental investigation and collected clinical specimens from the case and symptomatic contacts to test for influenza virus. The genomic sequences of the isolated virus were determined and characterised. Findings The unsubtyped influenza A virus was identified as the H6N1 subtype, based on sequences of the genes encoding haemagglutinin and neuraminidase. The source of infection was not established. Sequence analyses showed that this human isolate was highly homologous to chicken H6N1 viruses in Taiwan and had been generated through interclade reassortment. Notably, the virus had a G228S substitution in the haemagglutinin protein that might increase its affinity for the human α2-6 linked sialic acid receptor. Interpretation This is the first report of human infection with a wild avian influenza A H6N1 virus. A unique clade of H6N1 viruses with a G228S substitution of haemagglutinin have circulated persistently in poultry in Taiwan. These viruses continue to evolve and accumulate changes, increasing the potential risk of human-to-human transmission. Our report highlights the continuous need for preparedness for a pandemic of unpredictable and complex avian influenza. Funding Taiwan Centres for Disease Control.


title: Commentary on the management of total laryngectomy patients during the COVID‐19 pandemic

text: The coronavirus disease‐2019 (COVID‐19) pandemic has rapidly spread across the world, placing unprecedented strain on the health care system. Health care resources including hospital beds, ICUs, as well as personal protective equipment are becoming increasingly rationed and scare commodities. In this environment, the laryngectomee (patient having previously undergone a total laryngectomy) continues to represent a unique patient with unique needs. Given their surgically altered airway, they pose a challenge to manage for the otolaryngologist within the current COVID‐19 pandemic. In this brief report, we present special considerations and best practice recommendations in the management of total laryngectomy patients. We also discuss recommendations for laryngectomy patients and minimizing community exposures.


title: Harnessing the privatisation of China's fragmented health-care delivery

text: Although China's 2009 health-care reform has made impressive progress in expansion of insurance coverage, much work remains to improve its wasteful health-care delivery. Particularly, the Chinese health-care system faces substantial challenges in its transformation from a profit-driven public hospital-centred system to an integrated primary care-based delivery system that is cost effective and of better quality to respond to the changing population needs. An additional challenge is the government's latest strategy to promote private investment for hospitals. In this Review, we discuss how China's health-care system would perform if hospital privatisation combined with hospital-centred fragmented delivery were to prevail—population health outcomes would suffer; health-care expenditures would escalate, with patients bearing increasing costs; and a two-tiered system would emerge in which access and quality of care are decided by ability to pay. We then propose an alternative pathway that includes the reform of public hospitals to pursue the public interest and be more accountable, with public hospitals as the benchmarks against which private hospitals would have to compete, with performance-based purchasing, and with population-based capitation payment to catalyse coordinated care. Any decision to further expand the for-profit private hospital market should not be made without objective assessment of its effect on China's health-policy goals.


Colchicin treatment of COVID‐19 presenting with cutaneous rash and myopericarditis


title: Diagnostic utility of aqueocentesis and aqueous humor analysis in dogs and cats with anterior uveitis

text: OBJECTIVE: To evaluate diagnostic utility of aqueous humor analysis in animals with anterior uveitis. ANIMALS: Client‐owned dogs (n = 12) and cats (n = 10). PROCEDURES: Examination findings and diagnostic test results including aqueous humor cytology were compared. RESULTS: Disease duration prior to aqueocentesis was not significantly different between dogs with idiopathic anterior uveitis and those with an etiologic diagnosis, but was shorter in cats with feline infectious peritonitis (FIP) than those with idiopathic uveitis. Microbial nucleic acids, antigens, or antibodies against them were seldom found in blood/serum; however, serum feline coronavirus titers ≥1:6400 were detected only in cats with FIP. Aqueous humor cytology was diagnostic in no cats and two dogs, both with neoplasia. Although aqueous humor contained predominantly neutrophils in cats with FIP and large reactive lymphocytes and plasma cells appeared more frequent in cats with idiopathic uveitis, neither clinical nor cytologic assessment of anterior chamber contents differed significantly between cats with idiopathic or FIP‐associated uveitis. Cytologically assessed plasma cell number was correlated with keratic precipitates and disease duration. Clinically detectable hyphema and cytologic erythrocyte number were correlated. However, cytologic cell grades and clinical grade of flare or cell numbers within the anterior chamber were not correlated. CONCLUSIONS: Aqueous humor cytology permitted diagnosis of neoplasia in dogs with anterior uveitis but was generally not helpful in cats. Poor correlation between clinical and cytologic assessment of cell numbers and type within the anterior chamber dictates that clinical grading should not be the sole criterion for electing to perform aqueocentesis.


title: An audit of the use of isolation facilities in a UK National Health Service trust

text: Summary To aid the ongoing battle against hospital-acquired infection in the UK, all acute National Health Service (NHS) trusts should have audit data about how dedicated isolation beds within the trust are being used. In a previously published audit, we demonstrated that one-third of patients admitted to a dedicated isolation room in Tayside were not thought to be an infection risk by experienced healthcare staff. Since this audit, Tayside's isolation facilities have moved from a small peripheral ‘fever’ hospital to a large central teaching hospital site. At the time of this move, and using the above audit data, we designed and implemented a guideline for general practitioners and hospital doctors regarding the admission of patients to an isolation bed. The aim of this study was to compare the use of isolation beds before and after the move to the new facilities, which we anticipated would increase the demand for isolation. The results show that by all three criteria used, the utilization of isolation beds has deteriorated following the move, mainly due to the increased admission of general medical ‘boarders’ and low-risk infection patients. At a time when hospital-acquired infections are increasing, NHS trusts should ensure that dedicated isolation beds are used appropriately.


docid: ylvqxpba

title: Debate around infection-dependent hemophagocytic syndrome in paediatrics

text: BACKGROUND: Hemophagocytic syndrome (HPS) is clinically defined as a combination of fever, liver dysfunction, coagulation abnormalities, pancytopenia, progressive macrophage proliferation throughout the reticuloendothelial system, and cytokine over-production, and may be primary or secondary to infectious, auto-immune, and tumoral diseases. The most consistent association is with viral infections but, as it is still debated whether any micro-organisms are involved in its pathogenesis, we critically appraised the literature concerning HPS and its relationship with infections. DISCUSSION: Infection-dependent HPS has been widely observed, but there are no data concerning its incidence in children. A better understanding of the pathophysiology of HPS may clarify the interactions between the immune system and the variously implicated potential infectious agents. Epstein-Barr virus (EBV) infection has been prominently associated with HPS, with clonal proliferation and the hyperactivation of EBV-infected T cells. However, a number of other viral, bacterial, fungal, and parasitic infections have been reported in association with HPS. In the case of low-risk HPS, corticosteroids and/or intravenous immunoglobulin or cyclosporine A may be sufficient to control the biological process, but etoposide is recommended as a means of reversing infection-dependent lymphohistiocytic dysregulation in high-risk cases. SUMMARY: HPS is a potential complication of various infections. A polymerase chain reaction search for infectious agents including EBV, cytomegalovirus and Leishmania is recommended in clinical settings characterised by non-remitting fever, organomegaly, cytopenia and hyperferritinemia.


title: Modified percutaneous tracheostomy in COVID‐19 critically ill patients

text: BACKGROUND: Percutaneous tracheostomy (PT) in patients with coronavirus disease (COVID‐19) included several critical steps associated with increased risk of aerosol generation. We reported a modified PT technique aiming to minimize the risk of aerosol generation and to increase the staff safety in COVID‐19 patients. METHODS: PT was performed with a modified technique including the use of a smaller endotracheal tube (ETT) cuffed at the carina during the procedure. RESULTS: The modified technique we proposed was successfully performed in three critically ill patients with COVID‐19. CONCLUSIONS: In COVID‐19 critically ill patients, a modified PT technique, including the use of a smaller ETT cuffed at the carina and fiber‐optic bronchoscope inserted between the tube and the inner surface of the trachea, may ensure a better airway management, respiratory function, patient comfort, and great safety for the staff.


title: Utility of serum procalcitonin values in patients with acute exacerbations of chronic obstructive pulmonary disease: a cautionary note

text: BACKGROUND: Serum procalcitonin levels have been used as a biomarker of invasive bacterial infection and recently have been advocated to guide antibiotic therapy in patients with chronic obstructive pulmonary disease (COPD). However, rigorous studies correlating procalcitonin levels with microbiologic data are lacking. Acute exacerbations of COPD (AECOPD) have been linked to viral and bacterial infection as well as noninfectious causes. Therefore, we evaluated procalcitonin as a predictor of viral versus bacterial infection in patients hospitalized with AECOPD with and without evidence of pneumonia. METHODS: Adults hospitalized during the winter with symptoms consistent with AECOPD underwent extensive testing for viral, bacterial, and atypical pathogens. Serum procalcitonin levels were measured on day 1 (admission), day 2, and at one month. Clinical and laboratory features of subjects with viral and bacterial diagnoses were compared. RESULTS: In total, 224 subjects with COPD were admitted for 240 respiratory illnesses. Of these, 56 had pneumonia and 184 had AECOPD alone. A microbiologic diagnosis was made in 76 (56%) of 134 illnesses with reliable bacteriology (26 viral infection, 29 bacterial infection, and 21 mixed viral bacterial infection). Mean procalcitonin levels were significantly higher in patients with pneumonia compared with AECOPD. However, discrimination between viral and bacterial infection using a 0.25 ng/mL threshold for bacterial infection in patients with AECOPD was poor. CONCLUSION: Procalcitonin is useful in COPD patients for alerting clinicians to invasive bacterial infections such as pneumonia but it does not distinguish bacterial from viral and noninfectious causes of AECOPD.


title: Ultrasound Teleguidance to Reduce Healthcare Worker Exposure to Coronavirus Disease 2019

text: The global spread of coronavirus disease 2019 has accelerated the adoption of technologies that facilitate patient care while reducing viral spread. We illustrate a proof of concept application of teleguidance to ultrasound-guided bedside procedures as an example of an innovative solution that has been used at our institution to maximize patient and provider safety.


title: Corticothérapie en ORL en contexte de pandémie COVID-19

text: RESUME Ces conseils de bonne pratique concernant les indications et les modalités de la corticothérapie en ORL en période d’épidémie COVID-19 ont été rédigés sous l’égide de l’Association Française d’Otologie et d’Oto-neurologie (AFON) et de la Société Française d’ORL et de Chirurgie Cervico-faciale (SFORL). Il n’y pas actuellement de données suggérant un danger ou un bénéfice particulier des corticoïdes dans la COVID-19, et il convient donc, tant que cette question n’est pas tranchée, de limiter leurs indications aux tableaux cliniques les plus sévères et pour lesquels il est bien établi que ce type de traitements a un effet favorable sur l’évolution des symptômes. Dans les paralysies faciales aiguës a frigore de Grade V ou VI dans la classification de House Brackmann, une corticothérapie orale d’une semaine est recommandée. Dans les surdités brutales avec un déficit auditif supérieur à 60 dB, une corticothérapie est là-aussi conseillée, soit sous la forme d’injections intratympaniques soit en cures orales d’une semaine. En rhinologie, il n’y a pas d’indication à une corticothérapie par voie générale dans le contexte actuel. En revanche, il est conseillé aux patients de poursuivre leur corticothérapie locale en spray nasal ou par inhalation. L’instauration de traitements par sprays nasaux de corticoïdes reste possible s’il n’existe pas d’alternative. Enfin, il n’y aucune indication aux corticothérapies par voie générale ou locale dans les infections ORL bactériennes.


title: Methylmalonic and malonic aciduria in a dog with progressive encephalomyelopathy

text: A 12 week old female Labrador retriever dog with signs of progressive diffuse degeneration of the brain and spinal cord was found to have methlymalonic and malonic aciduria. Over a 5 month period, the dog developed neurologic signs compatible with disease of the central nervous system with predominant diffuse cerebral and right lateralizing brainstem deficits. Gross pathological examination of the brain showed that the lateral, third, and fourth ventricles of the brain were markedly enlarged and associated with white and grey matter atrophy. Syringomyelia and hydromyelia of the central canal into the dorsal funiculus of the spinal cord beginning at the level of the cervical intumescence and extending to the lumbar intumescence was also present. Significant biochemical abnormalities include methylmalonic and malonic aciduria, mild lactic and pyruvic aciduria. There was also accumulation of citric acid cycle intermediates including succinic, aconitic, and fumaric acids. Disordered fatty acid oxidation was suggested by increased excretion of adipic, ethylmalonic, suberic and sebacic acids. Neither ketoacidosis nor hyperammonemia were present, and serum cobalamin levels were normal. Overall, this dog demonstrates an inborn error of metabolism resulting in abnormal organic acid accumulation associated with a neurodegenerative disease.


title: Toxin-Based Therapeutic Approaches

text: Protein toxins confer a defense against predation/grazing or a superior pathogenic competence upon the producing organism. Such toxins have been perfected through evolution in poisonous animals/plants and pathogenic bacteria. Over the past five decades, a lot of effort has been invested in studying their mechanism of action, the way they contribute to pathogenicity and in the development of antidotes that neutralize their action. In parallel, many research groups turned to explore the pharmaceutical potential of such toxins when they are used to efficiently impair essential cellular processes and/or damage the integrity of their target cells. The following review summarizes major advances in the field of toxin based therapeutics and offers a comprehensive description of the mode of action of each applied toxin.


title: No Direct Association Between Asthma and the Microbiome Based on Currently Available Techniques

text: Current uses of culture-independent tools in previous studies have shown a significant relationship between microbiota and asthma. Although these studies are relatively new, there is also evidence of the possibility of new therapeutic strategies for the treatment or prevention of asthma. This article retrospectively examines the possible association between microorganisms and asthma. Data on all patients with different types of asthma were collected from hospital charts from the Department of Internal Medicine, Saarland University Medical Center, Germany, within the study period of 2011 to 2012. The tracheal secretions of asthmatics obtained by bronchoalveolar lavage, bronchial aspirates through flexible bronchoscopy, and directly in sputum were examined microbiologically for microorganisms. Thirty-one (10.47%, 95% CI, 6.98–13.96) of a total of 296 patients were found to have asthma microorganisms in their airways. We could not establish a causal relationship between microorganisms and asthma based on the results of our study (P = 0.893). Additionally, acute respiratory infections did not affect the microbiological colonization in asthmatics’ airways (P = 0.472). We were unable to find a direct association between asthma and the microbiome based on existing diagnostic techniques.


title: MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins

text: BACKGROUND: Host responses to viral infection include both immune activation and programmed cell death. The mitochondrial antiviral signaling adaptor, MAVS (IPS-1, VISA or Cardif) is critical for host defenses to viral infection by inducing type-1 interferons (IFN-I), however its role in virus-induced apoptotic responses has not been elucidated. PRINCIPAL FINDINGS: We show that MAVS causes apoptosis independent of its function in initiating IFN-I production. MAVS-induced cell death requires mitochondrial localization, is caspase dependent, and displays hallmarks of apoptosis. Furthermore, MAVS(−/−) fibroblasts are resistant to Sendai virus-induced apoptosis. A functional screen identifies the hepatitis C virus NS3/4A and the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) nonstructural protein (NSP15) as inhibitors of MAVS-induced apoptosis, possibly as a method of immune evasion. SIGNIFICANCE: This study describes a novel role for MAVS in controlling viral infections through the induction of apoptosis, and identifies viral proteins which inhibit this host response.


docid: yedxalqe

title: Fooling the coronavirus proofreading machinery

text: The first proofreading protein identified in RNA viruses might lead to new therapeutics against coronaviruses.


docid: bagpzmdv

title: Containing COVID-19 in rural and remote areas: experiences from China

text: Although the COVID-19 outbreak initially mainly affected highly urbanized settings, eventually it will reach rural and remote populations resulting in even worse outcomes due to the lack of access to testing, health care and slower implementation of nonpharmaceutical interventions. Here we describe the containment efforts in rural China.


docid: cszqykpu

title: Predicting commercially available antiviral drugs that may act on the novel coronavirus (2019-nCoV), Wuhan, China through a drug-target interaction deep learning model

text: The infection of a novel coronavirus found in Wuhan of China (2019-nCoV) is rapidly spreading, and the incidence rate is increasing worldwide. Due to the lack of effective treatment options for 2019-nCoV, various strategies are being tested in China, including drug repurposing. In this study, we used our pretrained deep learning-based drug-target interaction model called Molecule Transformer-Drug Target Interaction (MT-DTI) to identify commercially available drugs that could act on viral proteins of 2019-nCoV. The result showed that atazanavir, an antiretroviral medication used to treat and prevent the human immunodeficiency virus (HIV), is the best chemical compound, showing a inhibitory potency with Kd of 94.94 nM against the 2019-nCoV 3C-like proteinase, followed by efavirenz (199.17 nM), ritonavir (204.05 nM), and dolutegravir (336.91 nM). Interestingly, lopinavir, ritonavir, and darunavir are all designed to target viral proteinases. However, in our prediction, they may also bind to the replication complex components of 2019-nCoV with an inhibitory potency with Kd < 1000 nM. In addition, we also found that several antiviral agents, such as Kaletra, could be used for the treatment of 2019-nCoV, although there is no real-world evidence supporting the prediction. Overall, we suggest that the list of antiviral drugs identified by the MT-DTI model should be considered, when establishing effective treatment strategies for 2019-nCoV.


title: Preeclampsia‐like syndrome induced by severe COVID‐19: a prospective observational study

text: OBJECTIVES: To investigate the incidence of clinical, ultrasonographic and biochemical findings related to preeclampsia (PE) in pregnancies with COVID‐19, and to assess their accuracy to differentiate between PE and the PE‐like features associated with COVID‐19. DESIGN: A prospective, observational study. SETTING: Tertiary referral hospital. PARTICIPANTS: Singleton pregnancies with COVID‐19 at >20+0 weeks. METHODS: 42 consecutive pregnancies were recruited and classified into two groups: severe and nonsevere COVID‐19, according to the occurrence of severe pneumonia. Uterine artery pulsatility index (UtAPI) and angiogenic factors (soluble fms‐like tyrosine kinase‐1/placental growth factor [sFlt‐1/PlGF]) were assessed in women with suspected PE. MAIN OUTCOME MEASURES: Incidence of signs and symptoms related to PE, such as hypertension, proteinuria, thrombocytopenia, elevated liver enzymes, abnormal UtAPI and increased sFlt‐1/PlGF. RESULTS: 34 cases were classified as nonsevere and 8 as severe COVID‐19. Six (14.3%) women presented signs and symptoms of PE, all six being among the severe COVID‐19 cases (75.0%). However, abnormal sFlt‐1/PlGF and UtAPI could only be demonstrated in one case. Two cases remained pregnant after recovery from severe pneumonia and had a spontaneous resolution of the PE‐like syndrome. CONCLUSIONS: Pregnant women with severe COVID‐19 can develop a PE‐like syndrome that might be distinguished from actual PE by sFlt‐1/PlGF, LDH and UtAPI assessment. Health care providers should be aware of its existence and monitor pregnancies with suspected preeclampsia with caution.


title: Inactivated porcine reproductive and respiratory syndrome virus vaccine adjuvanted with Montanide™ Gel 01 ST elicits virus-specific cross-protective inter-genotypic response in piglets

text: Abstract The efficacy of a novel BEI-inactivated porcine reproductive and respiratory syndrome virus (PRRSV) candidate vaccine in pigs, developed at RIBSP Republic of Kazakhstan and delivered with an adjuvant Montanide™ Gel 01 ST (D/KV/ADJ) was compared with a commercial killed PRRSV vaccine (NVDC-JXA1, C/KV/ADJ) used widely in swine herds of the Republic of Kazakhstan. Clinical parameters (body temperature and respiratory disease scores), virological and immunological profiles [ELISA and virus neutralizing (VN) antibody titers], macroscopic lung lesions and viral load in the lungs (quantitative real-time PCR and cell culture assay) were assessed in vaccinated and both genotype 1 and 2 PRRSV challenged pigs. Our results showed that the commercial vaccine failed to protect pigs adequately against the clinical disease, viremia and lung lesions caused by the challenged field isolates, Kazakh strains of PRRSV type 1 and type 2 genotypes. In contrast, clinical protection, absence of viremia and lung lesions in D/KV/ADJ vaccinated pigs was associated with generation of VN antibodies in both homologous vaccine strain LKZ/2010 (PRRSV type 2) and a heterogeneous type 1 PRRSV strain (CM/08) challenged pigs. Thus, our data indicated the induction of cross-protective VN antibodies by D/KV/ADJ vaccine, and importantly demonstrated that an inactivated PRRSV vaccine could also induce cross-protective response across the viral genotype.


docid: kkpkoffv

title: Marketplaces as Public Spaces in Times of The Covid‐19 Coronavirus Outbreak: First Reflections

text: Marketplaces are regarded as quintessential public spaces, providing not only access to fresh produce but also functioning as important social infrastructures. However, many marketplaces closed down or changed fundamentally in response to the COVID‐19 coronavirus outbreak. In this paper, we reflect on the effects of the crisis on Dutch marketplaces from two interdependent analytical levels. From a ground level, we illustrate their ‘temporary death’ as public spaces and reflect on their changing social dynamics. From an organisational level, we analyse traders’ responses to the institutional measures taken to combat the crisis. Combining pre‐corona, in‐situ research with (social) media analysis, we show how a variegated institutional landscape of market regulation emerged. Whereas some markets closed down, others remained open in a highly regulated manner; representing merely economic infrastructures. Our first reflections lead to new avenues to explore how the COVID‐19 crisis affects the everyday geographies of public space.


title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries

text: BACKGROUND: To limit the spread of SARS-CoV-2, an evidence-based understanding of the symptoms is critical to inform guidelines for quarantining and testing. The most common features are purported to be fever and a new persistent cough, although the global prevalence of these symptoms remains unclear. The aim of this systematic review is to determine the prevalence of symptoms associated with COVID-19 worldwide. METHODS: We searched PubMed, Embase, CINAHL, AMED, medRxiv and bioRxiv on 5(th) April 2020 for studies of adults (>16 years) with laboratory test confirmed COVID-19. No language or publication status restrictions were applied. Data were independently extracted by two review authors into standardised forms. All datapoints were independently checked by three other review authors. A random-effects model for pooling of binomial data was applied to estimate the prevalence of symptoms, subgrouping estimates by country. I(2) was used to assess inter-study heterogeneity. RESULTS: Of 851 unique citations, 148 articles were included which comprised 24,410 adults with confirmed COVID-19 from 9 countries. The most prevalent symptoms were fever (78% [95% CI 75%-81%]; 138 studies, 21,701 patients; I(2) 94%), a cough (57% [95% CI 54%-60%]; 138 studies, 21,682 patients; I(2) 94%) and fatigue (31% [95% CI 27%-35%]; 78 studies, 13,385 patients; I(2) 95%). Overall, 19% of hospitalised patients required non-invasive ventilation (44 studies, 6,513 patients), 17% required intensive care (33 studies, 7504 patients), 9% required invasive ventilation (45 studies, 6933 patients) and 2% required extra-corporeal membrane oxygenation (12 studies, 1,486 patients). The mortality rate was 7% (73 studies, 10,402 patients). CONCLUSIONS: We confirm that fever and cough are the most prevalent symptoms of adults infected by SARS-CoV-2. However, there is a large proportion of infected adults which symptoms-alone do not identify.


title: A Single Injection of Human Neutralizing Antibody Protects against Zika Virus Infection and Microcephaly in Developing Mouse Embryos

text: Summary Zika virus (ZIKV) is a mosquito-transmitted flavivirus that is generally benign in humans. However, an emergent strain of ZIKV has become widespread, causing severe pre- and post-natal neurological defects. There is now an urgent need for prophylactic and therapeutic agents. To address this, we investigated six human monoclonal antibodies with ZIKV epitope specificity and neutralizing activity in mouse models of ZIKV infection and microcephaly. A single intraperitoneal injection of these antibodies conveyed distinct levels of adult and in utero protection from ZIKV infection, which closely mirrored their respective in vitro neutralizing activities. One antibody, ZK2B10, showed the most potent neutralization activity, completely protected uninfected mice, and markedly reduced tissue pathology in infected mice. Thus, ZK2B10 is a promising candidate for the development of antibody-based interventions and informs the rational design of ZIKV vaccine.


title: Role of electronic media in mitigating the psychological impacts of novel coronavirus (COVID-19)

text: Abstract The current research initiative focuses on the role of Pakistani media in eliminating panic and depression among health practitioners and the general public due to the outbreak of novel coronavirus (COVID-19). In Pakistan, electronic media is the most common source of information due to the higher rural population and the lower literacy rate and media's handling of COVID-19 coverage so far creates panic and depression. We suggest that special televised transmissions featuring psychologists and physiatrists should be aired to reduce the panic. Media also mitigates the stress of frontline medical staff by paying special attributes to them.


title: Husbandry of Dairy Animals – Goat: Replacement Management ☆

text: Abstract Raising replacement dairy kids begins with prenatal care of the doe. The doe needs to be properly vaccinated before kidding, be in proper body condition, and have good nutrition, including vitamins and minerals. A program to prevent caprine arthritis encephalitis must be instituted, which involves removal of the kid from the doe at birth, feeding heat treated colostrum the first day of life, and feeding with milk replacer, heat treated milk, or a mixture thereafter. Milk should be fed generously (3 times a day) to 2weeks of life. Milk consumption can become limited by feeding 0.5l per feeding, twice a day. More milk can be fed, by feeding 3 times a day or using acidified or cold milk procedures. A high-quality starter feed should be fed beginning the second week of life. A kid must be a minimum of 6weeks of age to be weaned, weigh at least 10kg, and have a starter intake of at least 250gday−1. Kids can be transitioned to weaning by reducing milk feeding to one time a day. After weaning, the kid should be fed 360g of starter feed per day and all of the high-quality hay they can eat. The kid should gain 150gday−1 from birth and weigh 35kg by 7months of age when they can be bred. Kid health problems can be prevented by consumption of adequate colostrum, well-ventilated environment, avoiding crowding, and good sanitation. Attention needs to be given to making gradual changes in feeding.


title: Unlocking bat immunology: establishment of Pteropus alecto bone marrow-derived dendritic cells and macrophages

text: Bats carry and shed many emerging infectious disease agents including Ebola virus and SARS-like Coronaviruses, yet they rarely display clinical symptoms of infection. Bat epithelial or fibroblast cell lines were previously established to study the bat immune response against viral infection. However, the lack of professional immune cells such as dendritic cells (DC) and macrophages has greatly limited the significance of current investigations. Using Pteropus alecto (P. alecto) GM-CSF plus IL4, FLT3L and CSF-1, we successfully generated bat bone marrow-derived DC and macrophages. Cells with the phenotype, morphology and functional features of monocyte-derived DC, bona fide DC or macrophages were obtained in GM-CSF/IL4, FLT3L or CSF-1 cultures, respectively. The successful generation of the first bat bone marrow-derived immune cells paves the way to unlocking the immune mechanisms that confer host resilience to pathogens in bats.


title: An In-hospital Pathway for Acute Coronary Syndrome Patients During the COVID-19 Outbreak: Initial Experience under Real-world Suboptimal Conditions

text: Unstructured Abstract In Lombardy (Italy), due to the COVID-19 outbreak, there is an urgent need to manage cardiovascular emergencies, including acute coronary syndrome (ACS), with appropriate standards of care and dedicated preventive measures and pathways against the risk of SARS-CoV-2 infection. For this reason, the Government of Lombardy decided to centralize the treatment of ACS patients in a limited number of centers, including our University Cardiology Institute that in the last four weeks became a cardiovascular emergency referral center in a regional hub and spoke system. Thus, we rapidly developed a customized pathway in order to allocate patients to the appropriate hospital ward, and treat them according to the ACS severity and the risk of suspected SARS-CoV-2 infection. We present here a protocol dedicated to ACS patients adopted in our center since March 13th 2020 and our initial experience in the management of ACS patients during the first four weeks of its use. Certainly, the protocol has room for further improvement as everyone's experience grows, but we hope that it could be a starting point, adaptable to different realities and local resources.


APOE e4 Genotype Predicts Severe COVID-19 in the UK Biobank Community Cohort


title: Chapter 9 Antimicrobial Use and Ecotoxicological Risks from Pandemics and Epidemics

text: Abstract Pandemics and epidemics represent an uncharacterized risk to human health—ranging from episodic to chronic pathogens and from chronic diseases. Society's capacity to respond to these threats with an even increasing range of pharmaceuticals presents a novel challenge to environmental scientists and public health officials. The environmental and human health risks posed by society's medical response to pandemics and epidemics will be discussed in the context of influenza as a case study and a range of existing pathogen and noncommunicable pathogen risks.


Access to Care for Dementia patients suffering from COVID-19


How to balance acute myocardial infarction and COVID-19: the protocols from Sichuan Provincial People’s Hospital


title: Restricted growth of U‐type infectious haematopoietic necrosis virus (IHNV) in rainbow trout cells may be linked to casein kinase II activity

text: Previously, we demonstrated that a representative M genogroup type strain of infectious haematopoietic necrosis virus (IHNV) from rainbow trout grows well in rainbow trout‐derived RTG‐2 cells, but a U genogroup type strain from sockeye salmon has restricted growth, associated with reduced genome replication and mRNA transcription. Here, we analysed further the mechanisms for this growth restriction of U‐type IHNV in RTG‐2 cells, using strategies that assessed differences in viral genes, host immune regulation and phosphorylation. To determine whether the viral glycoprotein (G) or non‐virion (NV) protein was responsible for the growth restriction, four recombinant IHNV viruses were generated in which the G gene of an infectious IHNV clone was replaced by the G gene of U‐ or M‐type IHNV and the NV gene was replaced by NV of U‐ or M‐type IHNV. There was no significant difference in the growth of these recombinants in RTG‐2 cells, indicating that G and NV proteins are not major factors responsible for the differential growth of the U‐ and M‐type strains. Poly I:C pretreatment of RTG‐2 cells suppressed the growth of both U‐ and M‐type IHNV, although the M virus continued to replicate at a reduced level. Both viruses induced type 1 interferon (IFN1) and the IFN1 stimulated gene Mx1, but the expression levels in M‐infected cells were significantly higher than in U‐infected cells and an inhibitor of the IFN1‐inducible protein kinase PKR, 2‐aminopurine (2‐AP), did not affect the growth of U‐ or M‐type IHNV in RTG‐2 cells. These data did not indicate a role for the IFN1 system in the restricted growth of U‐type IHNV in RTG‐2 cells. Prediction of kinase‐specific phosphorylation sites in the viral phosphoprotein (P) using the NetPhosK program revealed differences between U‐ and M‐type P genes at five phosphorylation sites. Pretreatment of RTG‐2 cells with a PKC inhibitor or a p38MAPK inhibitor did not affect the growth of the U‐ and M‐type viruses. However, 100 μm of the casein kinase II (CKII) inhibitor, 5,6‐dichloro‐1‐β‐d‐ribofuranosylbenzimidazole (DRB), reduced the titre of the U type 8.3‐fold at 24 h post‐infection. In contrast, 100 μm of the CKII inhibitor reduced the titre of the M type only 1.3‐fold at 48 h post‐infection. Our data suggest that the different growth of U‐ and M‐type IHNV in RTG‐2 cells may be linked to a differential requirement for cellular protein kinases such as CKII for their growth.


title: Nonserologic test for COVID‐19: How to manage?

text: BACKGROUND: Diagnosis of Severe Acute Respiratory Coranavirus‐2 (SARS‐CoV‐2) infection is currently based on real‐time PCR (RT‐PCR) performed on either nasopharyngeal (NPS) or oropharyngeal (OPS) swabs; saliva specimen collection can be used, too. Diagnostic accuracy of these procedures is suboptimal, and some procedural mistakes may account for it. METHODS AND RESULTS: The video shows how to properly collect secretions from the upper airways for nonserologic diagnosis of COVID‐19 by nasopharyngeal swab (NPS), oropharyngeal swab (OPS), and deep saliva collection after throat‐cleaning maneuver, all performed under videoendoscopic view by a trained ENT examiner. CONCLUSIONS: We recommend to perform NPS after elevation of the tip of the nose in order to reduce the risk of contamination from the nasal vestible, and to let it flow over the floor of the nasal cavity in parallel to the hard palate in order to reach the nasopharynx. Then the tip of the swab should be left in place for few seconds, and then rotated in order to achieve the largest absorption of nasopharyngeal secretions. Regards OPS, gentle anterior tongue depression should be used to avoid swab contamination from the oral cavity during collection of secretions from the posterior pharyngeal wall. These procedural tricks would enhance diagnostic reliability.


title: When are pathogen genome sequences informative of transmission events?

text: Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data.


title: Clinical Characteristics and Outcomes of 421 Patients with COVID-19 Treated in a Mobile Cabin Hospital

text: Abstract Background In December 2019, a novel coronavirus-associated pneumonia (COVID-19) was first detected in Wuhan, China. To prevent the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and treat patients with mild symptoms, sports stadiums and convention centers were reconstructed into mobile hospitals. Research Question Whether a mobile cabin hospital can provide a safe treatment site for patients with mild COVID-19 symptoms remains unknown. Study Design and Methods We retrospectively reviewed the medical records of 421 patients with COVID-19 admitted to a mobile cabin hospital in Wuhan from February 9th to March 5th, 2020. Clinical data comprised patient age, sex, clinical presentation, chest imaging, nucleic acid testing, length of hospitalization, and outcomes. Results The outcome was recovery and hospital discharge in 86% of patients, while 14.0% developed severe symptoms and were transferred to a designated hospital. The most common presenting symptoms were fever (60.6%) and cough (52.0%), while 5.2% showed no obvious symptoms. High fever (>39.0°C) was more common in severe cases than recovered cases (18.6% versus 6.6%). The distribution of lung lesions was peripheral in 85.0% of patients, multifocal in 69.4%, and bilateral in 68.2%. The most common pattern was ground-glass opacity (67.7%), followed by patchy shadowing (49.2%). The incidence of patchy shadowing was higher in severe patients (66.1%) than in those who recovered (31.8%, P<.0001). The median length of hospitalization was 17 (14–19) days, and the median time taken for positive real-time reverse transcriptase polymerase chain reaction results to become negative in recovered patients was 8 (6–10) days. Interpretation Mobile cabin hospitals provide a safe treatment site for patients with mild COVID-19 symptoms, and provide an effective isolation area to prevent the spread of SARS-CoV-2.


title: How would Australian hospital staff react to an avian influenza admission, or an influenza pandemic?

text: Objective: To estimate the expected staff absentee rates and work attitudes in an Australian tertiary hospital workforce in two hypothetical scenarios: (i) a single admission of avian influenza; and (ii) multiple admissions of human pandemic influenza. Methods: A survey conducted at hospital staff meetings between May and August 2006. Results: Out of 570 questionnaires distributed, 560 were completed. For scenario one, 72 (13%) indicated that they would not attend work, and an additional 136 (25%) would only work provided that immunizations and/or antiviral medications were immediately available, so that up to 208 (38%) would not attend work. For scenario two, 196 (36%) would not attend work, and an additional 95 (17%) would work only if immunizations and/or antiviral medications were immediately available, so that up to 291 (53%) staff would not attend work. Staff whose work required them to be in the ED (odds ratios 2.2 and 1.6 for each scenario respectively) or on acute medical wards (odds ratios 2.2 and 2.0 respectively) were more likely to work. Conclusion: High absenteeism among hospital staff should be anticipated if patients are admitted with either avian or pandemic influenza, particularly if specific antiviral preventative measures are not immediately available. Measures to maximize the safety of staff and their families would be important incentives to attend work. Education on realistic level of risk from avian and pandemic influenza, as well as the effectiveness of basic infection control procedures and personal protective equipment, would be useful in improving willingness to work.


title: The effect of severe acute respiratory syndrome on emergency airway management

text: Study objectives: From early March 2003 to late May 2003, severe acute respiratory syndrome (SARS) was detected in Singapore. Two hundred thirty-eight patients were infected; 33 died. Forty-two percent were health care workers. The whole medical system in the country was put under stress. One major public hospital became the designated SARS hospital. Emergency cases were diverted to the remaining public hospitals, of which Singapore General Hospital was the main recipient. The increase in workload, new infection control procedures including mandatory wearing of the positive airway pressure respirator and personal protective equipment (PPE), and limiting the number of person-contacts with each patient were thought to affect resuscitation and airway management. Our aim is to study the effects of wearing of PPE and the restriction in number of resuscitation personnel on airway management during the SARS crisis. Methods: The emergency department has an ongoing airway registry that prospectively captures patient demographics, diagnosis, indications for intubation, persons and discipline of intubating physician, number of attempts, method of intubation, success rates, and complications. The data were divided into 3 periods: (1) before PPE was instituted from November 1, 2002, to March 31, 2003; (2) during SARS (when PPE use was mandatory) from April 1 to July 31, 2003; and (3) after SARs (when PPE use was nonmandatory but encouraged) from August 1 to December 31, 2003. Results: There was no change in patient demographics during the 3 periods, but there was a change in the patient diagnoses in period 2, with decreases in the proportion of respiratory and cardiac cases and increases in neurology and trauma cases. These changes reverted to the previous distribution in period 3. The alarming discovery was that whereas in period 1 (pre-SARS), resident medical officers attempted intubations 45% of the time, this figure went down to 35% in period 2 (SARS) and 23% in period 3 (post-SARS). Anesthetists performed 1.2%, 8%, and 0% of emergency intubations in periods 1, 2, and 3, respectively. Attending emergency physicians performed 54%, 56%, and 77% of intubations in periods 1, 2, and 3, respectively. The complication/peri-intubation event rates were 10.5%, 9.9%, and 9.4% in periods 1, 2, and 3, respectively. The success rate for residents was 80.8%, 89%, and 86.2% in periods 1, 2, and 3, respectively. Conclusion: The wearing of PPE and positive airway pressure respirator is thought to make intubation more difficult, as seen by the increase in proportion of intubations performed by anesthetists in period 2 and by attending emergency physicians in periods 2 and 3. The infection control policy that restricts the number of health care staff attending to each patient may have influenced the department's decision to allow only the most confident or experienced personnel to manage the airway. The exposure of junior residents in emergency airway management during SARS and the immediate post-SARS period was decreased. This trend should be further monitored, and intervention may be necessary should it continue to decline.


title: Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

text: BACKGROUND: Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative approaches. RESULTS: We reconstruct over 1000 previously uncharacterized microbial species from 6 available NHP metagenomic cohorts, resulting in an increase of the mappable fraction of metagenomic reads by 600%. These novel species highlight that almost 90% of the microbial diversity associated with NHPs has been overlooked. Comparative analysis of this new catalog of taxa with the collection of over 150,000 genomes from human metagenomes points at a limited species-level overlap, with only 20% of microbial candidate species in NHPs also found in the human microbiome. This overlap occurs mainly between NHPs and non-Westernized human populations and NHPs living in captivity, suggesting that host lifestyle plays a role comparable to host speciation in shaping the primate intestinal microbiome. Several NHP-specific species are phylogenetically related to human-associated microbes, such as Elusimicrobia and Treponema, and could be the consequence of host-dependent evolutionary trajectories. CONCLUSIONS: The newly reconstructed species greatly expand the microbial diversity associated with NHPs, thus enabling better interrogation of the primate microbiome and empowering in-depth human and non-human comparative and co-diversification studies.


title: A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry

text: Molecular beacons are dual-labelled probes that are typically used in real-time PCR assays, but have also been conjugated with solid matrices for use in microarrays or biosensors. We have developed a fluid array system using microsphere-conjugated molecular beacons and the flow cytometer for the specific, multiplexed detection of unlabelled nucleic acids in solution. For this array system, molecular beacons were conjugated with microspheres using a biotin-streptavidin linkage. A bridged conjugation method using streptavidin increased the signal-to-noise ratio, allowing for further discrimination of target quantitation. Using beads of different sizes and molecular beacons in two fluorophore colours, synthetic nucleic acid control sequences were specifically detected for three respiratory pathogens, including the SARS coronavirus in proof-of-concept experiments. Considering that routine flow cytometers are able to detect up to four fluorescent channels, this novel assay may allow for the specific multiplex detection of a nucleic acid panel in a single tube.


title: Challenges and solutions for addressing critical shortage of supply chain for personal and protective equipment (PPE) arising from Coronavirus disease (COVID19) pandemic – Case study from the Republic of Ireland

text: Abstract Coronavirus (COVID-19) is highly infectious agent that causes fatal respiratory illnesses, which is of great global public health concern. Currently, there is no effective vaccine for tackling this COVID19 pandemic where disease countermeasures rely upon preventing or slowing person-to-person transmission. Specifically, there is increasing efforts to prevent or reduce transmission to front-line healthcare workers (HCW). However, there is growing international concern regarding the shortage in supply chain of critical one-time-use personal and protective equipment (PPE). PPE are heat sensitive and are not, by their manufacturer's design, intended for reprocessing. Most conventional sterilization technologies used in hospitals, or in terminal medical device sterilization providers, cannot effectively reprocess PPE due to the nature and severity of sterilization modalities. Contingency planning for PPE stock shortage is important. Solutions in the Republic of Ireland include use of smart communication channels to improve supply chain, bespoke production of PPE to meets gaps, along with least preferred option, use of sterilization or high-level disinfection for PPE reprocessing. Reprocessing PPE must consider material composition, functionality post treatment, along with appropriate disinfection. Following original manufacturer of PPE and regulatory guidance is important. Technologies deployed in the US, and for deployment in the Republic of Ireland, are eco-friendly, namely vaporised hydrogen peroxide (VH2O2), such as for filtering facepiece respirators and UV irradiation and High-level liquid disinfection (Actichlor+) is also been pursed in Ireland. Safeguarding supply chain of PPE will sustain vital healthcare provision and will help reduce mortality.


title: Biosafety Level 4 Laboratory User Training Program, China

text: Experienced, qualified personnel certified to work in high-level biocontainment laboratories contribute to the safe operation of these facilities. China began a training program for laboratory users after establishing its first Biosafety Level 4 laboratory, the Wuhan National Biosafety Laboratory (Level 4) of the Chinese Academy of Sciences. We provide an overview of the content of this training program, which can serve as a reference for developing national norms for high-containment laboratory training.


title: Antiviral Activity and Safety of Darunavir/Cobicistat for Treatment of COVID-19

text: BACKGROUND: We aimed to evaluate the antiviral activity and safety of Darunavir/Cobicistat (DRV/c) in treating COVID-19 patients. METHODS: In this single-center, randomized and open-label trial, mild patients with PCR confirmed COVID-19 were enrolled in Shanghai, China. Participants were randomized to receive DRV/c for 5 days on the top of interferon alpha 2b inhaling or interferon alpha 2b inhaling alone. The primary endpoint was the virological clearance rate of oropharyngeal swabs at day 7 after randomization in the intention-to-treat population. (clinicaltrials.gov: NCT04252274) RESULTS: From Jan 30, 2020 to Feb 6, 2020, a total of 30 patients were enrolled, of whom 18(60%) were male, aged 47·2±2·8 years. 63·3% (19/30) of the participants had fever and 46·7%(14/30) had cough at enrollment. The participants were randomized at 4(2-5) days after onset of symptoms. The proportions of negative PCR results at day 7 was 46·7%(7/15) and 60·0%(9/15) in the DRV/c and the control group (P=0·72), respectively. The viral clearance rate at day 3 was both 20%(3/15) in the two study groups while the number increased to 26·7%(4/15) in the DRV/c group and maintained 20%(3/15) in the control group at day 5. Fourteen days after randomization, 1 participant in the DRV/c group progressed to critical illness and discontinued DRV/c while all the patients in the control group were stable (P=1·0). The frequency of adverse events in the two groups were comparable. CONCLUSION: Five days of DRV/c did not increase the proportion of negative conversion than standard of care alone, although it was well tolerated.


docid: fgowncqp

title: Coronavirus Defective-Interfering RNA as an Expression Vector: The Generation of a Pseudorecombinant Mouse Hepatitis Virus Expressing Hemagglutinin-Esterase

text: Abstract We have developed an expression vector system using a defective-interfering (DI) RNA of mouse hepatitis virus (MHV), a prototype coronavirus, to deliver and express a foreign gene in MHV-infected cells. This vector contains an MHV intergenic sequence to promote the expression of foreign genes. In this study, we used this vector to introduce a hemagglutininesterase (HE) protein, an optional MHV structural protein, into the MHV-infected cells. The engineered HE protein could be efficiently incorporated into the virion which did not synthesize its own HE protein, thus generating a pseudorecombinant virus that expresses an exogenous HE protein. The engineered HE protein could be made distinguishable from the native protein by attaching an 8-amino-acid peptide tag at the carboxyl-terminus. Both the engineered and native HE proteins from the HE-producing virus train could be incorporated into the virion, thus generating phenotypically mixed virus parficles. We also showed that the HE-expressing DI RNA could be incorporated into viruses, and the engineered HE protein expressed in the infected cells for at least three serial virus passages. Furthermore, we have made two mutants, in which parts of the external domain of the HE protein have been deleted, to study the sequence requirements for the stable expression of HE and its incorporation into MHV virions. Although both of the mutant HE proteins could be expressed in the MHV-infected cells, they failed to be incorporated into virions, suggesting the importance of the extracellular domain of HE protein for its incorporation into virus particles. This vector system enabled the first successful incorporation of a selected coronaviral protein into virions and demonstrates its utility as an expression vector for studying the molecular biology of coronaviruses.


docid: mtzkyrmd

title: COVID-19: Protecting Healthcare Workers is a priority

text: In Italy, more infections among healthcare personnel than in China were recorded. As of April 05, 2020 12,252 health workers in Italy have tested positive for COVID-19, making up 10% of Italy's COVID-19 cases; furthermore, 80 medical doctors and 25 nurses have died. Protecting healthcare workers is crucial in order not to amplify the COVID-19 epidemics. Moreover, relocating the public health emergency response from the hospitals to the territory, by integrating the hospital into an overall epidemic response, is a priority for contrasting further COVID-19 waves.


title: Breed-specific variations in the coding region of toll-like receptor 4 in the domestic cat

text: Abstract Specific point mutations in the human toll-like receptor 4 (TLR4) confer altered risk for diverse diseases including sepsis, aspergillosis and inflammatory bowel disease. Some of these TLR4 polymorphisms are racially specific. We hypothesised that feline TLR4 polymorphisms might underlie an observed increased risk to infectious and inflammatory diseases in some cat breeds. The aim of this study was to identify breed-specific variations in the coding region of feline TLR4 and to model the effect of mutations on protein structure and function in silico. The entire coding region of TLR4 was sequenced in 8 groups (7 pure-bred, 1 crossbred) of domestic cats (Felis catus) comprising 158 individuals. Twenty-two single nucleotide polymorphisms (SNPs) were identified in TLR4, with 16 located in the coding region (11 non-synonymous) and four in the 3′UTR. Comparison of breed specific allelic frequencies indicated that Burmese and British shorthairs most commonly differed from other breeds. In silico analyses to predict the impact of the 11 non-synonymous variants indicated a deleterious effect on protein structure for one SNP (c.869 G > A), which was not associated with a specific breed. Overall, findings from this study do not support a role of TLR4 dysfunction in breed-predispositions to infectious diseases in domestic cats in Australia.


Definitions, differences and inequalities in times of COVID‐19: indigenous peoples in Mexico