title: To breastfeed or not to breastfeed? Lack of evidence on the presence of SARS-CoV-2 in breastmilk of pregnant women with COVID-19

text: A rapid systematic review was carried out to evaluate the current evidence related to the presence of SARS-CoV-2 in breast milk from pregnant women with COVID-19. Eight studies analyzing the presence of SARS-CoV-2 RNA in the breast milk of 24 pregnant women with COVID-19 during the third trimester of pregnancy were found. All patients had fever and/or symptoms of acute respiratory illness and chest computed tomography images indicative of COVID-19 pneumonia. Most pregnant women had cesarean delivery (91.7%) and two neonates had low birthweight (< 2 500 g). Biological samples collected immediately after birth from upper respiratory tract (throat or nasopharyngeal) of neonates and placental tissues showed negative results for the presence SARS-CoV-2 by RT-PCR test. No breast milk samples were positive for SARS-CoV-2 and, to date, there is no evidence on the presence of SARS-CoV-2 in breast milk of pregnant women with COVID-19. However, data are still limited and breastfeeding of women with COVID-19 remains a controversial issue. There are no restrictions on the use of milk from a human breast milk bank.


title: In vitro and ex vivo analyses of co-infections with swine influenza and porcine reproductive and respiratory syndrome viruses

text: Abstract Viral respiratory diseases remain problematic in swine. Among viruses, porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza virus (SIV), alone or in combination, are the two main known contributors to lung infectious diseases. Previous studies demonstrated that experimental dual infections of pigs with PRRSV followed by SIV can cause more severe disease than the single viral infections. However, our understanding of the impact of one virus on the other at the molecular level is still extremely limited. Thus, the aim of the current study was to determine the influence of dual infections, compared to single infections, in porcine alveolar macrophages (PAMs) and precision cut lung slices (PCLS). PAMs were isolated and PCLS were acquired from the lungs of healthy 8-week-old pigs. Then, PRRSV (ATCC VR-2385) and a local SIV strain of H1N1 subtype (A/Sw/Saskatchewan/18789/02) were applied simultaneously or with 3h apart on PAMs and PCLS for a total of 18h. Immuno-staining for both viruses and beta-tubulin, real-time quantitative PCR and ELISA assays targeting various genes (pathogen recognition receptors, interferons (IFN) type I, cytokines, and IFN-inducible genes) and proteins were performed to analyze the cell and the tissue responses. Interference caused by the first virus on replication of the second virus was observed, though limited. On the host side, a synergistic effect between PRRSV and SIV co-infections was observed for some transcripts such as TLR3, RIG-I, and IFNβ in PCLS. The PRRSV infection 3h prior to SIV infection reduced the response to SIV while the SIV infection prior to PRRSV infection had limited impact on the second infection. This study is the first to show an impact of PRRSV/SIV co-infection and superinfections in the cellular and tissue immune response at the molecular level. It opens the door to further research in this exciting and intriguing field.


title: A human coronavirus OC43 variant harboring persistence-associated mutations in the S glycoprotein differentially induces the unfolded protein response in human neurons as compared to wild-type virus

text: Abstract We have reported that human respiratory coronavirus OC43 (HCoV-OC43) is neurotropic and neuroinvasive in humans and mice, and that neurons are the primary target of infection in mice, leading to neurodegenerative disabilities. We now report that an HCoV-OC43 mutant harboring two persistence-associated S glycoprotein point mutations (H183R and Y241H), induced a stronger unfolded protein response (UPR) and translation attenuation in infected human neurons. There was a major contribution of the IRE1/XBP1 pathway, followed by caspase-3 activation and nuclear fragmentation, with no significant role of the ATF6 and eIF2-alpha/ATF4 pathways. Our results show the importance of discrete molecular viral S determinants in virus–neuronal cell interactions that lead to increased production of viral proteins and infectious particles, enhanced UPR activation, and increased cytotoxicity and cell death. As this mutant virus is more neurovirulent in mice, our results also suggest that two mutations in the S glycoprotein could eventually modulate viral neuropathogenesis.


title: Evaluating the impact of the multiplex respiratory virus panel polymerase chain reaction test on the clinical management of suspected respiratory viral infections in adult patients in a hospital setting

text: A retrospective cohort design was used to study the impact of a multiplex respiratory virus panel polymerase chain reaction test in 186 adult patients with suspected influenza-like illness. Decisions regarding continuation of empirical antiviral therapy appear to be impacted by the test. However, the impact on reducing antibiotic use remains unclear.


title: A design principle for a single-stranded RNA genome that replicates with less double-strand formation

text: Single-stranded RNA (ssRNA) is the simplest form of genetic molecule and constitutes the genome in some viruses and presumably in primitive life-forms. However, an innate and unsolved problem regarding the ssRNA genome is formation of inactive double-stranded RNA (dsRNA) during replication. Here, we addressed this problem by focusing on the secondary structure. We systematically designed RNAs with various structures and observed dsRNA formation during replication using an RNA replicase (Qβ replicase). From the results, we extracted a simple rule regarding ssRNA genome replication with less dsRNA formation (less GC number in loops) and then designed an artificial RNA that encodes a domain of the β-galactosidase gene based on this rule. We also obtained evidence that this rule governs the natural genomes of all bacterial and most fungal viruses presently known. This study revealed one of the structural design principles of an ssRNA genome that replicates continuously with less dsRNA formation.


title: Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing

text: BACKGROUND: Animal faeces comprise a community of many different microorganisms including bacteria and viruses. Only scarce information is available about the diversity of viruses present in the faeces of pigs. Here we describe a protocol, which was optimized for the purification of the total fraction of viral particles from pig faeces. The genomes of the purified DNA and RNA viruses were simultaneously amplified by PCR and subjected to deep sequencing followed by bioinformatic analyses. The efficiency of the method was monitored using a process control consisting of three bacteriophages (T4, M13 and MS2) with different morphology and genome types. Defined amounts of the bacteriophages were added to the sample and their abundance was assessed by quantitative PCR during the preparation procedure. RESULTS: The procedure was applied to a pooled faecal sample of five pigs. From this sample, 69,613 sequence reads were generated. All of the added bacteriophages were identified by sequence analysis of the reads. In total, 7.7% of the reads showed significant sequence identities with published viral sequences. They mainly originated from bacteriophages (73.9%) and mammalian viruses (23.9%); 0.8% of the sequences showed identities to plant viruses. The most abundant detected porcine viruses were kobuvirus, rotavirus C, astrovirus, enterovirus B, sapovirus and picobirnavirus. In addition, sequences with identities to the chimpanzee stool-associated circular ssDNA virus were identified. Whole genome analysis indicates that this virus, tentatively designated as pig stool-associated circular ssDNA virus (PigSCV), represents a novel pig virus. CONCLUSION: The established protocol enables the simultaneous detection of DNA and RNA viruses in pig faeces including the identification of so far unknown viruses. It may be applied in studies investigating aetiology, epidemiology and ecology of diseases. The implemented process control serves as quality control, ensures comparability of the method and may be used for further method optimization.


title: Clinical evaluation of real-time PCR assays for rapid diagnosis of SARS coronavirus during outbreak and post-epidemic periods

text: Abstract Background: The protocols of WHO network laboratories facilitated development of rapid diagnosis for SARS coronavirus (CoV) using reverse transcription (RT)-PCR assays. However, several reports have shown that conventional and real-time PCR assays were very specific for SARS CoV but lack sensitivity depending on the assay, specimen, and time course of disease. Objective: To evaluate an automatic nucleic acid extraction system and two standardized real-time PCR assays for rapid diagnosis of SARS CoV during outbreak and post-epidemic periods in Hong Kong. Study design: Specimens from clinically suspected SARS patients collected during outbreak and post-epidemic periods were tested by an automatic nucleic acid extraction system followed by our first generation conventional RT-PCR and two standardized real-time PCR assays (Artus GmbH, Germany and Roche Diagnostics, Germany). Paired serum samples were assayed for increasing titer against SARS CoV. Results: In the SARS epidemic, Artus and Roche PCR assays exhibited sensitivities of 87% and 85% for respiratory specimens (n =64), 91% and 88% for stool (n =44), and 82% for urine (n =29). A specificity of 100% was exhibited by both PCR assays except Artus attained only a 92% specificity for stool. For post-epidemic period, no SARS CoV was identified among 56 respiratory specimens by all PCR assays. Inhibitors to PCR assays were detected at an average rate of 7–8% among 202 clinical specimens. Conclusion: This study highlights the high throughput and performance of automatic RNA extraction in coordination with standardized real-time PCR assays suitable for large-scale routine diagnosis in case of future SARS epidemic. As no SARS CoV was detected among specimens collected during post-epidemic period, the positive predictive value of real-time PCR assays for detection of SARS CoV during low epidemic requires further evaluation.


Cardiac arrest precipitated by succinylcholine in a patient with COVID-19. Comment on Br J Anaesth 2020; xxx


title: How to Use a Prioritised Approach for Treating Hematological Disorders During the COVID-19 Pandemic in India?

text: The current pandemic coronavirus, SARS-CoV-2, is known to cause severe infection (COVID-19) in patients with comorbidities, particularly cancer or an immunosuppressed state. Most healthcare systems in the country are likely to be overwhelmed soon if the pandemic moves to a stage of community transmission. Currently, limited evidence is available for managing patients with hematological disorders during the COVID-19 pandemic. The current review summarises the possible challenges clinicians are likely to face, key considerations to guide decision making, and possible solutions to the anticipated challenges. Disease specific recommendations and possible guidance for decision making have been suggested for most hematologic diseases that are feasible in our health setup. It is not meant to replace individual clinical judgment, but to provide a template to formulate local policies.


title: Trachéotomie percutanée pour afflux saturant de patients COVID-19: expérience des ORL militaires déployés à Mulhouse

text: Résumé Objectifs: L’objectif principal était de montrer la faisabilité des trachéotomies percutanées réalisées par les ORL militaires lors de leur déploiement en urgence à l’Elément Militaire de Réanimation du Service de Santé des Armées (EMRSSA) à Mulhouse pour faire face à la situation sanitaire exceptionnelle liée au COVID-19. L’objectif secondaire était d’étudier la fiabilité et la sécurité de la procédure pour le patient et pour le personnel soignant, avec un risque de contamination virale iatrogène. Matériel et Méthodes: Une étude rétrospective monocentrique a été réalisée entre le 25 mars et le 25 avril 2020, chez 47 patients COVID-19 nécessitant une ventilation mécanique prolongée. Le critère d’inclusion était d’avoir bénéficié d’une trachéotomie percutanée. Résultats: 18 patients inclus consécutivement avaient bénéficié d’une trachéotomie percutanée avec succès malgré des conditions anatomiques défavorables (cou court : 83,3 %, surcharge pondérale ou obésité : 88,9%). Le délai médian de réalisation était de 11 jours après l’intubation, la durée moyenne de 7 minutes. La procédure était techniquement conforme dans 83,3 %, considérée comme facile (score d’auto-évaluation) dans 72,2 %, avec deux complications per-procédure mineures. Aucune conversion chirurgicale n’avait été observée. Une seule complication majeure hémorragique post-procédure tardive était notée. Conclusion: Cette étude a montré la faisabilité des trachéotomies percutanées par un ORL dans ces conditions à risque biologique COVID-19. La technique était rapide, facile et sûre et répondait aux exigences de sécurité pour le patient et le personnel soignant.


title: Transient inhibition of foot-and-mouth disease virus replication by siRNAs silencing VP1 protein coding region

text: Abstract Foot-and-mouth disease virus (FMDV) is the causative agent of foot-and-mouth disease, a severe, clinically acute, vesicular disease of cloven-hoofed animals. RNA interference (RNAi) is a mechanism for silencing gene expression post-transcriptionally that is being exploited as a rapid antiviral strategy. To identify efficacious small interfering RNAs (siRNAs) to inhibit the replication of FMDV, candidate siRNAs corresponding to FMDV VP1 gene were designed and synthesized in vitro using T7 RNA polymerase. In reporter assays, five siRNAs showed significant sequence-specific silencing effects on the expression of VP1-EGFP fusion protein from plasmid pVP1-EGFP-N1, which was cotransfected with siRNA into 293T cells. Furthermore, using RT-qPCR, viral titration and viability assay, we identified VP1-siRNA517, VP1-siRNA113 and VP1-siRNA519 that transiently acted as potent inhibitors of FMDV replication when BHK-21 cells were infected with FMDV. In addition, variations within multiple regions of the quasispecies of FMDV were retrospectively revealed by sequencing of FMDV genes, and a single nucleotide substitution was identified as the main factor in resistance to RNAi. Our data demonstrated that the three siRNA molecules synthesized with T7 RNA polymerase could have transient inhibitory effects on the replication of FMDV.


title: Synthesis and biological evaluation of 3-acyl-2-phenylamino-1,4-dihydroquinolin-4(1H)-one derivatives as potential MERS-CoV inhibitors

text: Abstract 3-Acyl-2-phenylamino-1,4-dihydroquinolin-4(1H)-one derivatives were synthesized and evaluated to show high anti-MERS-CoV inhibitory activities. Among them, 6,8-difluoro-3-isobutyryl-2-((2,3,4-trifluorophenyl)amino)quinolin-4(1H)-one (6u) exhibits high inhibitory effect (IC50 = 86 nM) and low toxicity (CC50 > 25 μM). Moreover, it shows good metabolic stability, low hERG binding affinity, no cytotoxicity, and good in vivo PK properties.


4 The Public Health Response to HIV/AIDS: What Have We Learned?


title: Cloning and further sequence analysis of the spike gene of attenuated porcine epidemic diarrhea virus DR13

text: The spike (S) gene of the attenuated porcine epidemic diarrhea virus (PEDV) DR13 was cloned and sequenced to further explore the functions of wild type PEDV and attenuated PEDV. Sequencing revealed a single large ORF of 4,149 nucleotides encoding a protein of 1,382 amino acids with predicted M (r) of 151 kDa. The coding region of the S gene of attenuated PEDV DR13 had 20 nucleotide changes that appeared to be significant determinants of function in that they produced changes in its predicted amino acid sequence. Notably, attenuated PEDV DR13 has previously been found to exhibit reduced pathogenicity in pigs. The regions containing these 20 nucleotide changes may therefore be crucial for PEDV pathogenicity. The attenuated PEDV DR13 S protein contains 28 Asn-Xaa-Ser/Thr sequons, 21 asparagines that are predicted to be N-glycosylated and a stretch of highly hydrophobic residues at positions 1,327–1,347, which is predicted to form an α-helix and to function as a membrane anchor. One (from N to K at 378) of the changes in the deduced amino acid sequence destroyed N-linked glycosylation sites, while another change (from N to S at 114) created a new one at a different location. These alterations in N-linked glycosylation sites reflected 3 nucleotide changes, which were related to the above-mentioned nucleotide changes and are suggested to influence the pathogenicity of attenuated PEDV DR13. Attenuated PEDV DR13 has 96.5, 96.4, 96.1, 93.9, 93.5 and 96.6% DNA sequence identities with CV777, Br1/87, JS-2004-2, Spk1, Chinju99 and parent DR13, respectively. Likewise, it shares 95.7, 95.4, 95.6, 92.0, 91.6 and 95.7% identity with those genes at the deduced amino acid sequence level. Phylogenetic analysis suggested that attenuated PEDV DR13 is closely related to CV777, Br1/87, JS-2004-2 and parent DR13, rather than to Spk1 and Chinju99 and is especially close to the Chinese PEDV strain JS-2004-2.


title: Cost-efficiency analysis of voluntary vaccination against n-serovar diseases using antibody-dependent enhancement: a game approach

text: Records of epidemics acknowledge immunological multi-serotype illnesses as an important aspect of the occurrence and control of contagious diseases. These patterns occur due to antibody-dependent-enhancement (ADE) among serotype diseases, which leads to infection of secondary infectious classes. One example of this is dengue hemorrhagic fever and dengue shock syndrome, which comprises the following four serotypes: DEN-1, DEN-2, DEN-3, and DEN-4. The evolutionary vaccination game approach is able to shed light on this long-standing issue in a bid to evaluate the success of various control programs. Although immunization is regarded as one of the most accepted approaches for minimizing the risk of infection, cost and efficiency are important factors that must also be considered. To analyze the [Formula: see text] serovar aspect alongside ADE consequence in voluntary vaccination, this study establishes a new mathematical epidemiological model that is dovetailed with evolutionary game theory, an approach through which we explored two vaccine programs: primary and secondary. Our findings illuminate that the ‘cost-efficiency’ effect for vaccination decision exhibits an impact on controlling [Formula: see text] serovar infectious diseases and should be designed in such a manner as to avoid adverse effects. Furthermore, our numerical result justifies the fact that adopting ADE significantly boosted emerging disease incidence, it also suggest that the joint vaccine policy works even better when the complex cyclical epidemic outbreak takes place among multi serotypes interactions. Research also exposes that the primary vaccine is a better controlling tool than the secondary; however, introducing a highly-efficiency secondary vaccine against secondary infection plays a key role to control the disease prevalence.


title: Détection des rotavirus humains dans les selles : Comparaison de cinq techniques

text: Summary The authors have tested 118 stools by five techniques used for the detection of rotaviruses in human faeces : electron microscopy, latex agglutination (Slidex Rota-kit : BioMérieux ; Rotalex : Orion Diagnostica) and ELISA (Enzygnost : Behring ; Bio-Enza-Bead : Bionetics). Reproducibility and specificity for all techniques were satisfactory. Comparison of the methods showed Enzygnost to be the most sensitive (89 %), followed by the two agglutination tests, then electron microscopy and least sensitive the Bio-Enza-Bead (56 %). For large — scale screening of faeces, it appeared that the latex agglutination test were preferable for reasons of simplicity, speed and cost.


title: Rapid manipulation of the porcine epidemic diarrhea virus genome by CRISPR/Cas9 technology

text: Abstract Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic enteric coronavirus causing lethal watery diarrhea in suckling piglets. Reverse genetics is a valuable tool to study the functions of viral genes and to generate vaccine candidates. In this study, a full-length infectious cDNA clone of the highly virulent PEDV strain AJ1102 was assembled in a bacterial artificial chromosome (BAC). The rescued virus (rAJ1102) exhibited similar proliferation characteristics in vitro to the wildtype AJ1102. Using CRISPR/Cas9 technology, a recombinant virus rAJ1102-ΔORF3-EGFP in which the ORF3 gene was replaced with an EGFP gene, was successfully generated, and its proliferation characteristics were compared with the parental rAJ1102. Importantly, it just took one week to construct the recombinant PEDV rAJ1102-ΔORF3-EGFP using this method, providing a more efficient platform for PEDV genome manipulation, which could also be applied to other RNA viruses.


title: B-04 Place de la fièvre Q dans les pneumopathies aiguës en Guyane française

text: Introduction et objectifs La fièvre Q aiguë se manifeste dans près de 90 % des cas par un tableau de pneumopathie en Guyane. Régulièrement, surviennent des cas groupés de pneumopathies à fièvre Q avec notamment des formes compliquées de détresse respiratoire. Afin de tenir compte de Coxiella burnetti, l’antibiothérapie de première intention de pneumonie aiguë associe l’amoxicilline à la doxycycline. Si cette attitude thérapeutique est justifiée par la gravité des formes cliniques observées, on ne sait pas en revanche, la fréquence de la fièvre Q parmi les pneumopathies prises en charge. Notre objectif principal était d’estimer la proportion de pneumopathies à Coxiella burnetti parmi les pneumopathies prises en charge et secondairement, de comparer leurs caractéristiques clinico-biologiques à celles des autres patients. Matériels et méthodes Étude rétrospective des données clinico-biologiques et radiologiques des pneumonies aiguës suivies du 01/05/2004 au 30/09/2007 dans l’unité des maladies infectieuses du CH de Cayenne. Résultats La fièvre Q a représenté 24 % des 139 pneumonies aiguës avec une prépondérance du sexe masculin. En cas de pneumonie à fièvre Q, la toux était volontiers plus sèche et les céphalées plus présentes. Au stade précoce, les paraméters biologiques ne permettaient pas d’orienter envers une fièvre Q. La durée médiane d’hospitalisation (4 jours) ainsi que l’âge médian (47 ans) des patients n’étaient pas différents en cas de coxiellose. Conclusion Coxiella burnetti a été responsable d’un quart des pneumonies aiguës prises en charge dans notre unité. Au stade précoce, peu de paramètres clinicobiologiques et radiologiques orientaient en sa faveur. En attendant des études pronostiques discriminantes, l’antibiothérapie probabiliste des pneumonies aiguës en Guyane doit tenir compte de Coxiella burnetti.


title: Dynamic Analysis of a Mathematical Model with Health Care Capacity for Pandemic COVID-19

text: The fact that no there exists yet an absolute treatment or vaccine for COVID-19, which was declared as a pandemic by the World Health Organization (WHO) in 2020, makes very important spread out over time of the epidemic in order to burden less on hospitals and prevent collapsing of the health care system. This case is a consequence of limited resources and is valid for all countries in the world facing with this serious threat. Slowing the speed of spread will probably make that the outbreak last longer, but it will cause lower total death count. In this study, a new SEIR epidemic model formed by taking into account the impact of health care capacity has been examined and local and global stability of the model has been analyzed. In addition, the model has been also supported by some numerical simulations.


title: Changing the use of HIV pre-exposure prophylaxis among men who have sex with men during the COVID-19 pandemic in Melbourne, Australia

text: We surveyed 204 MSM who were PrEP users. One in four daily PrEP users stopped taking PrEP during the COVID-19 pandemic and 5% switched to on-demand PrEP. Most men reduced PrEP use because they stopped having casual sex and reduced the number of casual partners during the COVID-19 pandemic.


title: Building, Hosting and Recruiting: A Brief Introduction to Running Behavioral Experiments Online

text: Researchers have ample reasons to take their experimental studies out of the lab and into the online wilderness. For some, it is out of necessity, due to an unforeseen laboratory closure or difficulties in recruiting on-site participants. Others want to benefit from the large and diverse online population. However, the transition from in-lab to online data acquisition is not trivial and might seem overwhelming at first. To facilitate this transition, we present an overview of actively maintained solutions for the critical components of successful online data acquisition: creating, hosting and recruiting. Our aim is to provide a brief introductory resource and discuss important considerations for researchers who are taking their first steps towards online experimentation.


title: Integration of patient-reported outcomes in multiregional confirmatory clinical trials

text: Abstract Introduction The increasing complexities of conducting multiregional trials and an evolving regulatory environment contribute to unprecedented new challenges for use of patient-reported outcome measures (PROMs) 1 1 Patient-reported outcome measures. within clinical trials. This paper presents these challenges and potential solutions. Methods Real-world examples and situations are reviewed from an industry and patient-reported outcome (PRO) 2 2 Patient-reported outcome. expert position. Conclusions An increase in the pursuit of new therapeutic targets, changes to the regulatory environment, and business pressures to expand clinical trials to more countries have significantly increased the complexity of confirmatory clinical studies that incorporate PROMs. Decisions to participate in collaborative efforts for endpoint development or proceed independently are made in the context of competing priorities of drug development timelines, drug differentiation strategies, the need for patient-related value messages, and the depth of a sponsor pipeline within specific disease areas. Study logistics are critically important; factors such as concept cultural relevancy, respondent literacy level, and quality of cross-cultural adaptation of PROMs must be evaluated when integrating into confirmatory clinical trials. Awareness of the issues relating to PROs in multiregional studies will enable companies to better plan studies and interpret results.


title: Detection of antibody-secreting cells specific for the cytomegalovirus and herpes simplex virus surface antigens

text: Abstract Infections with the herpes simplex virus (HSV) and the human cytomegalovirus (HCMV) can lead to life-threatening diseases, particularly in immunosuppressed patients. Furthermore, HSV infections at birth (herpes neonatorum) can result in a disseminated disease associated with a fatal multiorgan failure. Congenital HCMV infections can result in miscarriage, serious birth defects or developmental disabilities. Antibody-based interventions with hyperimmunoglobulins showed encouraging results in clinical studies, but clearly need to be improved. The isolation of highly neutralizing monoclonal antibodies is a promising strategy to establish potent therapy options against HSV and HCMV infections. Monoclonal antibodies are commonly isolated from hybridomas or EBV-immortalized B-cell clones. The screening procedure to identify virus-specific cells from a cell mixture is a challenging step, since most of the highly neutralizing antibodies target complex conformational epitopes on the virus surface. Conventional assays such as ELISA are based on purified viral proteins and inappropriate to display complex epitopes. To overcome this obstacle, we have established two full-virus based methods that allow screening for cells and antibodies targeting complex conformational epitopes on viral surface antigens. The methods are suitable to detect surface antigen-specific cells from a cell mixture and may facilitate the isolation of highly neutralizing antibodies against HSV and HCMV.


title: Activity of a purified His-tagged 3C-like proteinase from the coronavirus infectious bronchitis virus

text: Abstract Previous studies in vitro of the processing of cloned polyprotein fragments from the coronavirus infectious bronchitis virus (IBV) large open reading frame (ORF1), confirmed the activity of a predicted 3C-like proteinase (3CLP) domain and suggested that the proteinase is released autocatalytically from the polyprotein in the form of a 35 kDa protein, 3CLpro, capable of further cleavages in trans. In order to identify such cleavages within the ORF1 polyprotein mediated by 3CLpro, the proteinase was expressed in bacteria, purified and used in trans cleavage assays with polyprotein fragments lacking the 3CLP domain as targets. The proteinase was expressed as a polyprotein fragment which was able to process during expression in bacterial cells, releasing mature 3CLpro. A histidine (His6) tag was introduced close to the C-terminus of the proteinase to aid purification. Processing demonstrated by the tagged proteinase was indistinguishable from that of the wild-type enzyme indicating that the site chosen for the tag was permissive. From these studies we were able to demonstrate trans cleavages consistent with the use of most of the previously predicted or identified sites within the open reading frame of gene 1. This tentatively completes the processing map for the ORF1 region with respect to 3CLpro.


title: Respiratory viral infections in patients with chronic, obstructive pulmonary disease

text: Summary Objectives The purpose of the present study was to apply reverse transcription-PCR (RT-PCR) assays to clinical specimens collected from patients with acute respiratory illness and chronic obstructive pulmonary disease (COPD). Methods One hundred and ninety-four samples from two different study cohorts were analysed using RT-PCR assays for picornaviruses, coronaviruses 229E and OC43, influenza A and B viruses, respiratory syncytial virus, parainfluenza types 1–3 viruses, and human metapneumovirus and a PCR assay for adenoviruses. The results were added to results obtained previously using cell culture and serologic methods. Results RT-PCR assays identified an additional 35 respiratory virus-associated illnesses not identified previously by cell culture or serology (n=46). Picornaviruses and coronaviruses were the most common viral infections identified only by RT-PCR. Overall, 41.8% of the acute respiratory illnesses evaluated were associated with a respiratory virus infection, with picornaviruses, coronaviruses and influenza viruses being the most common infections recognized. No human metapneumovirus infections were identified by RT-PCR assay. Conclusions Respiratory viral infections are commonly associated with acute respiratory illness in COPD patients, and the use of RT-PCR assays significantly increases the ability to diagnose these infections.


title: The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak

text: The role of asymptomatic carriers in transmission poses challenges for control of the COVID-19 pandemic. Study of asymptomatic transmission and implications for surveillance and disease burden are ongoing, but there has been little study of the implications of asymptomatic transmission on dynamics of disease. We use a mathematical framework to evaluate expected effects of asymptomatic transmission on the basic reproduction number [Formula: see text] (i.e., the expected number of secondary cases generated by an average primary case in a fully susceptible population) and the fraction of new secondary cases attributable to asymptomatic individuals. If the generation-interval distribution of asymptomatic transmission differs from that of symptomatic transmission, then estimates of the basic reproduction number which do not explicitly account for asymptomatic cases may be systematically biased. Specifically, if asymptomatic cases have a shorter generation interval than symptomatic cases, [Formula: see text] will be over-estimated, and if they have a longer generation interval, [Formula: see text] will be under-estimated. Estimates of the realized proportion of asymptomatic transmission during the exponential phase also depend on asymptomatic generation intervals. Our analysis shows that understanding the temporal course of asymptomatic transmission can be important for assessing the importance of this route of transmission, and for disease dynamics. This provides an additional motivation for investigating both the importance and relative duration of asymptomatic transmission.


title: Discovery and Development of Antiviral Drugs for Biodefense: Experience of a Small Biotechnology Company

text: The unmet need for effective antivirals against potential agents of bioterrorism and emerging infections is obvious; however, the challenges to developing such drugs are daunting. Even with the passage of Project BioShield and more recently the BARDA legislation, there is still not a clear market for these types of drugs and limited federal funding available to support expensive drug development studies. SIGA Technologies, Inc. is a small biotech company committed to developing novel products for the prevention and treatment of severe infectious diseases, with an emphasis on products for diseases that could result from bioterrorism. Through trials and error SIGA has developed an approach to this problem in order to establish the infrastructure necessary to successfully advance new antiviral drugs from the discovery stage on through to licensure. The approach that we have taken to drug development is biology driven and dependent on a dispersive development model utilizing essential collaborations with academic, federal, and private sector partners. This consortium approach requires success in acquiring grants and contracts as well as iterative communication with the government and regulatory agencies. However, it can work as evidenced by the rapid progress of our lead antiviral against smallpox, ST-246, and should serve as the template for development of new antivirals against important biological pathogens.


title: Antiviral B cell and T cell immunity in the lungs

text: Respiratory viruses are frequent causes of repeated common colds, bronchitis and pneumonia, which often occur unpredictably as epidemics and pandemics. Despite those decimating effects on health and decades of intensive research, treatments remain largely supportive. The only commonly available vaccines are against influenza virus, and even these need improvement. The lung shares some features with other mucosal sites, but preservation of its especially delicate anatomical structures necessitates a fine balance of pro- and anti-inflammatory responses; well-timed, appropriately placed and tightly regulated T cell and B cell responses are essential for protection from infection and limitation of symptoms, whereas poorly regulated inflammation contributes to tissue damage and disease. Recent advances in understanding adaptive immunity should facilitate vaccine development and reduce the global effect of respiratory viruses.


title: Common Properties of Fusion Peptides from Diverse Systems

text: Although membrane fusion occurs ubiquitously and continuously in alleukaroytic cells, little is known about the mechanism that governs lipidbilayer fusion associated with any intracellular fusion reactions. Recentstudies of the fusion of enveloped viruses with host cell membranes havehelped to define the fusion process. The identification and characterizationof key proteins involved in fusion reactions have mainly driven recent advancesin our understanding of membrane fusion. The most important denominator amongthe fusion proteins is the fusion peptide. In this review, work done in thelast few years on the molecular mechanism of viral membrane fusion will behighlighted, focusing in particular on the role of the fusion peptide and themodification of the lipid bilayer structure. Much of what is known regardingthe molecular mechanism of viral membrane fusion has been gained using liposomesas model systems in which the molecular components of the membrane and the environmentare strictly controlled. Many amphilphilic peptides have a high affinity forlipid bilayers, but only a few sequences are able to induce membrane fusion. Thepresence of α-helical structure in at least part of the fusion peptideis strongly correlated with activity whereas, β-structure tends to beless prevalent, associated with non-native experimental conditions, and morerelated to vesicle aggregation than fusion. The specific angle of insertionof the peptides into the membrane plane is also found to be an importantcharacteristic for the fusion process. A shallow penetration, extending onlyto the central aliphatic core region, is likely responsible for the destabilization ofthe lipids required for coalescence of the apposing membranes and fusion.


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title: Regulation in markets facing uncertainty: The case of Australia

text: Abstract This paper explores the ways in which economic regulation accommodates uncertainty through an examination of experience of regulation in Australia against a background discussion of literature on regulatory risk and principles for good regulation. Regulation, typically in the form of incentive based price caps, often applies to aviation infrastructure, such as major airports and air navigation services. At the same time, the demand for aviation infrastructure services is uncertain and subject to external shocks. Two case studies in economic regulation of aviation infrastructure are examined. They cover a period of volatile demand associated with the collapse of a major domestic airline which coincided with the September 11 terrorist attacks in the US. One case study involves the application of price caps to newly privatized airports during 1997–2002. The other case study examines the development of a long term price path for air navigation services over 2002 to 2004. The case studies illustrate the important role played by regulatory design. The paper concludes that the design of the regulatory framework has an important role in ameliorating the risks associated with uncertainty.


title: Remaining hopeful

text: Jane Goodall has tirelessly fought for a better world for humans and wildlife, and with covid-19 she says there are reasons to stay positive, finds Donna Lu


title: Lockdown contained the spread of 2019 novel coronavirus disease in Huangshi city, China: Early epidemiological findings

text: BACKGROUND: To control the spread of 2019 novel coronavirus disease (COVID-19), China sealed Wuhan on Jan 23, 2020 and soon expanded lockdown to other twelve cities in Hubei province. We aimed to describe the epidemiological characteristics in one of the cities and highlight the effect of current implemented lockdown and nonpharmaceutical interventions. METHODS: We retrieved data of reported cases in Huangshi and Wuhan from publicly available disease databases. Local epidemiological data on suspected or confirmed cases in Huangshi were collected through field investigation. Epidemic curves were constructed with data on reported and observed cases. RESULTS: The accumulated confirmed COVID-19 cases and fatality in Huangshi were reported to be 1015 and 3.74% respectively, compared with 50006 and 5.08% in Wuhan till Mar 27, 2020. Right after Jan 24, the epidemic curve based on observed cases in Huangshi became flattened. Feb 1, 2020 was identified as the “turning point” as the epidemic in Huangshi faded soon afterwards. COVID-19 epidemic was characterized by mild cases in Huangshi, accounting for 82.66% of total cases. Moreover, 50 asymptomatic infections were identified in adults and children. Besides, we found confirmed cases in 19 familial clusters and 21 health care workers, supporting inter-human transmission. CONCLUSIONS: Our study reported the temporal dynamics and characteristics of the COVID-19 epidemic in Huangshi city, China, across the unprecedented intervention. Such new epidemiological inference might provide further guidance on current lockdown measures in high-risk cities and, subsequently, help improve public health intervention strategies against the pandemic on the country and global levels.


title: Chest CT of COVID-19 in patients with a negative first RT-PCR test: Comparison with patients with a positive first RT-PCR test

text: To compare clinical and imaging features between patients with an initial negative reverse-transcription-polymerase chain-reaction (RT-PCR) test and patients with an initial positive RT-PCR test. CT follow-up analysis in the negative RT-PCR group is also described. Thirty-three patients with SARS-CoV-2 infection confirmed by RT-PCR, with 216 lesions upon CT, were included. Demographic information and chest CT imaging features were collected. The average age in the whole study group was 46.9 ± 11.1 years, with 18 males and 15 females. Patients in the positive RT-PCR test group were more likely to have a fever than patients in the negative RT-PCR test group (85.7% vs 50%, P < .05). Lesions in the positive group were more likely to be located in the peripheral area than lesions in the negative group (83.6% vs 68.2%, P < .05). Regarding the appearance of 216 lesions, ground-glass opacities (GGOs) with consolidation (43.2%) was the most common appearance in the negative group, followed by pure GGOs (31.8%), while in the positive group, pure GGOs (32%) and GGOs with interlobular septal thickening (32.8%) were both most frequent, and the difference between them was evident (P < .05). For the follow-up analysis, the largest short-axis of a lesion was smaller upon follow-up (median size 13.6 mm vs 14 mm), albeit by a smaller margin. Pure GGOs decreased in frequency, from 31.3% to 21.3%, while consolidation increased in frequency, from 7.5% to 12.5%. The manifestations of COVID-19 in patients with a first negative RT-PCR test and patients with a positive first RT-PCR test are different to some extent. The consolidation component may increase after follow-up.


docid: govbbdlp

title: Standing your Ground to Exoribonucleases: Function of Flavivirus Long Non-coding RNAs

text: Members of the Flaviviridae (e.g. Dengue virus, West Nile virus, and Hepatitis C virus) contain a positive-sense RNA genome that encodes a large polyprotein. It is now also clear most if not all of these viruses also produce an abundant subgenomic long non-coding RNA. These non-coding RNAs, which are called subgenomicflavivirus RNAs (sfRNAs) or Xrn1-resistant RNAs (xrRNAs), are stable decay intermediates generated from the viral genomic RNA through the stalling of the cellular exoribonuclease Xrn1 at highly structured regions. Several functions of these flavivirus long non-coding RNAs have been revealed in recent years. The generation of these sfRNAs/xrRNAs from viral transcripts results in the repression of Xrn1 and the dysregulation of cellular mRNA stability. The abundant sfRNAs also serve directly as a decoy for important cellular protein regulators of the interferon and RNA interference antiviral pathways. Thus the generation of long non-coding RNAs from flaviviruses, hepaciviruses and pestiviruses likely disrupts aspects of innate immunity and may directly contribute to viral replication, cytopathology and pathogenesis.


title: Porcine deltacoronavirus nsp15 antagonizes interferon-β production independently of its endoribonuclease activity

text: Abstract Porcine deltacoronavirus (PDCoV) is an emerging swine coronavirus causing diarrhea and intestinal damage in nursing piglets. Previous work showed that PDCoV infection inhibits type I interferon (IFN) production. To further identify and characterize the PDCoV-encoded IFN antagonists will broaden our understanding of its pathogenesis. Nonstructural protein 15 (nsp15) encodes an endoribonuclease that is highly conserved among vertebrate nidoviruses (coronaviruses and arteriviruses) and plays a critical role in viral replication and transcription. Here, we found that PDCoV nsp15 significantly inhibits Sendai virus (SEV)-induced IFN-β production. PDCoV nsp15 disrupts the phosphorylation and nuclear translocation of NF-κB p65 subunit, but not antagonizes the activation of transcription factor IRF3. Interestingly, site-directed mutagenesis found that PDCoV nsp15 mutants (H129A, H234A, K269A) lacking endoribonuclease activity also suppress SEV-induced IFN-β production and NF-κB activation, suggesting that the endoribonuclease activity is not required for its ability to antagonize IFN-β production. Taken together, our results demonstrate that PDCoV nsp15 is an IFN antagonist and it inhibits interferon-β production via an endoribonuclease activity-independent mechanism.


docid: meevymhb

title: A novel porcine reproductive and respiratory syndrome virus vector system that stably expresses enhanced green fluorescent protein as a separate transcription unit

text: Here we report the rescue of a recombinant porcine reproductive and respiratory syndrome virus (PRRSV) carrying an enhanced green fluorescent protein (EGFP) reporter gene as a separate transcription unit. A copy of the transcription regulatory sequence for ORF6 (TRS6) was inserted between the N protein and 3′-UTR to drive the transcription of the EGFP gene and yield a general purpose expression vector. Successful recovery of PRRSV was obtained using an RNA polymerase II promoter to drive transcription of the full-length virus genome, which was assembled in a bacterial artificial chromosome (BAC). The recombinant virus showed growth replication characteristics similar to those of the wild-type virus in the infected cells. In addition, the recombinant virus stably expressed EGFP for at least 10 passages. EGFP expression was detected at approximately 10 h post infection by live-cell imaging to follow the virus spread in real time and the infection of neighbouring cells occurred predominantly through cell-to-cell-contact. Finally, the recombinant virus generated was found to be an excellent tool for neutralising antibodies and antiviral compound screening. The newly established reverse genetics system for PRRSV could be a useful tool not only to monitor virus spread and screen for neutralising antibodies and antiviral compounds, but also for fundamental research on the biology of the virus.


docid: bfrozfvg

title: Stable Benzotriazole Esters as Mechanism-Based Inactivators of the Severe Acute Respiratory Syndrome 3CL Protease

text: Severe acute respiratory syndrome (SARS) is caused by a newly emerged coronavirus that infected more than 8000 individuals and resulted in more than 800 fatalities in 2003. Currently, there is no effective treatment for this epidemic. SARS-3CL(pro) has been shown to be essential for replication and is thus a target for drug discovery. Here, a class of stable benzotriazole esters was reported as mechanism-based inactivators of 3CL(pro), and the most potent inactivator exhibited a k(inact) of 0.0011 s(−1) and a K(i) of 7.5 nM. Mechanistic investigation with kinetic and mass spectrometry analyses indicates that the active site Cys145 is acylated, and that no irreversible inactivation was observed with the use of the C145A mutant. In addition, a noncovalent, competitive inhibition became apparent by using benzotriazole ester surrogates in which the bridged ester-oxygen group is replaced with carbon.


title: Introduction to wastewater microbiology: special emphasis on hospital wastewater

text: The important role of proper sanitation in maintaining good public health has been confirmed in the past years. Wastewater treatment plants (WWTPs) serve as efficient processes in removing pathogens, organic pollutants, nutrients, and pharmaceuticals from wastewaters. However, the advance systems of treatment that we use today are the result of a series of inventions that have been performed since 19th century. This chapter explains the evolution of the wastewater origin and the treatment processes along with the developments in microbiology and pathology that led to the present-day scenario of research and advance facilities. Pharmaceuticals can easily enter the environment due to their incomplete degradation in the treatment processes and because of their adverse effects on organisms and environment they are becoming a matter of great concern. A brief discussion on the presence of pharmaceutical compounds in different environment sectors such as wastewater, WWTPs, and the natural aquatic environment has been provided.


What is the Role of Angiotensin Converting Enzyme 2 (ACE2) in COVID-19 Infection in Hypertensive, Diabetic Patients?


title: Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay

text: Abstract A method was developed for the quantitation of respiratory syncytial virus (RSV) based on real-time RT-PCR using a LightCycler instrument. A control real-time RT-PCR was undertaken on GAPDH mRNA (a human housekeeping gene) was carried out to standardise the non-homogeneous respiratory samples. The real-time RT-PCR method was one log more sensitive for the detection of RSV according to the endpoint dilution technique than the culture method or a conventional qualitative RT-PCR-hybridization-EIA. No cross-reactivity was observed with any of the viruses that could be found in the respiratory tract. RSV and GAPDH were quantified in nasal aspirates from 75 children hospitalised for acute respiratory tract disease: 31 (41.3%) were positive according to the immunofluorescence assay (IFA), 34 (45.3%) were culture-positive and 42 (56%) were positive according to our real-time RT-PCR method. The sensitivity, specificity, positive and negative predictive values of the real-time RT-PCR were 100, 90, 92, 100%, respectively. The samples found to be positive for RSV were classified according to the severity of the disease. The mean number of RSV RNA copies was higher in the severe disease group than in the non-severe group 4.05×107 vs 9.1×106 (P=0.055). However, the mean ratio of RSV RNA copies to GAPDH mRNA copies was 42.8 in the severe group, and 22.2 in non-severe group (P=NS).


title: LC3 conjugation system in mammalian autophagy

text: Abstract Autophagy is the bulk degradation of proteins and organelles, a process essential for cellular maintenance, cell viability, differentiation and development in mammals. Autophagy has significant associations with neurodegenerative diseases, cardiomyopathies, cancer, programmed cell death, and bacterial and viral infections. During autophagy, a cup-shaped structure, the preautophagosome, engulfs cytosolic components, including organelles, and closes, forming an autophagosome, which subsequently fuses with a lysosome, leading to the proteolytic degradation of internal components of the autophagosome by lysosomal lytic enzymes. During the formation of mammalian autophagosomes, two ubiquitylation-like modifications are required, Atg12-conjugation and LC3-modification. LC3 is an autophagosomal ortholog of yeast Atg8. A lipidated form of LC3, LC3-II, has been shown to be an autophagosomal marker in mammals, and has been used to study autophagy in neurodegenerative and neuromuscular diseases, tumorigenesis, and bacterial and viral infections. The other Atg8 homologues, GABARAP and GATE-16, are also modified by the same mechanism. In non-starved rats, the tissue distribution of LC3-II differs from those of the lipidated forms of GABARAP and GATE-16, GABARAP-II and GATE-16-II, suggesting that there is a functional divergence among these three modified proteins. Delipidation of LC3-II and GABARAP-II is mediated by hAtg4B. We review the molecular mechanism of LC3-modification, the crosstalk between LC3-modification and mammalian Atg12-conjugation, and the cycle of LC3-lipidation and delipidation mediated by hAtg4B, as well as recent findings concerning the other two Atg8 homologues, GABARAP and GATE-16. We also highlight recent findings regarding the pathobiology of LC3-modification, including its role in microbial infection, cancer and neuromuscular diseases.


title: Characterization of a variant virus isolated from neural cell culture after infection of mouse coronavirus JHMV

text: Abstract Our previous experiments showed that a variant virus with a larger envelope glycoprotein encoded by a larger mRNA3 (cl-2) multiplied predominantly in the brain of rats after wild type (wt) JHMV infection (F. Taguchi, S. Siddell, H. Wege, and V. ter Meulen, 1985, J. Virol., 54, 429–435). We could isolate similar but not identical variant virus after infection of cultured neural cells from rat brain with wt JHMV (designated CNS virus), which also had a larger mRNA3 and produced larger envelope E2 glycoprotein in infected cells. CNS virus multiplied to a higher degree in cultured astrocytes from rat than wt JHMV and cl-2. During infection with these variant viruses in neural cells, virus populations generated did not change, in contrast to consistent selection of viruses with larger mRNA3 after wt JHMV infections. CNS virus produced abundant mRNA2a as well as 65K glycoprotein while the productions of both were trace in cl-2 infected cells. The present experiments, together with our previous observation, suggest that the larger E2 glycoprotein may be of importance for the replication in rat brain cells.


title: Evidence of genetic diversity generated by recombination among avian coronavirus IBV

text: Previously, we demonstrated that the DE072 strain of IBV is a recombinant which has an IBV strain D1466-like sequence in the S gene. Herein, we analyzed the remaining 3.8 kb 3′ end of the genome, which includes Gene 3, Gene 4, Gene 5, Gene 6, and the 3′ non-coding region of the DE072 and D1466 strains. Those two viruses had high nucleotide similarity in Gene 4. However, the other individual genes had a much different level of sequence similarity with the same gene of the other IBV strains. The genome of five IBV strains, of which the complete sequence of the 3′ end of the genome has been determined, were divided at an intergenic (IG) consensus sequence (CTGAACAA or CTTAACAA) and compared phylogenetically. Phylogenetic trees of different topology indicated that the consensus IG sequences and the highly conserved sequence around this regions may serve as recombination ‘hot spots’. Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Presumably this occurs because the consensus IG sequence serves as the template switching site for the viral encoded polymerase.


title: Predicting the angiotensin converting enzyme 2 (ACE2) utilizing capability as the receptor of SARS-CoV-2

text: Abstract SARS-CoV-2, the newly identified human coronavirus causing severe pneumonia pandemic, was probably originated from Chinese horseshoe bats. However, direct transmission of the virus from bats to humans is unlikely due to lack of direct contact, implying the existence of unknown intermediate hosts. Angiotensin converting enzyme 2 (ACE2) is the receptor of SARS-CoV-2, but only ACE2s of certain species can be utilized by SARS-CoV-2. Here, we evaluated and ranked the receptor-utilizing capability of ACE2s from various species by phylogenetic clustering and sequence alignment with the currently known ACE2s utilized by SARS-CoV-2. As a result, we predicted that SARS-CoV-2 tends to utilize ACE2s of various mammals, except murines, and some birds, such as pigeon. This prediction may help to screen the intermediate hosts of SARS-CoV-2.


title: Chapter 11 m-Health in Public Health Practice A Constellation of Current Evidence

text: Abstract Beyond the earlier skepticism that greeted its usefulness and applicability in public health practice, m-Health has continued to gain significant support and acceptability among public health practitioners in terms of the ease with which its features and reach have been harnessed to address global disease prevention and health promotion objectives. Research evidence over the past few decades suggest the positive effect of adopting m-Health in improving knowledge dissemination, creating and sustaining motivation for positive health behavior changes or practices, and empowering individuals, communities and populations to take greater responsibility for their health. This chapter examines historical and current literature evidence of m-Health application in public health practice, its impact on global population health and future prospects.


title: Lonicera japonica Thunb.: Ethnopharmacology, phytochemistry and pharmacology of an important traditional Chinese medicine

text: Abstract Ethnopharmacological relevance Lonicera japonica Thunb. (Caprifoliaceae), a widely used traditional Chinese medicine, was known as Jin Yin Hua (Chinese: ), Ren Dong and Japanese honeysuckle. It was taken to treat the exopathogenic wind-heat, epidemic febrile diseases, sores, carbuncles and some infectious diseases. At the same time, Lonicera japonica could be used as healthy food, cosmetics, ornamental groundcover, and so on. Aim of the review The present paper reviewed the ethnopharmacology, the biological activities, toxicology and phytochemistry of Lonicera japonica. Materials and methods Information on Lonicera japonica was gathered via the Internet (using Google Scholar, Baidu Scholar, Elsevier, ACS, Medline Plus, CNKI and Web of Science) and libraries. Additionally, information also was obtained from some local books and brilliant scholars on ethnopharmacology. Results More than 140 chemical compounds have been isolated, and the main compositions are essential oils, organic acids and flavones, etc. Lonicera japonica and its active principles possess wide pharmacological actions, such as anti-inflammatory, antibacterial, antiviral, antioxidative and hepatoprotective activities. Conclusions As an important traditional Chinese medicine, further studies on Lonicera japonica can lead to the development of new drugs and therapeutics for various diseases, and how to utilize it better should be paid more attentions.


Primary Characterization of SARS Coronavirus Strain Frankfurt 1


title: Ultrasound in managing extrapulmonary tuberculosis: a randomized controlled two-center study

text: BACKGROUND: Patients with clinically suspected tuberculosis are often treated empirically, as diagnosis - especially of extrapulmonary tuberculosis - remains challenging. This leads to an overtreatment of tuberculosis and to underdiagnosis of possible differential diagnoses. METHODS: This open-label, parallel-group, superiority randomized controlled trial is done in a rural and an urban center in Tanzania. HIV-positive and -negative adults (≥18 years) with clinically suspected extrapulmonary tuberculosis are randomized in a 1:1 ratio to an intervention- or control group, stratified by center and HIV status. The intervention consists of a management algorithm including extended focused assessment of sonography for HIV and tuberculosis (eFASH) in combination with chest X-ray and microbiological tests. Treatment with anti-tuberculosis drugs is started, if eFASH is positive, chest X-ray suggests tuberculosis, or a microbiological result is positive for tuberculosis. Patients in the control group are managed according national guidelines. Treatment is started if microbiology is positive or empirically according to the treating physician. The primary outcome is the proportion of correctly managed patients at 6 months (i.e patients who were treated with anti-tuberculosis treatment and had definite or probable tuberculosis, and patients who were not treated with anti-tuberculosis treatment and did not have tuberculosis). Secondary outcomes are the proportion of symptom-free patients at two and 6 months, and time to death. The sample size is 650 patients. DISCUSSION: This study will determine, whether ultrasound in combination with other tests can increase the proportion of correctly managed patients with clinically suspected extrapulmonary tuberculosis, thus reducing overtreatment with anti-tuberculosis drugs. TRIAL REGISTRATION: PACTR, Registration number: PACTR201712002829221, registered December 1st 2017.


title: Molecular and Serological Tests for COVID-19. A Comparative Review of SARS-CoV-2 Coronavirus Laboratory and Point-of-Care Diagnostics

text: Validated and accurate laboratory testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a crucial part of the timely management of Coronavirus Disease 2019 (COVID-19) disease, supporting the clinical decision-making process for infection control at the healthcare level and detecting asymptomatic cases. This would facilitate an appropriate treatment, a prompt isolation and consequently deceleration of the pandemic. Various laboratory tests can identify the genetic material of SARS-CoV-2 that causes COVID-19 in specimens, or specific anti-viral antibodies in blood/serum. Due to the current pandemic situation, a development of point-of-care diagnostics (POCD) allows us to substantially accelerate taking clinical decisions and implement strategic planning at the national level of preventative measures. This review summarizes and compares the available POCD and those currently under development, including quantitative reverse transcription PCR (RT-qPCR), serology immunoassays (SIAs) and protein microarray method (PMM) designed for standard and rapid COVID-19 diagnosis.


title: Antiviral activity of four types of bioflavonoid against dengue virus type-2

text: BACKGROUND: Dengue is a major mosquito-borne disease currently with no effective antiviral or vaccine available. Effort to find antivirals for it has focused on bioflavonoids, a plant-derived polyphenolic compounds with many potential health benefits. In the present study, antiviral activity of four types of bioflavonoid against dengue virus type -2 (DENV-2) in Vero cell was evaluated. Anti-dengue activity of these compounds was determined at different stages of DENV-2 infection and replication cycle. DENV replication was measured by Foci Forming Unit Reduction Assay (FFURA) and quantitative RT-PCR. Selectivity Index value (SI) was determined as the ratio of cytotoxic concentration 50 (CC(50)) to inhibitory concentration 50 (IC(50)) for each compound. RESULTS: The half maximal inhibitory concentration (IC(50)) of quercetin against dengue virus was 35.7 μg mL(-1 )when it was used after virus adsorption to the cells. The IC(50 )decreased to 28.9 μg mL(-1 )when the cells were treated continuously for 5 h before virus infection and up to 4 days post-infection. The SI values for quercetin were 7.07 and 8.74 μg mL(-1), respectively, the highest compared to all bioflavonoids studied. Naringin only exhibited anti-adsorption effects against DENV-2 with IC(50 )= 168.2 μg mL(-1 )and its related SI was 1.3. Daidzein showed a weak anti-dengue activity with IC(50 )= 142.6 μg mL(-1 )when the DENV-2 infected cells were treated after virus adsorption. The SI value for this compound was 1.03. Hesperetin did not exhibit any antiviral activity against DENV-2. The findings obtained from Foci Forming Unit Reduction Assay (FFURA) were corroborated by findings of the qRT-PCR assays. Quercetin and daidzein (50 μg mL(-1)) reduced DENV-2 RNA levels by 67% and 25%, respectively. There was no significant inhibition of DENV-2 RNA levels with naringin and hesperetin. CONCLUSION: Results from the study suggest that only quercetin demonstrated significant anti-DENV-2 inhibitory activities. Other bioflavonoids, including daidzein, naringin and hesperetin showed minimal to no significant inhibition of DENV-2 virus replication. These findings, together with those previously reported suggest that select group of bioflavonoids including quercetin and fisetin, exhibited significant inhibitory activities against dengue virus. This group of flavonoids, flavonol, could be investigated further to discover the common mechanisms of inhibition of dengue virus replication.


title: Prevalence and molecular epidemiology of human coronavirus HKU1 in patients with acute respiratory illness

text: In 2005, human coronavirus HKU1 (HCoV‐HKU1) was isolated and identified from a 71‐year‐old man with pneumonia in Hong Kong. To identify and classify genotypes of HCoV‐HKU1 in Korea, a sensitive, specific, and quantitative real‐time polymerase chain reaction (PCR) assay was developed and analyzed the sequences of HCoV‐HKU1 isolated in Korea. A total of 1,985 respiratory specimens taken from patients with acute respiratory illness were tested for HCoV‐HKU1 from January 2007 to May 2008. The major clinical symptoms associated with HCoV‐HKU1 infection were examined statistically and sequence variations of the RNA‐dependent RNA polymerase (RdRp), spike, and nucleocapsid genes were also analyzed. Fifty cases (2.5%) HCoV‐HKU1 were identified by real‐time PCR and viral loads ranged from 6.7 × 10(4) to 1.6 × 10(9) copies/ml. The clinical symptoms of HCoV‐HKU1 infection included rhinorrhea (72%), cough (64%), nasal congestion (56%), fever (32%), sputum (30%), sore throat (18%), chills (16%), postnasal discharge (14%), and tonsillar hypertrophy (10%). There was a seasonal distribution of HCoV‐HKU1 infection, peaking in winter and spring. Both genotypes A and B were detected but no recombination between them was found. This is the first report on the identification and genotyping of HCoV‐HKU1 as a causative agent of acute respiratory illness in Korea. The data suggest that at least two genotypes, A and B, of HCoV‐HKU1 with scattered silent mutations were circulating in Korea from 2007 to 2008. J. Med. Virol. 85:309–314, 2013. © 2012 Wiley Periodicals, Inc.


title: Small animal reproduction: Scientific facts versus dogmas or unverified beliefs

text: Small Animal Reproduction is a rather recent topic in the field of Animal Reproduction. Although some continuing educational societies aim to improve the level of general knowledge, published scientific facts are still limited, and there are many hypotheses or affirmations that remain unverified or even sometimes dogmatic or empirical. Through examples, this article reviews the main causes that may sometimes challenge a veterinary practitioner faced with a dog or a cat presenting reproductive problems. It could be difficult to orientate the diagnosis or the therapeutic approach, not knowing if what is found in the literature is a scientific proof or just an unverified affirmation. This problem may result from the fact that there are still physiological processes that remain unclear, but also that some common beliefs are based on old studies that have not been repeated or verifiedIn addition, to make it more challenging to seek for the information, there are unverifiedaffirmations,unclear nomenclature, clinical conditions which have not been standardized in the literature, clinical conditions mostly described through case reports, lack of studies on specific topics, areas of small animal reproduction that have been neglected by researchers, contradictory data or even studies that lack objectivity. The growing interest for research in Small Animal Reproduction will probably reduce the gap between unverified beliefs and scientific facts.


title: Respiratory support in patients with COVID-19 (outside ICU)

text: Abstract With first cases noted towards the end of 2019 in China, COVID19 infection was rapidly become a devastating pandemic. Even if most patients present with a mild to moderate form of the disease, the estimated prevalence of COVID19-related severe acute respiratory failure (ARF) is 15-20% and 2-12% needed intubation and mechanical ventilation. In addition to mechanical ventilation some other techniques of respiratory support could be used in some forms of COVID19 related ARF. This position paper of the Respiratory Support and Chronic Care Group of the French Society of Respiratory Diseases is intended to help respiratory clinicians involved in care of COVID19 pandemic in the rational use of non-invasive techniques such as oxygen therapy, CPAP, non-invasive ventilation and high flow oxygen therapy in managing patients outside ICU. The aims are: 1) to focus both on the place of each technique and in describing practical tips (types of devices and circuit assemblies) aimed to limit the risk of caregivers when using those techniques at high risk spreading of viral particles. 2) to propose a step-by-step strategy to manage ARF outside ICU


docid: jrqdyfbg

title: Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts

text: Abstract The porcine reproductive and respiratory syndrome virus (PRRSV) glycoprotein 4 (GP4) resembles a typical type I membrane protein in its structure but lacks a hydrophilic tail at the C-terminus, suggesting that GP4 may be a lipid-anchored membrane protein. Using the human decay-accelerating factor (DAF; CD55), a known glycosyl-phosphatidylinositol (GPI) lipid-anchored protein, chimeric constructs were made to substitute the GPI-anchor domain of DAF with the putative lipid-anchor domain of GP4, and their membrane association and lipase cleavage were determined in cells. The DAF-GP4 fusion protein was transported to the plasma membrane and was cleaved by phosphatidylinositol-specific phospholipase C (PI-PLC), indicating that the C-terminal domain of GP4 functions as a GPI anchor. Mutational studies for residues adjacent to the GPI modification site and characterization of respective mutant viruses generated from infectious cDNA clones show that the ability of GP4 for membrane association corresponded to virus viability and growth characteristics. The residues T158 (ω−2, where ω is the GPI moiety at E160), P159 (ω−1), and M162 (ω+2) of GP4 were determined to be important for virus replication, with M162 being of particular importance for virus infectivity. The complete removal of the peptide–anchor domain in GP4 resulted in a complete loss of virus infectivity. The depletion of cholesterol from the plasma membrane of cells reduced the virus production, suggesting a role of lipid rafts in PRRSV infection. Remarkably, GP4 was found to co-localize with CD163 in the lipid rafts on the plasma membrane. Since CD163 has been reported as a cellular receptor for PRRSV and GP4 has been shown to interact with this receptor, our data implicates an important role of lipid rafts during entry of the virus.


title: Pulmonary Artery Thrombectomy – A Life Saving Treatment in a Patient with Presumed COVID‐19 complicated by a massive Pulmonary Embolus

text: To our knowledge, we report the first case of percutaneous pulmonary thrombectomy and catheter directed thrombolysis for massive pulmonary embolism (PE) in a patient with presumed severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Standard treatments of anticoagulation and systemic thrombolysis were unsuccessful and the patient continued to deteriorate. Percutaneous pulmonary thrombectomy and locally delivered thrombolysis was a life‐saving treatment; the patient continues to improve and is currently being nursed on a standard ward. This report highlights the diagnostic challenge of COVID‐19 due to the low sensitivity of the nasopharyngeal swab test and the importance of imaging in managing patients with Novel Coronavirus Pneumonia (NCP). Additionally, it emphasises the need for interventional radiologists and haematologists to work alongside our critical care colleagues to deliver life‐saving treatment in this fight against COVID‐19.


docid: txvbfzst

title: Detection of a broad range of human adenoviruses in respiratory tract samples using a sensitive multiplex real‐time PCR assay

text: Human adenoviruses (hAdVs) are associated with acute respiratory tract infections in pediatric populations and have been identified as a cause of outbreaks in institutional settings. Rapid diagnosis of hAdV infection is critical for appropriate and timely management. This study reports the design and validation of a sensitive and specific multiplex real‐time PCR for the detection of a broad range of hAdV serotypes in respiratory samples. The assay targets the conserved region of the hAdV hexon gene and utilizes hydrolysis probes for the detection of amplified products. The assay was evaluated using retrospectively (n = 864) and prospectively (n = 11,451) collected samples from November 2005 to July 2006. Seasonality studies and analysis of outbreaks was conducted over a 2‐year period from January 2005 to December 2006 (n = 33,067 samples). The assay gave a hAdV positive rate of 7.1% (n = 811) for specimens tested prospectively and was able to detect a broad range of hAdV serotypes with good sensitivity and specificity. A high rate of co‐infection was noted (21.7%). Adenovirus infections were more prevalent in the young with a median age of 24 months for positive patients. Sequence analysis of hAdV positives showed that serotype 7 was the most prevalent followed by serotypes 2 and 3. Association of hAdVs with respiratory outbreaks was low at 2.3% (6 of 266 outbreaks tested) and no seasonal variation was observed for hAdV infections during the 2‐year study period. This assay can improve the detection of hAdVs in respiratory samples and can be used to provide valuable epidemiological information. J. Med. Virol. 80:856–865, 2008. © 2008 Wiley‐Liss, Inc.


title: Pathology and Pathogenesis of Severe Acute Respiratory Syndrome

text: Severe acute respiratory syndrome (SARS) is an emerging infectious viral disease characterized by severe clinical manifestations of the lower respiratory tract. The pathogenesis of SARS is highly complex, with multiple factors leading to severe injury in the lungs and dissemination of the virus to several other organs. The SARS coronavirus targets the epithelial cells of the respiratory tract, resulting in diffuse alveolar damage. Several organs/cell types may be infected in the course of the illness, including mucosal cells of the intestines, tubular epithelial cells of the kidneys, neurons of the brain, and several types of immune cells, and certain organs may suffer from indirect injury. Extensive studies have provided a basic understanding of the pathogenesis of this disease. In this review we describe the most significant pathological features of SARS, explore the etiological factors causing these pathological changes, and discuss the major pathogenetic mechanisms. The latter include dysregulation of cytokines/chemokines, deficiencies in the innate immune response, direct infection of immune cells, direct viral cytopathic effects, down-regulation of lung protective angiotensin converting enzyme 2, autoimmunity, and genetic factors. It seems that both abnormal immune responses and injury to immune cells may be key factors in the pathogenesis of this new disease.


title: Middle East respiratory syndrome coronavirus in pediatrics: a report of seven cases from Saudi Arabia

text: Infection with Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012 as an important respiratory disease with high fatality rates of 40%–60%. Despite the increased number of cases over subsequent years, the number of pediatric cases remained low. A review of studies conducted from June 2012 to April 19, 2016 reported 31 pediatric MERS-CoV cases. In this paper, we present the clinical and laboratory features of seven patients with pediatric MERS. Five patients had no underlying medical illnesses, and three patients were asymptomatic. Of the seven cases, four (57%) patients sought medical advice within 1–7 days from the onset of symptoms. The three other patients (43%) were asymptomatic and were in contact with patients with confirmed diagnosis of MERS-CoV. The most common presenting symptoms were fever (57%), cough (14%), shortness of breath (14%), vomiting (28%), and diarrhea (28%). Two (28.6%) patients had platelet counts of < 150 × 10(9)/L, and one patient had an underlying end-stage renal disease. The remaining patients presented with normal blood count, liver function, and urea and creatinine levels. The documented MERS-CoV Ct values were 32–38 for four of the seven cases. Two patients (28.6%) had abnormal chest radiographic findings of bilateral infiltration. One patient (14.3%) required ventilator support, and two patients (28.6%) required oxygen supplementation. All the seven patients were discharged without complications.


Reply to “Varicella-like exanthem as a specific COVID-19-associated skin manifestation: multicenter case series of 22 patients”: To consider varicella-like exanthem associated with COVID-19, virus varicella zoster and virus herpes simplex must be ruled out.


title: The conserved macrodomains of the non-structural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases

text: Human pathogenic positive single strand RNA ((+)ssRNA) viruses, including Chikungunya virus, pose severe health problems as for many neither efficient vaccines nor therapeutic strategies exist. To interfere with propagation, viral enzymatic activities are considered potential targets. Here we addressed the function of the viral macrodomains, conserved folds of non-structural proteins of many (+)ssRNA viruses. Macrodomains are closely associated with ADP-ribose function and metabolism. ADP-ribosylation is a post-translational modification controlling various cellular processes, including DNA repair, transcription and stress response. We found that the viral macrodomains possess broad hydrolase activity towards mono-ADP-ribosylated substrates of the mono-ADP-ribosyltransferases ARTD7, ARTD8 and ARTD10 (aka PARP15, PARP14 and PARP10, respectively), reverting this post-translational modification both in vitro and in cells. In contrast, the viral macrodomains possess only weak activity towards poly-ADP-ribose chains synthesized by ARTD1 (aka PARP1). Unlike poly-ADP-ribosylglycohydrolase, which hydrolyzes poly-ADP-ribose chains to individual ADP-ribose units but cannot cleave the amino acid side chain - ADP-ribose bond, the different viral macrodomains release poly-ADP-ribose chains with distinct efficiency. Mutational and structural analyses identified key amino acids for hydrolase activity of the Chikungunya viral macrodomain. Moreover, ARTD8 and ARTD10 are induced by innate immune mechanisms, suggesting that the control of mono-ADP-ribosylation is part of a host-pathogen conflict.


Do corticosteroids have a role in treating Ebola virus disease?


title: It's not all about COVID‐19: Pneumocystis pneumonia in the era of a respiratory outbreak

text: As the COVID‐19 pandemic continues to spread, hospitals have turned their focus to diagnosing COVID‐19 in patients who present with respiratory symptoms, and there is a risk of missing other differential diagnoses. We present two cases of newly diagnosed advanced HIV infection with Pneumocystis pneumonia (PCP) that were initially managed as suspect cases of COVID‐19, and in whom HIV was not initially considered.


docid: kkjrrejn

title: Hipertensión arterial pulmonar y COVID-19


docid: tijcxtwx

title: A novel coronavirus outbreak of global health concern


title: Democracy and Women's Health

text: New research on broader determinants of health has culminated into the new paradigm of social determinants of health. The fundamental view that underlies this new paradigm is that socioeconomic and political contexts in which people live have significant bearing upon their health and well-being. Unlike a wealth of research on socioeconomic determinants, few studies have focused on the role of political factors. Some of these studies examine the role of political determinants on health through their mediation with the labour environments and systems of welfare state. A few others study the relationship between polity regimes and population health more directly. However, none of them has a focus on women's health. This study explores the interactions, both direct and indirect, between democracy and women's health. In doing so, it identifies some of the main health vulnerabilities for women and explains, through a conceptual model, how democracy and respect for human rights interacts with women's health.


Offline: Why President Trump is wrong about WHO


title: Bridging the divide: global governance of trade and health

text: The main institutions responsible for governing international trade and health—the World Trade Organization (WTO), which replaced the General Agreement on Tariffs and Trade (GATT) in 1995, and WHO—were established after World War 2. For many decades the two institutions operated in isolation, with little cooperation between them. The growth and expansion of world trade over the past half century amid economic globalisation, and the increased importance of health issues to the functioning of a more interconnected world, brings the two domains closer together on a broad range of issues. Foremost is the capacity of each to govern their respective domains, and their ability to cooperate in tackling issues that lie at the intersection of trade and health. This paper discusses how the governance of these two areas relate to one another, and how well existing institutions work together.


title: Molecular detection of Enteropathogens from diarrheic stool of HIV positive patients in Gondar, Ethiopia

text: BACKGROUND: Infectious diarrhea is a common problem in the developing world, especially among people living with HIV/AIDS. Traditional diagnostic methods such as stool culture and microscopic examination are limited by resources and poor sensitivity. The use of molecular diagnostics for enteropathogen detection in this region of sub-Saharan Africa has not been fully explored. We sought to identify risk factors and characterize enteropathogens from diarrheic stools of HIV-positive patients in Gondar, Ethiopia using multiplex molecular panels targeting key infectious agents. METHODS: A cross-sectional study of 100 stool samples was performed. Samples were collected consecutively from HIV- positive patients presenting with diarrhea at University of Gondar Hospital clinic, a major center in NW Ethiopia. Genomic DNA was extracted from stool and processed using a multiplex molecular panel Allplex™ [Seegene, Canada]. Correlations between patient characteristics, symptoms, public health risk factors, and enteropathogen type (s) were studied. Eighty-six samples were successfully analyzed by molecular methods. RESULTS: The mean age was 35 with 43% male. Eighty percent lived in an urban area, 18% had access to well water only, and 81% practiced proper hand hygiene. The majority of patients (72%) were receiving HAART with a median CD4 cell count of 362/μL. Multiple pathogens were detected in 94% of specimens, with an average of 5 enteropathogens per sample. Common bacteria, viruses, and parasites detected were Shigella spp./enteroinvasive E. coli (80%), enterotoxigenic E. coli (73%), Norovirus (16%) and B. hominis (62%). CD4 cell count < 500/ μL was associated with the presence of viruses (p = 0.004) and the absence of STEC (p = 0.010). The use of HAART or CD4 levels was not associated with the number of enteropathogens detected. CONCLUSIONS: Diarrheic stool from HIV-positive outpatients in Gondar, Ethiopia had on average 5 enteropathogens present in their stool. Shigellaspp./enteroinvasive E. coli and enterotoxigenic E. coli are the major pathogens, not dissimilar to immunocompetent individuals in low income countries.


docid: kromgrnu

title: SARS

text: Severe acute respiratory syndrome (SARS) emerged in southern China in late 2002. It first spread within Guangdong Province and then to other parts of China. Via air travelers, it quickly reached various countries around the globe, causing several major hospital outbreaks. Within weeks, the causative agent, a previously unknown coronavirus (SARS-CoV), was identified, thanks to an unprecedented international effort led by the World Health Organization (WHO). Its origin was quickly traced to wild animals traded locally for culinary purposes. Masked palm civet and some other species seem to have acted as intermediate hosts. Since then, SARS-like coronaviruses were found in different bat species in China and elsewhere, and bats are now regarded as the wildlife reservoir for SARS-CoV. Fortunately, the SARS outbreak could be contained within months. Until July 2003, it had caused 8096 cases, with 774 deaths. Once adequate measures such as isolating patients and quarantining their contacts were strictly adhered to, further transmission between human beings could be interrupted. SARS is an example of how rapidly an infectious agent can spread in the modern world. At the same time, it should serve as a showcase of how international cooperation and modern science can help to combat the spread of infectious diseases.


title: Virological and serological findings in dogs with naturally occurring distemper

text: Abstract Canine distemper virus (CDV) is the cause of a severe and highly contagious disease in dogs. The unpredictable and variable course of CDV-related disease may hamper correct diagnosis of infection and makes it crucial the collection of samples suitable for laboratory confirmation. In the present study we were able to follow the disease in two dogs infected naturally, collecting different biological matrices during the entire period of infection. By real time RT-PCR, viral RNA was detected and quantified, suggesting that urine and rectal swabs would be useful for ante-mortem diagnosis of distemper in dogs, regardless of the clinical stage and form of the illness.


Commentary: When a cardiac surgeon takes care of patients with Coronavirus Disease 2019: It’s gonna be ok!


Frontiers in the Convergence of Bioscience and Information Technology


title: Respiratory infections in immunocompromised patients: Lung findings using chest computed tomography

text: Abstract Respiratory infections and subsequent complications are one of the leading causes of high mortality in immunocompromised patients. Although chest radiograph and computed tomography are the commonly used diagnostic tools for the early diagnosis of lung manifestations of infections, they lack the specificity for the wide range of chest infections which can occur in immunocompromised patients. Systematic analysis of the imaging findings in correlation with the clinical settings along with comparison with the old images can expedite early and accurate diagnosis for subsequent appropriate management. Computer tomography findings in immunocompromised patients with respiratory infections, with regards to various clinical settings, will be discussed here.


docid: jpxohpbj

title: Epidemic Trend of COVID-19 Transmission in India During Lockdown-1 Phase

text: To assess the current epidemic trend of COVID-19/SARS-CoV-2 in India, the epidemic dynamics of COVID-19 cases in India in terms of Case Fatality Rate (CFR), Case Recovery Rate (CRR) and Mortality rate (MR) COVID-19 have been evaluated during Lockdown-1. The analysis includes (i) epidemic curve of Covid-19 cases (ii) demographic analysis (iii) calculation of the CFR and CRR by different methods (iv) calculation of MR (v) Geo-temporal analysis (vi) epidemiological transmission factor (vii) evaluation of the effects and impact of infection, prevention and control in India. A total of 10,815 COVID-19 confirmed cases have been reported in 31 states/union territories as of April 14, 2020 with 9272 active cases (85.73%), 1190 cured/discharged (11%), and 353 deaths (3.23%). Among confirmed cases, most cases (59%) are aged 20–49 which is working age in India and 76% cases are reported for men. The median age of Indian COVID-19 patients found to be 39. As of April 14, the CFR per total cases in India is 3.32% and per closed cases is 23.27%. The CRR per total cases in India is 11.00% and per closed cases is 76.72%, which indicates that the recovery rate of COVID-19 is more than the fatality rate in India. The prevention and control measures taken by the state and central governments at all levels and measure of maintenance of social distancing by people have resulted in effective curbing in the COVID-19 transmission in India.


title: Common principles and intermediates of viral protein-mediated fusion: the HIV-1 paradigm

text: Enveloped viruses encode specialized fusion proteins which promote the merger of viral and cell membranes, permitting the cytosolic release of the viral cores. Understanding the molecular details of this process is essential for antiviral strategies. Recent structural studies revealed a stunning diversity of viral fusion proteins in their native state. In spite of this diversity, the post-fusion structures of these proteins share a common trimeric hairpin motif in which the amino- and carboxy-terminal hydrophobic domains are positioned at the same end of a rod-shaped molecule. The converging hairpin motif, along with biochemical and functional data, implies that disparate viral proteins promote membrane merger via a universal "cast-and-fold" mechanism. According to this model, fusion proteins first anchor themselves to the target membrane through their hydrophobic segments and then fold back, bringing the viral and cellular membranes together and forcing their merger. However, the pathways of protein refolding and the mechanism by which this refolding is coupled to membrane rearrangements are still not understood. The availability of specific inhibitors targeting distinct steps of HIV-1 entry permitted the identification of key conformational states of its envelope glycoprotein en route to fusion. These studies provided functional evidence for the direct engagement of the target membrane by HIV-1 envelope glycoprotein prior to fusion and revealed the role of partially folded pre-hairpin conformations in promoting the pore formation.


title: The 2(nd) sialic acid-binding site of influenza A virus neuraminidase is an important determinant of the hemagglutinin-neuraminidase-receptor balance

text: Influenza A virus (IAV) neuraminidase (NA) receptor-destroying activity and hemagglutinin (HA) receptor-binding affinity need to be balanced with the host receptor repertoire for optimal viral fitness. NAs of avian, but not human viruses, contain a functional 2(nd) sialic acid (SIA)-binding site (2SBS) adjacent to the catalytic site, which contributes to sialidase activity against multivalent substrates. The receptor-binding specificity and potentially crucial contribution of the 2SBS to the HA-NA balance of virus particles is, however, poorly characterized. Here, we elucidated the receptor-binding specificity of the 2SBS of N2 NA and established an important role for this site in the virion HA-NA-receptor balance. NAs of H2N2/1957 pandemic virus with or without a functional 2SBS and viruses containing this NA were analysed. Avian-like N2, with a restored 2SBS due to an amino acid substitution at position 367, was more active than human N2 on multivalent substrates containing α2,3-linked SIAs, corresponding with the pronounced binding-specificity of avian-like N2 for these receptors. When introduced into human viruses, avian-like N2 gave rise to altered plaque morphology and decreased replication compared to human N2. An opposite replication phenotype was observed when N2 was combined with avian-like HA. Specific bio-layer interferometry assays revealed a clear effect of the 2SBS on the dynamic interaction of virus particles with receptors. The absence or presence of a functional 2SBS affected virion-receptor binding and receptor cleavage required for particle movement on a receptor-coated surface and subsequent NA-dependent self-elution. The contribution of the 2SBS to virus-receptor interactions depended on the receptor-binding properties of HA and the identity of the receptors used. We conclude that the 2SBS is an important and underappreciated determinant of the HA-NA-receptor balance. The rapid loss of a functional 2SBS in pandemic viruses may have served to balance the novel host receptor-repertoire and altered receptor-binding properties of the corresponding HA protein.


Recommendations on key practical measures in laparoscopic surgery during the COVID‐19 pandemic


title: Impacts of biodiversity on the emergence and transmission of infectious diseases

text: Current unprecedented declines in biodiversity reduce the ability of ecological communities to provide many fundamental ecosystem services. Here we evaluate evidence that reduced biodiversity affects the transmission of infectious diseases of humans, other animals and plants. In principle, loss of biodiversity could either increase or decrease disease transmission. However, mounting evidence indicates that biodiversity loss frequently increases disease transmission. In contrast, areas of naturally high biodiversity may serve as a source pool for new pathogens. Overall, despite many remaining questions, current evidence indicates that preserving intact ecosystems and their endemic biodiversity should generally reduce the prevalence of infectious diseases. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature09575) contains supplementary material, which is available to authorized users.


title: INFECCIÓN GRAVE POR CORONAVIRUS SARS-CoV-2: Experiencia en un hospital de tercer nivel con pacientes afectados por COVID-19 durante la pandemia 2020

text: Abstract Objective: To describe the clinical and respiratory characteristics of a cohort of 43 patients with COVID-19 after an evolutive period of 28 days. Design: A prospective, single-center observational study was carried out. Setting: Intensive care. Patients: Patients admitted due to COVID-19 and respiratory failure. Interventions: None. Variables: Automatic recording was made of demographic variables, severity parameters, laboratory data, assisted ventilation (HFO: high-flow oxygen therapy and IMV: invasive mechanical ventilation), oxygenation (PaO2, PaO2/FiO2) and complications. The patients were divided into three groups: survivors (G1), deceased (G2) and patients remaining under admission (G3). The chi-squared test or Fisher exact test (categorical variables) was used, along with the Mann-Whitney U-test or Wilcoxon test for analyzing the differences between medians. Statistical significance was considered for p<0.05. Results: A total of 43 patients were included (G1=28 [65.1%], G2=10 [23.3%] and G3=5[11.6%]), with a mean age of 65 years (range 52-72), 62% males, APACHE II 18 (15-24), SOFA 6 (4-7). Arterial hypertension (30.2%) and obesity (25.6%) were the most frequent comorbidities. High-flow oxygen therapy was used in 62.7% of the patients, with failure in 85%. In turn, 95% of the patients required IMV and 85% received ventilation in prone decubitus. In the general population, initial PaO2/FiO2 improved after 7 days (165 [125-210] vs.194 [153-285]; p=0.02), in the same way as in G1 (164 [125-197] vs. 207 [160-294]; p=0.07), but not in G2 (163 [95-197] vs. 135 [85-177]). No bacterial coinfection was observed. The incidence of IMV-associated pneumonia was high (13 episodes/1000 days of IMV). Conclusions: Patients with COVID-19 require early IMV, a high frequency of ventilation in prone decubitus, and have a high incidence of failed HFO. The lack of improvement of PaO2/FiO2 at 7 days could be a prognostic marker. Resumen Objetivo: Describir las características clínicas y respiratorias de una cohorte de 43 pacientes con COVID-19 tras 28 días de evolución. Diseño: Prospectivo observacional en un solo centro Ámbito: Medicina intensiva Pacientes: Pacientes ingresados por COVID-19 e insuficiencia respiratoria Intervenciones: Ninguna Variables: Se obtuvieron de forma automática variables demográficas, de gravedad, de laboratorio, de asistencia ventilatoria recibida (OAF: oxigenoterapia alto flujo y VMI: ventilación mecánica invasiva), de oxigenación (PaO2, PaO2/FiO2) y de complicaciones. Los pacientes se dividieron en 3 grupos: supervivientes(G1), fallecidos(G2) y aquellos que continuaban ingresados(G3). Se utilizó “chi” cuadrado o Fisher (variables categóricas) y “U” Mann-Whitney o Wilcoxon para analizar la diferencia entre medianas. Se consideró significativo un valor de p<0.05. Resultados: Se incluyeron 43 pacientes (G1=28[65,1%],G2=10[23,3%] y G3=5[11,6%]), edad 65(52-72) años, 62% hombres, APACHE II 18(15-24), SOFA 6(4-7), Hipertensión arterial(30,2%) y obesidad(25,6%) fueron las comorbilidades más frecuentes. La OAF fue usada en el 62,7% de pacientes, 85% fracasó. El 95% de los pacientes necesitó VMI y el 85% ventilación en prono. En la población general, la PaO2/FiO2 inicial mejoró a los 7 días (165[125-210] vs. 194[153-285], p=0.02), al igual que en G1(164[125-197] vs. 207[160-294], p=0.07) pero no en G2 (163[95-197] vs. 135[85-177]). No se observó co-infección bacteriana. El desarrollo de neumonía asociada a la VMI fue elevado (13 episodios/1000 días de VMI) Conclusiones: Los pacientes con Covid-19 requieren VMI precoz, elevada frecuencia de ventilación en prono y presentan alta prevalencia de fracaso a OAF. La falta de mejoría de la PaO2/FiO2 a los 7 días podría ser un marcador de pronóstico.


title: Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea

text: Abstract Porcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae family, is an enveloped, positive-sense, single-stranded RNA virus, which causes severe diarrhea and dehydration in suckling pigs. We detected three PEDV strains from ten small intestine samples from piglets with acute diarrhea and we determined the complete genome sequences of the reemerging Korean PEDV field isolates, except for the noncoding regions from both ends. The complete genome sequences of the strains were identical or almost identical (one synonymous single-nucleotide polymorphism (SNP) in the ORF1a/1b genomic sequence). Interestingly, comparative genome analysis of recent Korean PEDV isolates and other strains revealed that the complete genome sequences of recent Korean strains were almost identical (99.9%) to those of the US PEDV strains isolated in 2013. These results suggest that the three reemerging Korean strains are distinct from previous endemic Korean PEDV strains and has been recently introduced into Korea from oversea with high likelihood.