title: Genomic organization and adaptive evolution of IGHC genes in marine mammals

text: Abstract Immunoglobulins are important elements of the adaptive immune system that bind to an immense variety of microbial antigens to neutralize infectivity and specify effector functions. In the present study, the immunoglobulin heavy chain constant region (IGHC) genes from marine mammals were identified and compared with those of their terrestrial relatives to explore their genomic organization and evolutionary characteristics. The genomic organization of marine mammal IGHC genes was shown to be conservative with other eutherian mammals. Stronger signals of positive selection on IGHC were revealed in terrestrial mammals than that in marine mammals with the branch-site model, displaying different selective pressure, which might suggest their divergent adaptations to contrasted environments.


title: What does the future hold for clinical microbiology?

text: In the past decade, clinical microbiology laboratories have undergone important changes with the introduction of molecular biology techniques and laboratory automation. In the future, there will be a need for more rapid diagnoses, increased standardization of testing and greater adaptability to cope with new threats from infectious microorganisms, such as agents of bioterrorism and emerging pathogens. The combination of the new tools that are now being developed in research laboratories, the general reorganization of clinical laboratories and improved communication between physicians and clinical microbiologists should lead to profound changes in the way that clinical microbiologists work.


title: Equine Rhinitis A Virus Infection in Thoroughbred Racehorses—A Putative Role in Poor Performance?

text: The aim of this study was to identify respiratory viruses circulating amongst elite racehorses in a training yard by serological testing of serial samples and to determine their impact on health status and ability to race. A six-month longitudinal study was conducted in 30 Thoroughbred racehorses (21 two-year-olds, five three-year-olds and four four-year-olds) during the Flat racing season. Sera were tested for the presence of antibodies against equine herpesvirus 1 and 4 (EHV-1 and EHV-4) and equine rhinitis viruses A and B (ERAV and ERBV) by complement fixation (CF) and equine arteritis virus (EAV) by ELISA. Antibodies against equine influenza (EI) were measured by haemagglutination inhibition (HI). Only ERAV was circulating in the yard throughout the six-month study period. Seroconversion to ERAV frequently correlated with clinical respiratory disease and was significantly associated with subsequent failure to race (p = 0.0009). Over 55% of the two-year-olds in the study seroconverted to ERAV in May and June. In contrast, only one seroconversion to ERAV was observed in the older horses. They remained free of any signs of respiratory disease and raced successfully throughout the study period. The importance of ERAV as a contributory factor in the interruption of training programmes for young horses may be underestimated.


title: Contrast‐Enhanced Ultrasound in Patients With COVID‐19: Pneumonia, Acute Respiratory Distress Syndrome, or Something Else?

text: Coronavirus disease 2019 (COVID‐19) represents a very heterogeneous disease. Some aspects of COVID‐19 pneumonia question the real nature of ground glass opacities and its consolidative lesions. It has been hypothesized that COVID‐19 lung involvement could represent not only a viral effect but also an immune response induced by the infection, causing epithelial/endothelial lesions and coagulation disorders. We report 3 cases of COVID‐19 pneumonia in which contrast‐enhanced ultrasound was suggestive of consolidations with perfusion defects, at least in part caused by ischemic or necrotic changes and not only by inflammatory or atelectasis events.


title: Chapter 25 Therapeutic use of monoclonal antibodies: general aspects and challenges for drug delivery

text: Abstract Monoclonal antibodies are routinely used in several fields but the great challenge has been their use as therapeutic agents for the treatment of diseases, such as breast cancer, leukemia, asthma, macular degeneration, arthritis, Crohn’s disease, and transplants, among others. Monoclonal antibodies are protein molecules made in the laboratory from hybridoma cells by recombinant DNA technology. Important advances have been made over the past decade to improve some critical points, such as safety and efficacy of the first generation of therapeutic antibodies. This type of molecules presents a significant challenge from the pharmaceutical point of view due to their characteristics, such as molecular size, stability, and solubility. In this chapter we have attempted to identify the major issues associated with therapeutic approaches, formulating drawbacks and delivering antibody drugs, particularly focused on the challenges and opportunities that these present for the future.


title: Analysis of severe acute respiratory syndrome coronavirus structural proteins in virus‐like particle assembly

text: SARS‐CoV has four major structural proteins: the N, S, M, and E proteins. To investigate the mechanism of SARS‐CoV assembly, we cloned the genes encoding these four proteins into the eukaryotic expression vector pCAGGS and transfected them into 293T cells. When all four expression vectors were co‐transfected VLP formed, as confirmed using electron microscopy. Using a rabbit polyclonal antibody specific to the N protein, N‐protein‐containing particles similar in size to the VLP were also observed by immunoelectron microscopy, indicating that the VLP contained the N protein. Co‐immunoprecipitation analyses demonstrated an interaction between the N and M proteins, suggesting that N protein binds directly to M protein to be incorporated into VLP.


title: Persistent Airway Obstruction After Virus Infection Is Not Associated With Airway Inflammation

text: Abstract Background:This study examined the contribution of airway inflammation to the delayed lung function recovery that occurs in some people following virus-induced asthma exacerbations. Methods:Subjects (n = 40) were recruited at hospital admission for acute asthma exacerbation. Respiratory virus infection was diagnosed by viral nucleic acid detection and/or cell culture, using induced sputum, nasal, or throat swabs. Data collected included lung function, answers to common cold and asthma control questionnaires, and induced sputum cellular profiles. Subjects were reexamined 4 to 6 weeks postexacerbation and were compared with stable asthmatic subjects (n = 26) who had been recruited from ambulatory care clinics. Results:Persistent airway obstruction, defined as lung function improvement at follow-up (ie, change in FEV1percent predicted [Δ%FEV1]) of <15%, was observed in 10 subjects (25%). Airway recovery (Δ%FEV1, ≥ 15%) was observed in the remaining subjects (30 subjects; 75%). During the acute episode, the airway-recovery group had increased total cell count (p = 0.019), increased number of neutrophils (p = 0.005), and increased percentage of neutrophils (p = 0.0043) compared to the group of stable subjects with asthma. Postexacerbation, the airway-recovery group had reduced numbers of neutrophils and an increased percentage of eosinophils. In contrast, during exacerbation, subjects with persistent airway obstruction showed no differences in inflammatory cell counts compared to stable subjects with asthma, nor did cell counts change postexacerbation. Symptoms improved in both groups postexacerbation. However, in the persistent-airway-obstruction group, asthma remained uncontrolled. Conclusion:Persistent airway obstruction and uncontrolled asthma are observed in some people after viral asthma exacerbations. These abnormalities are not associated with inflammatory cell influx into the airway lining fluid during the exacerbation and may reflect the involvement of noncellular elements. Further work should explore other mechanisms leading to incomplete airway recovery.


docid: csiknjsm

title: The classification of viruses infecting the respiratory tract

text: Abstract Following the boom in respiratory virology in the 1960s, species of rhinoviruses, coronaviruses, enteroviruses, adenoviruses, parainfluenza viruses and respiratory syncytial virus were added to influenza and measles viruses as causes of respiratory tract infection. In restricted patient groups, such as the immunocompromised, members of the family of herpesviruses including herpes simplex, cytomegalovirus, varicella-zoster virus, Epstein-Barr virus and human herpes virus 6 have also been associated with respiratory disease. This list of pathogens was extended last year with the discovery of a novel virus, the human metapneumovirus. More than 200 antigenically distinct viruses have been documented as causes of sporadic or epidemic respiratory infections in infants, children and adults. However, this varied and diverse group can be divided among six distinct families. Understanding some of the basic biology of these families gives an insight into possible strategies for diagnosis, control and therapy.


title: Influenza-like illness outbreaks in nursing homes in Corsica, France, 2014–2015: epidemiological and molecular characterization

text: BACKGROUND: To study the molecular epidemiology of the influenza outbreaks in nursing homes (NHs) to determine whether multiple influenza strains were involved. METHODS: From September to December 2014, NHs in Corsica were invited to participate in an ongoing daily epidemiological and microbiological surveillance for influenza-like illness (ILI) among residents and health care workers (HCWs). RESULTS: The study involved 12 NHs. Respiratory illness meeting the ILI case definition was observed among 44 residents from whom 22 specimens were collected. Of the 22 residents with a nasopharyngeal sample, 13 (59 %) were positive for at least one of the 11 pathogens analysed. Among these 13 patients, 11 (92 %) presented a confirmed influenza (A/H3N2) and two had another respiratory virus: one human metapneumovirus and one human coronavirus. Of patients with a confirmed influenza A(H3N2), 10 (91 %) were vaccinated against influenza during the 2014–2015 season. Two influenza outbreaks were reported in two NHs, caused by influenza A(H3N2) strains belonging to cluster 3C.3 and 3C.2a. Although antivirals were available, prophylaxis was not used. CONCLUSIONS: Phylogenetic analysis seems to suggest no multiple introduction into the two NHs reporting the two influenza A(H3N2) outbreaks. A number of factors could have contributed to transmitting influenza in NHs including, the absence of administration of antiviral treatment for prophylaxis of all residents/staff regardless of immunization status because of the poor vaccine match during each outbreak, the intensive contacts with incompletely protected residents and HCWs, and the low adherence of NHs to notification of ILI outbreaks to the health authorities. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40064-016-2957-z) contains supplementary material, which is available to authorized users.


title: Medical Tourism

text: Searches of the literature or Internet using the term “medical tourism” produce two sets of articles: travel for the purpose of delivering health care or travel for the purpose of seeking health care. The first usage primarily appears in the medical literature and is beyond the scope of this article, which focuses on travel to seek health care. Still, there are some aspects these two topics have in common: both are affected by ease and speed of international travel and communication associated with globalization, and both raise questions about continuity of care as well as issues related to cultural, language, and legal differences; both also raise questions about ethics. This article describes some of the motivating factors, contributing elements, and challenges in elucidating trends, as well as implications for clinicians who provide pretravel advice and those who care for ill returning travelers.


title: Prevention of Infectious Diseases in Athletes

text: The sports medicine physician may face challenging issues regarding infectious diseases when dealing with teams or highly competitive athletes who have difficulties taking time off to recover. One must treat the individual sick athlete and take the necessary precautions to contain the spread of communicable disease to the surrounding team, staff, relatives, and other contacts. This article reviews preventive strategies for infectious disease in athletes, including immunization recommendations and prophylaxis guidelines, improvements in personal hygiene and prevention of spread of infectious organisms by direct contact, insect-borne disease precautions, and prevention of sexually transmitted diseases. A special emphasis on immunizations focuses on pertussis, influenza, and meningococcal prophylaxis.


title: Toll-like receptors and signalling in spermatogenesis and testicular responses to inflammation—a perspective

text: Abstract It is self-evident that infection and inflammation in the reproductive tract can inhibit male fertility, but the observation that fertility may also be compromised by systemic inflammation and disease is more difficult to explain. Recent studies implicating microbial pattern-recognition receptors, such as the Toll-like receptors (TLRs), as well as inflammatory cytokines and their signalling pathways, in testicular function have cast new light on this mysterious link between infection/inflammation and testicular dysfunction. It is increasingly evident that signalling pathways normally involved in controlling inflammation play fundamental roles in regulating Sertoli cell activity and responses to reproductive hormones, in addition to promoting immune responses within the testis. Many of the negative effects of inflammation on spermatogenesis may be attributed to elevated production of inflammation-related gene products within the circulation and the testis, which subsequently exert disruptive effects on spermatogenic cell development and survival, as well as the ability of the Sertoli cells to provide support for spermatogenesis. These interactions have important implications for testicular dysfunction and disease, and may eventually provide new opportunities for therapeutic interventions.


title: Genetic diversity of bat orthohepadnaviruses in China and a proposed new nomenclature

text: Abstract The orthohepadnaviruses, which include the major human pathogen hepatitis B virus, exist in a wide range of hosts. Since 2013, a large group of orthohepadnaviruses has been identified in bats worldwide and classified as 4 species within the genus Orthohepadnavirus. To further investigate orthohepadnaviruses in the Chinese bat population, 554 archived bat samples from 20 colonies covering 3 southern provinces were screened with results showing that 9 (1.6%) were positive. A systematic phylogenetic analysis has indicated the need for a new nomenclature for bat hepatitis B virus-like viruses: BtHBV, with the addition of 3 new species, one being divided into 6 genotypes. Viruses identified here shared 9.0–19.2% full genome divergence and classified into 3 different genotypes. This study illustrates the genetic diversity of orthohepadnaviruses in the Chinese bat population, and emphasizes need for further investigation of their public health significance.


Correction to Lancet Gastroenterol Hepatol 2020; 5: 430–31


title: An improved reverse genetics system for generation of bovine viral diarrhea virus as a BAC cDNA

text: Abstract Full length cDNA clones of bovine viral diarrhea virus (BVDV) with a low-copy number plasmid backbone have not proven to be stable when propagated in bacteria. To improve stability, pBAS, a bacterial artificial chromosome (BAC) plasmid was used to construct a full length cDNA clone of BVDV strain SD1, which has a genomic size of 12.3kb. The resulting clone pBSD1 was propagated stably for at least 10 passages in three different Escherichia coli strains at two different incubation temperatures as determined by sequencing the progeny plasmids. In vitro transcripts derived from pBSD1 were homologous in size and had an infectious efficiency as high as ∼5.0×105 FFU/μg RNA in MDBK cells. The recovered virus, BSD1, harbored the five artificially introduced silent point mutations as genetic markers and was similar to wild type SD1 in viral growth kinetics, RNA replication, and protein expression. This BAC clone provides a stable reverse genetics system for manipulation and study of BVDV genes.


title: Comparative Impact of Individual Quarantine vs. Active Monitoring of Contacts for the Mitigation of COVID-19: a modelling study

text: BACKGROUND: Voluntary individual quarantine and voluntary active monitoring of contacts are core disease control strategies for emerging infectious diseases, such as COVID-19. Given the impact of quarantine on resources and individual liberty, it is vital to assess under what conditions individual quarantine can more effectively control COVID-19 than active monitoring. As an epidemic grows, it is also important to consider when these interventions are no longer feasible, and broader mitigation measures must be implemented. METHODS: To estimate the comparative efficacy of these case-based interventions to control COVID-19, we fit a stochastic branching model to reported parameters for the dynamics of the disease. Specifically, we fit to the incubation period distribution and each of two sets of the serial interval distribution: a shorter one with a mean serial interval of 4.8 days and a longer one with a mean of 7.5 days. To assess variable resource settings, we consider two feasibility settings: a high feasibility setting with 90% of contacts traced, a half-day average delay in tracing and symptom recognition, and 90% effective isolation; and low feasibility setting with 50% of contacts traced, a two-day average delay, and 50% effective isolation. FINDINGS: Our results suggest that individual quarantine in high feasibility settings where at least three-quarters of infected contacts are individually quarantined contains an outbreak of COVID-19 with a short serial interval (4.8 days) 84% of the time. However, in settings where this performance is unrealistically high and the outbreak continues to grow, so too will the burden of the number of contacts traced for active monitoring or quarantine. When resources are prioritized for scalable interventions such as social distancing, we show active monitoring or individual quarantine of high-risk contacts can contribute synergistically to mitigation efforts. INTERPRETATION: Our model highlights the urgent need for more data on the serial interval and the extent of presymptomatic transmission in order to make data-driven policy decisions regarding the cost-benefit comparisons of individual quarantine vs. active monitoring of contacts. To the extent these interventions can be implemented they can help mitigate the spread of COVID-19.


title: Enhancement of immunostimulatory properties of exosomal vaccines by incorporation of fusion-competent G protein of vesicular stomatitis virus

text: Exosomes have been proposed as candidates for therapeutic immunization. The present study demonstrates that incorporation of the G protein of vesicular stomatitis virus (VSV-G) into exosome-like vesicles (ELVs) enhances their uptake and induces the maturation of dendritic cells. Targeting of VSV-G and ovalbumin as a model antigen to the same ELVs increased the cross-presentation of ovalbumin via an endosomal acidification mechanism. Immunization of mice with VSV-G and ovalbumin containing ELVs led to an increased IgG2a antibody response, expansion of antigen-specific CD8 T cells, strong in vivo CTL responses, and protection from challenge with ovalbumin expressing tumor cells. Thus, incorporation of VSV-G and targeting of antigens to ELVs are attractive strategies to improve exosomal vaccines.


title: Association between Mannose-Binding Lectin Gene Polymorphisms and Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Infection

text: BackgroundGenetic determinants of susceptibility to severe acute respiratory syndrome coronavirus (SARS-CoV) infection remain unknown. We assessed whether mannose-binding lectin (MBL) gene polymorphisms were associated with susceptibility to SARS-CoV infection or disease severity in an ethnically homogeneous population born in northern China MethodsThe frequencies of 1 mutation in codon 54 and 3 promoter polymorphisms at nt −550, −221, and 4 were ascertained in 352 patients with SARS and 392 control subjects, by means of polymerase chain reaction direct sequencing ResultsOf 352 patients with SARS and 392 control subjects, 120 (34.4%) and 91 (23.2%) were carriers of the codon 54 variant, respectively (odds ratio [OR], 1.73 [95% confidence interval {CI}, 1.25–2.39]; P=.00086). A total of 123 (36.0%) of 352 patients with SARS and 100 (25.5%) of 392 control subjects had haplotype pairs associated with medium or low expression of MBL (OR, 1.67 [95% CI, 1.21–2.29]; P=.00187). The population-attributable fraction of patients with SARS that was associated with having the codon 54 variant was 20.1% (95% CI, 7.9%–32.3%) Conclusions MBL gene polymorphisms were significantly associated with susceptibility to SARS-CoV infection; this might be explained by the reduced expression of functional MBL secondary to having the codon 54 variant


title: Infectious Bronchitis Virus as a Vector for the Expression of Heterologous Genes

text: The avian coronavirus infectious bronchitis virus (IBV) is the causative agent of the respiratory disease infectious bronchitis of domestic fowl, and is controlled by routine vaccination. To explore the potential use of IBV as a vaccine vector a reverse genetics system was utilised to generate infectious recombinant IBVs (rIBVs) expressing the reporter genes enhanced green fluorescent protein (eGFP) or humanised Renilla luciferase (hRluc). Infectious rIBVs were obtained following the replacement of Gene 5 or the intergenic region (IR) with eGFP or hRluc, or the replacement of ORFs 3a and 3b with hRluc. The replacement of Gene 5 with an IBV codon-optimised version of the hRluc gene also resulted in successful rescue of infectious rIBV. Reporter gene expression was confirmed by fluorescence microscopy, or luciferase activity assays, for all successfully rescued rIBVs following infection of primary chick kidney (CK) cells. The genetic stability of rIBVs was analysed by serial passage on CK cells. Recombinant IBV stability varied depending on the genome region being replaced, with the reporter genes maintained up to at least passage 8 (P8) following replacement of Gene 5, P7 for replacement of the IR and P5 for replacement of ORFs 3a and 3b. Codon-optimisation of the hRluc gene, when replacing Gene 5, resulted in an increase in genome stability, with hRluc expression stable up to P10 compared to P8 for standard hRluc. Repeated passaging of rIBVs expressing hRluc at an MOI of 0.01 demonstrated an increase in stability, with hRluc expression stable up to at least P12 following the replacement of Gene 5. This study has demonstrated that heterologous genes can be incorporated into, and expressed from a range of IBV genome locations and that replacement of accessory Gene 5 offers a promising target for realising the potential of IBV as a vaccine vector for other avian pathogens.


title: Enhancement and Neutralization of Feline Infectious Peritonitis Virus Infection in Feline Macrophages by Neutralizing Monoclonal Antibodies Recognizing Different Epitopes

text: The interaction between the enhancing and neutralizing activities of three monoclonal antibodies (MAbs) (5‐6‐2, 6‐4‐2 and 7‐4‐1) to the spike protein of feline infectious peritonitis virus (FIPV) strain 79‐1146 was determined using feline macrophages. At a high MAb concentration, all of the three MAbs completely inhibited the FIPV infection at 37 C. However, two of them (6‐4‐2 and 7‐4‐1) enhanced FIPV infection when either the MAb concentration or reaction temperature was lowered. These MAbs also exerted an immediate infectivity‐enhancing activity for up to 10 min of reaction and by 20 min, neutralizing activities were observed. Only MAb 5‐6‐2 consistently showed neutralizing activity regardless of the reaction conditions. Competition with sera from cats experimentally infected with FIPV strain 79‐1146 or feline enteric coronavirus strain 79‐1683 showed that the two epitopes recognized by MAb 5‐6‐2 and MAb 6‐4‐2, respectively, are also recognized by the natural host.


title: Antimicrobial use Guidelines for Treatment of Respiratory Tract Disease in Dogs and Cats: Antimicrobial Guidelines Working Group of the International Society for Companion Animal Infectious Diseases

text: Respiratory tract disease can be associated with primary or secondary bacterial infections in dogs and cats and is a common reason for use and potential misuse, improper use, and overuse of antimicrobials. There is a lack of comprehensive treatment guidelines such as those that are available for human medicine. Accordingly, the International Society for Companion Animal Infectious Diseases convened a Working Group of clinical microbiologists, pharmacologists, and internists to share experiences, examine scientific data, review clinical trials, and develop these guidelines to assist veterinarians in making antimicrobial treatment choices for use in the management of bacterial respiratory diseases in dogs and cats.


docid: ghwhgkdm

title: A global bibliometric analysis of Plesiomonas-related research (1990 – 2017)

text: Plesiomonas shigelloides is an emerging pathogen with damaging effects on human health such as gastroenteritis and extraintestinal infections. Here, we carried out a bibliometric survey that aimed to examine publication trends in Plesiomonas-related research by time and place, international collaborative works, identify gaps and suggest directions for future research. The search term “Plesiomonas shigelloides” was used to retrieve articles published between 1990 and 2017 from the Web of Science database. Only primary research articles were included in the analysis. A total of 155 articles were published within the survey period, with an average of 5.54±2.66 articles per year and an annual growth rate of −0.8%. Research output peaked in 2000 and 2006 (each accounting for 7.7% of the total). The United States ranked first in terms of numbers of articles (n = 29, 18.1%) and total citations (n = 451). Cameroon, Canada, Cuba, Switzerland and Turkey co-shared the 10(th) position each with 2 articles (1.3%). Research collaboration was low (collaboration index = 3. 32). In addition to Plesiomonas shigelloides (n = 82, 52.9%), the top Authors Keywords and research focus included lipopolysaccharide and nuclear magnetic resonance (n = 13, 8.4%). Diarrhea (n = 43, 27.7%), Aeromonas species (n = 41, 26.5%) and infections (n = 31, 20.0%) were also highly represented in Keywords-Plus. Authors’ collaborations and coupling networks formed two mega-clusters which nodes were shared solely by authors from high-income countries. The common conceptual framework in retrieved articles determined by K-means clustering revealed three clusters with sizes of 7, 16, and 29, representing research responses focused on extraintestinal and gastroenteritis, P. shigelloides lipopolysaccharide structure, and co-infections, respectively. Our bibliometric analysis revealed a global diminishing research in Plesiomonas; greater research outcomes from high-income countries compared to others and low collaboration with developing countries.


title: Middle East Respiratory Syndrome Coronavirus in Dromedaries in Ethiopia Is Antigenically Different From the Middle East Isolate EMC

text: Middle East respiratory syndrome (MERS) is an emerging respiratory disease caused by the MERS coronavirus (MERS-CoV). MERS has been endemic to Saudi Arabia since 2012. The reservoir of MERS-CoV is the dromedary camel, suggesting that MERS is primarily a zoonotic disease. MERS-CoV is common in dromedaries throughout the Middle East, North Africa, and East Africa as evidenced by neutralizing antibodies against MERS-CoV; however, human cases have remained limited to the Middle East. To better understand the cause of this difference, the virological properties of African camel MERS-CoV were analyzed based on the spike (S) protein in Ethiopia. Nasal swabs were collected from 258 young dromedaries (≤ 2 years old) in the Afar region of Ethiopia, of which 39 were positive for MERS-CoV, as confirmed by genetic tests. All positive tests were exclusive to the Amibara woreda region. Using next-generation sequencing, two full-length genomes of Amibara isolates were successfully decoded; both isolates belonged to the C2 clade based on phylogenetic analysis of full-length and S protein sequences. Recombinant EMC isolates of MERS-CoV, in which the S protein is replaced with those of Amibara isolates, were then generated to test the roles of these proteins in viral properties. Amibara S recombinants replicated more slowly in cultured cells than in EMC S recombinants. In neutralizing assays, Amibara S recombinants were neutralized by lower concentrations of sera from both Ethiopian dromedaries and EMC isolate (wild-type)-immunized mouse sera, relative to the EMC S recombinants, indicating that viruses coated in the Amibara S protein were easier to neutralize than the EMC S protein. Neutralization experiments performed using S1/S2 chimeric recombinants of the EMC and Amibara S proteins showed that the neutralization profile was dependent on the S1 region of the S protein. These results suggest that the slower viral replication and the ease of neutralization seen in the Ethiopian MERS-CoV are due to strain-specific differences in the S protein and may account for the absence of human MERS-CoV cases in Ethiopia.


title: CHAPTER 4 Keeping Track of Viruses

text: Publisher Summary This chapter introduces basic concepts of virology and exemplifies the usage of current technology for identifying and tracking viral pathogens. Virus structure, lifestyle, replication strategies, classication, the varied modes of transmission, infection, and disease manifestations are focussed upon in the chapter. Viruses are extremely simple “life” forms without metabolic capacity, organelles, translational machinery, or autonomous replicative potential; the essential elements of a virus are consequently minimal. A virus enters the host through any opportunistic opening of the body—; such as minute breaks in the skin barrier or mucosal linings of the eye, nose, etc. Antibodies produced during an infection often have the ability to bind the virus and reduce infectivity. An immediate question to solve during a virus outbreak is the mechanism by which the virus spreads. Viruses frequently infect animal or insect vectors that serve to pass the virus to humans. By identifying the virus through sequence analysis, a hypothetical reservoir can be predicted by the placement of the sequence on the phylogenetic tree‥ The varied modes of transmission, infection, and disease manifestations as they relate to the different diagnostic methods for virus identification are highlighted. Examples of naturally emerging viruses; such as Sin Nombre, Nipah, West Nile conclude the chapter. New technologies that allow the creation of manmade or “engineered” viruses, new frontiers in viral diagnostics, and a few thoughts on the future of virology are also presented. The global eradication of smallpox ranks as one of humankind's greatest accomplishments yet many viral challenges remain. HIV, hepatitis B and C, influenza, dengue, rotavirus, and many other viral diseases continue to affect tens of millions.


Traditional Chinese medicine contributes to the treatment of COVID-19 patients


title: Treatment–donation-stockpile dynamics in ebola convalescent blood transfusion therapy

text: Abstract The interim guidance issued by the World Health Organization during the West Africa 2014 Ebola outbreak provides guidelines on the use of convalescent blood from Ebola survivors for transfusion therapy. Here we develop a novel mathematical model, based on the interim guidance, to examine the nonlinear transmission–treatment–donation–stockpile dynamics during an Ebola outbreak and with a large scale use of the transfusion therapy in the population. We estimate the reduction of case fatality ratio by introducing convalescent blood transfusion as a therapy, and inform optimal treatment–donation–stockpile strategies to balance the treatment need for case fatality ratio reduction and the strategic need of maintaining a minimal blood bank stockpile for other control priorities.


title: Estimating the transmission potential of supercritical processes based on the final size distribution of minor outbreaks

text: Use of the final size distribution of minor outbreaks for the estimation of the reproduction numbers of supercritical epidemic processes has yet to be considered. We used a branching process model to derive the final size distribution of minor outbreaks, assuming a reproduction number above unity, and applying the method to final size data for pneumonic plague. Pneumonic plague is a rare disease with only one documented major epidemic in a spatially limited setting. Because the final size distribution of a minor outbreak needs to be normalized by the probability of extinction, we assume that the dispersion parameter (k) of the negative-binomial offspring distribution is known, and examine the sensitivity of the reproduction number to variation in dispersion. Assuming a geometric offspring distribution with k = 1, the reproduction number was estimated at 1.16 (95% confidence interval: 0.97–1.38). When less dispersed with k = 2, the maximum likelihood estimate of the reproduction number was 1.14. These estimates agreed with those published from transmission network analysis, indicating that the human-to-human transmission potential of the pneumonic plague is not very high. Given only minor outbreaks, transmission potential is not sufficiently assessed by directly counting the number of offspring. Since the absence of a major epidemic does not guarantee a subcritical process, the proposed method allows us to conservatively regard epidemic data from minor outbreaks as supercritical, and yield estimates of threshold values above unity.


title: Evaluation of a multiplex ligation-dependent probe amplification assay for the detection of respiratory pathogens in oncological patients

text: Abstract Background Respiratory tract infections are widespread and may cause significant morbidity and mortality in immunosuppressed populations such as oncological patients. Objectives The RealAccurate Respiratory RT PCR Kit covering 14 respiratory viruses was compared to the RespiFinder Smart22, a broad-spectrum multiplex ligation-dependent probe amplification (MLPA) test, targeting 22 viral and bacterial respiratory pathogens. Study design After verification of its analytical performance, the clinical performance of the RespiFinder Smart22 was evaluated by re-analysis of 96 respiratory samples from oncological patients. Additionally, the time to result (TTR) of both methods was compared. Results The analytical performance of the RespiFinder Smart22 fulfilled all previously specified criteria. Concordant results in both assays were achieved in 74.0% of all clinical specimens and in 91.2% when only positive results were taken into account. The RespiFinder Smart22 yielded additional results in a total of 22 (22.9% of 96) samples due to higher test sensitivity and a broader, highly multiplexed spectrum of pathogens. The TTR of a typical routine test consisting of three samples were 206 and 356min for the RealAccurate Respiratory RT PCR Kit and the RespiFinder Smart22, respectively. However, hands-on time was reduced by 59.0% applying the MLPA method. Conclusions In our hands, the RespiFinder Smart22 showed excellent analytical performance while hands-on time was halved in comparison to the RT PCR method. Regarding the clinical evaluation, the MLPA method provided additional results in 22.9% (22/96) of specimens due to its comprehensive format, higher test sensitivity and the capability to detect 22 pathogens compared to 14 with the RealAccurate Respiratory RT PCR Kit.


title: Nursing care of patients with severe acute respiratory syndrome in the intensive care unit: case reports in Hong Kong

text: Abstract Severe acute respiratory syndrome (SARS) was diagnosed in more than 8437 patients in 25 countries between February and July 2003. During this period the World Health Organisation issued a global alert about SARS and together with the Centre for Disease Control have coordinated their efforts to investigate its pathogenesis and treatment. The outbreak in Hong Kong has been dramatic due to its geographical proximity with Guangdong province, China where the first case of SARS was reported. SARS has been described as a rapidly progressive, sometimes fatal pneumonia with a case fatality rate of 7.6% requiring intensive care. The four case reports illustrate a number of important points concerning the recognition, treatment, management and prevention of SARS, and highlights the importance of considering vigilant assessment and monitoring of patients with SARS. The purpose of this paper is to share our experiences in caring for critically ill patients with SARS in the intensive care unit to nurses globally in order to reduce SARS’ morbidity and mortality as well as to protect nurses and other healthcare workers from this disease that is so far threatening the community at large.


title: Nanomaterial-based sensors for the detection of biological threat agents

text: The danger posed by biological threat agents and the limitations of modern detection methods to rapidly identify them underpins the need for continued development of novel sensors. The application of nanomaterials to this problem in recent years has proven especially advantageous. By capitalizing on large surface/volume ratios, dispersability, beneficial physical and chemical properties, and unique nanoscale interactions, nanomaterial-based biosensors are being developed with sensitivity and accuracy that are starting to surpass traditional biothreat detection methods, yet do so with reduced sample volume, preparation time, and assay cost. In this review, we start with an overview of bioagents and then highlight the breadth of nanoscale sensors that have recently emerged for their detection.


title: The intergenic recombinant HLA-B*46:01 has a distinctive peptidome which includes KIR2DL3 ligands

text: HLA-B*46:01 was formed by an intergenic mini-conversion, between HLA-B*15:01 and HLA-C*01:02, in South-East Asia during the last 50,000 years and has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B*46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B*46:01 has a low diversity peptidome that is distinct from those of its parents. A minority (21%) of HLA-B*46:01 peptides, with common C-terminal characteristics, form ligands for KIR2DL3. The HLA-B*46:01 peptidome is predicted to be enriched for peptide antigens derived from Mycobacterium leprae. Overall, the results indicate that the distinctive peptidome and functions of HLA-B*46:01 provide carriers with resistance to leprosy, which drove its rapid rise in frequency in South-East Asia.


title: Viral Etiology of Acute Exacerbations of COPD in Hong Kong

text: Introduction Viral respiratory infections may precipitate acute exacerbations of COPD (AECOPD). However, little is known about viral etiology related to AECOPD in Asia. We aimed to study the viral etiology of AECOPD in Hong Kong. Methods Patients admitted to an acute hospital in Hong Kong with AECOPD were recruited prospectively from May 1, 2004, to April 30, 2005. Nasopharyngeal aspirate was collected and assessed by polymerase chain reaction (PCR) and viral culture. Spirometry was performed in the stable phase at 2 to 3 months after hospital discharge. Results There were 262 episodes of AECOPD among 196 patients (mean age, 75.7 ± 7.7 years [± SD]; 160 men). Mean FEV1 was 39.6 ± 18.9% of predicted normal, and FEV1/FVC ratio was 58.0 ± 15.2%. Fifty-eight episodes (22.1%) yielded positive viral PCR results. The viruses identified were influenza A (7.3%), coronavirus OC43 (4.6%), rhinovirus (3.1%), influenza B (2.7%), and respiratory syncytial virus (2.3%). The diagnostic yield of viral identification by PCR was 2.7 times higher than that based on conventional viral culture. The rates of identifying a positive viral etiology by PCR were similar among the subjects with FEV1 ≥ 50%, ≥ 30 to 50%, and < 30% of predicted normal. Viral infection appeared to have no effect on subsequent readmissions or mortality rate over a study period of 1 year Conclusion Influenza A and two less-attended viruses, coronavirus OC43 and rhinovirus, were the common etiologic agents in patients hospitalized with AECOPD in Hong Kong. These should be considered in developing diagnostic and intervening strategies pertaining to AECOPD.


title: Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

text: BACKGROUND: The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxins evolve rapidly hampering the identification of these proteins by sequence analysis. Here we analyze an unexpectedly widespread superfamily of toxin domains most of which possess RNase activity. RESULTS: The HEPN superfamily is comprised of all α-helical domains that were first identified as being associated with DNA polymerase β-type nucleotidyltransferases in prokaryotes and animal Sacsin proteins. Using sensitive sequence and structure comparison methods, we vastly extend the HEPN superfamily by identifying numerous novel families and by detecting diverged HEPN domains in several known protein families. The new HEPN families include the RNase LS and LsoA catalytic domains, KEN domains (e.g. RNaseL and Ire1) and the RNase domains of RloC and PrrC. The majority of HEPN domains contain conserved motifs that constitute a metal-independent endoRNase active site. Some HEPN domains lacking this motif probably function as non-catalytic RNA-binding domains, such as in the case of the mannitol repressor MtlR. Our analysis shows that HEPN domains function as toxins that are shared by numerous systems implicated in intra-genomic, inter-genomic and intra-organismal conflicts across the three domains of cellular life. In prokaryotes HEPN domains are essential components of numerous toxin-antitoxin (TA) and abortive infection (Abi) systems and in addition are tightly associated with many restriction-modification (R-M) and CRISPR-Cas systems, and occasionally with other defense systems such as Pgl and Ter. We present evidence of multiple modes of action of HEPN domains in these systems, which include direct attack on viral RNAs (e.g. LsoA and RNase LS) in conjunction with other RNase domains (e.g. a novel RNase H fold domain, NamA), suicidal or dormancy-inducing attack on self RNAs (RM systems and possibly CRISPR-Cas systems), and suicidal attack coupled with direct interaction with phage components (Abi systems). These findings are compatible with the hypothesis on coupling of pathogen-targeting (immunity) and self-directed (programmed cell death and dormancy induction) responses in the evolution of robust antiviral strategies. We propose that altruistic cell suicide mediated by HEPN domains and other functionally similar RNases was essential for the evolution of kin and group selection and cell cooperation. HEPN domains were repeatedly acquired by eukaryotes and incorporated into several core functions such as endonucleolytic processing of the 5.8S-25S/28S rRNA precursor (Las1), a novel ER membrane-associated RNA degradation system (C6orf70), sensing of unprocessed transcripts at the nuclear periphery (Swt1). Multiple lines of evidence suggest that, similar to prokaryotes, HEPN proteins were recruited to antiviral, antitransposon, apoptotic systems or RNA-level response to unfolded proteins (Sacsin and KEN domains) in several groups of eukaryotes. CONCLUSIONS: Extensive sequence and structure comparisons reveal unexpectedly broad presence of the HEPN domain in an enormous variety of defense and stress response systems across the tree of life. In addition, HEPN domains have been recruited to perform essential functions, in particular in eukaryotic rRNA processing. These findings are expected to stimulate experiments that could shed light on diverse cellular processes across the three domains of life. REVIEWERS: This article was reviewed by Martijn Huynen, Igor Zhulin and Nick Grishin


title: Impact du SARS-CoV2 sur la structuration de la prise en charge du cancer : exemple de la tenue des RCP de cancérologie en Occitanie

text: Résumé Ce travail étudie l’impact de l’épidémie de SARS-CoV2 et des recommandations qui ont été diffusées depuis le 16 mars sur l’activité des RCP. L’activité des RCP d’Occitanie a été mesurée à partir des fiches RCP extraites du Dossier Communicant de Cancérologie qui regroupe toutes les RCP. L’activité précédant le confinement a été comparée à celles des périodes de confinement (jusqu’au 24 avril) et des périodes équivalentes en 2019. Les critères de jugement étaient le nombre de réunions tenues, le nombre moyen de dossiers examinés par réunion, dont les premières présentations, et le nombre moyen de médecins présents. Les 191 RCP ont organisé 3 943 réunions et étudié 72 070 dossiers (dont 30 127 premières soumissions). On a observé une baisse de 8 % du nombre de réunions après le confinement. Le nombre de dossiers examinés a diminué de 23 % dans le mois suivant et jusqu’à 33 % dans la troisième quinzaine. Le nombre de médecins participant aux réunions a diminué initialement de 25 %. L’impact a été plus important dans la partie méditerranéenne de la région. Cette première étude à l’échelle d’une région montre que si l’impact de l’épidémie sur le nombre de RCP qui se sont réunies a été modeste, et que les RCP ont suivi les recommandations d’optimisation du quorum, la diminution du nombre de premières présentations laisse présager un retard au diagnostic et à la prise en charge des patients. Elle devra être complétée par des travaux qualitatifs et quantitatifs afin d’estimer l’impact réel de l’épidémie sur la prise en charge globale oncologique. Summary This work examines the impact of the SARS-CoV2 epidemic and the organizational recommendations that have been issued since March 16 on tumor boards (TB) activity. The tumor board activity was measured from tumor board sheets extracted from the oncologic electronic file between January 7, 2019 and April 24, 2020. The pre-containment activity was compared to the activity of the containment periods but also to the equivalent periods in 2019. The number of meetings held, the average number of files reviewed per meeting including first presentations and the average number of physicians’ attendance were the evaluation criteria. The study covered 191 TB that held 3,943 multidisciplinary team meetings (MTM) and reviewed 72070 files (including 30127 first submissions). There was a moderate decrease of 8 % in the number of meetings after March 16, 2020. The number of files examined decreased by 23 % in the following month and even more by 33 % in the third period. The physicians’ number who attended MTM also decreased by 25 %. The negative impact was higher in the Mediterranean part of the region. This first study of tumor board activity, covering a large region but little affected by the pandemic, shows that its impact on the participation to the MTM has been moderate. In addition, tumor boards have followed the recommendations for optimizing quorum. However, the decrease in average MTM activity, particularly for first submissions, suggests a potential delay in patient management. Complementary qualitative and quantitative works are warranted to estimate the real impact on carcinologic outcomes.


title: Triaging algorithm for Head & Neck oncology follow-up patients in COVID-19 climate

text: Abstract The current climate is one of uncertainty and immeasurable tragedy for people afflicted by the pandemic of SARS-CoV-2 virus infection. As professionals, we have a duty of care towards all patients especially the vulnerable and those suffering with life-threatening illnesses such as oral cancer. We present a safe & objective triaging method for afflicted with this disease in the prevailing morbid situation.


Diagnosis of Aorto‐Iliac Thrombosis in a Quarter Horse Foal Using Doppler Ultrasound and Nuclear Scintigraphy


title: COVID-19 and rhinology, from the consultation room to the operating theatre

text: ABSTRACT The purpose of this article is to give rhinologists advice on how to adapt their standard practice during the COVID-19 pandemic. The main goal of these recommendations is to protect healthcare workers against COVID-19 while continuing to provide emergency care so as to prevent loss of chance for patients. We reviewed our recommendations concerning consultations, medical prescriptions and surgical activity in rhinology.


title: Chapter 691 Arterivirus Serine Endopeptidase

text: The third edition of the Handbook of Proteolytic Enzymes aims to be a comprehensive reference work for the enzymes that cleave proteins and peptides, and contains over 800 chapters. Each chapter is organized into sections describing the name and history, activity and specificity, structural chemistry, preparation, biological aspects, and distinguishing features for a specific peptidase. The subject of Chapter 691 is Arterivirus Serine Endopeptidase. Keywords Arterivirus, nidovirus, RNA virus, replicase polyproteins, non-structural protein 4, autoproteolytic proteinase, polyprotein processing, RNA virus, multiple-cleavage proteinase.


title: Coronavirus Protein Processing and RNA Synthesis Is Inhibited by the Cysteine Proteinase Inhibitor E64d

text: Abstract Mouse hepatitis virus strain A59 (MHV-A59) encodes within the 22-kb gene 1 a large polypretain containing three proteinase domains with proven or predicted cysteine catalytic residues. E64d, a specific, irreversible inhibitor of cysteine (thiol) proteinases, inhibits the processing of the gene 1 polyprotein. Specifically, E64d blocks the carboxy-terminal cleavage of p65, E64d also inhibits replication of MHV-A59 in murine DBT cells in a dose-dependent manner, resulting in reduced virus titers and viral syncytia formation. This inhibition of replication is associated with a rapid shutoff of new viral RNA synthesis, in a manner similar to that seen in the presence of cycloheximide. The E64d-associated inhibition of RNA synthesis likely results from E64d-specific inhibition of processing of the gene 1 polyprotein, resulting in inactive proteinase or replicase proteins. These results indicate that processing of the MHV-A59 gene 1-encoded polyprotein is required throughout infection to sustain RNA synthesis and virus replication.


title: Multiplex PCR reveals that viruses are more frequent than bacteria in children with cystic fibrosis

text: Abstract Background Cystic fibrosis is a degenerative disease characterized by progressive epithelial secretory gland dysfunction associated with repeated respiratory infections. Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Multiplex PCR enables screening for many viruses involved in respiratory infections. Objectives This study aimed to evaluate the frequency of viruses and bacteria in respiratory specimens from children with cystic fibrosis and to clarify the incidence and characteristics (seasonality and age of patients) of different viruses detected in children with cystic fibrosis. Study design In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14days. We analyzed viruses in nasopharyngeal-swab specimens with multiplex PCR and bacteria in sputum with standard methods. Results We analyzed 368 paired specimens from 33 children. We detected viruses in 154 (41.8%) and bacteria in 132 (35.9%). Bacteria were commoner in spring and summer; viruses were commoner in autumn and winter. In every season, Staphylococcus aureus was the commonest bacteria and rhinovirus was the commonest virus. Nearly all infections with Haemophilus influenzae occurred in autumn and winter. Viruses were more prevalent in children <5 years old, and bacteria were more prevalent in children ≥12 years old. Conclusions Multiplex PCR screening for respiratory viruses is feasible in children with cystic fibrosis; the clinical implications of screening warrant further study.


title: British Columbia's biotechnology industry: blending research, business and lifestyle

text: An overview of British Columbia's biotechnology industry.


title: Oligonucleotide probes in infectious bronchitis virus diagnosis and strain identification

text: Abstract Genomic RNA fingerprints of infectious bronchitis virus (IBV) strains M41 and Conn46 were prepared to identify T1 RNase-resistant oligonucleotides ‘unique’ to each of the two IBV strains. Such oligonucleotides were subsequently eluted from the gels and their nucleotide sequences determined. When oligonucleotide probes of those sequences were synthesized and used in a dot-blot hybridization assay, the probes lacked IBV strain-specificity and reacted with the RNAs of homologous as well as heterologous IBV strains. Based on these results, the methods used in this study need to be applied to a large number of oligonucleotide probes, to find one or a few that might be suitable as IBV strain- or serotype-specific oligonucleotide probes.


title: Virus-induced ER stress and the unfolded protein response

text: The accumulation of unfolded or misfolded proteins in the lumen of the endoplasmic reticulum (ER) results in ER stress that triggers cytoprotective signaling pathways, termed the unfolded protein response (UPR), to restore and maintain homeostasis in the ER or to induce apoptosis if ER stress remains unmitigated. The UPR signaling network encompasses three core elements, i.e., PKR-like ER kinase (PERK), activating transcription factor 6 (ATF6), and inositol-requiring protein-1 (IRE1). Activation of these three branch pathways of the UPR leads to the translation arrest and degradation of misfolded proteins, the expression of ER molecular chaperones, and the expansion of the ER membrane to decrease the load of proteins and increase the protein-folding capacity in the ER. Recently, the essential roles of the UPR have been implicated in a number of mammalian diseases, particularly viral diseases. In virus-infected cells, the cellular translation machinery is hijacked by the infecting virus to produce large amounts of viral proteins, which inevitably perturbs ER homeostasis and causes ER stress. This review summarizes current knowledge about the UPR signaling pathways, highlights two identified UPR pathways in plants, and discuss progress in elucidating the UPR in virus-infected cells and its functional roles in viral infection.


Induction of lactogenic immunity to transmissible gastroenteritis virus of swine using an attenuated coronavirus mutant able to survive in the physicochemical environment of the digestive tract


docid: owenhaln

title: Avian coronavirus Spike Glycoprotein Ectodomain Shows a Low Codon Adaptation to Gallus gallus with Virus-Exclusive Codons in Strategic Amino Acids Positions

text: This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1–507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC × GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.


HIV/AIDS trends in China


title: Epidemiology and disease control in everyday beef practice

text: It is important for food animal veterinarians to understand the interaction among animals, pathogens, and the environment, in order to implement herd-specific biosecurity plans. Animal factors such as the number of immunologically protected individuals influence the number of individuals that a potential pathogen is able to infect, as well as the speed of spread through a population. Pathogens differ in their virulence and contagiousness. In addition, pathogens have various methods of transmission that impact how they interact with a host population. A cattle population's environment includes its housing type, animal density, air quality, and exposure to mud or dust and other health antagonists such as parasites and stress; these environmental factors influence the innate immunity of a herd by their impact on immunosuppression. In addition, a herd's environment also dictates the “animal flow” or contact and mixing patterns of potentially infectious and susceptible animals. Biosecurity is the attempt to keep infectious agents away from a herd, state, or country, and to control the spread of infectious agents within a herd. Infectious agents (bacteria, viruses, or parasites) alone are seldom able to cause disease in cattle without contributing factors from other infectious agents and/or the cattle's environment. Therefore to develop biosecurity plans for infectious disease in cattle, veterinarians must consider the pathogen, as well as environmental and animal factors.


docid: azqbbsfr

title: A real-time TaqMan® RT-PCR assay with an internal amplification control for rapid detection of transmissible gastroenteritis virus in swine fecal samples

text: Abstract A TaqMan probe-based real-time RT-PCR assay was developed for simultaneous detection of RNA of transmissible gastroenteritis virus (TGEV) in pig fecal samples and RNA of enhanced green fluorescent protein (EGFP) added exogenously as an internal amplification control. The TGEV primers and probe were designed to be specific to a portion of the S gene sequence conserved in all TGEV isolates, but absent in the closely related porcine respiratory coronaviruses. The optimized TaqMan assay detected a minimum of 2.8 copies of in vitro transcribed RNA of the target S gene and RNA extracted from 1 TCID50/ml of TGEV. Using 113 clinical samples received at our diagnostic laboratory over a 4-year period, the performance of the assay was tested and compared with that of a previously described nested RT-PCR assay. All the fecal samples which tested positive for TGEV by the nested RT-PCR assay also tested positive by the TaqMan assay. However, approximately 9% of the samples that tested negative by the nested RT-PCR assay tested positive by the TaqMan assay. These results indicate that the developed TaqMan assay is a highly sensitive diagnostic test for rapid detection of TGEV in pig fecal samples.


title: Business of business is more than business: Managing during the Covid crisis

text: Abstract The economic impact of the lock down and social distancing policy of the governments has been devastating on business. Should business look out for its own interest or deploy its resources and capabilities to fight the coronavirus even at the expense of short-term losses? This paper suggests that business and society are two peas in a pod and are mutually interdependent. One cannot survive without the other. The purpose of business is more than business. It is to nurture all of its stakeholders (employees, customers, suppliers, and community) and not just the investors. This is still common in many small-town manufacturing companies whose families, and their families, live in the community. The paper suggests several implications for B to B companies including developing a stakeholder scorecard, becoming a better customer to suppliers, and redefine the purpose of business.


title: Domestic waste recycling, collective action and economic incentive: The case in Hong Kong

text: Abstract Efficacy of waste recycling is one of the key determinants of environmental sustainability of a city. Like other pro-environmental activities, waste recycling cannot be successfully accomplished by just one or two people, but only by a concerted effort of the community. The collective-action dilemma creates a common underlying difficulty in formulating workable solutions to many environmental problems. With a view to the non-excludability of the outcome, rationality drives people to free-ride efforts of others in waste recycling. To solve this free-rider problem, some scholars suggest the use of economic incentive. This article attempts to study the impacts of reward schemes on waste recycling behaviour of residents in 122 private housing estates in Hong Kong. The study is differentiable from the others as the latter mainly focus on domestic waste recycling in low-rise low-density housing while this one looks into the same in a high-rise high-density residential setting. According to the results of analyses on a set of aggregate data, reward schemes are found to have a significant positive relationship with the per-household weight of recyclables collected, keeping other things constant. The research findings suggest that economic incentives do work in promoting waste recycling in Hong Kong. Practical and policy implications follow.


title: Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses

text: A novel coronavirus (SARS-CoV-2) is the causative agent of an emergent severe respiratory disease (COVID-19) in humans that is threatening to result in a global health crisis. By using genomic, sequence, structural and evolutionary analysis, we show that Alpha- and Beta-CoVs possess several novel families of immunoglobulin (Ig) domain proteins, including ORF8 and ORF7a from SARS-related coronaviruses and two protein groups from certain Alpha-CoVs. Among them, ORF8 is distinguished in being rapidly evolving, possessing a unique insert and a hypervariable position among SARS-CoV-2 genomes in its predicted ligand-binding groove. We also uncover many Ig proteins from several metazoan viruses which are distinct in sequence and structure but share an architecture comparable to that of CoV Ig domain proteins. Hence, we propose that deployment of Ig domain proteins is a widely-used strategy by viruses, and SARS-CoV-2 ORF8 is a potential pathogenicity factor which evolves rapidly to counter the immune response and facilitate the transmission between hosts.


title: Detection of HBoV DNA in idiopathic lung fibrosis, Cologne, Germany

text: Abstract We report two confirmed cases of usual interstitial pneumonia (UIP) associated with infection of the human bocavirus (HBoV). In one case HBoV was identified in the bronchoalveolar lavage (BAL) during an acute exacerbation as well as post mortem in different tissues giving raise to the hypothesis that HBoV infections trigger UIP or could be a causative agent and be a systemic component in UIP. In the other case, the UIP was confirmed by radiological methods and HBoV was detected in the BAL during an acute exacerbation. Both cases give raise to the hypothesis that HBoV could be a causative agent of UIP or could contribute to its development and/or acute exacerbations.


title: Integrating epitope data into the emerging web of biomedical knowledge resources

text: The recognition of immune epitopes is an important molecular mechanism of the vertebrate immune system to discriminate between self and non-self. Increasing amounts of data on immune epitopes are becoming available due to technological advances in epitope-mapping techniques and the availability of genomic information for pathogens. Organizing this data poses a challenge that is similar to the successful effort that was required to organize genomic data, which needed the establishment of centralized databases that complement the primary literature to make the data readily accessible and searchable by researchers. As described in this Innovation article, the Immune Epitope Database and Analysis Resource aims to achieve the same for the more complex and context-dependent information on immune epitopes, and to integrate this data with existing and emerging knowledge resources.


title: The Novel Compound Heterozygous Mutations of ECEL1 Identified in a Family with Distal Arthrogryposis Type 5D

text: INTRODUCTION: Distal arthrogryposis type 5D (DA5D) is an autosomal recessive disease. The clinical symptoms include contractures of the joints of limbs, especially camptodactyly of the hands and/or feet, unilateral ptosis, a round-shaped face, arched eyebrows, and micrognathia, without ophthalmoplegia. ECEL1 is a DA5D causative gene that encodes a membrane-bound metalloprotease. ECEL1 plays important roles in the final axonal arborization of motor nerves in limb skeletal muscles and neuromuscular junction formation during prenatal development. METHODS: A DA5D family with webbing of the elbows and fingers was recruited. We performed whole-exome sequencing (WES) and filtered mutations by disease-causing genes of arthrogryposis multiplex congenita (AMC). Mutational analysis and cosegregation confirmation were then performed. RESULTS: We identified novel compound heterozygous mutations of ECEL1 (NM_004826: c.69C>A, p.C23∗ and c.1810G>A, p.G604R) in the proband. CONCLUSIONS: We detected causative mutations in a DA5D family, expanding the spectrum of known ECEL1 mutations and contributing to the clinical diagnosis of DA5D.


title: The EPICENTRE (ESPNIC Covid pEdiatric Neonatal Registry) initiative: background and protocol for the international SARS-CoV-2 infections registry

text: The outbreak of SARS-CoV-2 is the worst healthcare emergency of this century, and its impact on pediatrics and neonatology is still largely unknown. The European Society for Pediatric and Neonatal Intensive Care (ESPNIC) launched the EPICENTRE (ESPNIC Covid pEdiatric Neonatal Registry) international, multicenter, and multidisciplinary initiative to study the epidemiology, clinical course, and outcomes of pediatric and neonatal SARS-CoV-2 infections. EPICENTRE background and aims are presented together with protocol details. EPICENTRE is open to centers all over the world, and this will allow to provide a pragmatic picture of the epidemic, with a particular attention to pediatric and neonatal critical care issues. Conclusions: EPICENTRE will allow researchers to clarify the epidemiology, clinical presentation, and outcomes of pediatric and neonatal SARS-CoV-2 infection, refining its clinical management and hopefully providing new insights for clinicians.


title: Investigation of the Functional Roles of Host Cell Proteins Involved in Coronavirus Infection Using Highly Specific and Scalable RNA Interference (RNAi) Approach

text: Since its identification in the 1990s, the RNA interference (RNAi) pathway has proven extremely useful in elucidating the function of proteins in the context of cells and even whole organisms. In particular, this sequence-specific and powerful loss-of-function approach has greatly simplified the study of the role of host cell factors implicated in the life cycle of viruses. Here, we detail the RNAi method we have developed and used to specifically knock down the expression of ezrin, an actin binding protein that was identified by yeast two-hybrid screening to interact with the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) spike (S) protein. This method was used to study the role of ezrin, specifically during the entry stage of SARS-CoV infection.


title: SARS‐CoV‐2 and human milk: What is the evidence?

text: The novel coronavirus SARS‐CoV‐2 has emerged as one of the most compelling and concerning public health challenges of our time. To address the myriad issues generated by this pandemic, an interdisciplinary breadth of research, clinical and public health communities has rapidly engaged to collectively find answers and solutions. One area of active inquiry is understanding the mode(s) of SARS‐CoV‐2 transmission. Although respiratory droplets are a known mechanism of transmission, other mechanisms are likely. Of particular importance to global health is the possibility of vertical transmission from infected mothers to infants through breastfeeding or consumption of human milk. However, there is limited published literature related to vertical transmission of any human coronaviruses (including SARS‐CoV‐2) via human milk and/or breastfeeding. Results of the literature search reported here (finalized on 17 April 2020) revealed a single study providing some evidence of vertical transmission of human coronavirus 229E; a single study evaluating presence of SARS‐CoV in human milk (it was negative); and no published data on MERS‐CoV and human milk. We identified 13 studies reporting human milk tested for SARS‐CoV‐2; one study (a non‐peer‐reviewed preprint) detected the virus in one milk sample, and another study detected SARS‐CoV‐2 specific IgG in milk. Importantly, none of the studies on coronaviruses and human milk report validation of their collection and analytical methods for use in human milk. These reports are evaluated here, and their implications related to the possibility of vertical transmission of coronaviruses (in particular, SARS‐CoV‐2) during breastfeeding are discussed.


Eritema multiforme inducido por hidroxicloroquina en paciente con COVID-19


title: SARS-CoV-2 antibody characterization in emergency department, hospitalized and convalescent patients by two semi-quantitative immunoassays

text: BACKGROUND: In the ongoing COVID-19 pandemic, there is an urgent need for comprehensive performance evaluation and clinical utility assessment of serological assays to understand the immune response to SARS-CoV-2. METHODS: IgM/IgG and total antibodies against SARS-CoV-2 were measured by a cyclic enhanced fluorescence assay (CEFA) and a microsphere immunoassay (MIA), respectively. Independent performance evaluation included imprecision, reproducibility, specificity and cross-reactivity (CEFA n=320, MIA n=364). Clinical utility was evaluated by both methods in 87 patients at initial emergency department visit, 28 during subsequent hospitalizations (106 serial samples), and 145 convalescent patients. Totally 916 patients and 994 samples were evaluated. RESULTS: Agreement of CEFA and MIA was 90.4%-94.5% (Kappa: 0.81-0.89) in 302 samples. CEFA and MIA detected SARS-CoV-2 antibodies in 26.2% and 26.3%, respectively, of ED patients. Detection rates increased over time reaching 100% after 21 days post-symptom onset. Longitudinal antibody kinetic changes by CEFA and MIA measurements correlated well and exhibited three types of seroconversion. Convalescent sera showed a wide range of antibody levels. CONCLUSION: Rigorously validated CEFA and MIA assays are reliable for detecting antibodies to SARS-CoV-2 and show promising clinical utility when evaluating immune response in hospitalized and convalescent patients, but are not useful for early screening at patient’s initial ED visit.


title: Selective depletion of glycyrrhizin from Si-Ni-San, a traditional Chinese prescription, blocks its effect on contact sensitivity in mice and recovers adhesion and metalloproteinases production of T lymphocytes

text: Abstract In the present study, we performed to selectively deplete glycyrrhizin from Si-Ni-San, a traditional Chinese prescription that consists of 4 Chinese herbs including Radix Glycyrrhizae Uralensis, and examined its influence on the suppressing activity of Si-Ni-San against contact sensitivity in mice. An immunoaffinity column was made by covalently coupling the polyclonal antibody, obtained by the immunization with glycyrrhizin–BSA conjugate, to CNBr-activated Sepharose 4B. By using this column, glycyrrhizin in Si-Ni-San was selectively and almost completely depleted from the whole extract, which was confirmed by high-performance liquid chromatography (HPLC). Both 200 mg/kg of Si-Ni-San and 10 mg/kg of glycyrrhizin, the dose corresponding to its proportion contained in Si-Ni-San, significantly reduced the ear swelling of picryl chloride (PCl)-induced ear contact sensitivity in mice and the inhibition by Si-Ni-San was stronger than that by glycyrrhizin. The adhesion activity to type IV collagen of the isolated spleen cells from PCl-sensitized mice was significantly decreased by both Si-Ni-San and glycyrrhizin. However, the glycyrrhizin-depleted sample of Si-Ni-San (Si-Ni-SanGL−) only showed a slight inhibition on the cell adhesion. Furthermore, the spleen cells from PCl-sensitized mice produced more matrix metalloproteinase (MMP)-2 and -9 than naive spleen cells did, and both Si-Ni-San and glycyrrhizin remarkably reduced MMP-2 and MMP-9 production. In contrast, Si-Ni-SanGL− only showed a slight inhibition. These results suggest that glycyrrhizin may act as one of the active constituents of Si-Ni-San in inhibiting delayed-type hypersensitivity reaction via down-regulating the MMP production and the cell adhesion to extracellular matrix. The present study also provides a new approach to recognize and validate an active constituent in traditional prescription through a selective depletion.


title: Diagnosis of human metapneumovirus and rhinovirus in patients with respiratory tract infections by an internally controlled multiplex real-time RNA PCR

text: Abstract Background: Adequate laboratory diagnosis of human rhinoviruses (hRV) and human metapneumoviruses (hMPV) requires molecular methods as viral culture lacks sensitivity. However, setting up individual PCRs for all respiratory viruses is not practical so preferentially multiplex PCRs are used. Objectives: To develop for routine diagnosis a rapid real-time PCR assay for detection of hRV and hMPV including an internal control in a single tube multiplex reaction using probes carrying different fluorophores to discriminate targets. Study design: The multiplex real-time RNA PCR was optimized to include the internal control virus and a total of 358 respiratory samples from 239 patients taken over a one-year period were analyzed by the multiplex assay. Results: The multiplex assay with co-amplification of the internal control was as sensitive and specific as the individual assays. Application of this assay on clinical samples from 239 patients in a one-year period resulted in an incidence of hRV and hMPV of 41/239 (17.1%) and 6/239 (2.5%), respectively. Inhibition, defined as poor internal control amplification, was detected in 8 (2.2%) samples. Culture was performed on these samples and only four hRV were detected. Conclusions: This real-time PCR method enables sensitive diagnosis of these two respiratory pathogens with the potential to expand the assay as part of a full molecular respiratory viral screen.


title: Production of Authentic SARS-CoV Mpro with Enhanced Activity: Application as a Novel Tag-cleavage Endopeptidase for Protein Overproduction

text: Abstract The viral proteases have proven to be the most selective and useful for removing the fusion tags in fusion protein expression systems. As a key enzyme in the viral life-cycle, the main protease (Mpro) is most attractive for drug design targeting the SARS coronavirus (SARS-CoV), the etiological agent responsible for the outbreak of severe acute respiratory syndrome (SARS) in 2003. In this study, SARS-CoV Mpro was used to specifically remove the GST tag in a new fusion protein expression system. We report a new method to produce wild-type (WT) SARS-CoV Mpro with authentic N and C termini, and compare the activity of WT protease with those of three different types of SARS-CoV Mpro with additional residues at the N or C terminus. Our results show that additional residues at the N terminus, but not at the C terminus, of Mpro are detrimental to enzyme activity. To explain this, the crystal structures of WT SARS-CoV Mpro and its complex with a Michael acceptor inhibitor were determined to 1.6 Å and 1.95 Å resolution respectively. These crystal structures reveal that the first residue of this protease is important for sustaining the substrate-binding pocket and inhibitor binding. This study suggests that SARS-CoV Mpro could serve as a new tag-cleavage endopeptidase for protein overproduction, and the WT SARS-CoV Mpro is more appropriate for mechanistic characterization and inhibitor design.


title: Confronting an influenza pandemic with inexpensive generic agents: can it be done?

text: Summary Avian influenza A H5N1 presents a serious and possibly imminent pandemic threat. In such an event, adequate supplies of affordable vaccines and antiviral agents will be unavailable to most people in the world. In view of the overwhelming need for effective alternatives, generic agents that target the host immune response or the pandemic virus should be considered. Many scientists doubt the effectiveness of these agents. Nonetheless, several studies suggest that statins improve outcomes in patients with bacteraemia and pneumonia and might be similarly effective against influenza. An experimental study has shown that the fibrate gemfibrozil, a peroxisome proliferator-activated receptor (PPAR) α agonist, reduces mortality in H2N2 influenza virus-infected mice. There is substantial molecular cross-talk between statins and PPAR agonists, and their clinical effects are additive in patients with cardiovascular diseases. Chloroquine increases endosomal pH, impairing influenza virus release into the cytosol. Statins, fibrates, and chloroquine are produced as generic medications in developing countries. They are inexpensive, could be stockpiled, and would be available on the first pandemic day. With a lack of realistic alternatives for confronting the next pandemic, research is urgently needed to determine whether these and other generic agents could mitigate the effects of what might otherwise become an unprecedented global public-health crisis.


title: IoT-based cloud framework to control Ebola virus outbreak

text: Ebola is a deadly infectious virus that spreads very quickly through human-to-human transmission and sometimes death. The continuous detection and remote monitoring of infected patients are required in order to prevent the spread of Ebola virus disease (EVD). Healthcare services based on Internet of Things (IoT) and cloud computing technologies are emerging as a more effective and proactive solution which provides remote continuous monitoring of patients. A novel architecture based on Radio Frequency Identification Device (RFID), wearable sensor technology, and cloud computing infrastructure is proposed for the detection and monitoring of Ebola infected patients. The aim of this work is to prevent the spreading of the infection at the early stage of the outbreak. The J48 decision tree is used to evaluate the level of infection in a user depending on his symptoms. RFID is used to automatically sense the close proximity interactions (CPIs) between users. Temporal Network Analysis (TNA) is applied to describe and monitor the current state of the outbreak using the CPI data. The performance and accuracy of our proposed model are evaluated on Amazon EC2 cloud using synthetic data of two million users. Our proposed model provided 94 % accuracy for the classification and 92 % of the resource utilization.


Reflections on travel-associated infections in Europe


title: Herpes simplex virus type 1 and Alzheimer’s disease: increasing evidence for a major role of the virus

text: Herpes simplex virus type 1 (HSV1), when present in brain of carriers of the type 4 allele of the apolipoprotein E gene (APOE), has been implicated as a major factor in Alzheimer’s disease (AD). It is proposed that virus is normally latent in many elderly brains but reactivates periodically (as in the peripheral nervous system) under certain conditions, for example stress, immunosuppression, and peripheral infection, causing cumulative damage and eventually development of AD. Diverse approaches have provided data that explicitly support, directly or indirectly, these concepts. Several have confirmed HSV1 DNA presence in human brains, and the HSV1-APOE-ε4 association in AD. Further, studies on HSV1-infected APOE-transgenic mice have shown that APOE-e4 animals display a greater potential for viral damage. Reactivated HSV1 can cause direct and inflammatory damage, probably involving increased formation of beta amyloid (Aβ) and of AD-like tau (P-tau)—changes found to occur in HSV1-infected cell cultures. Implicating HSV1 further in AD is the discovery that HSV1 DNA is specifically localized in amyloid plaques in AD. Other relevant, harmful effects of infection include the following: dynamic interactions between HSV1 and amyloid precursor protein (APP), which would affect both viral and APP transport; induction of toll-like receptors (TLRs) in HSV1-infected astrocyte cultures, which has been linked to the likely effects of reactivation of the virus in brain. Several epidemiological studies have shown, using serological data, an association between systemic infections and cognitive decline, with HSV1 particularly implicated. Genetic studies too have linked various pathways in AD with those occurring on HSV1 infection. In relation to the potential usage of antivirals to treat AD patients, acyclovir (ACV) is effective in reducing HSV1-induced AD-like changes in cell cultures, and valacyclovir, the bioactive form of ACV, might be most effective if combined with an antiviral that acts by a different mechanism, such as intravenous immunoglobulin (IVIG).


title: Cell surface α2,3-linked sialic acid facilitates Zika virus internalization

text: The emergence of neurotropic Zika virus (ZIKV) raised a public health emergency of global concern. ZIKV can cross the placental barrier and infect foetal brains, resulting in microcephaly, but the pathogenesis of ZIKV is poorly understood. With recent findings reporting AXL as a type I interferon antagonist rather than an entry receptor, the exact entry mechanism remains unresolved. Here we report that cell surface sialic acid plays an important role in ZIKV infection. Removal of cell surface sialic acid by neuraminidase significantly abolished ZIKV infection in Vero cells and human induced-pluripotent stem cells-derived neural progenitor cells. Furthermore, knockout of the sialic acid biosynthesis gene encoding UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase resulted in significantly less ZIKV infection of both African and Asian lineages. Huh7 cells deficient in α2,3-linked sialic acid through knockout of ST3 β-galactoside-α2,3-sialyltransferase 4 had significantly reduced ZIKV infection. Removal of membrane-bound, un-internalized virus with pronase treatment revealed the role of sialic acid in ZIKV internalization but not attachment. Sialyllactose inhibition studies showed that there is no direct interaction between sialic acid and ZIKV, implying that sialic acid could be mediating ZIKV-receptor complex internalization. Identification of α2,3-linked sialic acid as an important host factor for ZIKV internalization provides new insight into ZIKV infection and pathogenesis.


Cirugía urológica funcional y COVID-19 : cómo y por qué hay que retomar ya la actividad quirúrgica adaptados a la nueva realidad


title: Adenoviruses Associated with Acute Respiratory Diseases Reported in Beijing from 2011 to 2013

text: BACKGROUND: Adenovirus is one of the most common causes of viral acute respiratory infections. To identify the types of human adenoviruses (HAdVs) causing respiratory illness in Beijing, a sentinel surveillance project on the viral aetiology of acute respiratory infection was initiated in 2011. PRINCIPAL FINDINGS: Through the surveillance project, 4617 cases of respiratory infections were identified during 2011-2013. Throat swabs (pharynx and tonsil secretions) were collected from all the patients, and 15 different respiratory viruses were screened by multiplex one-step PCR method. 45 were identified as adenovirus-positive from sporadic and outbreak cases of respiratory infection by a multiplex one-step RT-PCR method, and a total of 21 adenovirus isolates were obtained. Five HAdV types among three species, including HAdV-3 (species HAdV-B), HAdV-4 (species HAdV-E), HAdV-7 (species HAdV-B), HAdV-55 (species HAdV-B), and an undefined HAdV type (species HAdV-C) were identified. The comparison results of the penton base, hexon, and fiber gene sequences of the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and those from the GenBank database indicated significant spatial and temporal conservation and stability of sequences within the genome; however, the phylogenetic relationship indicated that both strain BJ04 and strain BJ09 isolated in 2012 and 2013, respectively, may have recombined between HAdV-1 genome and HAdV-2 genome within species HAdV-C, indicating intraspecies recombination. CONCLUSIONS: This study confirmed that at least 5 HAdV types including HAdV-3, HAdV-4, HAdV-7, HAdV-55 and an undefined HAdV type were co-circulating and were the causative agents of respiratory tract infections in recent years in Beijing. HAdV-3, HAdV-4, HAdV-7, and HAdV-55 showed the apparent stability of the genomes, while intraspecies recombination was identified in strain BJ04 and BJ09. The recombinants carrying penton base gene of HAdV-1 as well as hexon and fiber genes of HAdV-2 might be a novel type of HAdV worthy of further study.


title: Short and long term impacts of COVID-19 on the pharmaceutical sector

text: BACKGROUND: The novel coronavirus disease 2019 (COVID-19) was characterized as a global pandemic by the WHO on March 11th, 2020. This pandemic had major effects on the health market, the pharmaceutical sector, and was associated with considerable impacts; which may appear in short and long-term time-horizon and need identification and appropriate planning to reduce their socio-economic burden. OBJECTIVES: Current short communication study assessed pharmaceutical market crisis during the COVID-19 era; discussing short- and long-term impacts of the pandemic on the pharmaceutical sector. RESULTS: Short-term impacts of COVID-19 pandemic includes demand changes, regulation revisions, research and development process changes and the shift towards tele-communication and tele-medicine. In addition, industry growth slow-down, approval delays, moving towards self-sufficiency in pharm-production supply chain and trend changes in consumption of health-market products along with ethical dilemma could be anticipated as long-term impacts of COVID-19 pandemic on pharmaceutical sector in both global and local levels. CONCLUSION: The pandemic of COVID-19 poses considerable crisis on the health markets, including the pharmaceutical sector; and identification of these effects, may guide policy-makers towards more evidence-informed planning to overcome accompanying challenges. [Figure: see text]


title: Equine coronavirus: An emerging enteric virus of adult horses

text: Equine coronavirus (ECoV) is an emerging virus associated clinically and epidemiologically with fever, depression, anorexia and less frequently colic and diarrhoea in adult horses. Sporadic cases and outbreaks have been reported with increased frequency since 2010 from Japan, the USA and more recently from Europe. A faeco‐oral transmission route is suspected and clinical or asymptomatic infected horses appear to be responsible for direct and indirect transmission of ECoV. A presumptive clinical diagnosis of ECoV infection may be suggested by clinical presentation, haematological abnormalities such as leucopenia due to lymphopenia and/or neutropenia. Confirmation of ECoV infection is provided by specific ECoV nucleic acid detection in faeces by quantitative PCR (qPCR) or demonstration of coronavirus antigen by immunohistochemistry or electron microscopy in intestinal biopsy material obtained ante or post mortem. The disease is generally self‐limiting and horses typically recover with symptomatic supportive care. Complications associated with disruption of the gastrointestinal barrier have been reported in some infected horses and include endotoxaemia, septicaemia and hyperammonaemia‐associated encephalopathy. Although specific immunoprophylactic measures have been shown to be effective in disease prevention for closely‐related coronaviruses such as bovine coronavirus (BCoV), such strategies have yet not been investigated for horses and disease prevention is limited to basic biosecurity protocols. This article reviews current knowledge concerning the aetiology, epidemiology, clinical signs, diagnosis, pathology, treatment and prevention of ECoV infection in adult horses.


title: Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series

text: BACKGROUND: In December, 2019, the newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, causing COVID-19, a respiratory disease presenting with fever, cough, and often pneumonia. WHO has set the strategic objective to interrupt spread of SARS-CoV-2 worldwide. An outbreak in Bavaria, Germany, starting at the end of January, 2020, provided the opportunity to study transmission events, incubation period, and secondary attack rates. METHODS: A case was defined as a person with SARS-CoV-2 infection confirmed by RT-PCR. Case interviews were done to describe timing of onset and nature of symptoms and to identify and classify contacts as high risk (had cumulative face-to-face contact with a confirmed case for ≥15 min, direct contact with secretions or body fluids of a patient with confirmed COVID-19, or, in the case of health-care workers, had worked within 2 m of a patient with confirmed COVID-19 without personal protective equipment) or low risk (all other contacts). High-risk contacts were ordered to stay at home in quarantine for 14 days and were actively followed up and monitored for symptoms, and low-risk contacts were tested upon self-reporting of symptoms. We defined fever and cough as specific symptoms, and defined a prodromal phase as the presence of non-specific symptoms for at least 1 day before the onset of specific symptoms. Whole genome sequencing was used to confirm epidemiological links and clarify transmission events where contact histories were ambiguous; integration with epidemiological data enabled precise reconstruction of exposure events and incubation periods. Secondary attack rates were calculated as the number of cases divided by the number of contacts, using Fisher's exact test for the 95% CIs. FINDINGS: Patient 0 was a Chinese resident who visited Germany for professional reasons. 16 subsequent cases, often with mild and non-specific symptoms, emerged in four transmission generations. Signature mutations in the viral genome occurred upon foundation of generation 2, as well as in one case pertaining to generation 4. The median incubation period was 4·0 days (IQR 2·3–4·3) and the median serial interval was 4·0 days (3·0–5·0). Transmission events were likely to have occurred presymptomatically for one case (possibly five more), at the day of symptom onset for four cases (possibly five more), and the remainder after the day of symptom onset or unknown. One or two cases resulted from contact with a case during the prodromal phase. Secondary attack rates were 75·0% (95% CI 19·0–99·0; three of four people) among members of a household cluster in common isolation, 10·0% (1·2–32·0; two of 20) among household contacts only together until isolation of the patient, and 5·1% (2·6–8·9; 11 of 217) among non-household, high-risk contacts. INTERPRETATION: Although patients in our study presented with predominately mild, non-specific symptoms, infectiousness before or on the day of symptom onset was substantial. Additionally, the incubation period was often very short and false-negative tests occurred. These results suggest that although the outbreak was controlled, successful long-term and global containment of COVID-19 could be difficult to achieve. FUNDING: All authors are employed and all expenses covered by governmental, federal state, or other publicly funded institutions.


title: Implementation of the Hospital Emergency Incident Command System during an outbreak of severe acute respiratory syndrome (SARS) at a hospital in Taiwan, ROC

text: Abstract We sought to describe the implementation of the Hospital Emergency Incident Command System (HEICS) at National Cheng Kung University Hospital (NCKUH) in Taiwan, ROC during the outbreak of severe acute respiratory syndrome (SARS) in early 2003. We administered a 14-question survey via structured interviews to individuals occupying activated HEICS leadership positions at NCKUH to identify the organization, structure, and function of the HEICS units and subunits they led and the job actions they performed from 25 March to 16 June 2003 Thirty-three of 38 persons (87%) occupying 39 of 44 (89%) activated HEICS leadership positions directly participated in the survey. The participants collectively reported: 1) the creation of four new HEICS unit leader positions and corresponding units during the outbreak, including the infection control officer (administrative section) and SARS assessment, isolation, and critical care unit leaders (operations section); 2) the creation of six new HEICS subunits, including functional areas for fever screening, SARS assessment, and resuscitation outside the hospital, and SARS patient care, SARS critical care, and employee isolation inside the hospital; and 3) the performance of new job actions related to infection control by all HEICS unit leaders. HEICS provides a flexible framework that seems to have assisted NCKUH in the organization of its emergency response to the SARS outbreak in Taiwan, ROC.


docid: ihsqbtxu

title: Mutational Analysis of the Murine Coronavirus Spike Protein: Effect on Cell-to-Cell Fusion

text: Abstract The spike (S) protein of murine coronavirus strain A59 (MHV-A59) is a type I membrane protein that induces membrane fusion. In this study we have analyzed the role of two domains in the S protein on fusion. The 180-kDa mature S protein is partially cleaved into two 90-kDa subunits during transport to the plasma membrane. We have identified several amino acids that are important for cleavage of S, and we show that cleavage is not strictly required for fusion. However, the level of cleavage seems to influence the fusion kinetics. After introduction of an arginine at position P2to mimick the MHV-JHM cleavage site, full cleavage of the spike protein was obtained. Further, we analyzed the effect of mutations in the transmembrane (TM) domain of the S protein. Maturation and cell surface expression of the mutant proteins were not affected, and all proteins became acylated. The mutant in which the predicted transmembrane domain was shortened did not induce syncytia. From a group of mutants in which several conserved cysteines in the TM domain had been replaced by serines, one was unable to induce syncytia, another showed delayed syncytia formation, and the third mutant induced syncytia as did the wild-type protein. The potential role of the transmembrane domain in fusion is discussed.


title: The rational design of vaccines

text: This review provides an insight into the various opportunities for vaccine intervention, analysis of strategies for vaccine development, vaccine ability to modulate immune responses and resultant rational vaccine design. In addition, wider aspects are considered, such as biotechnological advances, advances in immunological understanding and host–pathogen interactions. The key question addressed here is, with all our research and understanding, have we reached a new echelon in vaccine development, that of rational design?


title: Rotavirus Disrupts Calcium Homeostasis by NSP4 Viroporin Activity

text: Many viruses alter intracellular calcium homeostasis. The rotavirus nonstructural protein 4 (NSP4), an endoplasmic reticulum (ER) transmembrane glycoprotein, increases intracellular levels of cytoplasmic Ca(2+) ([Ca(2+)]cyto) through a phospholipase C-independent pathway, which is required for virus replication and morphogenesis. However, the NSP4 domain and mechanism that increases [Ca(2+)]cyto are unknown. We identified an NSP4 domain (amino acids [aa] 47 to 90) that inserts into membranes and has structural characteristics of viroporins, a class of small hydrophobic viral proteins that disrupt membrane integrity and ion homeostasis to facilitate virus entry, assembly, or release. Mutational analysis showed that NSP4 viroporin activity was mediated by an amphipathic α-helical domain downstream of a conserved lysine cluster. The lysine cluster directed integral membrane insertion of the viroporin domain and was critical for viroporin activity. In epithelial cells, expression of wild-type NSP4 increased the levels of free cytoplasmic Ca(2+) by 3.7-fold, but NSP4 viroporin mutants maintained low levels of [Ca(2+)]cyto, were retained in the ER, and failed to form cytoplasmic vesicular structures, called puncta, which surround viral replication and assembly sites in rotavirus-infected cells. When [Ca(2+)]cyto was increased pharmacologically with thapsigargin, viroporin mutants formed puncta, showing that elevation of calcium levels and puncta formation are distinct functions of NSP4 and indicating that NSP4 directly or indirectly responds to elevated cytoplasmic calcium levels. NSP4 viroporin activity establishes the mechanism for NSP4-mediated elevation of [Ca(2+)]cyto, a critical event that regulates rotavirus replication and virion assembly.