title: Implications of SARS-CoV-2 Genetic Diversity and Mutations on Pathogenicity of COVID-19 and Biomedical Interventions

text: ABSTRACT Objective Coronavirus disease 2019 (COVID-19) has caused an unprecedented global health emergency. The COVID-19 pandemic has claimed over 350,000 human lives within five months of its emergence, especially in the USA and the European continent. This study analysed the implications of the genetic diversity and mutations in SARS-CoV-2 on its virulence diversity and investigated how these factors could affect the successful development and application of antiviral chemotherapy, immunotherapy, serodiagnosis, and vaccination. Methods All the suitable and eligible full text articles published between 31st December 2019 and 31st May 2020 were filtered and extracted from “PubMed”, “Scopus”, “Web of Science”, and “Hinari” and were critically reviewed. We used the Medical Subject Headings (MeSH) terms “COVID-19, “Mutation”, “Genetic diversity”, “SARS-CoV-2”, “Virulence”, “Pathogenicity”, “Evolution” and “SARS-CoV-2 transmission” for this search. Results Our search showed that SARS-CoV-2 has persistently undergone significant mutations in various parts of its non-structural proteins (NSPs), including NSP2 and NSP3, S protein, and RNA-dependent RNA polymerase (RdRp). In particular, the S protein was found to be the key determinant of evolution, transmission, and virulence of SARS-CoV-2, and could be a potential target for vaccine development. Additionally, RdRp could be a major target in the development of antivirals for the treatment of COVID-19. Conclusion Given the critical importance of mutations in the pathogenicity of SARS-CoV-2 and in the development of sero-diagnostics, antivirals, and vaccines, this study recommends continuous molecular surveillance of SARS-CoV-2. This approach would potentially prompt identification of new mutants and their impact on ongoing biomedical interventions and COVID-19 control measures.


title: Use of renin–angiotensin–aldosterone system inhibitors and risk of COVID-19 requiring admission to hospital: a case-population study

text: BACKGROUND: Concerns have been raised about the possibility that inhibitors of the renin–angiotensin–aldosterone system (RAAS) could predispose individuals to severe COVID-19; however, epidemiological evidence is lacking. We report the results of a case-population study done in Madrid, Spain, since the outbreak of COVID-19. METHODS: In this case-population study, we consecutively selected patients aged 18 years or older with a PCR-confirmed diagnosis of COVID-19 requiring admission to hospital from seven hospitals in Madrid, who had been admitted between March 1 and March 24, 2020. As a reference group, we randomly sampled ten patients per case, individually matched for age, sex, region (ie, Madrid), and date of admission to hospital (month and day; index date), from Base de datos para la Investigación Farmacoepidemiológica en Atención Primaria (BIFAP), a Spanish primary health-care database, in its last available year (2018). We extracted information on comorbidities and prescriptions up to the month before index date (ie, current use) from electronic clinical records of both cases and controls. The outcome of interest was admission to hospital of patients with COVID-19. To minimise confounding by indication, the main analysis focused on assessing the association between COVID-19 requiring admission to hospital and use of RAAS inhibitors compared with use of other antihypertensive drugs. We calculated odds ratios (ORs) and 95% CIs, adjusted for age, sex, and cardiovascular comorbidities and risk factors, using conditional logistic regression. The protocol of the study was registered in the EU electronic Register of Post-Authorisation Studies, EUPAS34437. FINDINGS: We collected data for 1139 cases and 11 390 population controls. Among cases, 444 (39·0%) were female and the mean age was 69·1 years (SD 15·4), and despite being matched on sex and age, a significantly higher proportion of cases had pre-existing cardiovascular disease (OR 1·98, 95% CI 1·62–2·41) and risk factors (1·46, 1·23–1·73) than did controls. Compared with users of other antihypertensive drugs, users of RAAS inhibitors had an adjusted OR for COVID-19 requiring admission to hospital of 0·94 (95% CI 0·77–1·15). No increased risk was observed with either angiotensin-converting enzyme inhibitors (adjusted OR 0·80, 0·64–1·00) or angiotensin-receptor blockers (1·10, 0·88–1·37). Sex, age, and background cardiovascular risk did not modify the adjusted OR between use of RAAS inhibitors and COVID-19 requiring admission to hospital, whereas a decreased risk of COVID-19 requiring admission to hospital was found among patients with diabetes who were users of RAAS inhibitors (adjusted OR 0·53, 95% CI 0·34–0·80). The adjusted ORs were similar across severity degrees of COVID-19. INTERPRETATION: RAAS inhibitors do not increase the risk of COVID-19 requiring admission to hospital, including fatal cases and those admitted to intensive care units, and should not be discontinued to prevent a severe case of COVID-19. FUNDING: Instituto de Salud Carlos III.


title: Anti-HCV, nucleotide inhibitors, repurposing against COVID-19

text: Abstract Aims A newly emerged Human Coronavirus (HCoV) is reported two months ago in Wuhan, China (COVID-19). Until today >2700 deaths from the 80,000 confirmed cases reported mainly in China and 40 other countries. Human to human transmission is confirmed for COVID-19 by China a month ago. Based on the World Health Organization (WHO) reports, SARS HCoV is responsible for >8000 cases with confirmed 774 deaths. Additionally, MERS HCoV is responsible for 858 deaths out of about 2500 reported cases. The current study aims to test anti-HCV drugs against COVID-19 RNA dependent RNA polymerase (RdRp). Materials and methods In this study, sequence analysis, modeling, and docking are used to build a model for Wuhan COVID-19 RdRp. Additionally, the newly emerged Wuhan HCoV RdRp model is targeted by anti-polymerase drugs, including the approved drugs Sofosbuvir and Ribavirin. Key findings The results suggest the effectiveness of Sofosbuvir, IDX-184, Ribavirin, and Remidisvir as potent drugs against the newly emerged HCoV disease. Significance The present study presents a perfect model for COVID-19 RdRp enabling its testing in silico against anti-polymerase drugs. Besides, the study presents some drugs that previously proved its efficiency against the newly emerged viral infection.


title: Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks

text: Enteric viruses play an important role in the Brazilian poultry industry due to the economic impact of resulting low yields of broilers, layers, and breeders. The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The aim of this study was to identify single and multiple infections using data obtained from 270 samples from eleven Brazilian states, corresponding to the period between 2010 and 2017. This was accompanied by an analysis of the relationship between the age of birds, clinical signs, and geographical distribution, using Polymerase Chain Reaction (PCR) and Reverse Transcription-PCR (RT-PCR) techniques. Twenty-five profiles of virus combinations were detected. Single infections were encountered in 86.3% of samples, and multiple infections were present in the remaining 13.7%. Both single and multiple infections affected all kinds of commercial chickens with digestive problems, stunting syndrome, decreases in egg and meat production, increased mortality, and respiratory signs. FAdV-I, ChPV, CAstV, ANV, and ARtV were mostly detected in young broilers, in contrast with IBV, which was detected in hens from one to greater than 51 weeks of age. These results exhibit the complexity of enteric diseases and the still poorly understood role of each pathogen as a unique etiological agent.


title: Factors Associated with Preventive Behaviours of COVID-19 among Hospital Staff in Iran in 2020: An Application of the Protection Motivation Theory

text: Abstract This study was conducted for predicting preventive behaviours of healthcare workers (HCW) towards Covid-19 based on the Protection Motivation Theory (PMT). This cross-sectional and analytical study was conducted on 761 HCW in Hamadan, Iran, using multi-stage random sampling. The preventive behaviours against COVID-19 among HCW were assessed at a relatively desirable level. Based on the PMT, threat and coping appraisal were predictors of protection motivation to conduct COVID-19 preventive behaviours (P<0.001). The intention was also predictive of COVID-19 preventive behaviours (P<0.001). Consideration of personnel's self-efficacy and their knowledge regarding the effectiveness of protective behaviours in designing staff training programs are recommended.


title: Respiratory hygiene in emergency departments: Compliance, beliefs, and perceptions

text: BACKGROUND: Low respiratory hygiene compliance among health care workers of emergency departments has become a major concern in the spread of respiratory infections. Our objective was to determine the compliance with respiratory hygiene of triage nurses at 2 university hospital centers and to identify factors influencing compliance to the respiratory hygiene principles of emergency health care workers. METHODS: A 2-part, cross-sectional, descriptive study was conducted at 2 training centers. An anonymous observation of compliance with respiratory hygiene by triage emergency nurses was performed. A self-administered, voluntary questionnaire on attitudes, perceptions, and knowledge of respiratory hygiene guidelines was distributed to the health care workers at the emergency department of the 2 hospital sites. RESULTS: Median objective compliance with respiratory hygiene measures of triage nurses was 22% (interquartile range [IQR], 11%-33%). Median perceived compliance of the health care workers was 68% (IQR, 61%-79%). Median actual knowledge score was 75% (IQR, 75%-100%). Overall, 91.9% of respondents believed that the mask was an effective preventive measure. The main obstacles toward mask wearing by the health care worker were “tendency to forget” (37.8%) and “discomfort” (35.1%). CONCLUSION: The compliance rate at our institution is very low. We identified a few factors affecting adherence to respiratory hygiene measures that are of potential use in targeting groups and formulating recommendations.


title: Expression and regulation of the neutral amino acid transporter B(0)AT1 in rat small intestine

text: Absorption of neutral amino acids across the luminal membrane of intestinal enterocytes is mediated by the broad neutral amino acid transporter B(0)AT1 (SLC6A19). Its intestinal expression depends on co-expression of the membrane-anchored peptidase angiotensin converting enzyme 2 (ACE2) and is additionally enhanced by aminopeptidase N (CD13). We investigated in this study the expression of B(0)AT1 and its auxiliary peptidases as well as its transport function along the rat small intestine. Additionally, we tested its possible short- and long-term regulation by dietary proteins and amino acids. We showed by immunofluorescence that B(0)AT1, ACE2 and CD13 co-localize on the luminal membrane of small intestinal villi and by Western blotting that their protein expression increases in distal direction. Furthermore, we observed an elevated transport activity of the neutral amino acid L-isoleucine during the nocturnal active phase compared to the inactive one. Gastric emptying was delayed by intragastric application of an amino acid cocktail but we observed no acute dietary regulation of B(0)AT1 protein expression and L-isoleucine transport. Investigation of the chronic dietary regulation of B(0)AT1, ACE2 and CD13 by different diets revealed an increased B(0)AT1 protein expression under amino acid-supplemented diet in the proximal section but not in the distal one and for ACE2 protein expression a reverse localization of the effect. Dietary regulation for CD13 protein expression was not as distinct as for the two other proteins. Ring uptake experiments showed a tendency for increased L-isoleucine uptake under amino acid-supplemented diet and in vivo L-isoleucine absorption was more efficient under high protein and amino acid-supplemented diet. Additionally, plasma levels of branched-chain amino acids were elevated under high protein and amino acid diet. Taken together, our experiments did not reveal an acute amino acid-induced regulation of B(0)AT1 but revealed a chronic dietary adaptation mainly restricted to the proximal segment of the small intestine.


title: Health care workers’ perceptions and reported use of respiratory protective equipment: A qualitative analysis

text: BACKGROUND: Little is known about health care workers’ (HCW) perceptions of, or experiences using, respiratory protective equipment (RPE). We sought to characterize their perceptions and identify reasons underlying inappropriate use. METHODS: We conducted 12 focus groups with nurses and nursing assistants at 4 medical centers. We analyzed the thematic content of 73 discrete “stories” told by focus group participants. RESULTS: We identified 5 story types surrounding RPE use: 1) policies are known and seen during work routines; 2) during protocol lapses, use is reinforced through social norms; 3) clinical experiences sometimes supersede protocol adherence; 4) when risk perception is high, we found concern regarding accessing RPE; and 5) HCWs in emergency departments were viewed as not following protocol because risk was ever-present. DISCUSSION: HCWs were aware of the importance of RPE and protocols for using it, and these supported use when protocol lapses occurred. However, protocol adherence was undermined by clinical experience, perceived risk, and the distinct context of the emergency department where patients continually arrive with incomplete or delayed diagnoses. CONCLUSIONS: Protocols, visual cues, and social norms contribute to a culture of safety. This culture can be undermined when HCWs experience diagnostic uncertainty or they mistrust the protocol and instead rely on their clinical experiences.


title: Pathogeneses of respiratory infections with virulent and attenuated vaccinia viruses

text: BACKGROUND: Respiratory infection with the neurovirulent vaccinia virus (VV) strain Western Reserve (WR) results in an acute infection of the lung followed by dissemination of the virus to other organs and causes lethality in mice. The mechanisms of lethality are not well-understood. In this study, we analyzed virus replication and host immune responses after intranasal infection with lethal and non-lethal doses of VV using the WR strain and the less virulent Wyeth strain. RESULTS: The WR strain replicated more vigorously in the lung and in the brain than the Wyeth strain. There were, however, no differences between the virus titers in the brains of mice infected with the higher lethal dose and the lower non-lethal dose of WR strain, suggesting that the amount of virus replication in the brain is unlikely to be the sole determining factor of lethality. The WR strain grew better in primary mouse lung cells than the Wyeth strain. Lethal infection with WR strain was associated with a reduced number of lymphocytes and an altered phenotype of the T cells in the lung compared to non-lethal infections with the WR or Wyeth strains. Severe thymus atrophy with a reduction of CD4 and CD8 double positive T cells was also observed in the lethal infection. CONCLUSION: These results suggest that the lethality induced by intranasal infection with a high dose of the WR strain is caused by the higher replication of virus in lung cells and immune suppression during the early phase of the infection, resulting in uncontrolled virus replication in the lung.


title: Therapeutic strategies for critically ill patients with COVID-19

text: Since the 2019 novel coronavirus disease (COVID-19) outbreak originated from Wuhan, Hubei Province, China, at the end of 2019, it has become a clinical threat to the general population worldwide. Among people infected with the novel coronavirus (2019-nCoV), the intensive management of the critically ill patients in intensive care unit (ICU) needs substantial medical resource. In the present article, we have summarized the promising drugs, adjunctive agents, respiratory supportive strategies, as well as circulation management, multiple organ function monitoring and appropriate nutritional strategies for the treatment of COVID-19 in the ICU based on the previous experience of treating other viral infections and influenza. These treatments are referable before the vaccine and specific drugs are available for COVID-19.


title: Mutational Analysis of the SARS Virus Nsp15 Endoribonuclease: Identification of Residues Affecting Hexamer Formation

text: The severe acute respiratory syndrome (SARS) coronavirus virus non-structural protein 15 is a Mn2+-dependent endoribonuclease with specificity for cleavage at uridylate residues. To better understand structural and functional characteristics of Nsp15, 22 mutant versions of Nsp15 were produced in Escherichia coli as His-tagged proteins and purified by metal-affinity and ion-exchange chromatography. Nineteen of the mutants were soluble and were analyzed for enzymatic activity. Six mutants, including four at the putative active site, were significantly reduced in endoribonuclease activity. Two of the inactive mutants had unusual secondary structures compared to the wild-type protein, as measured by circular dichroism spectroscopy. Gel-filtration analysis, velocity sedimentation ultracentrifugation, and native gradient pore electrophoresis all showed that the wild-type protein exists in an equilibrium between hexamers and monomers in solution, with hexamers dominating at micromolar protein concentration, while native gradient pore electrophoresis also revealed the presence of trimers. A mutant in the N terminus of Nsp15 was impaired in hexamer formation and had low endoribonuclease activity, suggesting that oligomerization is required for endoribonuclease activity. This idea was supported by titration experiments showing that enzyme activity was strongly concentration-dependent, indicating that oligomeric Nsp15 is the active form. Three-dimensional reconstruction of negatively stained single particles of Nsp15 viewed by transmission electron microscopic analysis suggested that the six subunits were arranged as a dimer of trimers with a number of cavities or channels that may constitute RNA binding sites.


title: Management of the ACC/AHA Stage D Patient Cardiac Transplantation

text: Over the last 4 decades, cardiac transplantation has become the preferred therapy for select patients with end-stage heart disease. Heart transplantation is indicated in patients with heart failure despite optimal medical and device therapy, manifesting as intractable angina, refractory heart failure, or intractable ventricular arrhythmias. This article provides an overview of heart transplantation in the current era, focusing on the evaluation process for heart transplantation, the physiology of the transplanted heart, immunosuppressive regimens, and early and long-term complications.


title: China's unique role in the field of global health

text: Abstract China's participation in global governance, inspired by the 17 United Nations Sustainable Development Goals, is driven by the guiding principle of “building a community of shared future for mankind”. China has been promoting the Belt and Road Initiative and South-South Cooperation and has made significant contributions to the prosperity of human beings. Along with the opportunities that globalization brought about such as the World Health Organization and the boom in the economy, global health challenges also emerged. This resulted in certain obstacles for China when it sought to advocate the Belt and Road Initiative and when it attempted to carry out its strategy to address global health issues. What are the emerging challenges for global health? What can China do for global health? Why does global health need China? We tried to address these questions as China's global engagement continues to expand in the new era. This article makes the case for Chinese approaches, including getting involved in public health, being consistent in addressing local conditions, sharing China's experience with handling health services, and strengthening government-led action while being guided by relative policies. China has a lot to offer in the promotion of global health and in overcoming the challenges and risks that this goal currently faces. Thus, China should be considered an inseparable part of global health governance and bilateral health development cooperation.


title: Future of Medical Decision Support Systems

text: After having an introduction to the essential topics, the previous chapters have all provided effective use of deep learning for diagnosis of important diseases, as they are base for the medical decision support systems. There are of course many more research aspects to be discussed but if is also a good approach to focus on some insights regarding future of medical decision support systems.


title: Environmental Cleaning in Resource-Limited Settings

text: PURPOSE OF REVIEW: Environmental surfaces in healthcare facilities, particularly in a patient room, are a critical pathway for healthcare-associated pathogen transmission. Despite well-established guides and recommendations regarding environmental surface cleaning and disinfection, there are several challenges in resource-limited settings. This viewpoint article will discuss the practice of environmental cleaning in resource-limited settings including challenges and relationship between environment and healthcare-associated infections in this setting and outlines pre-requisites to overcome these challenges. RECENT FINDINGS: Despite several barriers and challenges, environmental cleaning is a crucial component to help reduce transmission of healthcare-associated infections and multi-drug-resistant pathogens as well as emerging infectious disease-associated pathogens in resource-limited settings. However, there is a need to develop a multi-modal strategy together with a mechanism for monitor and feedback to improve the practices of environmental cleaning in resource-limited settings. SUMMARY: Additional researches on the barriers and implementation gaps and the role of collaborative network as well as how to apply technology would provide significant insights on the practices of environmental cleaning in resource-limited settings.


title: Project IDentif.AI: Harnessing Artificial Intelligence to Rapidly Optimize Combination Therapy Development for Infectious Disease Intervention

text: In 2019/2020, the emergence of coronavirus disease 2019 (COVID‐19) resulted in rapid increases in infection rates as well as patient mortality. Treatment options addressing COVID‐19 included drug repurposing, investigational therapies such as remdesivir, and vaccine development. Combination therapy based on drug repurposing is among the most widely pursued of these efforts. Multi‐drug regimens are traditionally designed by selecting drugs based on their mechanism of action. This is followed by dose‐finding to achieve drug synergy. This approach is widely‐used for drug development and repurposing. Realizing synergistic combinations, however, is a substantially different outcome compared to globally optimizing combination therapy, which realizes the best possible treatment outcome by a set of candidate therapies and doses toward a disease indication. To address this challenge, the results of Project IDentif.AI (Identifying Infectious Disease Combination Therapy with Artificial Intelligence) are reported. An AI‐based platform is used to interrogate a massive 12 drug/dose parameter space, rapidly identifying actionable combination therapies that optimally inhibit A549 lung cell infection by vesicular stomatitis virus within three days of project start. Importantly, a sevenfold difference in efficacy is observed between the top‐ranked combination being optimally and sub‐optimally dosed, demonstrating the critical importance of ideal drug and dose identification. This platform is disease indication and disease mechanism‐agnostic, and potentially applicable to the systematic N‐of‐1 and population‐wide design of highly efficacious and tolerable clinical regimens. This work also discusses key factors ranging from healthcare economics to global health policy that may serve to drive the broader deployment of this platform to address COVID‐19 and future pandemics.


title: Immunogenicity and antigenic relationships among spike proteins of porcine epidemic diarrhea virus subtypes G1 and G2

text: Porcine epidemic diarrhea virus (PEDV) is a coronavirus that infects cells lining the small intestine of swine, resulting in vomiting, diarrhea, and dehydration. The amino acid sequence of the spike (S) protein, which is the principal target recognized by host immune cells, has multiple mutations that distinguish the two PEDV genotypes, G1 and G2. To determine whether these mutations lead to changes in antigenicity, as suggested by the failure of PEDV vaccines in China, we first optimized the codons of typical S genes of the CV777 vaccine strain (G1 subtype) and LNCT2 strain (G2 subtype) and expressed the recombinant full-length sequence of the S protein in a eukaryotic expression system. The IgG antibody levels of serum from mice immunized with purified S protein were markedly high. Antigenicity was compared by detection of polyclonal antibodies (PAbs) against the virus and S protein using an enzyme-linked immunosorbent assay (ELISA), an indirect immunofluorescence assay (IFA), and a serum cross-neutralization (SN) assay. Reactivity with the PAbs revealed significant cross-reactivity between the two PEDV subtypes, although there was a twofold difference in the antigenic responses based on PAb titers in the ELISA and IFA. Consistent with the variation in the S gene sequences, the SN titer suggested differences in the neutralization activity of the S protein between the two subtypes, which could explain the antigenic variation between the PEDV subtypes G1 and G2.


title: Exploring the Uptake of Advance Care Planning in Older Adults: An Integrative Review

text: CONTEXT: Advance Care Planning (ACP) is essential to elicit goals, values, and preferences of care in older adults with serious illness and on trajectories of frailty. An exploration of ACP uptake in older adults may identify barriers and facilitators. OBJECTIVE: To conduct an integrative review of research on the uptake of ACP in older adults, and create a conceptual model of the findings. METHODS: Using Whittemore and Knafl’s methodology, we systematically searched four electronic databases of ACP literature in older adults from 1996 through December 2019. Critical appraisal tools were utilized to assess study quality and articles were categorized according to level of evidence. Statistical and thematic analysis was then undertaken. RESULTS: Among 1081 studies, 78 met inclusion criteria. Statistical analysis evaluated ACP and variables within the domains of demographics, psychosocial, disability and functioning, and miscellaneous variables. Thematic analysis identified a central category of enhanced communication, followed by categories of: (1) provider role and preparation; (2) patient/family relationship patterns; (3) standardized processes and structured approaches; (4) contextual influences; and (5) missed opportunities. A conceptual model depicted categories and relationships. CONCLUSIONS: Enhanced communication and ACP facilitators improve uptake of ACP. Clinicians should be cognizant of these factors. This review provides a guide for clinicians who are considering implementation strategies to facilitate ACP in real-world settings.


title: Laboratory-acquired infections: Are microbiologists at risk?

text: Exposure of laboratory workers to infectious agents in the clinical microbiology laboratory continues to be an occupational risk. This risk is mitigated by the application of safety guidelines issued by regulatory agencies and professional organizations. The Clinical and Laboratory Standards Institute (fomerly NCCLS) published a guidance document (M29-A3) in 2005 on the risk of transmission of infectious agents in the laboratory, preventative measures to reduce risk, and management of exposure to infectious agents. The key to a safe workplace is employees who are knowledgeable of the routes of transmission of infectious agents in the laboratory setting and apply safety principles and work practices to reduce the risk.


Thoughts about Public Space During Covid‐19 Pandemic


title: CEACAM1 recognition by bacterial pathogens is species-specific

text: BACKGROUND: Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), an immunoglobulin (Ig)-related glycoprotein, serves as cellular receptor for a variety of Gram-negative bacterial pathogens associated with the human mucosa. In particular, Neisseria gonorrhoeae, N. meningitidis, Moraxella catarrhalis, and Haemophilus influenzae possess well-characterized CEACAM1-binding adhesins. CEACAM1 is typically involved in cell-cell attachment, epithelial differentiation, neovascularisation and regulation of T-cell proliferation, and is one of the few CEACAM family members with homologues in different mammalian lineages. However, it is unknown whether bacterial adhesins of human pathogens can recognize CEACAM1 orthologues from other mammals. RESULTS: Sequence comparisons of the amino-terminal Ig-variable-like domain of CEACAM1 reveal that the highest sequence divergence between human, murine, canine and bovine orthologues is found in the β-strands comprising the bacteria-binding CC'FG-face of the Ig-fold. Using GFP-tagged, soluble amino-terminal domains of CEACAM1, we demonstrate that bacterial pathogens selectively associate with human, but not other mammalian CEACAM1 orthologues. Whereas full-length human CEACAM1 can mediate internalization of Neisseria gonorrhoeae in transfected cells, murine CEACAM1 fails to support bacterial internalization, demonstrating that the sequence divergence of CEACAM1 orthologues has functional consequences with regard to bacterial recognition and cellular invasion. CONCLUSIONS: Our results establish the selective interaction of several human-restricted bacterial pathogens with human CEACAM1 and suggest that co-evolution of microbial adhesins with their corresponding receptors on mammalian cells contributes to the limited host range of these highly adapted infectious agents.


title: The Global Impact of the Coronavirus Pandemic

text: The coronavirus pandemic has engulfed the nations of the world for the first five months of 2020 and altered the pace, fabric and nature of our lives. In this overview accompanying the Special Issue of Cytokine & Growth Factor Reviews, we examine some of the many social and scientific issues impacted by SARS-CoV2 – personal lives, economy, scientific communication, the environment. International members of Istituto Pasteur in Rome and INITIATE, the Marie Curie Training Network reflect on the lasting global impact of the coronavirus pandemic.


title: The rapid transformation of cardiac surgery practice in the coronavirus disease 2019 (COVID-19) pandemic: Insights and clinical strategies from a center at the epicenter

text: BACKGROUND: The onset of the coronavirus disease 2019 (COVID-19) pandemic has forced our cardiac surgery program and hospital to enact drastic measures that has forced us to change how we care for cardiac surgery patients, assist with COVID-19 care, and enable support for the hospital in terms of physical resources, providers, and resident training. METHODS: In this review, we review the cardiovascular manifestations of COVID-19 and describe our system-wide adaptations to the pandemic, including the use of telemedicine, how a severe reduction in operative volume affected our program, the process of redeployment of staff, repurposing of residents into specific task teams, the creation of operation room intensive care units, and the challenges that we faced in this process. RESULTS: We offer a revised set of definitions of surgical priority during this pandemic and how this was applied to our system, followed by specific considerations in coronary/valve, aortic, heart failure and transplant surgery. Finally, we outline a path forward for cardiac surgery for the near future. CONCLUSIONS: We recognize that individual programs around the world will eventually face COVID-19 with varying levels of infection burden and different resources, and we hope this document can assist programs to plan for the future.


title: (Indoor) isolation, stress and physical inactivity: vicious circles accelerated by Covid‐19?

text: The Covid‐19 epidemic necessitates the application of strict isolation strategies to curb virus spreading. Isolation of individuals in combination with fear of contagion, quarantine and stigma, as well as with potential (mis)information overload (“infodemic”)(1), however, causes chronic stress and is associated with a burden on mental health, posing risk factors for anxiety and depression. It is well understood that chronic stress is a major modulator of immunity(2) and thus directly influences probability of infection.


title: Spike proteins of novel MERS-coronavirus isolates from North- and West-African dromedary camels mediate robust viral entry into human target cells

text: Abstract The highly pathogenic Middle East respiratory syndrome (MERS)-related coronavirus (CoV) is transmitted from dromedary camels, the natural reservoir, to humans. For at present unclear reasons, MERS cases have so far only been observed in the Arabian Peninsula, although MERS-CoV also circulates in African dromedary camels. A recent study showed that MERS-CoV found in North/West- (Morocco) and West-African (Burkina Faso and Nigeria) dromedary camels are genetically distinct from Arabian viruses and have reduced replicative capacity in human cells, potentially due to amino acid changes in one or more viral proteins. Here, we show that the spike (S) proteins of the prototypic Arabian MERS-CoV strain, human betacoronavirus 2c EMC/2012, and the above stated African MERS-CoV variants do not appreciably differ in expression, DPP4 binding and ability to drive entry into target cells. Thus, virus-host-interactions at the entry stage may not limit spread of North- and West-African MERS-CoV in human cells.


title: Epidemiology, Pathogenesis, and Treatment of the Common Cold

text: Objective Reading this article will reinforce the reader's knowledge of the pathogenesis of the common cold. The rationale for current and potential therapies for the common cold are reviewed in the context of current concepts of the pathogenesis of these illnesses. Data sources and study selection A MEDLINE literature search was done using the search terms common cold, rhinovirus, and viral respiratory infection. The search was restricted to the English language. Articles were selected for review if the title and/or abstract suggested the content was relevant to the subject of this review. The bibliographies of selected articles were used as a source of additional literature. Results Recent studies suggest that the host response to the virus is an important contributor to the pathogenesis of the common cold. Inflammatory mediators, especially the pro-inflammatory cytokines, appear to be an important component of this response and present an attractive target for new interventions for common cold therapies. Currently available treatments for the common cold have limited efficacy against specific symptoms. These therapies should be selected to treat the specific symptoms that are perceived to be the most bothersome by the patient.


title: Engagement and Education: Care of the Critically Ill and Injured During Pandemics and Disasters: CHEST Consensus Statement

text: BACKGROUND: Engagement and education of ICU clinicians in disaster preparedness is fragmented by time constraints and institutional barriers and frequently occurs during a disaster. We reviewed the existing literature from 2007 to April 2013 and expert opinions about clinician engagement and education for critical care during a pandemic or disaster and offer suggestions for integrating ICU clinicians into planning and response. The suggestions in this article are important for all of those involved in a pandemic or large-scale disaster with multiple critically ill or injured patients, including front-line clinicians, hospital administrators, and public health or government officials. METHODS: A systematic literature review was performed and suggestions formulated according to the American College of Chest Physicians (CHEST) Consensus Statement development methodology. We assessed articles, documents, reports, and gray literature reported since 2007. Following expert-informed sorting and review of the literature, key priority areas and questions were developed. No studies of sufficient quality were identified upon which to make evidence-based recommendations. Therefore, the panel developed expert opinion-based suggestions using a modified Delphi process. RESULTS: Twenty-three suggestions were formulated based on literature-informed consensus opinion. These suggestions are grouped according to the following thematic elements: (1) situational awareness, (2) clinician roles and responsibilities, (3) education, and (4) community engagement. Together, these four elements are considered to form the basis for effective ICU clinician engagement for mass critical care. CONCLUSIONS: The optimal engagement of the ICU clinical team in caring for large numbers of critically ill patients due to a pandemic or disaster will require a departure from the routine independent systems operating in hospitals. An effective response will require robust information systems; coordination among clinicians, hospitals, and governmental organizations; pre-event engagement of relevant stakeholders; and standardized core competencies for the education and training of critical care clinicians.


title: Establishment of feline intestinal epithelial cell cultures for the propagation and study of feline enteric coronaviruses

text: Feline infectious peritonitis (FIP) is the most feared infectious cause of death in cats, induced by feline infectious peritonitis virus (FIPV). This coronavirus is a virulent mutant of the harmless, ubiquitous feline enteric coronavirus (FECV). To date, feline coronavirus (FCoV) research has been hampered by the lack of susceptible cell lines for the propagation of serotype I FCoVs. In this study, long-term feline intestinal epithelial cell cultures were established from primary ileocytes and colonocytes by simian virus 40 (SV40) T-antigen- and human Telomerase Reverse Transcriptase (hTERT)-induced immortalization. Subsequently, these cultures were evaluated for their usability in FCoV research. Firstly, the replication capacity of the serotype II strains WSU 79–1683 and WSU 79–1146 was studied in the continuous cultures as was done for the primary cultures. In accordance with the results obtained in primary cultures, FCoV WSU 79–1683 still replicated significantly more efficient compared to FCoV WSU 79–1146 in both continuous cultures. In addition, the cultures were inoculated with faecal suspensions from healthy cats and with faecal or tissue suspensions from FIP cats. The cultures were susceptible to infection with different serotype I enteric strains and two of these strains were further propagated. No infection was seen in cultures inoculated with FIPV tissue homogenates. In conclusion, a new reliable model for FCoV investigation and growth of enteric field strains was established. In contrast to FIPV strains, FECVs showed a clear tropism for intestinal epithelial cells, giving an explanation for the observation that FECV is the main pathotype circulating among cats.


title: Ubiquitination, Ubiquitin-like Modifiers, and Deubiquitination in Viral Infection

text: Ubiquitin is important for nearly every aspect of cellular physiology. All viruses rely extensively on host machinery for replication; therefore, it is not surprising that viruses connect to the ubiquitin pathway at many levels. Viral involvement with ubiquitin occurs either adventitiously because of the unavoidable usurpation of cellular processes, or for some specific purpose selected for by the virus to enhance viral replication. Here, we review current knowledge of how the ubiquitin pathway alters viral replication and how viruses influence the ubiquitin pathway to enhance their own replication.


title: Deubiquitinating Enzymes Related to Autophagy: New Therapeutic Opportunities?

text: Autophagy is an evolutionary conserved catabolic process that allows for the degradation of intracellular components by lysosomes. This process can be triggered by nutrient deprivation, microbial infections or other challenges to promote cell survival under these stressed conditions. However, basal levels of autophagy are also crucial for the maintenance of proper cellular homeostasis by ensuring the selective removal of protein aggregates and dysfunctional organelles. A tight regulation of this process is essential for cellular survival and organismal health. Indeed, deregulation of autophagy is associated with a broad range of pathologies such as neuronal degeneration, inflammatory diseases, and cancer progression. Ubiquitination and deubiquitination of autophagy substrates, as well as components of the autophagic machinery, are critical regulatory mechanisms of autophagy. Here, we review the main evidence implicating deubiquitinating enzymes (DUBs) in the regulation of autophagy. We also discuss how they may constitute new therapeutic opportunities in the treatment of pathologies such as cancers, neurodegenerative diseases or infections.


title: Tracking and predicting growth areas in science

text: We explore the possibility of using co-citation clusters over three time periods to track the emergence and growth of research areas, and predict their near term change. Data sets are from three overlapping six-year periods: 1996-2001, 1997-2002 and 1998-2003. The methodologies of co-citation clustering, mapping, and string formation are reviewed, and a measure of cluster currency is defined as the average age of highly cited papers relative to the year span of the data set. An association is found between the currency variable in a prior period and the percentage change in cluster size and citation frequency in the following period. The conflating factor of “single-issue clusters” is discussed and dealt with using a new metric called in-group citation.


Correction to Lancet Public Health 2020; 5; e261–70


title: Proteasome Inhibitors Enhance Bacteriophage Lambda (λ) Mediated Gene Transfer in Mammalian Cells

text: Bacteriophage lambda vectors can transfer their genomes into mammalian cells, resulting in expression of phage-encoded genes. However, this process is inefficient. Experiments were therefore conducted to delineate the rate limiting step(s) involved, using a phage vector that contains a mammalian luciferase reporter gene cassette. The efficiency of phage-mediated gene transfer in mammalian cells was quantitated, in the presence or absence of pharmacologic inhibitors of cell uptake and degradation pathways. Inhibitors of lysosomal proteases and proteasome inhibitors strongly enhanced phage-mediated luciferase expression, suggesting that these pathways contribute to the destruction of intracellular phage particles. In contrast, inhibition of endosome acidification had no effect on phage-mediated gene transfer, presumably because phage lambda is tolerant to extended exposure to low pH. These findings provide insights into the pathways by which phage vectors enter and transduce mammalian cells, and suggest that it may be possible to pharmacologically enhance the efficiency of phage-mediated gene transfer in mammalian cells. Finally, the data also suggest that the proteasome complex may serve as an innate defense mechanism that restricts the infection of mammalian cells by diverse viral agents.


title: Comparison of clinical and microbiological diagnoses for older adults with COVID-19 in Wuhan: a retrospective study

text: BACKGROUND: The potential differences between a clinical diagnosis of coronavirus disease 2019 (COVID-19) (i.e., symptoms without positive virus test) and a microbiological diagnosis (i.e., positive virus test results) of COVID-19 are not known. AIMS: This study explored the differences between the two types of COVID-19 diagnosis among older patients in terms of clinical characteristics and outcomes. METHODS: A total of 244 inpatients aged ≥ 60 years with COVID-19 were included in this study, of whom 52 were clinically diagnosed and 192 were microbiologically diagnosed. Clinical and laboratory data on hospital admission and outcomes (discharged or died in hospital) of all patients were retrieved from medical records retrospectively. Patients who met the criteria for clinical diagnosis with negative virus test results were assigned to the clinical diagnosis group, whereas those with positive virus test results were assigned to the microbiological diagnosis group. After univariate analyses, two propensity score analyses [i.e., covariate adjustment using propensity score (CAPS) and propensity score matching (PSM)] were conducted to control bias. RESULTS: The clinical and microbiological diagnosis groups demonstrated significant differences in outcomes and in the majority of laboratory findings. After propensity score analyses, many differences between the two groups disappeared and the rate of mortality had no statistically significant difference (P = 0.318 and 0.828 for CAPS and PSM, respectively). CONCLUSIONS: Patients with similar signs, symptoms, and laboratory and imaging findings as confirmed COVID-19 cases may have a similar mortality risk, regardless of the virus test results, and require timely intervention to reduce their mortality.


title: The liaison between respiratory failure and high blood pressure: evidence from COVID-19 patients

text: In COVID-19 patients respiratory failure is associated with increase systemic blood pressure conceivably due to the modulation of renin-angiotensin-aldosterone system by SARS-CoV-2 infection.


title: Improved survival rates in patients with H1N1 acute respiratory failure in Korea between 2009 and 2016

text: There was a pandemic of influenza A (H1N1) in 2009; in Korea, there was also an H1N1 epidemic in 2016. We aim to investigate whether survival had improved in the setting of recent advances in intensive care unit (ICU) management. We conducted a retrospective analysis of acute respiratory failure patients with H1N1 influenza pneumonia in 2016 and 2009 respectively at two tertiary referral hospitals in Korea. A total of 28 patients were treated in 2016, and 34 in 2009. There was no significant difference in SOFA scores on ICU admission day. In-hospital mortality was significantly lower in patients of 2016 compared to those of 2009 (18% vs. 44% P = 0.028). By multivariable analyses, the treatment year 2016 was associated with a greater likelihood of survival. Compared to the patients treated in 2009, those treated in 2016 were one seventh as likely to die after adjusting for other clinical variables (hazard ratio for mortality, 0.15; 95% confidence interval. 0.03–0.63, P = 0.010). Improved survival in patients who underwent extracorporeal membrane oxygenation treatment (in-hospital mortality, 17% vs. 60%, P = 0.242) and decreased tidal volumes during mechanical ventilation (median 5.4 mL/kg vs. median 9.2 mL/kg, P = 0.018) were observed in 2016 compared to 2009. Treatment outcomes for patients with H1N1 acute respiratory failure improved from 2009 to 2016 in two tertiary referral centers in South Korea.


title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response

text: ABSTRACT We report a patient who had travelled to Japan presented mild respiratory symptom during the COVID-19 infection outbreak period. There was transient existence of SARS-CoV-2 RNA in his oropharynx. The RNA was absent in the six respiratory specimens that were subsequently tested. Anti-SARS-CoV-2 antibody response in the acute and convalescent sera were absent. The reported case indicates that transient colonization of SARS-CoV-2 in the upper respiratory tract is possible without inciting any antibody response against the virus.


Diabetes during the COVID‐19 Pandemic: A Global Call to Reconnect with Patients and Emphasize Lifestyle Changes and Optimise Glycemic and Blood Pressure Control


title: Potential of Black Soldier Fly Production for Pacific Small Island Developing States

text: SIMPLE SUMMARY: The black soldier fly is an insect of which the larvae can eat almost any organic matter, including organic waste. The larvae are edible and can be fed to livestock, fish, or even people. Around the world, black soldier fly farms and composting facilities are being established to process waste into animal feed, with economic and environmental benefits. The Pacific Small Island Developing States stand to benefit greatly from black soldier fly farming to solve multiple problems they face, due in large part to overpopulation, urbanization, and climate change. We reviewed the pressing issues in each of these nations, how black soldier fly production could help them, and which obstacles need to be cleared to make this possible. ABSTRACT: Organic waste such as food waste and livestock manure is a serious concern in the Pacific Islands, where landfills are overflowing and illegal dumping of waste threatens the fragile ecosystems. Organic waste also attracts filth flies, some of which are vectors for pathogens that cause human disease. The black soldier fly, Hermetia illucens, has tremendous potential for the Pacific Islands. Capable of digesting almost any organic matter and converting it into insect biomass, black soldier flies are already being used around the world to process organic waste into larvae. The system can be adapted to large-scale municipal composting as well as small sizes for individual livestock farms or even urban households. The larvae can be fed live to fish or poultry, processed into feed comparable to fishmeal or soy meal, or even used to generate biofuel. Thus, the fly not only eliminates waste, but also can improve the sustainability of livestock production. The Pacific Small Island Developing States stand to benefit immensely from black soldier fly bioconversion facilities, used primarily as a means to compost organic waste; however, several knowledge gaps must first be addressed. We reviewed the state of black soldier flies in the Pacific and identified where their use shows the most promise. Research priorities for the field include fly surveys and bioconversion assays using Pacific crop waste.


title: Clinical analysis of risk factors for severe COVID-19 patients with type 2 diabetes()

text: AIMS: To describe characteristics of COVID-19 patients with type 2 diabetes and to analyze risk factors for severity. METHODS: Demographics, comorbidities, symptoms, laboratory findings, treatments and outcomes of COVID-19 patients with diabetes were collected and analyzed. RESULTS: Seventy-four COVID-19 patients with diabetes were included. Twenty-seven patients (36.5%) were severe and 10 patients (13.5%) died. Higher levels of blood glucose, serum amyloid A (SAA), C reactive protein and interleukin 6 were associated with severe patients compared to non-severe ones (P < 0.05). Levels of albumin, cholesterol, high density lipoprotein, small and dense low density lipoprotein and CD4(+) T lymphocyte counts in severe patients were lower than those in non-severe patients (P < 0.05). Logistic regression analysis identified decreased CD4(+) T lymphocyte counts (odds ratio [OR] = 0.988, 95%Confidence interval [95%CI] 0.979–0.997) and increased SAA levels (OR = 1.029, 95%CI 1.002–1.058) as risk factors for severity of COVID-19 with diabetes (P < 0.05). CONCLUSIONS: Type 2 diabetic patients were more susceptible to COVID-19 than overall population, which might be associated with hyperglycemia and dyslipidemia. Aggressive treatment should be suggested, especially when these patients had low CD4(+) T lymphocyte counts and high SAA levels.


title: The COVID‐19 epidemic of manuscripts

text: In the midst of the novel coronavirus pandemic—referred to as COVID‐19—there has been much uncertainty. We remain uncertain about its precise origin, its structure and composition, how best to test for it, or for resulting immunity, whether or not exposure leads to immunity, whether or not disposable surgical masks are effective, why men and some ethnic minorities are more susceptible and just exactly what the death rate as a result of this virus is. However, one thing is absolutely clear, there has been an epidemic of manuscripts on the subject of COVID‐19 to nursing journals and, amongst these new manuscripts the rejection rate is, unfortunately, very high.


title: ISG15 in antiviral immunity and beyond

text: The host response to viral infection includes the induction of type I interferons and the subsequent upregulation of hundreds of interferon-stimulated genes. Ubiquitin-like protein ISG15 is an interferon-induced protein that has been implicated as a central player in the host antiviral response. Over the past 15 years, efforts to understand how ISG15 protects the host during infection have revealed that its actions are diverse and pathogen-dependent. In this Review, we describe new insights into how ISG15 directly inhibits viral replication and discuss the recent finding that ISG15 modulates the host damage and repair response, immune response and other host signalling pathways. We also explore the viral immune-evasion strategies that counteract the actions of ISG15. These findings are integrated with a discussion of the recent identification of ISG15-deficient individuals and a cellular receptor for ISG15 that provides new insights into how ISG15 shapes the host response to viral infection.


title: Signal detection as the first line of defence in tourism crisis management

text: The vulnerability of the tourism industry to a range of crises has attracted many scholars to investigate the crisis strategies and practices employed by destinations and tourism organizations mainly with regards to crisis preparedness, containment and damage limitation, crisis recovery and subsequent learning. One over-looked area has been that of crisis signal detection. This paper proposes a three-stage conceptual framework for crisis signal detection consisting of signal scanning, capture and transmission to the crisis response centre. With this framework as a basis, 16 corporate level executives of international tourism organizations were interviewed in order to explore the significance of signal detection in their crisis management practice and the challenges faced in each of these three stages. The findings offer insights into the design of crisis management mechanisms and open areas for further research.


title: Infections in pediatric solid organ transplant recipients

text: Despite the progress made in graft and patient survival in recent years, infectious complications remain a major source of morbidity and mortality in pediatric solid organ transplant recipients. The risk of infection after transplant is determined by the interaction of several factors, including age, type of organ transplanted, type and intensity of immunosuppression, environmental exposures, and the consequences of invasive procedures. Compared with adult transplant recipients, children are at higher risk of developing primary infection with various organisms after transplantation, as they often lack previous immunity from natural exposure to many microbes and often have not completed their primary immunization series at the time of transplantation. This article provides an overview of the risk factors, timing, and types of infectious complications associated with organ transplantation in children.


title: SPINT2 inhibits proteases involved in activation of both influenza viruses and metapneumoviruses

text: Abstract Viruses possessing class I fusion proteins require proteolytic activation by host cell proteases to mediate fusion with the host cell membrane. The mammalian SPINT2 gene encodes a protease inhibitor that targets trypsin-like serine proteases. Here we show the protease inhibitor, SPINT2, restricts cleavage-activation efficiently for a range of influenza viruses and for human metapneumovirus (HMPV). SPINT2 treatment resulted in the cleavage and fusion inhibition of full-length influenza A/CA/04/09 (H1N1) HA, A/Aichi/68 (H3N2) HA, A/Shanghai/2/2013 (H7N9) HA and HMPV F when activated by trypsin, recombinant matriptase or KLK5. We also demonstrate that SPINT2 was able to reduce viral growth of influenza A/CA/04/09 H1N1 and A/X31 H3N2 in cell culture by inhibiting matriptase or TMPRSS2. Moreover, inhibition efficacy did not differ whether SPINT2 was added at the time of infection or 24 h post-infection. Our data suggest that the SPINT2 inhibitor has a strong potential to serve as a novel broad-spectrum antiviral.


title: The Virome of the Human Respiratory Tract

text: The human respiratory tract virome is defined here as the viruses present in the human respiratory tract that can infect human cells. Sensitive, culture-independent molecular assays (polymerase chain reaction and high-throughput sequencing) reveal that in addition to common viruses that cause acute, symptomatic infections the virome also includes viruses that do not cause clinical symptoms, have unknown pathogenic effect, or cause symptoms but are not among the most common viral respiratory tract pathogens. These molecular tools provide means for better defining the virome and studying the effects of viral infections on the dynamics of chronic lung diseases.


title: An Unexpected Outbreak of Middle East Respiratory Syndrome Coronavirus Infection in the Republic of Korea, 2015

text: This report includes a summary of a current outbreak of the Middle East Respiratory Syndrome Coronavirus infection in the Republic of Korea as of June 23, 2015. Epidemiologic, clinical, and laboratory investigations of this outbreak are ongoing.


title: Requirements for empirical immunogenicity trials, rather than structure-based design, for developing an effective HIV vaccine

text: The claim that it is possible to rationally design a structure-based HIV-1 vaccine is based on misconceptions regarding the nature of protein epitopes and of immunological specificity. Attempts to use reverse vaccinology to generate an HIV-1 vaccine on the basis of the structure of viral epitopes bound to monoclonal neutralizing antibodies have failed so far because it was not possible to extrapolate from an observed antigenic structure to the immunogenic structure required in a vaccine. Vaccine immunogenicity depends on numerous extrinsic factors such as the host immunoglobulin gene repertoire, the presence of various cellular and regulatory mechanisms in the immunized host and the process of antibody affinity maturation. All these factors played a role in the appearance of the neutralizing antibody used to select the epitope to be investigated as potential vaccine immunogen, but they cannot be expected to be present in identical form in the host to be vaccinated. It is possible to rationally design and optimize an epitope to fit one particular antibody molecule or to improve the paratope binding efficacy of a monoclonal antibody intended for passive immunotherapy. What is not possible is to rationally design an HIV-1 vaccine immunogen that will elicit a protective polyclonal antibody response of predetermined efficacy. An effective vaccine immunogen can only be discovered by investigating experimentally the immunogenicity of a candidate molecule and demonstrating its ability to induce a protective immune response. It cannot be discovered by determining which epitopes of an engineered antigen molecule are recognized by a neutralizing monoclonal antibody. This means that empirical immunogenicity trials rather than structural analyses of antigens offer the best hope of discovering an HIV-1 vaccine.


title: Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis

text: A large number of viruses can individually and concurrently cause various respiratory illnesses. Metagenomic sequencing using next-generation sequencing (NGS) technology is capable of identifying a variety of pathogens. Here, we describe a method using a large panel of oligo probes to enrich sequence targets of 34 respiratory DNA and RNA viruses that reduces non-viral reads in NGS data and achieves high performance of sequencing-based pathogen identification. The approach can be applied to total nucleic acids purified from respiratory swabs stored in viral transport medium. Illumina TruSeq RNA Access Library procedure is used in targeted sequencing of respiratory viruses. The samples are subjected to RNA fragmentation, random reverse transcription, random PCR amplification, and ligation with barcoded library adaptors. The libraries are pooled and subjected to two rounds of enrichments by using a large panel of oligos designed to capture whole genomes of 34 respiratory viruses. The enriched libraries are amplified and sequenced using Illumina MiSeq sequencing system and reagents. This method can achieve viral detection sensitivity comparable with molecular assay and obtain partial to complete genome sequences for each virus to allow accurate genotyping and variant analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this chapter (10.1007/978-1-4939-8682-8_10) contains supplementary material, which is available to authorized users.


title: Evaluation of the survivability of MS2 viral aerosols deposited on filtering face piece respirator samples incorporating antimicrobial technologies

text: BACKGROUND: Respiratory protective devices exposed to pathogenic microorganisms present a potential source of transmission of infection during handling. In this study, the efficacy of 4 antimicrobial respirators to decontaminate MS2, a surrogate for pathogenic viruses, was evaluated and compared with control N95 filtering face piece respirators, which did not contain any known antimicrobial components. METHODS: MS2 containing droplet nuclei were generated using a Collison nebulizer and loaded onto respirator coupons at a face velocity of 13.2 cm/seconds for 30 minutes. The coupons were incubated at 2 different temperature and relative humidity (RH) conditions and analyzed for viable MS2 at different time intervals. RESULTS: Results showed that log(10) reduction of MS2 was not statistically significant (P > .05) between the control and antimicrobial respirator coupons, when stored at 22°C and 30% RH up to 20 hours. Coupons from 1 of the 4 antimicrobial respirators showed an average MS2 log(10) reduction of 3.7 at 37°C and 80% RH for 4 hours, which was statistically significant (P ≤ .05) compared with coupons from the control respirators. CONCLUSION: Results from this study suggest that MS2 virus decontamination efficacy of antimicrobial respirators is dependent on the antimicrobial agent and storage conditions.


title: MERS, SARS, and Ebola: The Role of Super-Spreaders in Infectious Disease

text: Super-spreading occurs when a single patient infects a disproportionate number of contacts. The 2015 MERS-CoV, 2003 SARS-CoV, and to a lesser extent 2014–15 Ebola virus outbreaks were driven by super-spreaders. We summarize documented super-spreading in these outbreaks, explore contributing factors, and suggest studies to better understand super-spreading.


title: Trend analysis of mortality rates and causes of death in children under 5 years old in Beijing, China from 1992 to 2015 and forecast of mortality into the future: an entire population-based epidemiological study

text: OBJECTIVES: To analyse trends in mortality and causes of death among children aged under 5 years in Beijing, China between 1992 and 2015 and to forecast under-5 mortality rates (U5MRs) for the period 2016–2020. METHODS: An entire population-based epidemiological study was conducted. Data collection was based on the Child Death Reporting Card of the Beijing Under-5 Mortality Rate Surveillance Network. Trends in mortality and leading causes of death were analysed using the χ(2) test and SPSS 19.0 software. An autoregressive integrated moving average (ARIMA) model was fitted to forecast U5MRs between 2016 and 2020 using the EViews 8.0 software. RESULTS: Mortality in neonates, infants and children aged under 5 years decreased by 84.06%, 80.04% and 80.17% from 1992 to 2015, respectively. However, the U5MR increased by 7.20% from 2013 to 2015. Birth asphyxia, congenital heart disease, preterm/low birth weight and other congenital abnormalities comprised the top five causes of death. The greatest, most rapid reduction was that of pneumonia by 92.26%, with an annual average rate of reduction of 10.53%. The distribution of causes of death differed among children of different ages. Accidental asphyxia and sepsis were among the top five causes of death in children aged 28 days to 1 year and accident was among the top five causes in children aged 1–4 years. The U5MRs in Beijing are projected to be 2.88‰, 2.87‰, 2.90‰, 2.97‰ and 3.09‰ for the period 2016–2020, based on the predictive model. CONCLUSION: Beijing has made considerable progress in reducing U5MRs from 1992 to 2015. However, U5MRs could show a slight upward trend from 2016 to 2020. Future considerations for child healthcare include the management of birth asphyxia, congenital heart disease, preterm/low birth weight and other congenital abnormalities. Specific preventative measures should be implemented for children of various age groups.


Improving antibiotic stewardship in COVID-19: bacterial co-infection is less common than with influenza


title: Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)—Novel insights into camelid immunity

text: Abstract Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, causing functional and structural changes in target proteins. Protein deimination causes generation of neo-epitopes, affects gene regulation and also allows for protein moonlighting. Furthermore, PADs have been found to be a phylogenetically conserved regulator for extracellular vesicle (EVs) release. EVs are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins in serum and serum-EVs are described for the first time in camelids, using the llama (Lama glama L. 1758) as a model animal. We report a poly-dispersed population of llama serum EVs, positive for phylogenetically conserved EV-specific markers and characterised by TEM. In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. In serum, 60 deiminated proteins were identified that were not in EVs, and 25 deiminated proteins were found to be unique to EVs, with 43 shared deiminated protein hits between both serum and EVs. Deiminated histone H3, a marker of neutrophil extracellular trap formation, was also detected in llama serum. PAD homologues were identified in llama serum by Western blotting, via cross reaction with human PAD antibodies, and detected at an expected 70 kDa size. This is the first report of deiminated proteins in serum and EVs of a camelid species, highlighting a hitherto unrecognized post-translational modification in key immune and metabolic proteins in camelids, which may be translatable to and inform a range of human metabolic and inflammatory pathologies.


title: Gene expression profiling of bovine bronchial epithelial cells exposed in vitro to bovine herpesvirus 1 and Mannheimia haemolytica

text: Abstract Bovine respiratory disease (BRD) often occurs when active respiratory virus infections (BHV-1, etc.) impair resistance to Mannheimia haemolytica infection in the lower respiratory tract. The interactions that occur when the respiratory epithelium encounters these viral and bacterial pathogens are poorly understood. We used Agilent bovine gene microarray chips containing 44,000 transcripts to elucidate bovine bronchial epithelial cell (BBEC) responses following in vitro exposure to BHV-1 alone, M. haemolytica alone, or both BHV-1 and M. haemolytica. Microarray analysis revealed differential regulation (>2-fold) of 978 transcripts by BHV-1 alone, 2040 transcripts by M. haemolytica alone, and 2189 genes by BHV-1 and M. haemolytica in combination. M. haemolytica treatment produced significantly greater inductions (>10-fold) of several inflammation associated genes, such as CXCL2, IL-6, IL-1α, e-selectin, and IL-8, than to BHV-1 alone. Functional analysis of the microarray data revealed a significant upregulation of genes involved in important biological processes such as inflammation (TNF-α, IL-8, Tlr-2, IL-1, CXCL2, CSF2), vascular functions (VEGF, EDN2) and leukocyte migration (ICAM1, IL-16) during a co-infection with BHV-1 and M. haemolytica compared to either pathogen alone. This study provides evidence to support that lung epithelial cells are a source of mediators that may promote inflammatory changes observed during bovine respiratory disease.


The age of telemedicine is upon us


title: DExD/H-box RNA helicases as mediators of anti-viral innate immunity and essential host factors for viral replication

text: Abstract Traditional functions of DExD/H-box helicases are concerned with RNA metabolism; they have been shown to play a part in nearly every cellular process that involves RNA. On the other hand, it is accepted that DexD/H-box helicases also engage in activities that do not require helicase activity. A number of DExD/H-box helicases have been shown to be involved in anti-viral immunity. The RIG-like helicases, RIG-I, mda5 and lgp2, act as important cytosolic pattern recognition receptors for viral RNA. Detection of viral nucleic acids by the RIG-like helicases or other anti-viral pattern recognition receptors leads to the induction of type I interferons and pro-inflammatory cytokines. More recently, additional DExD/H-box helicases have also been implicated to act as cytosolic sensors of viral nucleic acids, including DDX3, DDX41, DHX9, DDX60, DDX1 and DHX36. However, there is evidence that at least some of these helicases might have more downstream functions in pattern recognition receptor signalling pathways, as signalling adaptors or transcriptional regulators. In an interesting twist, a lot of DExD/H-box helicases have also been identified as essential host factors for the replication of different viruses, suggesting that viruses ‘hijack’ their RNA helicase activities for their benefit. Interestingly, DDX3, DDX1 and DHX9 are among the helicases that are required for the replication of a diverse range of viruses. This might suggest that these helicases are highly contested targets in the ongoing ‘arms race’ between viruses and the host immune system. This article is part of a Special Issue entitled: The Biology of RNA helicases — Modulation for life.


title: New nsp8 isoform suggests mechanism for tuning viral RNA synthesis

text: During severe acute respiratory syndrome coronavirus (SARS-CoV) infection, the activity of the replication/transcription complexes (RTC) quickly peaks at 6 hours post infection (h.p.i) and then diminishes significantly in the late post-infection stages. This “down-up-down” regulation of RNA synthesis distinguishes different viral stages: primary translation, genome replication, and finally viron assembly. Regarding the nsp8 as the primase in RNA synthesis, we confirmed that the proteolysis product of the primase (nsp8) contains the globular domain (nsp8C), and indentified the resectioning site that is notably conserved in all the three groups of coronavirus. We subsequently crystallized the complex of SARS-CoV nsp8C and nsp7, and the 3-D structure of this domain revealed its capability to interfuse into the hexadecamer super-complex. This specific proteolysis may indicate one possible mechanism by which coronaviruses to switch from viral infection to genome replication and viral assembly stages.


title: Feline Infectious Peritonitis Virus Nsp5 Inhibits Type I Interferon Production by Cleaving NEMO at Multiple Sites

text: Feline infectious peritonitis (FIP), caused by virulent feline coronavirus, is the leading infectious cause of death in cats. The type I interferon (type I IFN)-mediated immune responses provide host protection from infectious diseases. Several coronaviruses have been reported to evolve diverse strategies to evade host IFN response. However, whether feline infectious peritonitis virus (FIPV) antagonizes the type I IFN signaling remains unclear. In this study, we demonstrated that FIPV strain DF2 infection not only failed to induce interferon-β (IFN-β) and interferon-stimulated gene (ISG) production, but also inhibited Sendai virus (SEV) or polyinosinic-polycytidylic acid (poly(I:C))-induced IFN-β production. Subsequently, we found that one of the non-structural proteins encoded by the FIPV genome, nsp5, interrupted type I IFN signaling in a protease-dependent manner by cleaving the nuclear factor κB (NF-κB) essential modulator (NEMO) at three sites—glutamine132 (Q132), Q205, and Q231. Further investigation revealed that the cleavage products of NEMO lost the ability to activate the IFN-β promoter. Mechanistically, the nsp5-mediated NEMO cleavage disrupted the recruitment of the TRAF family member-associated NF-κB activator (TANK) to NEMO, which reduced the phosphorylation of interferon regulatory factor 3 (IRF3), leading to the inhibition of type I IFN production. Our research provides new insights into the mechanism for FIPV to counteract host innate immune response.


title: Progress and Perspective of Antiviral Protective Material

text: Public health events caused by viruses pose a significant risk to humans worldwide. From December 2019 till now, the rampant novel 2019 coronavirus (SAR-CoV-2) has hugely impacted China and over world. Regarding a commendable means of protection, mask technology is relatively mature, though most of the masks cannot effectively resist the viral infections. The key material of the mask is a non-woven material, which makes the barrier of virus through filtration. Due to the lack of the ability to kill the viruses, masks are prone to cross-infection and become an additional source of infection after being discarded. If the filteration and antiviral effects can be simultaneously integrated into the mask, it will be more effcient, work for a longer time and create less difficulty in post-treatment. This mini-review presents the advances in antiviral materials, different mechanisms of their activity, and their potential applications in personal protective fabrics. Furthermore, the article addresses the future challenges and directions of mask technology.


title: Space-Time Surveillance of Negative Emotions after Consecutive Terrorist Attacks in London

text: Terrorist attacks pose significant threats to mental health. There is dearth information about the impact of consecutive terrorist attacks on space-time concentrations of emotional reactions. This study collected (1) Twitter data following the two terrorist attacks in London in March and June of 2017, respectively, and (2) deprivation data at small areal levels in the United Kingdom. The space-time permutation model was used to detect the significant clusters of negative emotions, including fear, sadness, and anger in tweets. Logistic regression models were used to examine the social deprivation of communities associated with negative tweeting. The results reported two significant clusters after the March attack, one was in London, ten days after the attack, and the other was far from the attack site between Manchester and Birmingham, three days after the attack. Attention to the reoccurring attack in June diminished quickly. The socially deprived communities experienced double disadvantage—sending fewer tweets but expressing more negative emotions than their counterparts. The findings suggest that terrorism can affect public emotions far and broad. There is a potential for surveillance to rapidly identify geographically concentrated emotions after consecutive or prolonged disasters using social media data.


title: A review of early experience in lung ultrasound (LUS) in the diagnosis and management of COVID-19

text: Abstract A novel coronavirus (2019-nCoV) was identified as the cause of a cluster of pneumonia in Wuhan, China at the end of 2019. Since then more than four million confirmed cases of coronavirus disease 2019 (COVID-19) have been reported around the globe. The current gold standard for etiological diagnosis is reverse transcription polymerase chain reaction (rRT-PCR) analysis of respiratory tract specimens, but the test has a high false-negative rate due to both nasopharyngeal swab sampling error and viral burden. Hence diagnostic imaging has emerged as a fundamental component of current management of COVID-19 patients. Currently, high-resolution computed tomography (CT) is the main imaging tool for primary diagnosis and evaluation of disease severity in patients. Lung ultrasound (LUS) imaging has become a safe bedside imaging alternative that does no expose the patient to radiation, and minimizes the risk of contamination. Although the number of studies to date are limited, LUS findings have demonstrated high diagnostic sensitivity and accuracy, comparable to those of chest CT scans. In this article we review the current state of art of LUS in evaluating pulmonary changes induced by COVID-19. The goal is to identify characteristic sonographic findings most suited for the diagnosis of COVID-19 pneumonia infections.


title: Dissecting RNA recombination in vitro: role of RNA sequences and the viral replicase.

text: Molecular mechanisms of RNA recombination were studied in turnip crinkle carmovirus (TCV), which has a uniquely high recombination frequency and non-random crossover site distribution among the recombining TCV-associated satellite RNAs. To test the previously proposed replicase-driven template-switching mechanism for recombination, a partially purified TCV replicase preparation (RdRp) was programed with RNAs resembling the putative in vivo recombination intermediates. Analysis of the in vitro RdRp products revealed efficient generation of 3'-terminal extension products. Initiation of 3'-terminal extension occurred at or close to the base of a hairpin that was a recombination hotspot in vivo. Efficient generation of the 3'-terminal extension products depended on two factors: (i) a hairpin structure in the acceptor RNA region and (ii) a short base-paired region formed between the acceptor RNA and the nascent RNA synthesized from the donor RNA template. The hairpin structure bound to the RdRp, and thus is probably involved in its recruitment. The probable role of the base-paired region is to hold the 3' terminus near the RdRp bound to the hairpin structure to facilitate 3'-terminal extension. These regions were also required for in vivo RNA recombination between TCV-associated sat-RNA C and sat-RNA D, giving crucial and direct support for a replicase-driven template-switching mechanism of RNA recombination.


Re: “Strategy for the practice of digestive and oncological surgery during the Covid-19 epidemic”


title: Towards antivirals against chikungunya virus

text: Abstract Chikungunya virus (CHIKV) has re-emerged in recent decades, causing major outbreaks of chikungunya fever in many parts of Africa and Asia, and since the end of 2013 also in Central and South America. Infections are usually associated with a low mortality rate, but can proceed into a painful chronic stage, during which patients may suffer from polyarthralgia and joint stiffness for weeks and even several years. There are no vaccines or antiviral drugs available for the prevention or treatment of CHIKV infections. Current therapy therefore consists solely of the administration of analgesics, antipyretics and anti-inflammatory agents to relieve symptoms. We here review molecules that have been reported to inhibit CHIKV replication, either as direct-acting antivirals, host-targeting drugs or those that act via a yet unknown mechanism. This article forms part of a symposium in Antiviral Research on “Chikungunya discovers the New World.”


title: Thromboembolic Findings in COVID-19 Autopsies: Pulmonary Thrombosis or Embolism?

text: In their article, Lax and colleagues reported the frequent occurrence of pulmonary thrombosis in a series of autopsies of patients with COVID-19. The editorialist discusses how these findings help to further inform our emerging understanding of thromboembolic disease in COVID-19.


title: Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3

text: Abstract Severe acute respiratory syndrome coronavirus (SARS-CoV) is an inefficient inducer of interferon (IFN) response. It expresses various proteins that effectively circumvent IFN production at different levels via distinct mechanisms. Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. We also found that proteins 8b and 8ab could physically interact with IRF3. Overexpression of 8b and 8ab resulted in the reduction of poly (I:C)-induced IRF3 dimerization and inhibition of the IFN-β signaling pathway. This counteracting effect was partially mediated by protein 8b/8ab-induced degradation of IRF3 in a ubiquitin-proteasome-dependent manner. Taken together, we propose that SARS-CoV may exploit the unique functions of proteins 8b and 8ab as novel mechanisms to overcome the effect of IFN response during virus infection.


title: Novel guanosine derivatives against Zika virus polymerase in silico

text: The Zika virus (ZIKV) outbreak, which started in the year 2015, is considered the fastest and most widely spread outbreak reported for this flavivirus. The polymerase domain of the NS5 protein has been targeted in other viral infections and is recognized as a suitable target in ZIKV infection. Different novel modified compounds against ZIKV NS5 have been tested in silico. A few structures have been solved for ZIKV polymerase and deposited in the protein data bank website. Two of these solved structures (with a resolution of less than 1.9 A) are used in this study to test the binding of 74 novel compounds in silico. Molecular docking is used to quantify the binding affinities of ZIKV polymerase and compare it to the hepatitis C virus NS5B. A total of 19 novel compounds revealed results that are either similar to or better than the physiological molecule, guanosine triphosphate. Water molecules are found to facilitate the binding of the compounds to ZIKV RNA‐dependent RNA polymerase (RdRp) structures. The presented 19 novel compounds represent good binders to ZIKV RdRp and could be suitable candidates for developing a new and effective anti‐ZIKV polymerase nucleotide inhibitor.


title: Face touching: A frequent habit that has implications for hand hygiene

text: BACKGROUND: There is limited literature on the frequency of face-touching behavior as a potential vector for the self-inoculation and transmission of Staphylococcus aureus and other common respiratory infections. METHODS: A behavioral observation study was undertaken involving medical students at the University of New South Wales. Their face-touching behavior was observed via videotape recording. Using standardized scoring sheets, the frequency of hand-to-face contacts with mucosal or nonmucosal areas was tallied and analyzed. RESULTS: On average, each of the 26 observed students touched their face 23 times per hour. Of all face touches, 44% (1,024/2,346) involved contact with a mucous membrane, whereas 56% (1,322/2,346) of contacts involved nonmucosal areas. Of mucous membrane touches observed, 36% (372) involved the mouth, 31% (318) involved the nose, 27% (273) involved the eyes, and 6% (61) were a combination of these regions. CONCLUSION: Increasing medical students' awareness of their habituated face-touching behavior and improving their understanding of self-inoculation as a route of transmission may help to improve hand hygiene compliance. Hand hygiene programs aiming to improve compliance with before and after patient contact should include a message that mouth and nose touching is a common practice. Hand hygiene is therefore an essential and inexpensive preventive method to break the colonization and transmission cycle associated with self-inoculation.


Public Health Measures to Slow Community Spread of Coronavirus Disease 2019


title: An empirical test of the midpoint rooting method

text: The outgroup method is widely used to root phylogenetic trees. An accurate root indication, however, strongly depends on the availability of a proper outgroup. An alternate rooting method is the midpoint rooting (MPR). In this case, the root is set at the midpoint between the two most divergent operational taxonomic units. Although the midpoint rooting algorithm has been extensively used, the efficiency of this method in retrieving the correct root remains untested. In the present study, we empirically tested the success rate of the MPR in obtaining the outgroup root for a given phylogenetic tree. This was carried out by eliminating outgroups in 50 selected data sets from 33 papers and rooting the trees with the midpoint method. We were thus able to compare the root position retrieved by each method. Data sets were separated into three categories with different root consistencies: data sets with a single outgroup taxon (54% success rate for MPR), data sets with multiple outgroup taxa that showed inconsistency in root position (82% success rate), and data sets with multiple outgroup taxa in which root position was consistent (94% success rate). Interestingly, the more consistent the outgroup root is, the more successful MPR appears to be. This is a strong indication that the MPR method is valuable, particularly for cases where a proper outgroup is unavailable.


title: InfectiousDiseases ofPoverty, the first five years

text: Although the focus in the area of health research may be shifting from infectious to non-communicable diseases, the infectious diseases of poverty remain a major burden of disease of global health concern. A global platform to communicate and share the research on these diseases is needed to facilitate the translation of knowledge into effective approaches and tools for their elimination. Based on the “One health, One world” mission, a new, open-access journal, Infectious Diseases of Poverty (IDP), was launched by BioMed Central in partnership with the National Institute of Parasitic Diseases (NIPD), Chinese Center for Disease Control and Prevention (China CDC) on October 25, 2012. Its aim is to identify and assess research and information gaps that hinder progress towards new interventions for a particular public health problem in the developing world. From the inaugural IDP issue of October 25, 2012, a total of 256 manuscripts have been published over the following five years. Apart from a small number of editorials, opinions, commentaries and letters to the editor, the predominant types of publications are research articles (69.5%) and scoping reviews (21.5%). A total of 1 081 contributing authors divided between 323 affiliations across 68 countries, territories and regions produced these 256 publications. The journal is indexed in major international biomedical databases, including Web of Science, PubMed, Scopus and Embase. In 2015, it was assigned its first impact factor (4.11), which is now 2.13. During the past five years, IDP has received manuscripts from 90 countries, territories and regions across six continents with an annual acceptance rate of all contributions maintained at less than 40%. Content analysis shows that neglected tropical diseases (NTDs), followed by the “Big Three” (HIV/AIDS, malaria and tuberculosis) and infectious diseases in general comprise 88% of all publications. In addition, a series of 10 thematic issues, covering 118 publications in all, was published as separate parts of the first five volumes. These publications were cited 975 times, which equals an average of 8.3 times per publication. The current challenge is to identify cutting-edge research topics and attract and to publish first-rate publications leading to increasing importance and impact of the journal in its field. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40249-017-0310-6) contains supplementary material, which is available to authorized users.


title: Surveillance of adenoviruses and noroviruses in European recreational waters

text: Abstract Exposure to human pathogenic viruses in recreational waters has been shown to cause disease outbreaks. In the context of Article 14 of the revised European Bathing Waters Directive 2006/7/EC (rBWD, CEU, 2006) a Europe-wide surveillance study was carried out to determine the frequency of occurrence of two human enteric viruses in recreational waters. Adenoviruses were selected based on their near-universal shedding and environmental survival, and noroviruses (NoV) selected as being the most prevalent gastroenteritis agent worldwide. Concentration of marine and freshwater samples was done by adsorption/elution followed by molecular detection by (RT)-PCR. Out of 1410 samples, 553 (39.2%) were positive for one or more of the target viruses. Adenoviruses, detected in 36.4% of samples, were more prevalent than noroviruses (9.4%), with 3.5% GI and 6.2% GII, some samples being positive for both GI and GII. Of 513 human adenovirus-positive samples, 63 (12.3%) were also norovirus-positive, whereas 69 (7.7%) norovirus-positive samples were adenovirus-negative. More freshwater samples than marine water samples were virus-positive. Out of a small selection of samples tested for adenovirus infectivity, approximately one-quarter were positive. Sixty percent of 132 nested-PCR adenovirus-positive samples analysed by quantitative PCR gave a mean value of over 3000 genome copies per L of water. The simultaneous detection of infectious adenovirus and of adenovirus and NoV by (RT)PCR suggests that the presence of infectious viruses in recreational waters may constitute a public health risk upon exposure. These studies support the case for considering adenoviruses as an indicator of bathing water quality.


title: Loop-mediated isothermal amplification (LAMP): recent progress in research and development

text: Loop-mediated isothermal amplification (LAMP) is an established technology that continues to attract the attention of researchers in many fields. Research and development efforts on LAMP technology in recent years have focused on two major areas; first, the study of its clinical application as an approved in vitro diagnostics tool in Japan and certain other countries; and second, research aimed at further simplifying the LAMP test process. This review provides an overview of the status of LAMP on these two topics by summarizing research work conducted, in the main, after our previous review article.


title: Expression of elevated levels of pro‐inflammatory cytokines in SARS‐CoV‐infected ACE2(+) cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS

text: The authors have previously shown that acute lung injury (ALI) produces a wide spectrum of pathological processes in patients who die of severe acute respiratory syndrome (SARS) and that the SARS coronavirus (SARS‐CoV) nucleoprotein is detectable in the lungs, and other organs and tissues, in these patients. In the present study, immunohistochemistry (IHC) and in situ hybridization (ISH) assays were used to analyse the expression of angiotensin‐converting enzyme 2 (ACE2), SARS‐CoV spike (S) protein, and some pro‐inflammatory cytokines (PICs) including MCP‐1, TGF‐β1, TNF‐α, IL‐1β, and IL‐6 in autopsy tissues from four patients who died of SARS. SARS‐CoV S protein and its RNA were only detected in ACE2(+) cells in the lungs and other organs, indicating that ACE2‐expressing cells are the primary targets for SARS‐CoV infection in vivo in humans. High levels of PICs were expressed in the SARS‐CoV‐infected ACE2(+) cells, but not in the uninfected cells. These results suggest that cells infected by SARS‐CoV produce elevated levels of PICs which may cause immuno‐mediated damage to the lungs and other organs, resulting in ALI and, subsequently, multi‐organ dysfunction. Therefore application of PIC antagonists may reduce the severity and mortality of SARS. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


title: COVID-19: Precautionary Guidelines for Ophthalmologists

text: Several coronaviruses can infect humans, and the globally endemic human coronaviruses, HCoV-229E (human coronavirus 229E), HCoV-NL63 (human coronavirus NL63), and others, tend to cause mild respiratory diseases. The zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus type1 (SARS-CoV-1) have high fatality rates. In December 2019, the World Health Organization (WHO) was notified by Chinese authorities about an outbreak of pneumonia before the causative organism was identified in January 2020 as a novel coronavirus family. The WHO refers to the virus as coronavirus disease 2019 (COVID-19). Within several weeks, the outbreak has become an emergency, and many countries have since been affected. The method of transmission is not yet fully known but is thought to be mainly respiratory. Healthcare providers, particularly ophthalmologists, are at high risk of a COVID-19 infection through unprotected contact with eye secretions during routine ophthalmic examinations that involve the use of direct ophthalmoscopy and slit-lamp examinations, which are usually performed in a setting that allows for close doctor-patient contact. In light of these, specific measures are needed from an ophthalmic point of view to control the COVID-19 outbreak and to protect health care providers.


title: IL-12 RB1 Genetic Variants Contribute to Human Susceptibility to Severe Acute Respiratory Syndrome Infection among Chinese

text: BACKGROUND: Cytokines play important roles in antiviral action. We examined whether polymorphisms of interleukin (IL)-12 receptor B1 (IL-12RB1) affect the susceptibility to and outcome of severe acute respiratory syndrome (SARS). METHODS: A case-control study was carried out in Chinese SARS patients and healthy controls. The genotypes of 4SNPs on IL-12 RB1 gene, +705A/G,+1158T/C, +1196G/C and +1664 C/T, were determined by PCR-RFLP. Haplotypes were estimated from the genotype data using the expectation-maximisation algorithm. RESULTS: Comparison between patients and close contacts showed that individuals with the +1664 C/T (CT and TT) genotype had a 2.09-fold (95% confidence interval [CI], 1.90–7.16) and 2.34-fold (95% CI, 1.79–13.37) increased risk of developing SARS, respectively. For any of the other three polymorphisms, however, no significant difference can be detected in allele or genotype frequencies between patients and controls. Additionally, estimation of the frequencies of multiple-locus haplotypes revealed potential risk haplotypes (GCCT) for SARS infection. CONCLUSIONS: Our data indicate that genetic variants of IL12RB1confer genetic susceptibility to SARS infection, but not necessary associated with the progression of the disease in Chinese population.


title: Treatment of Middle East Respiratory Syndrome with a combination of lopinavir-ritonavir and interferon-β1b (MIRACLE trial): study protocol for a randomized controlled trial

text: BACKGROUND: It had been more than 5 years since the first case of Middle East Respiratory Syndrome coronavirus infection (MERS-CoV) was recorded, but no specific treatment has been investigated in randomized clinical trials. Results from in vitro and animal studies suggest that a combination of lopinavir/ritonavir and interferon-β1b (IFN-β1b) may be effective against MERS-CoV. The aim of this study is to investigate the efficacy of treatment with a combination of lopinavir/ritonavir and recombinant IFN-β1b provided with standard supportive care, compared to treatment with placebo provided with standard supportive care in patients with laboratory-confirmed MERS requiring hospital admission. METHODS: The protocol is prepared in accordance with the SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) guidelines. Hospitalized adult patients with laboratory-confirmed MERS will be enrolled in this recursive, two-stage, group sequential, multicenter, placebo-controlled, double-blind randomized controlled trial. The trial is initially designed to include 2 two-stage components. The first two-stage component is designed to adjust sample size and determine futility stopping, but not efficacy stopping. The second two-stage component is designed to determine efficacy stopping and possibly readjustment of sample size. The primary outcome is 90-day mortality. DISCUSSION: This will be the first randomized controlled trial of a potential treatment for MERS. The study is sponsored by King Abdullah International Medical Research Center, Riyadh, Saudi Arabia. Enrollment for this study began in November 2016, and has enrolled thirteen patients as of Jan 24-2018. TRIAL REGISTRATION: ClinicalTrials.gov, ID: NCT02845843. Registered on 27 July 2016. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13063-017-2427-0) contains supplementary material, which is available to authorized users.