title: Analysis of the molecular basis of neuropathogenesis of RNA viruses in experimental animals: relevance for human disease?

text: RNA viruses with segmented genomes were the first model used for molecular analysis of viral neuropathogenesis, since they could be analysed genetically by reassortment. Four viruses with non–segmented genomes have been used as models of neurovirulence and demyelinating disease: JHM coronavirus, Theiler's virus, Sindbis virus and Semliki Forest virus (SFV). Virus gene expression in the central nervous system of infected animals has been measured by in situ hybridization and immunocytochemistry. Cell tropism has been analysed by neural cell culture. Infectious clones have been constructed for Theiler's virus, Sindbis virus and SFV, and these allow analysis of the sequences involved in the determination of neuropathogenesis, through the construction of chimeric viruses and site–specific mutagenesis. Measles and rubella viruses have been studied in animal systems because of their importance for human disease. The importance of two recently discovered mechanisms of neuropathogenesis, antibody–induced modulation of virus multiplication, and persistence of virus in the absence of multiplication, remains to be assessed.


title: Hydroxychloroquine for Treatment of SARS‐CoV‐2 Infection? Improving Our Confidence in a Model‐Based Approach to Dose Selection

text: In less than six months, COVID-19 has spread from a marketplace in Wuhan, China to over 150 countries and territories of the world. Therapeutics are desperately needed to reduce the morbidity and mortality of this pandemic disease. It has been reported that hydroxychloroquine (HCQ) is active against SARS-CoV-2 in vitro, and this finding was quickly supported by an open label non-randomized clinical trial that provided the first published clinical evidence HCQ may be a treatment option.


title: Structural Definition of a Neutralization-sensitive Epitope on the MERS-CoV S1-NTD

text: Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the receptor-binding domain (RBD) on MERS-CoV spike (S) protein have been characterized, but much less is known about antibodies targeting non-RBD epitopes. Here we report the structural and functional characterization of G2, a neutralizing antibody targeting MERS-CoV S1 N-terminal domain (S1-NTD). Structures of G2 alone and in complex with the MERS-CoV S1-NTD defined a site of vulnerability comprising two loops, each of which contained a residue mutated in G2-escape variants. Cell-surface binding studies and in vitro competition experiments demonstrated that G2 strongly disrupts the attachment of MERS-CoV S to its receptor DDP4, with the inhibition requiring the native trimeric S conformation. These results advance our understanding of antibody-mediated neutralization of coronaviruses and should facilitate development of immunotherapeutics and vaccines against MERS-CoV.


title: Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011

text: BACKGROUND: In Africa, especially in West Africa, studies about the prevalence and diversity of respiratory viruses (influenza and others) in elderly people are largely lacking. In studies done elsewhere, it is well established that older people, when compared with younger adults, are at greater risk of significant morbidity and mortality from complications arising from influenza. The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal. METHODS: The recruitment period of this study was from January 2009 to December 2011. 232 patients aged 50 years and above presenting ILI cases were enrolled. Nasal-pharyngeal and/or oral pharyngeal swabs were collected from patients. RNA was extracted from 200 μl of each sample followed by a two-step real-time RT-PCR. The Anyplex™ II RV16 Detection kit was used for viral detection. The kit enabled the simultaneous detection of the presence of 16 respiratory viruses. RESULTS: 150 viruses were detected: influenza viruses (44.7%) and rhinoviruses (26.7%) were the most prevalent. We detected 13 human parainfluenza viruses (8.7%), 7 human respiratory syncytial viruses (4.7%), 6 coronaviruses (4%), 5 human metapneumoviruses (3.3%), 5 human adenoviruses (3.3%) and 1 human bocavirus (0.7%). 14 cases (6%) of dual virus infections and one triple viral detection case were encountered. 56 (56.6%) viruses detected were found in the 50-64 year old age group, 59 (76.6%; P < 0.001) from 65–74 year old age group and 35 (62.5%) were detected in the ≥75 year old age group. The viral co-infections were more frequent in the 65-74 age group (9/15). CONCLUSIONS: This pilot study demonstrates a variety of respiratory viruses in the elderly. It also highlights a high prevalence of these viruses in this age group. We speculate from these results that the impact of respiratory viruses other than influenza on the elderly has been considerably underestimated. A more exhaustive study seems necessary in order to provide a more complete picture of the burden of respiratory viruses on morbidity among adults over 50 years old in the sub-Saharan context.


title: The innate immune system: fighting on the front lines or fanning the flames of COVID-19?

text: Abstract The coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 has had devastating global impacts and will continue to have dramatic effects on public health for years to come. A better understanding of the immune response to SARS-CoV-2 will be critical for the application and development of therapeutics. The degree to which the innate immune response confers protection or induces pathogenesis through a dysregulated immune response remains unclear. In this review, we discuss what is known about the role of the innate immune system during SARS-CoV-2 infection, suggest directions for future studies, and evaluate proposed COVID-19 immunomodulating therapeutics.


title: Use of Unamplified RNA/cDNA–Hybrid Nanopore Sequencing for Rapid Detection and Characterization of RNA Viruses

text: Nanopore sequencing, a novel genomics technology, has potential applications for routine biosurveillance, clinical diagnosis, and outbreak investigation of virus infections. Using rapid sequencing of unamplified RNA/cDNA hybrids, we identified Venezuelan equine encephalitis virus and Ebola virus in 3 hours from sample receipt to data acquisition, demonstrating a fieldable technique for RNA virus characterization.


title: The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2

text: SARS-CoV-2 infection can lead to acute respiratory syndrome in patients, which can be due in part to dysregulated immune signalling. We analyze here the occurrences of CpG dinucleotides, which are putative pathogen-associated molecular patterns, along the viral sequence. Carrying out a comparative analysis with other ssRNA viruses and within the Coronaviridae family, we find the CpG content of SARS-CoV-2, while low compared to other betacoronaviruses, widely fluctuates along its primary sequence. While the CpG relative abundance and its associated CpG force parameter [1] are low for the spike protein (S) and comparable to circulating seasonal coronaviruses such as HKU1, they are much greater and comparable to SARS and MERS for the 3’-end of the viral genome. In particular, the nucleocapsid protein (N), whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3’UTRs of all subgenomic RNA, has high CpG content. We speculate this dual nature of CpG content can confer to SARS-CoV-2 high ability to both enter the host and trigger pattern recognition receptors (PRRs) in different contexts. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic. Using a new application of selective forces on dinucleotides to estimate context driven mutational processes, we find that synonymous mutations seem driven both by the viral codon bias and by the high value of the CpG force in the N protein, leading to a loss in CpG content. Sequence motifs preceding these CpG-loss-associated loci match recently identified binding patterns of the Zinc Finger anti-viral Protein (ZAP) protein.


title: Les causes de l’émergence des maladies infectieuses

text: SUMMARY The most infectious diseases that veterinarians and doctors believed to have vanquished in the 1980s in developed countries, have repeatedly talked about them in an often dramatic way in the 2000s. Foot-and-mouth disease devastated British herds in 2001, bovine tuberculosis, which had been hoped for eradication after 50 years of fighting, has re-emerged in the United Kingdom and France... At the same time, new infectious diseases, often zoonotic, have appeared in animals and in humans : HP avian influenza H5N1 in 2003, SARS in 2003, the MERS-CoVin2012… The reasons for these emergences are multiple because each disease has its own determinants. However, three main groups of factors can be cited: the evolution of pathogens (RNA viruses in particular), environmental changes favoring the development of vectors and reservoirs, and human behavior. The constant movement of humans, animals and their products on the planet, densification of populations and massive displacements linked to conflicts are probably at the heart of these evolutions. For the future, the challenges are to understand the infectious risks linked to these evolutions in order to try to prevent them. Epidemiology through surveillance and investigation will be tomorrow more than ever, at the heart of the prevention of infectious diseases.


title: What Internet Services Would Patients Like From Hospitals During an Epidemic? Lessons From the SARS Outbreak in Toronto

text: BACKGROUND: International health organizations and officials are bracing for a pandemic. Although the 2003 severe acute respiratory syndrome (SARS) outbreak in Toronto did not reach such a level, it created a unique opportunity to identify the optimal use of the Internet to promote communication with the public and to preserve health services during an epidemic. OBJECTIVE: The aim of the study was to explore patients’ attitudes regarding the health services that might be provided through the Internet to supplement those traditionally available in the event of a future mass emergency situation. METHODS: We conducted “mask-to-mask” surveys of patients at three major teaching hospitals in Toronto during the second outbreak of SARS. Patients were surveyed at the hospital entrances and selected clinics. Descriptive statistics and logistic regression models were used for the analysis. RESULTS: In total, 1019 of 1130 patients responded to the survey (90% overall response rate). With respect to Internet use, 70% (711/1019) used the Internet by themselves and 57% (578/1019) with the help of a friend or family member. Of the Internet users, 68% (485/711) had already searched the World Wide Web for health information, and 75% (533/711) were interested in communicating with health professionals using the Internet as part of their ongoing care. Internet users expressed interest in using the Web for the following reasons: to learn about their health condition through patient education materials (84%), to obtain information about the status of their clinic appointments (83%), to send feedback to the hospital about how to improve its services (77%), to access screening tools to help determine if they were potentially affected by the infectious agent responsible for the outbreak (77%), to renew prescriptions (75%), to consult with their health professional about nonurgent matters (75%), and to access laboratory test results (75%). Regression results showed that younger age, higher education, and English as a first language were predictors of patients’ interest in using Internet services in the event of an epidemic. CONCLUSION: Most patients are willing and able to use the Internet as a means to maintain communication with the hospital during an outbreak of an infectious disease such as SARS. Hospitals should explore new ways to interact with the public, to provide relevant health information, and to ensure continuity of care when they are forced to restrict their services.


Evidence of mother-newborn infection with COVID-19


Endoscopy units and the COVID-19 Outbreak: A Multi-Center Experience from Italy


title: Angiotensin-converting enzyme polymorphism affects outcome of local Chinese with acute lung injury

text: Summary Introduction Acute Lung Injury (ALI) with genetic predisposition is fatal. Relationship between angiotensin-converting enzyme insertion/deletion (ACE I/D) polymorphism and the prognosis of local Chinese patients with ALI was investigated; meanwhile, the mechanisms involved were explored. Methods 101 ALI patients, 408 non-ALI patients and 236 healthy blood donors were enrolled. ACE I/D polymorphism was detected by polymerase chain reaction, then ACE genotype (II, ID, DD) and allele (I, D) frequencies were compared. Clinical data of ALI patients was calculated. Also, peripheral blood mononuclear cells (PBMC) were isolated from healthy volunteers with different ACE genotypes. Lipopolysaccharide (LPS)-induced ACE gene mRNA expression and ACE activity was measured. Results There was no significant difference in the frequencies of the genotypes and alleles. Acute Physiology and Chronic Health Evaluation (APACHE) II score was higher in DD subgroup than in II subgroup (19.7 ± 8.7 and 15.6 ± 6.2; P < 0.05). The 28-day mortality was significantly different (17.4%, 26.8%, and 64.3% for II, ID, and DD; P = 0.013). DD genotype was the independent prognostic factor for 28-day outcome. Furthermore, LPS-induced ACE mRNA expression and ACE activity from PBMC in DD genotype subgroup were both significantly higher than those in the other two subgroups. Conclusions ACE I/D polymorphism is a prognostic factor for ALI. Patients with the DD genotype have higher mortality of ALI. Polymorphism influences the expression of ACE gene in LPS-stimulated PBMC, DD genotype leads to higher level of mRNA and enzyme activity. It may be one of the mechanisms involved.


title: Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

text: Summary Early detection and effective treatment of severe COVID-19 patients remain major challenges. Here, we performed proteomic and metabolomic profiling of sera from 46 COVID-19 and 53 control individuals. We then trained a machine learning model using proteomic and metabolomic measurements from a training cohort of 18 non-severe and 13 severe patients. The model was validated using ten independent patients, seven of which were correctly classified. Targeted proteomics and metabolomics assays were employed to further validate this molecular classifier in a second test cohort of 19 new COVID-19 patients, leading to 16 correct assignments. We identified molecular changes in the sera of COVID-19 patients compared to other groups implicating dysregulation of macrophage, platelet degranulation and complement system pathways, and massive metabolic suppression. This study revealed characteristic protein and metabolite changes in the sera of severe COVID-19 patients, which might be used in selection of potential blood biomarkers for severity evaluation.


title: Physical Collection Efficiency of Filter Materials for Bacteria and Viruses

text: The purpose of this study was to determine the physical collection efficiency of commercially available filters for collecting airborne bacteria, viruses, and other particles in the 10–900 nm (nanometer) size range. Laboratory experiments with various polytetrafluoroethylene (PTFE), polycarbonate (PC) and gelatin filters in conjunction with Button™ Inhalable samplers and three-piece cassettes were undertaken. Both biological and non-biological test aerosols were used: Bacillus atrophaeus, MS2, polystyrene latex (PSL), and sodium chloride (NaCl). The B.atrophaeus endospores had an aerodynamic diameter of 900 nm, whereas MS2 virion particles ranged from 10 to 80 nm. Monodisperse 350 nm PSL particles were used as this size was believed to have the lowest filtration efficiency. NaCl solution (1% weight by volume) was used to create a polydisperse aerosol in the 10–600 nm range. The physical collection efficiency was determined by measuring particle concentrations size-selectively upstream and downstream of the filters. The PTFE and gelatin filters showed excellent collection efficiency (>93%) for all of the test particles. The PC filters showed lower collection efficiency for small particles especially <100 nm. Among the tested filters, the lowest collection efficiencies, 49 and 22%, were observed for 1 and 3-μm pore size PC filters at the particle sizes of 47 and 63 nm, respectively. The results indicate that the effect of filter material is more significant for the size range of single virions than for bacteria. The effect of filter loading was examined by exposing filters to mixtures of PSL particles, which aimed at mimicking typical indoor dust levels and size distributions. A 4-h loading did not cause significant change in the physical collection efficiency of the tested filters.


Prolonged Duration of SARS-CoV-2 Viral Positivity in a Crohn’s Disease Patient


title: Immune evasion during foot‐and‐mouth disease virus infection of swine

text: Summary: The interface between successful pathogens and their hosts is often a tenuous balance. In acute viral infections, this balance involves induction and inhibition of innate responses. Foot‐and‐mouth disease virus (FMDV) is considered one of the most contagious viruses known and is characterized by rapid induction of clinical disease in cloven hoofed animals exposed to infection. Viral shedding is extensive before the equally rapid resolution of acute disease. This positive strand RNA virus is an extremely successful pathogen, due in part to the ability to interrupt the innate immune response. Previous reviews have described the inhibition of cellular innate responses in the infected cell both in vitro and in vivo. Here, we present a review of virus inhibition of cells that are a source of antiviral function in swine. Particularly in the case of dendritic cells and natural killer cells, the virus has evolved mechanisms to interrupt the normal function of these important mediators of innate function, even though these cells are not infected by the virus. Understanding how this virus subverts the innate response will provide valuable information for the development of rapidly acting biotherapeutics to use in response to an outbreak of FMDV.


title: Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis

text: Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Here, we comprehensively review this rapidly expanding field, describing the structures and enzymatic activities of viral macrodomains, and discussing their roles in viral replication and pathogenesis.


title: Effect of bunching of cilia and their interplay on muco-ciliary transport

text: Abstract Cilia are hair-like organelles projecting from a eukaryotic cell, used either for locomotion or as sensors. Cilia commonly occur in patches. To take this into consideration, we represent cilia in multiple patches, instead of the conventional ‘dense mat’ representation. We focus on the combined action and interplay of these patches. The effects of varying the frequency, spacing and phase lag of the beating of one cilia bunch with respect to the beating of adjacent patches are studied. We model the Airway Surface Liquid (ASL) as a three-layer structure. The possibility of an optimum frequency of beating is noted and the change of mucous flow under different spacing and phase differences are observed.


title: Life Goes On

text: Purpose Due to the emergence of the new coronavirus 2019 and the lack of sufficient information about infected patients, this study was conducted to investigate the chest high-resolution computed tomography (HRCT) findings of patients infected with the new coronavirus 2019 Methods This cross-sectional study was performed on COVID-19 patients referred to Medical Imaging Centers of Sari, Mazandaran, Iran, on March 2020 for computed tomography (CT) scan Symptomatic patients were referred to the Medical Imaging Center for diagnosis confirmation through CT scan In addition to age and sex, HRCT findings were collected from the picture archiving and communication system (PACS) for further evaluations Results Out of 552 patients with mean age of 51 2 ± 14 8 years, the male/female ratio was 1 38 to 1 The most common expressive findings in patients were ground-glass opacity (GGO) (87 3%), peripheral distribution (82 4%), and posterior distribution (81 5%) The most conflicting findings in patients were pleural effusion (7 6%), peribronchovascular distribution (7 6%), and lymphadenopathy (5 1%) The peripheral distribution (p = 0 034), round opacities (p = 0 02), single lobe (p = 0 003), and pleural effusion (p = 0 037) were significant in people under and over 50 years of age Conclusion In summary, the present study indicated that in addition to GGO, peripheral distribution findings could be a vital diagnostic choice in COVID-19 patients


title: Structural characterization and immunomodulating activities of a novel polysaccharide from Nervilia fordii

text: Abstract Nervilia fordii (Hance) Schltr. has been widely used as a medicinal and edible herb in Southwest China and Southeast Asia. In this study, NFP-1, a new water-soluble polysaccharidewith a purity of 97.8%, was purified from water extract of Nervilia fordii by DEAE-cellulose and Sephadex G-100 chromatography. NFP-1 has a relative molecular weight of 950 kDa determined by high performance gel-permeation chromatography (HPGPC). Its monosaccharide compositions were analyzed by high performance liquid chromatography (HPLC) after pre-column derivatizing its hydrolysate with 1-phenyl-3-methyl-5-pyrazolone (PMP). NFP-1 mainly consists of galactose, arabinose, rhamnose, and galacturonic acid. Based on FT-IR, methylation and GC–MS analysis, and NMR, the structure unit of NFP-1 was established as →4)-α-Rhap-(2→ 4)-α-GalpA-(1→2)-α-Rhap-(1→2)-α-Rhap-(4→1)-β-Galp-T containing two branch chains of →2,4)-α-Rhap-(1→5)-α-Araf-(1→3)-α-Araf-(1→, and →2,4)-α-Rhap-(1→4)-β-Galp-(1→. The immunomodulatory assays revealed the dual-functionalities of NFP-1. NFP-1 could significantly induce the secretion of nitric oxide (NO), and promote the secretions of TNF-α, IL-6, and IL-1β in RAW264.7 macrophages. NFP-1 could also significantly inhibit the production of NO, depress the secretions of TNF-α, IL-6 and IL-1β in RAW264.7 macrophages activated by lipopolysaccharide (LPS), and promote the production of IL-10 meanwhile. Our study suggested that Nervilia fordii could be an ideal medicinal or functional food due to its dual immunomodulatory activities.


Viruses and Autoimmune Diseases


title: Strategies of highly pathogenic RNA viruses to block dsRNA detection by RIG-I-like receptors: Hide, mask, hit

text: Abstract Double-stranded RNA (dsRNA) is synthesized during the course of infection by RNA viruses as a byproduct of replication and transcription and acts as a potent trigger of the host innate antiviral response. In the cytoplasm of the infected cell, recognition of the presence of viral dsRNA as a signature of “non-self” nucleic acid is carried out by RIG-I-like receptors (RLRs), a set of dedicated helicases whose activation leads to the production of type I interferon α/β (IFN-α/β). To overcome the innate antiviral response, RNA viruses encode suppressors of IFN-α/β induction, which block RLRs recognition of dsRNA by means of different mechanisms that can be categorized into: (i) dsRNA binding and/or shielding (“hide”), (ii) dsRNA termini processing (“mask”) and (iii) direct interaction with components of the RLRs pathway (“hit”). In light of recent functional, biochemical and structural findings, we review the inhibition mechanisms of RLRs recognition of dsRNA displayed by a number of highly pathogenic RNA viruses with different disease phenotypes such as haemorrhagic fever (Ebola, Marburg, Lassa fever, Lujo, Machupo, Junin, Guanarito, Crimean-Congo, Rift Valley fever, dengue), severe respiratory disease (influenza, SARS, Hendra, Hantaan, Sin Nombre, Andes) and encephalitis (Nipah, West Nile).


title: Detection of viral agents in fecal specimens of monkeys with diarrhea

text: Background Diarrheal disease is a major cause of morbidity and mortality in humans and animals, including non human primates. While the diagnostics for gastrointestinal bacterial and parasitic pathogens and their etiological role in disease are well established, little is known about the epidemiology, prevalence and role of viral agents in diarrheal illness among monkeys. Methods We collected fecal specimens from monkeys with diarrhea that were housed in two primate colonies, the Institute of Laboratory Animal Sciences, Beijing, China and the Yerkes National Primate Research Center, Georgia, USA. We screened these fecal specimens for rotaviruses and enteric adenoviruses 40/41 by using commercial EIA kits (Rotaclone and Adenoclone), enteroviruses by RT‐PCR and Southern blot hybridization, and picobirnaviruses by polyacrylamide gel electrophoresis and silver staining. Some of the specimens were examined by EM for coronaviruses and noroviruses. Results Of the 92 specimens from China, we found 63 (68%) positive for viruses, including enteroviruses (52%), enteric adenoviruses (21%), rotaviruses (20%), and picobirnaviruses (2%). Coronaviruses were detected in some specimens. Mixed infection of two or more viral agents was seen in 23 (25%) specimens. In the US collection, we detected enteroviruses and enteric adenoviruses in 76% (45/59) and 14% (7/50) of the specimens, respectively. Electron microscopy showed norovirus‐like particles in some specimens from both colonies. Conclusions Our findings indicate endemic infections with enteric viruses in monkeys of both colonies. The availability of new simian rotaviruses, enteric adenoviruses, enteroviruses, and coronaviruses and the discovery of noroviruses and picobirnaviruses may allow us to develop better diagnostics for these agents and determine which of these agents are clearly associated with gastroenteritis in monkeys.


title: Comparison of Common Respiratory Virus Peak Incidence Among Varying Age Groups in Rhode Island, 2012-2016

text: This case series study assesses the seasonality of respiratory viral infections among different age groups in Rhode Island from 2012 to 2016.


At home dose escalation of Propranolol for Infantile Hemangiomas during the COVID‐19 Pandemic


title: Value of Autopsy Emphasized in the Case Report of a Single Patient with Middle East Respiratory Syndrome

text: This commentary highlights the article by Ng et al, emphasizing the need for autopsies to better model infectious diseases such as Middle East respiratory syndrome.


title: If it’s not one thing, HIF’s another: immunoregulation by hypoxia inducible factors in disease

text: Hypoxia Inducible Factors (HIFs) have emerged in recent years as critical regulators of immunity. Localised, low oxygen tension is a hallmark of inflamed and infected tissues. Subsequent myeloid cell HIF stabilisation plays key roles in the innate immune response, alongside emerging oxygen‐independent roles. Manipulation of regulatory proteins of the HIF transcription factor family can profoundly influence inflammatory profiles, innate immune cell function and pathogen clearance and, as such, has been proposed as a therapeutic strategy against inflammatory diseases. The direction and mode of HIF manipulation as a therapy is dictated by the inflammatory properties of the disease in question, with innate immune cell HIF reduction being, in general, advantageous during chronic inflammatory conditions, while upregulation of HIF is beneficial during infections. The therapeutic potential of targeting myeloid HIFs, both genetically and pharmacologically, has been recently illuminated in vitro and in vivo, with an emerging range of inhibitory and activating strategies becoming available. This review focuses on cutting edge findings that uncover the roles of myeloid cell HIF signalling on immunoregulation in the contexts of inflammation and infection, and explores future directions of potential therapeutic strategies.


title: Macro Domain from Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Is an Efficient ADP-ribose Binding Module: CRYSTAL STRUCTURE AND BIOCHEMICAL STUDIES

text: The newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) encodes the conserved macro domain within non-structural protein 3. However, the precise biochemical function and structure of the macro domain is unclear. Using differential scanning fluorimetry and isothermal titration calorimetry, we characterized the MERS-CoV macro domain as a more efficient adenosine diphosphate (ADP)-ribose binding module than macro domains from other CoVs. Furthermore, the crystal structure of the MERS-CoV macro domain was determined at 1.43-Å resolution in complex with ADP-ribose. Comparison of macro domains from MERS-CoV and other human CoVs revealed structural differences in the α1 helix alters how the conserved Asp-20 interacts with ADP-ribose and may explain the efficient binding of the MERS-CoV macro domain to ADP-ribose. This study provides structural and biophysical bases to further evaluate the role of the MERS-CoV macro domain in the host response via ADP-ribose binding but also as a potential target for drug design.


title: Computational Analysis of Multiparametric Flow Cytometric Data to Dissect B Cell Subsets in Vaccine Studies

text: The generation of the B cell response upon vaccination is characterized by the induction of different functional and phenotypic subpopulations and is strongly dependent on the vaccine formulation, including the adjuvant used. Here, we have profiled the different B cell subsets elicited upon vaccination, using machine learning methods for interpreting high-dimensional flow cytometry data sets. The B cell response elicited by an adjuvanted vaccine formulation, compared to the antigen alone, was characterized using two automated methods based on clustering (FlowSOM) and dimensional reduction (t-SNE) approaches. The clustering method identified, based on multiple marker expression, different B cell populations, including plasmablasts, plasma cells, germinal center B cells and their subsets, while this profiling was more difficult with t-SNE analysis. When undefined phenotypes were detected, their characterization could be improved by integrating the t-SNE spatial visualization of cells with the FlowSOM clusters. The frequency of some cellular subsets, in particular plasma cells, was significantly higher in lymph nodes of mice primed with the adjuvanted formulation compared to antigen alone. Thanks to this automatic data analysis it was possible to identify, in an unbiased way, different B cell populations and also intermediate stages of cell differentiation elicited by immunization, thus providing a signature of B cell recall response that can be hardly obtained with the classical bidimensional gating analysis. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.


Obesity and COVID‐19: The mTOR pathway as a possible culprit


title: Mapping Climate Change Vulnerabilities to Infectious Diseases in Europe

text: Background: The incidence, outbreak frequency, and distribution of many infectious diseases are generally expected to change as a consequence of climate change, yet there is limited regional information available to guide decision making. Objective: We surveyed government officials designated as Competent Bodies for Scientific Advice concerning infectious diseases to examine the degree to which they are concerned about potential effects of climate change on infectious diseases, as well as their perceptions of institutional capacities in their respective countries. Methods: In 2007 and 2009/2010, national infectious disease experts from 30 European Economic Area countries were surveyed about recent and projected infectious disease patterns in relation to climate change in their countries and the national capacity to cope with them. Results: A large majority of respondents agreed that climate change would affect vector-borne (86% of country representatives), food-borne (70%), water-borne (68%), and rodent-borne (68%) diseases in their countries. In addition, most indicated that institutional improvements are needed for ongoing surveillance programs (83%), collaboration with the veterinary sector (69%), management of animal disease outbreaks (66%), national monitoring and control of climate-sensitive infectious diseases (64%), health services during an infectious disease outbreak (61%), and diagnostic support during an epidemic (54%). Conclusions: Expert responses were generally consistent with the peer-reviewed literature regarding the relationship between climate change and vector- and water-borne diseases, but were less so for food-borne diseases. Shortcomings in institutional capacity to manage climate change vulnerability, identified in this assessment, should be addressed in impact, vulnerability, and adaptation assessments.


title: Association of Obesity with Disease Severity among Patients with COVID‐19

text: OBJECTIVE: To explore the potential association of obesity and other chronic diseases with severe outcomes, such as intensive care unit (ICU) admission and invasive mechanical ventilation (IMV), in patients hospitalized with COVID‐19. METHODS: Retrospective cohort of 103 patients hospitalized with COVID‐19. Demographic data, past medical history and hospital course were collected and analyzed. A multivariate logistic regression analysis was implemented to examine associations. RESULTS: From February 17th to April 5th, 103 consecutive patients were hospitalized with COVID‐19. Among them, 41 patients (39.8%) were admitted to the ICU and 29 (70.7%) required (IMV). The prevalence of obesity was 47.5% (49/103). In a multivariate analysis, severe obesity (BMI ≥35 kg/m2) was associated with ICU admission (aOR 5.39; 95% CI:1.13‐25.64). Moreover, patients who required IMV, were more likely to have had heart disease (aOR 3.41; 95% CI:1.05‐11.06), obesity (BMI=30‐34.9 kg/m2) (aOR 6.85; 95% CI: 1.05‐44.82) or severe obesity (BMI≥35 kg/m2) (aOR 9.99; 95% CI:1.39‐71.69). CONCLUSION: In our analysis, severe obesity (BMI ≥35 kg/m2) was associated with ICU admission, while history of heart disease and obesity (BMI ≥30 kg/m2) were independently associated with the use of IMV. Increased vigilance and aggressive treatment of patients with obesity and COVID‐19 are warranted.


title: Analysis of the sex ratio of reported gonorrhoea incidence in Shenzhen, China

text: OBJECTIVE: To assess the clinical process of gonorrhoea diagnosis and report in China, and to determine the difference of sex ratio between reported incidence based on reporting data and true diagnosis rate based on reference tests of gonorrhoea. SETTING: A total of 26 dermatology and sexually transmitted disease (STD) departments, 34 obstetrics-gynaecology clinics and 28 urology outpatient clinics selected from 34 hospitals of Shenzhen regarded as our study sites. PARTICIPANTS: A total of 2754 participants were recruited in this study, and 2534 participants completed the questionnaire survey and provided genital tract secretion specimens. There were 1106 male and 1428 female participants. Eligible participants were patients who presented for outpatient STD care at the selected clinics for the first time in October 2012 were at least 18 years old, and were able to give informed consent. OUTCOME MEASURES: Untested rate, true-positive rate, false-negative rate and unreported rate of gonorrhoea, as well as reported gonorrhoea incidence sex ratio and true diagnosis sex ratio were calculated and used to describe the results. RESULTS: 2534 participants were enrolled in the study. The untested rate of gonorrhoea among females was significantly higher than that among males (female 88.1%, male 68.3%, p=0.001). The male-to-female sex ratios of untested rate, true-positive rate, false-negative rate and unreported rate were 1:1.3, 1.2:1, 1:1.6 and 1:1.4, respectively. The reported gonorrhoea incidence sex ratio of new diagnosed gonorrhoea was 19.8:1 (male vs female: 87/1106 vs 5/1420), while the true diagnosis sex ratio was 2.5:1 (male vs female: 161/1106 vs 84/1420). These data indicate that the sex ratio of reported gonorrhoea incidence has been overestimated by a factor of 7.9 (19.8/2.5). CONCLUSIONS: We found the current reported gonorrhoea incidence and sex ratios to be inaccurate due to underestimations of gonorrhoea incidence, especially among women.


title: Deubiquitylating enzymes and drug discovery: emerging opportunities

text: More than a decade after a Nobel Prize was awarded for the discovery of the ubiquitin–proteasome system and clinical approval of proteasome and ubiquitin E3 ligase inhibitors, first-generation deubiquitylating enzyme (DUB) inhibitors are now approaching clinical trials. However, although our knowledge of the physiological and pathophysiological roles of DUBs has evolved tremendously, the clinical development of selective DUB inhibitors has been challenging. In this Review, we discuss these issues and highlight recent advances in our understanding of DUB enzymology and biology as well as technological improvements that have contributed to the current interest in DUBs as therapeutic targets in diseases ranging from oncology to neurodegeneration. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrd.2017.152) contains supplementary material, which is available to authorized users.


title: Parainfluenza virus type 3 outbreak in a neonatal intensive care unit

text: Parainfluenza virus (PIV) is a respiratory pathogen in young children and is second only to the respiratory syncytial virus (RSV) as a cause of lower respiratory tract infection. PIV type 3 (PIV3) is the most severe. Herein we describe an outbreak of PIV3 in three infants in a neonatal intensive care unit. They were diagnosed on virus culture from pharyngeal swabs. We prevented the spread of the virus using standard infection control procedures and isolation of the symptomatic infants. One infant had severe chronic lung disease and was complicated with recurrent wheezing for a long time. Because RSV and PIV have many structural, pathogenic, epidemiologic, and clinical similarities, we speculate that PIV infection causes recurrent wheezing, as observed with RSV infection. Therefore, physicians must consider recurrent wheezing at the time of treatment of PIV infection early in life.


title: A severe refractory COVID-19 patient responding to convalescent plasma; A case series

text: INTRODUCTION: Although some medicines are under research, currently, no specific antiviral drug has been approved to target 2019 novel coronavirus. In this report two severe cases of 2019 novel coronavirus disease (COVID-19) patients have been described who received convalescent plasma (CP). CASE REPORT: Two male cases (a 46-year-old and a 56-year-old) after being diagnosed with severe COVID-19, they deteriorated despite supportive care and antiviral therapy. They started to improve with CP infusion both clinically and radiologically. Finally they were discharged in a very well condition with negative virology tests. CONCLUSION: CP might be an effective therapy for severe COVID-19 patients.


title: Economic reforms and health insurance in China()

text: During the 1990s, Chinese state-owned enterprises (SOEs) and collective enterprises continually decreased coverage of public health insurance to their employees. This paper investigates this changing pattern of health insurance coverage in China using panel data from the China Nutrition and Health Survey (1991–2000). It is the first attempt in this literature that tries to identify precisely the effects of specific policies and reforms on health insurance coverage in the transitional period of China. The fixed effects linear model clustering at the province level is used for estimation, and results are compared to alternative models, including pooled OLS, random effects GLS model and fixed effects logit model. Strong empirical evidence is found that unemployment as a side effect of the Open Door Policy, and the deregulation of SOE and collective enterprises were the main causes for the decreasing trend. For example, urban areas that were highly affected by the Open Door Policy were associated with 17 percentage points decrease in the insurance coverage. Moreover, I found evidence that the gaps between SOE and non-SOE employees, collective and non-collective employees, urban and rural employees have considerably decreased during the ten years.


Factors involved in low susceptibility to covid-19: an adaptation of high altitude inhabitants


title: A Comparative Analysis of Factors Influencing Two Outbreaks of Middle Eastern Respiratory Syndrome (MERS) in Saudi Arabia and South Korea

text: In 2012, an emerging viral infection was identified in Saudi Arabia that subsequently spread to 27 additional countries globally, though cases may have occurred elsewhere. The virus was ultimately named Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV), and has been endemic in Saudi Arabia since 2012. As of September 2019, 2468 laboratory-confirmed cases with 851 associated deaths have occurred with a case fatality rate of 34.4%, according to the World Health Organization. An imported case of MERS occurred in South Korea in 2015, stimulating a multi-month outbreak. Several distinguishing factors emerge upon epidemiological and sociological analysis of the two outbreaks including public awareness of the MERS outbreak, and transmission and synchronization of governing healthcare bodies. South Korea implemented a stringent healthcare model that protected patients and healthcare workers alike through prevention and high levels of public information. In addition, many details about MERS-CoV virology, transmission, pathological progression, and even the reservoir, remain unknown. This paper aims to delineate the key differences between the two regional outbreaks from both a healthcare and personal perspective including differing hospital practices, information and public knowledge, cultural practices, and reservoirs, among others. Further details about differing emergency outbreak responses, public information, and guidelines put in place to protect hospitals and citizens could improve the outcome of future MERS outbreaks.


title: Neutralizing human recombinant antibodies against herpes simplex virus type 1 glycoproteins B from a phage-displayed scFv antibody library

text: Abstract The HSV-1 envelope glycoprotein B (gB) plays a critical role in virus entry into host cells. Neutralizing antibodies can therefore potentially prevent virus entry into target cells and cell-to-cell spread of infection. Our present study focused on the selection of neutralizing single-chain Fv (scFv) antibodies of a phage-displayed nonimmune human scFv antibody library against gB of HSV-1. To enrich specific scFvs, two phage antibodies were isolated against amino acid residues 31–43 derived from the N-terminal part of gB using panning technique. Two scFvs, scFv-gB1 and scFv-gB2, with frequencies of 45% and 20% were obtained from scFv clones after performing PCR and MvaI fingerprinting. In phage ELISA analysis, both gB1 and gB2 scFvs demonstrated high reactivity with the gB peptide. In the neutralization assay, scFv-gB1 and scFv-gB2 represented neutralizing effects of 55% and 59%, respectively. Upon further enhancement of the neutralizing effects of these antibodies, they can be considered as new potential alternatives in the treatment and prophylaxis of HSV-1 infections.


title: Transcriptome sequencing and development of an expression microarray platform for the domestic ferret

text: BACKGROUND: The ferret (Mustela putorius furo) represents an attractive animal model for the study of respiratory diseases, including influenza. Despite its importance for biomedical research, the number of reagents for molecular and immunological analysis is restricted. We present here a parallel sequencing effort to produce an extensive EST (expressed sequence tags) dataset derived from a normalized ferret cDNA library made from mRNA from ferret blood, liver, lung, spleen and brain. RESULTS: We produced more than 500000 sequence reads that were assembled into 16000 partial ferret genes. These genes were combined with the available ferret sequences in the GenBank to develop a ferret specific microarray platform. Using this array, we detected tissue specific expression patterns which were confirmed by quantitative real time PCR assays. We also present a set of 41 ferret genes with even transcription profiles across the tested tissues, indicating their usefulness as housekeeping genes. CONCLUSION: The tools developed in this study allow for functional genomic analysis and make further development of reagents for the ferret model possible.


title: A Drill Down Analysis of the Pandemic COVID-19 cases in India using PDE

text: A key question prevails among all individuals today is how the disease, COVID-19 would propagate in an environment in which it is left unconstrained wherein, assertive efforts to mitigate the disease’s adverse effects are in headway. In the present study, the drilldown analysis of Covid-19 cases in India is presented and also discusses the prevention methods needed to break the chain of spread of virus.


title: An antibiotic stewardship programme to reduce inappropriate antibiotic prescribing for acute respiratory infections in rural Chinese primary care facilities: study protocol for a clustered randomised controlled trial

text: BACKGROUND: Inappropriate prescribing of antibiotics for acute respiratory infections at the primary care level represents the major source of antibiotic misuse in healthcare, and is a major driver for antimicrobial resistance worldwide. In this study we will develop, pilot and evaluate the effectiveness of a comprehensive antibiotic stewardship programme in China’s primary care hospitals to reduce inappropriate prescribing of antibiotics for acute respiratory infections among all ages. METHODS: We will use a parallel-group, cluster-randomised, controlled, superiority trial with blinded outcome evaluation but unblinded treatment (providers and patients). We will randomise 34 primary care hospitals from two counties within Guangdong province into the intervention and control arm (1:1 overall ratio) stratified by county (8:9 within-county ratio). In the control arm, antibiotic prescribing and management will continue through usual care. In the intervention arm, we will implement an antibiotic stewardship programme targeting family physicians and patients/caregivers. The family physician components include: (1) training using new operational guidelines, (2) improved management and peer-review of antibiotic prescribing, (3) improved electronic medical records and smart phone app facilitation. The patient/caregiver component involves patient education via family physicians, leaflets and videos. The primary outcome is the proportion of prescriptions for acute respiratory infections (excluding pneumonia) that contain any antibiotic(s). Secondary outcomes will address how frequently specific classes of antibiotics are prescribed, how frequently key non-antibiotic alternatives are prescribed and the costs of consultations. We will conduct a qualitative process evaluation to explore operational questions regarding acceptability, cultural appropriateness and burden of technology use, as well as a cost-effectiveness analysis and a long-term benefit evaluation. The duration of the intervention will be 12 months, with another 24 months’ post-trial long-term follow-up. DISCUSSION: Our study is one of the first trials to evaluate the effect of an antibiotic stewardship programme in primary care settings in a low- or middle-income country (LMIC). All interventional activities will be designed to be embedded into routine primary care with strong local ownership. Through the trial we intend to impact on clinical practice and national policy in antibiotic prescription for primary care facilities in rural China and other LMICs. TRIAL REGISTRATION: ISRCTN, ID: ISRCTN96892547. Registered on 18 August 2019.


title: Harnessing Adenosine A2A Receptors as a Strategy for Suppressing the Lung Inflammation and Thrombotic Complications of COVID-19: Potential of Pentoxifylline and Dipyridamole

text: Counterproductive lung inflammation and dysregulated thrombosis contribute importantly to the lethality of advanced COVID-19. Adenosine A2A receptors (A2AR), expressed by a wide range of immune cells, as well as endothelial cells and platelets, exert cAMP-mediated anti-inflammatory and anti-thrombotic effects that potentially could be highly protective in this regard. The venerable drug pentoxifylline (PTX) exerts both anti-inflammatory and antithrombotic effects that reflect its ability to boost the responsiveness of A2AR to extracellular adenosine. The platelet-stabilizing drug dipyridamole (DIP) blocks intracellular uptake of extracellularly-generated adenosine, thereby up-regulating A2AR signaling in a way that should be functionally complementary to the impact of PTX in that regard. Moreover, DIP has recently been reported to slow the cellular replication of SARS-CoV-2 in clinically feasible concentrations. Both PTX and DIP are reasonably safe, well-tolerated, widely available, and inexpensive drugs. When COVID-19 patients can be treated within several days of symptom onset, using PTX + DIP in conjunction with hydroxychloroquine (HCQ) and an antibiotic - azithromycin (AZM) or doxycycline – might be warranted. HCQ and AZM can suppress SARS-CoV-2 proliferation in vitro and may slow the cell-to-cell spread of the virus; a large case series evaluating this combination in early-stage patients reported an impressively low mortality rate. However, whereas HCQ and AZM can promote QT interval lengthening and may be contraindicated in more advanced COVID-19 entailing cardiac damage, doxycycline has no such effect and exerts a potentially beneficial anti-inflammatory action. In contrast to HCQ, we propose that the combination of PTX + DIP can be used in both early and advanced stages of COVID-19. Concurrent use of certain nutraceuticals – yeast beta-glucan, zinc, vitamin D, spirulina, phase 2 inducers, N-acetylcysteine, glucosamine, quercetin, and magnesium – might also improve therapeutic outcomes in COVID-19.


title: Role of free radicals in viral pathogenesis and mutation

text: Oxygen radicals and nitric oxide (NO) are generated in excess in a diverse array of microbial infections. Emerging concepts in free radical biology are now shedding light on the pathogenesis of various diseases. Free‐radical induced pathogenicity in virus infections is of great importance, because evidence suggests that NO and oxygen radicals such as superoxide are key molecules in the pathogenesis of various infectious diseases. Although oxygen radicals and NO have an antimicrobial effect on bacteria and protozoa, they have opposing effects in virus infections such as influenza virus pneumonia and several other neurotropic virus infections. A high output of NO from inducible NO synthase, occurring in a variety of virus infections, produces highly reactive nitrogen oxide species, such as peroxynitrite, via interaction with oxygen radicals and reactive oxygen intermediates. The production of these various reactive species confers the diverse biological functions of NO. The reactive nitrogen species cause oxidative tissue injury and mutagenesis through oxidation and nitration of various biomolecules. The unique biological properties of free radicals are further illustrated by recent evidence showing accelerated viral mutation by NO‐induced oxidative stress. NO appears to affect a host's immune response, with immunopathological consequences. For example, NO is reported to suppress type 1 helper T cell‐dependent immune responses during infections, leading to type 2 helper T cell‐biased immunological host responses. NO‐induced immunosuppression may thus contribute to the pathogenesis of virus infections and help expansion of quasispecies population of viral pathogens. This review describes the pathophysiological roles of free radicals in the pathogenesis of viral disease and in viral mutation as related to both nonspecific inflammatory responses and immunological host reactions modulated by NO. Copyright © 2001 John Wiley & Sons, Ltd.


title: A case of Bacillus cereus bacteremia in a COVID-19 patient treated with steroids

text: This report describes a case of Bacillus cereus bacteremia in a COVID-19 patient with prior inhalational steroid use and inpatient steroid treatment for COVID-19 pulmonary symptoms. The case herein is intended to illustrate an uncommon presentation of B. cereus bacteremia and highlight the increased likelihood for the occurrence of this bacteremia in patients with COVID-19 and concomitant steroid use.


The new coronavirus and the risk to children's health


title: Glial cell type-specific changes in spinal dipeptidyl peptidase 4 expression and effects of its inhibitors in inflammatory and neuropatic pain

text: Altered pain sensations such as hyperalgesia and allodynia are characteristic features of various pain states, and remain difficult to treat. We have shown previously that spinal application of dipeptidyl peptidase 4 (DPP4) inhibitors induces strong antihyperalgesic effect during inflammatory pain. In this study we observed low level of DPP4 mRNA in the rat spinal dorsal horn in physiological conditions, which did not change significantly either in carrageenan-induced inflammatory or partial nerve ligation-generated neuropathic states. In naïve animals, microglia and astrocytes expressed DPP4 protein with one and two orders of magnitude higher than neurons, respectively. DPP4 significantly increased in astrocytes during inflammation and in microglia in neuropathy. Intrathecal application of two DPP4 inhibitors tripeptide isoleucin-prolin-isoleucin (IPI) and the antidiabetic drug vildagliptin resulted in robust opioid-dependent antihyperalgesic effect during inflammation, and milder but significant opioid-independent antihyperalgesic action in the neuropathic model. The opioid-mediated antihyperalgesic effect of IPI was exclusively related to mu-opioid receptors, while vildagliptin affected mainly delta-receptor activity, although mu- and kappa-receptors were also involved. None of the inhibitors influenced allodynia. Our results suggest pathology and glia-type specific changes of DPP4 activity in the spinal cord, which contribute to the development and maintenance of hyperalgesia and interact with endogenous opioid systems.


title: Dos terapias conocidas podrían ser efectivas como adyuvantes en el paciente crítico infectado por COVID-19

text: Resumen La neumonía causada por coronavirus, que se originó en Wuhan, China, a finales de 2019, se ha extendido por todo el mundo convirtiéndose en una pandemia. Desafortunadamente, a día de hoy no existe ninguna vacuna específica para el virus COVID-19, y el tratamiento está siendo de soporte con añadido de antivirales y otros fármacos, sin que hasta la fecha se haya evidenciado un beneficio claro. Muchos de estos pacientes se deterioran rápidamente y requieren ser intubados y ventilados mecánicamente, lo que está provocando el colapso del sistema sanitario en muchos países debido a la falta de ventiladores y de camas de críticos. En este documento revisamos dos terapias adyuvantes sencillas de aplicar, sin efectos deletéreos y de un coste bajo que podrían ser de utilidad para el tratamiento de la infección por coronavirus agudo severo asociado al síndrome respiratorio agudo (SARS-CoV-2). La vitaminaC, un potente antioxidante, se ha convertido en una terapia relevante debido a sus beneficios potenciales cuando se administra por vía intravenosa. El efecto potencial de la vitaminaC en la reducción de la inflamación en los pulmones podría desempeñar un papel clave en la lesión pulmonar causada por la infección por coronavirus. Otra posible terapia eficaz es el ozono. Pese a la controversia que siempre le ha acompañado, se ha estudiado y utilizado ampliamente durante muchos años y su eficacia se ha demostrado en múltiples estudios. Sin embargo, nuestro objetivo no es hacer una revisión exhaustiva de dichas terapias sino difundir sus efectos beneficiosos. Obviamente, los ensayos clínicos son necesarios, pero dado el potencial beneficio de estas terapias, recomendamos incorporarlas al arsenal terapéutico para el tratamiento del SARS-CoV-2. Abstract Pneumonia caused by coronavirus, which originated in Wuhan, China, in late 2019, has been spread around the world already becoming a pandemic. Unfortunately, there is not yet a specific vaccine or effective antiviral drug for treating COVID-19. Many of these patients deteriorate rapidly and require intubation and are mechanically ventilated, which is causing the collapse of the health system in many countries due to lack of ventilators and intensive care beds. In this document we review two simple adjuvant therapies to administer, without side effects, and low cost that could be useful for the treatment of acute severe coronavirus infection associated with acute respiratory syndrome (SARS-CoV-2). VitaminC, a potent antioxidant, has emerged as a relevant therapy due to its potential benefits when administered intravenous. The potential effect of vitaminC in reducing inflammation in the lungs could play a key role in lung injury caused by coronavirus infection. Another potential effective therapy is ozone: it has been extensively studied and used for many years and its effectiveness has been demonstrated so far in multiples studies. Nevertheless, our goal is not to make an exhaustive review of these therapies but spread the beneficial effects themselves. Obviously clinical trials are necessaries, but due to the potential benefit of these two therapies we highly recommended to add to the therapeutic arsenal.


title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012

text: Abstract One of the major problems of avian infectious bronchitis virus (IBV) is the frequent emergence of new variants. In the present study 205 tracheal swabs and organs were collected from broilers and layers chicken farms during January to August 2012 from 19 governorates all over Egypt. The chickens demonstrated respiratory signs and mortality. Out of the examined samples, 130 of which (about 64%) of suspected farms were positive for IBV with real time RT-PCR. 13 IBV-positive samples were selected for further isolation and characterization. Isolation in specific pathogen free (SPF) embryos was carried out after studies three blind successive passages and the hypervariable region of spike protein1 (SP1) was amplified by RT-PCR and sequenced to study the genetic diversity between the isolated viruses. Phylogenetic analysis of the obtained sequences of 13 isolates compared with other IBV strains from the Middle East and worldwide reveled that 11 out of the 13 isolates had close relationship the Israeli variants (IS/885 and IS/1494/06) with nucleotide homology reached up to 89.9% and 82.3%, respectively. Only two isolates had close relationship with CR/88121 and 4/91 viruses with identities of 95% and 96%, respectively. This study indicates existence of two variant groups of IBV circulating in Egypt during 2012. Group I was similar but distinguishable from Israeli variant IS/885 and group II was related to 4/91 and CR/88121 vaccine strains. There was no geographical link between the 2 groups as they were distributed all over the country. These findings necessitate the need to revise the vaccination programs and control measures for IBV.


title: Diagnostic Performance of a Rapid Point of Care Test for SARS‐CoV‐2 in an Urban ED Setting

text: The ability to rapidly and accurately identify a patient's COVID‐19 status has had significant impact on emergency departments (ED) and health systems globally. Since the identification of SARS‐CoV‐2 illness in the United States, there has been rapid development in patient testing capacity following initial challenges including sparse availability. This was made possible by increasing availability of diagnostic molecular tests in several formats, from laboratory based traditional, RT‐PCR methods to near patient testing rapid point of care PCR tests.


title: Modeling and detection of respiratory-related outbreak signatures

text: BACKGROUND: Time series methods are commonly used to detect disease outbreak signatures (e.g., signals due to influenza outbreaks and anthrax attacks) from varying respiratory-related diagnostic or syndromic data sources. Typically this involves two components: (i) Using time series methods to model the baseline background distribution (the time series process that is assumed to contain no outbreak signatures), (ii) Detecting outbreak signatures using filter-based time series methods. METHODS: We consider time series models for chest radiograph data obtained from Midwest children's emergency departments. These models incorporate available covariate information such as patient visit counts and smoothed ambient temperature series, as well as time series dependencies on daily and weekly seasonal scales. Respiratory-related outbreak signature detection is based on filtering the one-step-ahead prediction errors obtained from the time series models for the respiratory-complaint background. RESULTS: Using simulation experiments based on a stochastic model for an anthrax attack, we illustrate the effect of the choice of filter and the statistical models upon radiograph-attributed outbreak signature detection. CONCLUSION: We demonstrate the importance of using seasonal autoregressive integrated average time series models (SARIMA) with covariates in the modeling of respiratory-related time series data. We find some homogeneity in the time series models for the respiratory-complaint backgrounds across the Midwest emergency departments studied. Our simulations show that the balance between specificity, sensitivity, and timeliness to detect an outbreak signature differs by the emergency department and the choice of filter. The linear and exponential filters provide a good balance.


title: Periodic solutions and bifurcation in an S I S epidemic model with birth pulses

text: Abstract The dynamical behavior of an S I S epidemic model with birth pulses and a varying population is discussed analytically and numerically. This paper investigates the existence and stability of the infection-free periodic solution and the endemic periodic solution. By using discrete maps, the center manifold theorem, and the bifurcation theorem, the conditions of existence for bifurcation of the positive periodic solution are derived. Moreover, numerical results for phase portraits, periodic solutions, and bifurcation diagrams, which are illustrated with an example, are in good agreement with the theoretical analysis.


Cancer disparities in the COVID‐19 era


title: Leadership, Management and Command in the time of the Coronavirus

text: The Covid-19 pandemic that swept through the world in late 2019 and through 2020 provides a test not just for all societies and their leadership, but for leadership theory. In a world turned upside down, when many conventions are disposed of, it is clear that things will not return to the status quo ante any time soon, if ever. In the light of these challenges, this short paper suggests we might reconsider the way governments and their leaders act against the frame of societal problems, originally established by Rittell and Webber in 1973. I suggest that all three modes of decision-making (Leadership, Management and Command) are necessary because of the complex and complicated nature of the problem and conclude that while Command is appropriate for certain times and issues, it also poses long-term threats, especially if the context is ignored.


title: Molecular detection of novel picornaviruses in chickens and turkeys

text: Fecal specimens, including swabs and litter extracts, collected from chickens, domestic ducks, turkeys, and Canadian geese were tested using degenerate primers targeting regions encoding for conserved amino acid motifs (YGDD and DY(T/S)(R/K/G)WDST) in calicivirus RNA-dependent RNA polymerases. Similar motifs are also present in other RNA viruses. Two fecal specimens and 18 litter extracts collected from chickens and turkeys yielded RT-PCR products. BLAST search and phylogenetic analysis revealed that all amplicons represented picornaviruses that clustered into two major groups. Four chicken and one turkey samples yielded 250 bp amplicons with 84–91% nucleotide identity to the recently described turkey hepatitis viruses, while 280 and 283 bp amplicons obtained from 11 chicken and 4 turkey samples represented novel picornaviruses with the closest nucleotide identity to kobuviruses (54–61%) and turdiviruses (47–54%). Analysis of 2.2–3.2 kb extended genome sequences including the partial P2 (2C) and complete P3 (3A, 3B (VPg), 3C(pro), and 3D(pol)) regions of selected strains indicated that viruses yielding the 280/283 bp amplicons represent a putative new genus of Picornaviridae. The 3′-non-translated region (NTR) of the turkey hepatitis-like viruses described in this study was significantly longer (641–654 nt) than that of any of the other piconaviruses and included a putative short open reading frame (ORF). In summary, we report the molecular detection of novel picornaviruses that appear to be endemic in both chickens and turkeys.


title: AI4COVID-19: AI enabled preliminary diagnosis for COVID-19 from cough samples via an app

text: BACKGROUND: The inability to test at scale has become humanity's Achille's heel in the ongoing war against the COVID-19 pandemic. A scalable screening tool would be a game changer. Building on the prior work on cough-based diagnosis of respiratory diseases, we propose, develop and test an Artificial Intelligence (AI)-powered screening solution for COVID-19 infection that is deployable via a smartphone app. The app, named AI4COVID-19 records and sends three 3-s cough sounds to an AI engine running in the cloud, and returns a result within 2 min. METHODS: Cough is a symptom of over thirty non-COVID-19 related medical conditions. This makes the diagnosis of a COVID-19 infection by cough alone an extremely challenging multidisciplinary problem. We address this problem by investigating the distinctness of pathomorphological alterations in the respiratory system induced by COVID-19 infection when compared to other respiratory infections. To overcome the COVID-19 cough training data shortage we exploit transfer learning. To reduce the misdiagnosis risk stemming from the complex dimensionality of the problem, we leverage a multi-pronged mediator centered risk-averse AI architecture. RESULTS: Results show AI4COVID-19 can distinguish among COVID-19 coughs and several types of non-COVID-19 coughs. The accuracy is promising enough to encourage a large-scale collection of labeled cough data to gauge the generalization capability of AI4COVID-19. AI4COVID-19 is not a clinical grade testing tool. Instead, it offers a screening tool deployable anytime, anywhere, by anyone. It can also be a clinical decision assistance tool used to channel clinical-testing and treatment to those who need it the most, thereby saving more lives.


title: Mesoniviridae: a proposed new family in the order Nidovirales formed by a single species of mosquito-borne viruses

text: Recently, two independent surveillance studies in Côte d’Ivoire and Vietnam, respectively, led to the discovery of two mosquito-borne viruses, Cavally virus and Nam Dinh virus, with genome and proteome properties typical for viruses of the order Nidovirales. Using a state-of-the-art approach, we show that the two insect nidoviruses are (i) sufficiently different from other nidoviruses to represent a new virus family, and (ii) related to each other closely enough to be placed in the same virus species. We propose to name this new family Mesoniviridae. Meso is derived from the Greek word “mesos” (in English “in the middle”) and refers to the distinctive genome size of these insect nidoviruses, which is intermediate between that of the families Arteriviridae and Coronaviridae, while ni is an abbreviation for “nido”. A taxonomic proposal to establish the new family Mesoniviridae, genus Alphamesonivirus, and species Alphamesonivirus 1 has been approved for consideration by the Executive Committee of the ICTV.


title: Do We Need a Coronavirus (Safeguards) Act 2020? Proposed Legal Safeguards for Digital Contact Tracing and Other Apps in the COVID-19 Crisis

text: The focus of this Preview is “The Coronavirus (Safeguards) Bill 2020: Proposed protections for digital interventions and in relation to immunity certificates,” published by Lilian Edwards, professor of law, innovation and society at Newcastle Law School and a member of the NHSX Ethical Advisory Board (CV19 App).


title: End-of-life care in patients with a highly transmissible respiratory virus: implications for COVID-19

text: Symptom management and end-of-life care are core skills for all physicians, although in ordinary times many anesthesiologists have fewer occasions to use these skills. The current coronavirus disease (COVID-19) pandemic has caused significant mortality over a short time and has necessitated an increase in provision of both critical care and palliative care. For anesthesiologists deployed to units caring for patients with COVID-19, this narrative review provides guidance on conducting goals of care discussions, withdrawing life-sustaining measures, and managing distressing symptoms.


title: Anti-SARS-CoV IgG response in relation to disease severity of severe acute respiratory syndrome

text: Abstract Background The association between a robust or depressed antibody response and clinical severity of SARS remains unknown. Objectives To study seroconversion and the magnitude of IgG responses in a SARS cohort with different disease severities. Study design and method A retrospective analysis of all acute and convalescent-phase sera collected from a cohort of laboratory-confirmed SARS cases. Anti-SARS-CoV IgG antibody was detected using indirect immunofluorescence technique and quantified by two-fold serial dilutions. Characteristics of patients who seroconverted “early” (<median interval) were compared to those documented to remain sero-negative during the same time interval. Median IgG levels in convalescent-phase sera (collected within 30 days) were compared among patients with different disease severities. Correlations between IgG levels and important laboratory parameters were assessed. Results A total of 325 laboratory-confirmed SARS cases were analyzed; of which 301 (92.6%) had anti-SARS-CoV IgG detected in their sera at the time of sampling. IgG was first detected on day 4 of illness; seroconversion occurred at a median of 16 days (range 4–35 days), and IgG peak levels were reached in the fourth week. Early seroconversion (<day 16) occurred more frequently among patients who required ICU-admission (χ 2; p =0.011). Higher IgG levels were detected in patients who required supplemental oxygen (Mann–Whitney; p =0.002), ICU-admission (p =0.001), had negative pre-discharge fecal RT-PCR results (p =0.004), and lymphopenia at presentation (p =0.028). Peak IgG titres also correlated positively with peak LDH levels (Spearman's r =+0.360; p <0.001) among survivors. Conclusions Severe SARS is associated with a more robust IgG response.


title: Leukocyte-Derived IFN-α/β and Epithelial IFN-λ Constitute a Compartmentalized Mucosal Defense System that Restricts Enteric Virus Infections

text: Epithelial cells are a major port of entry for many viruses, but the molecular networks which protect barrier surfaces against viral infections are incompletely understood. Viral infections induce simultaneous production of type I (IFN-α/β) and type III (IFN-λ) interferons. All nucleated cells are believed to respond to IFN-α/β, whereas IFN-λ responses are largely confined to epithelial cells. We observed that intestinal epithelial cells, unlike hematopoietic cells of this organ, express only very low levels of functional IFN-α/β receptors. Accordingly, after oral infection of IFN-α/β receptor-deficient mice, human reovirus type 3 specifically infected cells in the lamina propria but, strikingly, did not productively replicate in gut epithelial cells. By contrast, reovirus replicated almost exclusively in gut epithelial cells of IFN-λ receptor-deficient mice, suggesting that the gut mucosa is equipped with a compartmentalized IFN system in which epithelial cells mainly respond to IFN-λ that they produce after viral infection, whereas other cells of the gut mostly rely on IFN-α/β for antiviral defense. In suckling mice with IFN-λ receptor deficiency, reovirus replicated in the gut epithelium and additionally infected epithelial cells lining the bile ducts, indicating that infants may use IFN-λ for the control of virus infections in various epithelia-rich tissues. Thus, IFN-λ should be regarded as an autonomous virus defense system of the gut mucosa and other epithelial barriers that may have evolved to avoid unnecessarily frequent triggering of the IFN-α/β system which would induce exacerbated inflammation.


title: Comparative global epidemiology of influenza, respiratory syncytial and parainfluenza viruses, 2010–2015

text: Summary Objectives To improve our understanding of the global epidemiology of common respiratory viruses by analysing their contemporaneous incidence at multiple sites. Methods 2010–2015 incidence data for influenza A (IAV), influenza B (IBV), respiratory syncytial (RSV) and parainfluenza (PIV) virus infections were collected from 18 sites (14 countries), consisting of local (n = 6), regional (n = 9) and national (n = 3) laboratories using molecular diagnostic methods. Each site submitted monthly virus incidence data, together with details of their patient populations tested and diagnostic assays used. Results For the Northern Hemisphere temperate countries, the IAV, IBV and RSV incidence peaks were 2–6 months out of phase with those in the Southern Hemisphere, with IAV having a sharp out-of-phase difference at 6 months, whereas IBV and RSV showed more variable out-of-phase differences of 2–6 months. The tropical sites Singapore and Kuala Lumpur showed fluctuating incidence of these viruses throughout the year, whereas subtropical sites such as Hong Kong, Brisbane and Sydney showed distinctive biannual peaks for IAV but not for RSV and PIV. Conclusions There was a notable pattern of synchrony of IAV, IBV and RSV incidence peaks globally, and within countries with multiple sampling sites (Canada, UK, Australia), despite significant distances between these sites.


SARS transmission: language and droplet production


title: Knowledge and practices regarding Middle East Respiratory Syndrome Coronavirus among camel handlers in a Slaughterhouse, Kenya, 2015

text: Dromedary camels are implicated as reservoirs for the zoonotic transmission of Middle East Respiratory Syndrome coronavirus (MERS‐CoV) with the respiratory route thought to be the main mode of transmission. Knowledge and practices regarding MERS among herders, traders and slaughterhouse workers were assessed at Athi‐River slaughterhouse, Kenya. Questionnaires were administered, and a check list was used to collect information on hygiene practices among slaughterhouse workers. Of 22 persons, all washed hands after handling camels, 82% wore gumboots, and 65% wore overalls/dustcoats. None of the workers wore gloves or facemasks during slaughter processes. Fourteen percent reported drinking raw camel milk; 90% were aware of zoonotic diseases with most reporting common ways of transmission as: eating improperly cooked meat (90%), drinking raw milk (68%) and slaughter processes (50%). Sixteen (73%) were unaware of MERS‐CoV. Use of personal protective clothing to prevent direct contact with discharges and aerosols was lacking. Although few people working with camels were interviewed, those met at this centralized slaughterhouse lacked knowledge about MERS‐CoV but were aware of zoonotic diseases and their transmission. These findings highlight need to disseminate information about MERS‐CoV and enhance hygiene and biosafety practices among camel slaughterhouse workers to reduce opportunities for potential virus transmission.


title: In vitro antiviral activity of phlorotannins isolated from Ecklonia cava against porcine epidemic diarrhea coronavirus infection and hemagglutination

text: Despite the prepdominat agent causing severe entero-pathogenic diarrhea in swine, there are no effective therapeutical treatment of porcine epidemic diarrhea virus (PEDV). In this study, we evaluated the antiviral activity of five phlorotannins isolated from Ecklonia cava (E. cava) against PEDV. In vitro antiviral activity was tested using two different assay strategies: (1) blockage of the binding of virus to cells (simultaneous-treatment assay) and (2) inhibition of viral replication (post-treatment assay). In simultaneous-treatment assay, compounds 2–5 except compound 1 exhibited antiviral activities of a 50% inhibitory concentration (IC(50)) with the ranging from 10.8 ± 1.4 to 22.5 ± 2.2 μM against PEDV. Compounds 1–5 were completely blocked binding of viral spike protein to sialic acids at less than 36.6 μM concentrations by hemagglutination inhibition. Moreover, compounds 4 and 5 of five phlorotannins inhibited viral replication with IC(50) values of 12.2 ± 2.8 and 14.6 ± 1.3 μM in the post-treatment assay, respectively. During virus replication steps, compounds 4 and 5 exhibited stronger inhibition of viral RNA and viral protein synthesis in late stages (18 and 24 h) than in early stages (6 and 12 h). Interestingly, compounds 4 and 5 inhibited both viral entry by hemagglutination inhibition and viral replication by inhibition of viral RNA and viral protein synthesis, but not viral protease. These results suggest that compounds isolated from E. cava have strong antiviral activity against PEDV, inhibiting viral entry and/or viral replication, and may be developed into natural therapeutic drugs against coronavirus infection.


title: Interferon gamma (IFNγ) +874A/T gene polymorphism in South Indian ischemic stroke patients

text: BACKGROUND: Ischemic stroke is a complex vascular and metabolic process resulting in neuronal death and progression with time. Cytokines play a role in immune response and also maintains the normal homeostatic environment of the central nervous system. IFN-γ is one of the key effector cytokines produced by NK and T cells that enhances microbicidal activity of macrophages and neutrophils. PURPOSE: As the association of IFNγ +874A/T gene polymorphism with stroke has not been investigated in Indian population, we wanted to evaluate the association of this polymorphism with ischemic stroke in a South Indian population. METHODS: We genotyped 171 ischemic stroke patients and 153 age-matched control subjects. RESULTS: Statistical analysis showed a significant association of TT homozygote with ischemic stroke (OR=1.9, 95% CI=1.05-3.43, p=0.03), while AA (OR= 0.84, 95% CI=0.54–1.31, p=0.46) and AT(OR=0.80, 95% CI=0.51-1.26, p=0.34) genotypes were not significantly associated. A and T allele frequencies in stroke were 58.78% and 41.22% as against 65.36% and 34.64% in control group, respectively, thus, suggesting no statistically significant differences in the A (OR=0.75, 95% CI=0.54–1.03, p=0.08) and T (OR=1.32, 95% CI=0.96– 1.82, p=0.08) allele frequencies between the two groups. CONCLUSION: We conclude that the IFN-γ +874 TT genotype is associated with the increased risk of ischemic stroke.


title: The need for GIScience in mapping COVID-19

text: Since first being tracked in late 2019 in China, the effects of the COVID-19 coronavirus have shaped global patterns of morbidity and mortality as well as exposed the strengths and limitations of health care systems and social safety nets. Without question, reporting of its impact has been bolstered in large part through near real-time daily mapping of cases and fatalities. Though these maps serve as an effective political and social tool in communicating disease impact, most visualizations largely over-emphasize their usefulness for tracking disease progression and appropriate responses. Messy and inconsistent health data are a big part of this problem, as is a paucity of high-resolution spatial data to monitor health outcomes. Another issue is that the ease of producing out-of-the box products largely out paces the response to the core challenges inherent in the poor quality of most geo-referenced data. Adopting a GIScience approach, and in particular, making use of location-based intelligence tools, can improve the shortcomings in data reporting and more accurately reveal how COVID-19 will have a long-term impact on global health.


title: Engineering a Replication-Competent, Propagation-Defective Middle East Respiratory Syndrome Coronavirus as a Vaccine Candidate

text: Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging coronavirus infecting humans that is associated with acute pneumonia, occasional renal failure, and a high mortality rate and is considered a threat to public health. The construction of a full-length infectious cDNA clone of the MERS-CoV genome in a bacterial artificial chromosome is reported here, providing a reverse genetics system to study the molecular biology of the virus and to develop attenuated viruses as vaccine candidates. Following transfection with the cDNA clone, infectious virus was rescued in both Vero A66 and Huh-7 cells. Recombinant MERS-CoVs (rMERS-CoVs) lacking the accessory genes 3, 4a, 4b, and 5 were successfully rescued from cDNA clones with these genes deleted. The mutant viruses presented growth kinetics similar to those of the wild-type virus, indicating that accessory genes were not essential for MERS-CoV replication in cell cultures. In contrast, an engineered mutant virus lacking the structural E protein (rMERS-CoV-ΔE) was not successfully rescued, since viral infectivity was lost at early passages. Interestingly, the rMERS-CoV-ΔE genome replicated after cDNA clone was transfected into cells. The infectious virus was rescued and propagated in cells expressing the E protein in trans, indicating that this virus was replication competent and propagation defective. Therefore, the rMERS-CoV-ΔE mutant virus is potentially a safe and promising vaccine candidate to prevent MERS-CoV infection. IMPORTANCE Since the emergence of MERS-CoV in the Arabian Peninsula during the summer of 2012, it has already spread to 10 different countries, infecting around 94 persons and showing a mortality rate higher than 50%. This article describes the development of the first reverse genetics system for MERS-CoV, based on the construction of an infectious cDNA clone inserted into a bacterial artificial chromosome. Using this system, a collection of rMERS-CoV deletion mutants has been generated. Interestingly, one of the mutants with the E gene deleted was a replication-competent, propagation-defective virus that could only be grown in the laboratory by providing E protein in trans, whereas it would only survive a single virus infection cycle in vivo. This virus constitutes a vaccine candidate that may represent a balance between safety and efficacy for the induction of mucosal immunity, which is needed to prevent MERS-CoV infection.


title: Modeling the transmission dynamics and control of rabies in China

text: Abstract Human rabies was first recorded in ancient China in about 556 BC and is still one of the major public-health problems in China. From 1950 to 2015, 130,494 human rabies cases were reported in Mainland China with an average of 1977 cases per year. It is estimated that 95% of these human rabies cases are due to dog bites. The purpose of this article is to provide a review about the models, results, and simulations that we have obtained recently on studying the transmission of rabies in China. We first construct a basic susceptible, exposed, infectious, and recovered (SEIR) type model for the spread of rabies virus among dogs and from dogs to humans and use the model to simulate the human rabies data in China from 1996 to 2010. Then we modify the basic model by including both domestic and stray dogs and apply the model to simulate the human rabies data from Guangdong Province, China. To study the seasonality of rabies, in Section 4 we further propose a SEIR model with periodic transmission rates and employ the model to simulate the monthly data of human rabies cases reported by the Chinese Ministry of Health from January 2004 to December 2010. To understand the spatial spread of rabies, in Section 5 we add diffusion to the dog population in the basic SEIR model to obtain a reaction–diffusion equation model and determine the minimum wave speed connecting the disease-free equilibrium to the endemic equilibrium. Finally, in order to investigate how the movement of dogs affects the geographically inter-provincial spread of rabies in Mainland China, in Section 6 we propose a multi-patch model to describe the transmission dynamics of rabies between dogs and humans and use the two-patch submodel to investigate the rabies virus clades lineages and to simulate the human rabies data from Guizhou and Guangxi, Hebei and Fujian, and Sichuan and Shaanxi, respectively. Some discussions are provided in Section 7.


title: Enteric viral infections as a cause of diarrhoea in the acquired immunodeficiency syndrome

text: Background and aims The role of non‐cytomegalovirus (CMV) enteric viral infection in causing diarrhoea in patients with human immunodeficiency virus (HIV) is poorly understood. We aimed to investigate the prevalence of these infections in acute and chronic diarrhoea. Methods Stool specimens from 377 HIV‐infected patients presenting with diarrhoea were studied prospectively for evidence of non‐CMV enteric viral infection. Patients with diarrhoea underwent investigation for gastrointestinal pathogens, including electron microscopic examination of stool for enteric viruses. We collected data on patients in whom enteric virus was identified and examined the association of enteric virus infection with diarrhoeal symptomatology. Results Eighty‐nine (10.3%) stool specimens from 60 (15.9%) HIV(+) individuals were positive for coronavirus (n = 13, 22%), rotavirus (n = 11, 18%), adenovirus (n = 30, 50%) and small round structured viruses (n = 5, 8%) or dual infection (n = 2, 3%). Thirty‐four of 52 (65%) patients available for analysis had acute diarrhoea, and 18/52 (35%) had chronic diarrhoea. Twenty‐three of 52 (44%) patients had a concurrent gut pathogen. After exclusion of concurrent pathogens enteric viral infections were found to be significantly associated with acute as opposed to chronic diarrhoea (P = 0.004). The presence of adenovirus colitis was significantly more likely to be associated with chronic diarrhoea (15/21 cases) than adenovirus isolated from stool alone (9/23 cases) (P = 0.03). There was a trend towards an association between adenovirus colitis and colonic cytomegalovirus infection (P = 0.06). Conclusion Enteric viral infection is strongly associated with acute diarrhoea in patients with HIV. Light microscopic examination of large bowel biopsies can identify adenovirus colitis which is significantly associated with chronic diarrhoea, and in addition may facilitate gastrointestinal co‐infection with CMV.


title: Mutations in the spike glycoprotein of human coronavirus OC43 modulate disease in BALB/c mice from encephalitis to flaccid paralysis and demyelination

text: The etiology of most neurodegenerative diseases of the central nervous system remains unknown and likely involves a combination of genetic susceptibility and environmental triggering factors. Given that exposure to numerous infectious pathogens occurs during childhood, and that some viral infections can lead to neurodegeneration and demyelination, it is conceivable that some viruses may act as triggering factors in neuropathogenesis. We have previously shown that the prototype OC43 strain of the common cold—associated human respiratory coronavirus has the capacity to infect human neuronal and glial cells and does persist in human brains. Moreover, it has neuroinvasive properties in susceptible BALB/c mice, where it leads to a chronic encephalitis with accompanying disabilities. Here, we show that mutations in the viral spike glycoprotein, reproducibly acquired during viral persistence in human neural cell cultures, led to a drastically modified virus-induced neuropathology in BALB/c mice, characterized by flaccid paralysis and demyelination. Even though infection by both mutated and wild-type viruses led to neuroinflammation, the modified neuropathogenesis induced by the mutated virus was associated with increased viral spread and significantly more CD4+ and CD8+ T-lymphocyte infiltration into the central nervous system, as well as significantly increased levels of the proinflammatory cytokine interleukin (IL)-6 and the chemokine CCL2 (monocyte chemoattractant protein [MCP]-1). Moreover, recombinant virus harboring the S glycoprotein mutations retained its neurotropism, productively infecting neurons. Therefore, interaction of a human respiratory coronavirus with the central nervous system may modulate virus and host factors resulting in a modified neuropathogenesis in genetically susceptible individuals.


title: Brief introduction of current technologies in isolation of broadly neutralizing HIV-1 antibodies

text: Abstract HIV/AIDS has become a worldwide pandemic. Before an effective HIV-1 vaccine eliciting broadly neutralizing monoclonal antibodies (bnmAbs) is fully developed, passive immunization for prevention and treatment of HIV-1 infection may alleviate the burden caused by the pandemic. Among HIV-1 infected individuals, about 20% of them generated cross-reactive neutralizing antibodies two to four years after infection, the details of which could provide knowledge for effective vaccine design. Recent progress in techniques for isolation of human broadly neutralizing antibodies has facilitated the study of passive immunization. The isolation and characterization of large panels of potent human broadly neutralizing antibodies has revealed new insights into the principles of antibody-mediated neutralization of HIV. In this paper, we review the current effective techniques in broadly neutralizing antibody isolation.


title: Capacity building in national influenza laboratories – use of laboratory assessments to drive progress

text: BACKGROUND: Laboratory testing is a fundamental component of influenza surveillance for detecting novel strains with pandemic potential and informing biannual vaccine strain selection. The United States (U.S.) Centers for Disease Control and Prevention (CDC), under the auspices of its WHO Collaborating Center for Influenza, is one of the major public health agencies which provides support globally to build national capacity for influenza surveillance. Our main objective was to determine if laboratory assessments supported capacity building efforts for improved global influenza surveillance. METHODS: In 2010, 35 national influenza laboratories were assessed in 34 countries, using a standardized tool. Post-assessment, each laboratory received a report with a list of recommendations for improvement. Uptake of recommendations were reviewed 3.2 mean years after the initial assessments and categorized as complete, in-progress, no action or no update. This was a retrospective study; follow-up took place through routine project management rather than at a set time-point post-assessment. WHO data on National Influenza Centre (NIC) designation, External Quality Assessment Project (EQAP) participation and FluNet reporting was used to measure laboratory capacity longitudinally and independently of the assessments. All data was further stratified by World Bank country income category. RESULTS: At follow-up, 81 % of 614 recommendations were either complete (350) or in-progress (145) for 32 laboratories (91 % response rate). The number of countries reporting to FluNet and the number of specimens they reported annually increased between 2005, when they were first funded by CDC, and 2010, the assessment year (p < 0.01). Improvements were also seen in EQAP participation and NIC designation over time and more so for low and lower-middle income countries. CONCLUSIONS: Assessments using a standardized tool have been beneficial to improving laboratory-based influenza surveillance. Specific recommendations helped countries identify and prioritize areas for improvement. Data from assessments helped CDC focus its technical assistance by country and region. Low and lower-middle income countries made greater improvements in their laboratories compared with upper-middle income countries. Future research could include an analysis of annual funding and technical assistance by country. Our approach serves as an example for capacity building for other diseases.


title: Infection prevention and control compliance in Tanzanian outpatient facilities: a cross-sectional study with implications for the control of COVID-19

text: Summary Background As coronavirus disease 2019 (COVID-19) spreads, weak health systems must not become a vehicle for transmission through poor infection prevention and control practices. We assessed the compliance of health workers with infection prevention and control practices relevant to COVID-19 in outpatient settings in Tanzania, before the pandemic. Methods This study was based on a secondary analysis of cross-sectional data collected as part of a randomised controlled trial in private for-profit dispensaries and health centres and in faith-based dispensaries, health centres, and hospitals, in 18 regions. We observed provider–patient interactions in outpatient consultation rooms, laboratories, and dressing rooms, and categorised infection prevention and control practices into four domains: hand hygiene, glove use, disinfection of reusable equipment, and waste management. We calculated compliance as the proportion of indications (infection risks) in which a health worker performed a correct action, and examined associations between compliance and health worker and facility characteristics using multilevel mixed-effects logistic regression models. Findings Between Feb 7 and April 5, 2018, we visited 228 health facilities, and observed at least one infection prevention and control indication in 220 facilities (118 [54%] dispensaries, 66 [30%] health centres, and 36 [16%] hospitals). 18 710 indications were observed across 734 health workers (49 [7%] medical doctors, 214 [29%] assistant medical officers or clinical officers, 106 [14%] nurses or midwives, 126 [17%] clinical assistants, and 238 [32%] laboratory technicians or assistants). Compliance was 6·9% for hand hygiene (n=8655 indications), 74·8% for glove use (n=4915), 4·8% for disinfection of reusable equipment (n=841), and 43·3% for waste management (n=4299). Facility location was not associated with compliance in any of the infection prevention and control domains. Facility level and ownership were also not significantly associated with compliance, except for waste management. For hand hygiene, nurses and midwives (odds ratio 5·80 [95% CI 3·91–8·61]) and nursing and medical assistants (2·65 [1·67–4·20]) significantly outperformed the reference category of assistant medical officers or clinical officers. For glove use, nurses and midwives (10·06 [6·68–15·13]) and nursing and medical assistants (5·93 [4·05–8·71]) also significantly outperformed the reference category. Laboratory technicians performed significantly better in glove use (11·95 [8·98–15·89]), but significantly worse in hand hygiene (0·27 [0·17–0·43]) and waste management (0·25 [0·14–0·44] than the reference category. Health worker age was negatively associated with correct glove use and female health workers were more likely to comply with hand hygiene. Interpretation Health worker infection prevention and control compliance, particularly for hand hygiene and disinfection, was inadequate in these outpatient settings. Improvements in provision of supplies and health worker behaviours are urgently needed in the face of the current pandemic. Funding UK Medical Research Council, Economic and Social Research Council, Department for International Development, Global Challenges Research Fund, Wellcome Trust.