title: A Balancing Act: MDA5 in Antiviral Immunity and Autoinflammation

text: Induction of interferons during viral infection is mediated by cellular proteins that recognise viral nucleic acids. MDA5 is one such sensor of virus presence and is activated by RNA. MDA5 is required for immunity against several classes of viruses, including picornaviruses. Recent work showed that mutations in the IFIH1 gene, encoding MDA5, lead to interferon-driven autoinflammatory diseases. Together with observations made in cancer cells, this suggests that MDA5 detects cellular RNAs in addition to viral RNAs. It is therefore important to understand the properties of the RNAs which activate MDA5. New data indicate that RNA length and secondary structure are features sensed by MDA5. We review these developments and discuss how MDA5 strikes a balance between antiviral immunity and autoinflammation.


title: Virtual application of in situ simulation during a pandemic

text: The coronavirus disease 2019 (COVID-19) pandemic introduced challenges to the use of simulation, including limited personal protective equipment and restricted time and personnel. Our use of video for in situ simulation aimed to circumvent these challenges and assist in the development of a protocol for protected intubation and simultaneously educate emergency department (ED) staff. We video-recorded a COVID-19 respiratory failure in situ simulation event, which was shared by a facilitator both virtually and in the ED. The facilitator led discussions and debriefs. We followed this with in situ run-throughs in which staff walked through the steps of the simulation in the ED, handling medications and equipment and becoming comfortable with use of isolation rooms. This application of in situ simulation allowed one simulation event to reach a wide audience, while allowing participants to respect social distancing, and resulted in the education of this audience and successful crowdsourcing for a protocol amidst a pandemic.


title: Role of MicroRNAs in Host Defense against Infectious Bursal Disease Virus (IBDV) Infection: A Hidden Front Line

text: Infectious bursal disease (IBD) is an acute, highly contagious and immunosuppressive avian disease caused by infectious bursal disease virus (IBDV). In recent years, remarkable progress has been made in the understanding of the pathogenesis of IBDV infection and the host response, including apoptosis, autophagy and the inhibition of innate immunity. Not only a number of host proteins interacting with or targeted by viral proteins participate in these processes, but microRNAs (miRNAs) are also involved in the host response to IBDV infection. If an IBDV–host interaction at the protein level is taken imaginatively as the front line of the battle between invaders (pathogens) and defenders (host cells), their fight at the RNA level resembles the hidden front line. miRNAs are a class of non-coding single-stranded endogenous RNA molecules with a length of approximately 22 nucleotides (nt) that play important roles in regulating gene expression at the post-transcriptional level. Insights into the roles of viral proteins and miRNAs in host response will add to the understanding of the pathogenesis of IBDV infection. The interaction of viral proteins with cellular targets during IBDV infection were previously well-reviewed. This review focuses mainly on the current knowledge of the host response to IBDV infection at the RNA level, in particular, of the nine well-characterized miRNAs that affect cell apoptosis, the innate immune response and viral replication.


title: Molecular Pathology in the Lungs of Severe Acute Respiratory Syndrome Patients

text: Severe acute respiratory syndrome (SARS) is a novel infectious disease with disastrous clinical consequences, in which the lungs are the major target organs. Previous studies have described the general pathology in the lungs of SARS patients and have identified some of the cell types infected by SARS coronavirus (SARS-CoV). However, at the time of this writing, there were no comprehensive reports of the cellular distribution of the virus in lung tissue. In this study, we have performed double labeling combining in situ hybridization with immunohistochemistry and alternating each of these techniques separately in consecutive sections to evaluate the viral distribution on various cell types in the lungs of seven patients affected with SARS. We found that SARS-CoV was present in bronchial epithelium, type I and II pneumocytes, T lymphocytes, and macrophages/monocytes. For pneumocytes, T lymphocytes, and macrophages, the infection rates were calculated. In addition, our present study is the first to demonstrate infection of endothelial cells and fibroblasts in SARS.


title: Is COVID-19 receiving ADE from other coronaviruses?

text: Abstract One of the most perplexing questions regarding the current COVID-19 coronavirus epidemic is the discrepancy between the severity of cases observed in the Hubei province of China and those occurring elsewhere in the world. One possible answer is antibody dependent enhancement (ADE) of SARS-CoV-2 due to prior exposure to other coronaviruses. ADE modulates the immune response and can elicit sustained inflammation, lymphopenia, and/or cytokine storm, one or all of which have been documented in severe cases and deaths. ADE also requires prior exposure to similar antigenic epitopes, presumably circulating in local viruses, making it a possible explanation for the observed geographic limitation of severe cases and deaths.


title: Indirect fluorescent antibody testing of nasopharyngeal swabs for influenza diagnosis in lung transplant recipients

text: Abstract Background: Rapid and reliable diagnosis of respiratory viral infections (RVI) in lung transplant recipients is essential to direct therapy of acute graft dysfunction and identify epidemic trends. Traditional techniques of serology and viral culture are limited by the lack of antibody response and delay in diagnosis. Methods: We examined the clinical utility of indirect fluorescent antibody (IFA) testing in adult lung transplant patients with suspected RVI, compared with serology and culture. Nasopharyngeal and throat swabs (NT) were obtained to sample epithelial cells, followed by application of monoclonal antibody to respiratory syncytial virus, adenovirus, parainfluenza 1–3 and influenza A and B. The Bartels Respiratory Viral Detection kit was used with IFA results available within 24 hours. Results: Nine of 18 patients tested positive for RVI with influenza A (n = 8) and influenza B (n = 1) detected. The sensitivity of IFA (67%) was higher than that of cell culture (45%). With intensive supportive therapy, infection was self-limiting in bronchiolitis obliterans syndrome (BOS) Grade 0–2 patients. However, patients with BOS Grade 3 manifested an acute exacerbation of airflow obstruction, which proved to be irreversible. Conclusions: Lung transplant patients with “flu-like” symptoms should proceed to IFA testing of NT swab specimens for early diagnosis. Samples collected within 7 days of symptom onset have high sensitivity as compared with serology and viral culture techniques.


title: Structure-based discovery of Middle East respiratory syndrome coronavirus fusion inhibitor

text: A novel human coronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), has caused outbreaks of a SARS-like illness with high case fatality rate. The reports of its person-to-person transmission through close contacts have raised a global concern about its pandemic potential. Here we characterize the six-helix bundle fusion core structure of MERS-CoV spike protein S2 subunit by X-ray crystallography and biophysical analysis. We find that two peptides, HR1P and HR2P, spanning residues 998–1039 in HR1 and 1251–1286 in HR2 domains, respectively, can form a stable six-helix bundle fusion core structure, suggesting that MERS-CoV enters into the host cell mainly through membrane fusion mechanism. HR2P can effectively inhibit MERS-CoV replication and its spike protein-mediated cell–cell fusion. Introduction of hydrophilic residues into HR2P results in significant improvement of its stability, solubility and antiviral activity. Therefore, the HR2P analogues have good potential to be further developed into effective viral fusion inhibitors for treating MERS-CoV infection. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/ncomms4067) contains supplementary material, which is available to authorized users.


title: WHO to decide whether MERS is global health emergency

text: A meeting on the threat from the MERS coronavirus has been called under a procedure used only once before – for the swine flu pandemic in 2009


title: Urinary Tract Infections Treatment/Comparative Therapeutics

text: Urinary tract infection (UTI) occurs when there is compromise of host defense mechanisms and a virulent microbe adheres, multiplies, and persists in a portion of the urinary tract. Most commonly, UTI is caused by bacteria, but fungi and viruses are possible. Urine culture and sensitivity are the gold standards for diagnosis of bacterial UTI. Identifying the location of infection (eg, bladder, kidney, prostate) as well as comorbidities (eg, diabetes mellitus, immunosuppression) is essential to guide the diagnostic and therapeutic plan. Antimicrobial agents are the mainstay of therapy for bacterial UTI and selected ideally based on culture and sensitivity.


title: Alphavirus-Based Vaccines

text: Alphavirus vectors have demonstrated high levels of transient heterologous gene expression both in vitro and in vivo and, therefore, possess attractive features for vaccine development. The most commonly used delivery vectors are based on three single-stranded encapsulated alphaviruses, namely Semliki Forest virus, Sindbis virus and Venezuelan equine encephalitis virus. Alphavirus vectors have been applied as replication-deficient recombinant viral particles and, more recently, as replication-proficient particles. Moreover, in vitro transcribed RNA, as well as layered DNA vectors have been applied for immunization. A large number of highly immunogenic viral structural proteins expressed from alphavirus vectors have elicited strong neutralizing antibody responses in multispecies animal models. Furthermore, immunization studies have demonstrated robust protection against challenges with lethal doses of virus in rodents and primates. Similarly, vaccination with alphavirus vectors expressing tumor antigens resulted in prophylactic protection against challenges with tumor-inducing cancerous cells. As certain alphaviruses, such as Chikungunya virus, have been associated with epidemics in animals and humans, attention has also been paid to the development of vaccines against alphaviruses themselves. Recent progress in alphavirus vector development and vaccine technology has allowed conducting clinical trials in humans.


title: Intracellular human antibody fragments recognizing the VP35 protein of Zaire Ebola filovirus inhibit the protein activity

text: BACKGROUND: Ebola hemorrhagic fever is caused by the Ebola filovirus (EBOV), which is one of the most aggressive infectious agents known worldwide. The EBOV pathogenesis starts with uncontrolled viral replication and subversion of both the innate and adaptive host immune response. The multifunctional viral VP35 protein is involved in this process by exerting an antagonistic action against the early antiviral alpha/beta interferon (IFN-α/β) response, and represents a suitable target for the development of strategies to control EBOV infection. Phage display technology permits to select antibodies as single chain Fragment variable (scFv) from an artificial immune system, due to their ability to specifically recognize the antigen of interest. ScFv is ideal for genetic manipulation and to obtain antibody constructs useful for targeting either antigens expressed on cell surface or intracellular antigens if the scFv is expressed as intracellular antibody (intrabody) or delivered into the cells. RESULTS: Monoclonal antibodies (mAb) in scFv format specific for the EBOV VP35 were isolated from the ETH-2 library of human recombinant antibodies by phage display technology. Five different clones were identified by sequencing, produced in E.coli and expressed in CHO mammalian cells to be characterized in vitro. All the selected scFvs were able to react with recombinant VP35 protein in ELISA, one of the scFvs being also able to react in Western Blot assay (WB). In addition, all scFvs were expressed in cell cytoplasm as intrabodies; a luciferase reporter gene inhibition assay performed in A549 cells showed that two of the scFvs can significantly hamper the inhibition of the IFN-β-induced RIG-I signaling cascade mediated by EBOV VP35. CONCLUSION: Five antibodies in scFv format recognize an active form of EBOV VP35 in ELISA, while one antibody also recognizes VP35 in WB. Two of these scFvs were also able to interfere with the intracellular activity of VP35 in a cell system in vitro. These findings suggest that such antibodies in scFv format might be employed to develop therapeutic molecules able to hamper EBOV infections.


title: Hospitalization and Critical Care of 109 Decedents with COVID-19 Pneumonia in Wuhan, China

text: Rationale: The current outbreak of coronavirus disease (COVID-19) pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, spreads across national and international borders. The overall death rate of COVID-19 pneumonia in the Chinese population was 4%. Objectives: To describe the process of hospitalization and critical care of patients who died of COVID-19 pneumonia. Methods: This was a multicenter observational study of 109 decedents with COVID-19 pneumonia from three hospitals in Wuhan. Demographic, clinical, laboratory, and treatment data were collected and analyzed, and the final date of follow-up was February 24, 2020. Results: The mean age of 109 decedents with COVID-19 pneumonia was 70.7 years, 35 patients (32.1%) were female, and 85 patients (78.0%) suffered from one or more underlying comorbidities. Multiple organ failure, especially respiratory failure and heart failure, appeared in all patients even at the early stage of disease. Overall, the mean time from onset of symptoms to death was 22.3 days. All 109 hospitalized patients needed admission to an intensive care unit (ICU); however, because of limited availability, only 51 (46.8%) could be admitted. The period from hospitalization to death in the ICU group and non-ICU group was 15.9 days (standard deviation = 8.8 d) and 12.5 days (8.6 d, P = 0.044), respectively. Conclusions: Mortality due to COVID-19 pneumonia was concentrated in patients above the age of 65 years, especially those with major comorbidities. Patients who were admitted to the ICU lived longer than those who were not. Our findings should aid in the recognition and clinical management of such infections, especially with regard to ICU resource allocation.


title: Newcastle Disease Virus: A Promising Vector for Viral Therapy, Immune Therapy, and Gene Therapy of Cancer

text: This review deals with the avian paramyxovirus Newcastle disease virus (NDV) and describes properties that explain its oncolytic activity, its tumor-selective replication behavior, and its immune-stimulatory capacity with human cells. The strong interferon response of normal cells upon contact with NDV appears to be the basis for the good tolerability of the virus in cancer patients and for its immune stimulatory properties, whereas the weak interferon response of tumor cells explains the tumor selectivity of replication and oncolysis. Various concepts for the use of this virus for cancer treatment are pointed out and results from clinical studies are summarized. Reverse genetics technology has made it possible recently to clone the genome and to introduce new foreign genes thus generating new recombinant viruses. These can, in the future, be used to transfer new therapeutic genes into tumors and also to immunize against new emerging pathogens. The modular nature of gene transcription, the undetectable rate of recombination, and the lack of a DNA phase in the replication cycle make NDV a suitable candidate for the rational design of a safe and stable vaccine and gene therapy vector.


title: Maternal and perinatal outcomes with COVID‐19: A systematic review of 108 pregnancies

text: INTRODUCTION: The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has exposed vulnerable populations to an unprecedented global health crisis. The knowledge gained from previous human coronavirus outbreaks suggests that pregnant women and their fetuses are particularly susceptible to poor outcomes. The objective of this study was to summarize the clinical manifestations and maternal and perinatal outcomes of COVID‐19 during pregnancy. MATERIAL AND METHODS: We searched databases for all case reports and series from 12 February to 4 April 2020. Multiple terms and combinations were used including COVID‐19, pregnancy, maternal mortality, maternal morbidity, complications, clinical manifestations, neonatal morbidity, intrauterine fetal death, neonatal mortality and SARS‐CoV‐2. Eligibility criteria included peer‐reviewed publications written in English or Chinese and quantitative real‐time polymerase chain reaction (PCR) or dual fluorescence PCR‐confirmed SARS‐CoV‐2 infection. Unpublished reports, unspecified date and location of the study or suspicion of duplicate reporting, cases with suspected COVID‐19 that were not confirmed by a laboratory test, and unreported maternal or perinatal outcomes were excluded. Data on clinical manifestations, maternal and perinatal outcomes including vertical transmission were extracted and analyzed. RESULTS: Eighteen articles reporting data from 108 pregnancies between 8 December 2019 and 1 April 2020 were included in the current study. Most reports described women presenting in the third trimester with fever (68%) and coughing (34%). Lymphocytopenia (59%) with elevated C‐reactive protein (70%) was observed and 91% of the women were delivered by cesarean section. Three maternal intensive care unit admissions were noted but no maternal deaths. One neonatal death and one intrauterine death were also reported. CONCLUSIONS: Although the majority of mothers were discharged without any major complications, severe maternal morbidity as a result of COVID‐19 and perinatal deaths were reported. Vertical transmission of the COVID‐19 could not be ruled out. Careful monitoring of pregnancies with COVID‐19 and measures to prevent neonatal infection are warranted.


title: Contrasting clinical outcomes in two cohorts of cats naturally infected with feline immunodeficiency virus (FIV)

text: Despite over 25 years of feline immunodeficiency virus (FIV) research, relatively little is known about the longitudinal course of FIV infection following natural infection. In contrast to published reports of experimental infections using lethal strains of the virus, clinical signs of naturally acquired FIV infection can be mild or inapparent, rather than life-threatening. In this prospective, longitudinal controlled study, based in Chicago, IL (n = 17) and Memphis, TN (n = 27), we investigated two cohorts of privately owned, naturally infected cats kept under different housing conditions. Cats in the Chicago cohort (Group 1) were kept in households of ≤2 cats, while the Memphis cohort (Group 2) comprised part of a large multi-cat household of over 60 cats kept indoors only, with unrestricted access to one another. The majority of cats from Group 1 did not display clinical signs consistent with immunodeficiency during the 22-month observation period. In contrast, the outcome of infection in Group 2 was dramatically different; 17/27 (63%) of cats lost a median of 51.3% of their bodyweight (P < 0.0005) and died during the study period, with lymphoma being the most common cause of mortality. Although the decrease in CD4+ T cell count between enrolment and terminal disease was significant (P = 0.0017), the CD4:CD8 ratio at the time of enrolment did not reliably distinguish FIV-positive cats classified as ‘healthy’ and ‘not healthy’ at either cohort. FIV load at enrolment was significantly lower in Group 1 than in Group 2 (P < 0.0001), but there were no significant differences at enrolment between healthy and not healthy cats at either group. In conclusion, the results of this study suggest that management and housing conditions impact on disease progression and survival times of FIV-positive cats.


title: A review on possible modes of actions of Chloroquine/ Hydroxychloroquine: Repurposing against SAR-COV-2 (COVID 19) pandemic

text: The chloroquine (CQ) and its analogue hydroxychloroquine (HCQ) have been used as frontline drugs for treatment and prophylaxis against all types of human malaria worldwide. Since late December 2019, humans have been under threat due to an outbreak of a novel coronavirus (SARS-CoV-2) disease (COVID-19; previously known as 2019-nCoV), since its first reported cases in Wuhan, China [1]. Consequently, the virus infection has been declared a pandemic. While the World is finding expedited approvals for the development of vaccine, which is time dependent, being preventative and not possibly a cure, physicians and countries’ leaders are considering several concerted clinical trials suggesting that this age-old antimalarial drug, CQ/HCQ could be a potent therapeutic agent against COVID-19 infection. Based on accumulating scientific reports, we have highlighted in this review, the different possible modes of action of chloroquine/hydroxychloroquine that could particularly justify its use against viral infections. Considering the global health crisis of the COVID-19 pandemic, the option of using the drugs and repurposing of old drugs in this instance, chloroquine and hydroxychloroquine, specifically, hydroxychloroquine in the treatment of SARS-CoV-2 could be the best choice. CQ/HCQ has diverse modes of action, like alteration of acidic environment inside lysosome, late endosomes, restriction further with endocytosis, exsosome release, phagolysosomal fusion in systematically and subsequently inhibition of cytokine storm in host cell. One or sum of diverse mechanisms might work against the viral infections and help prevent more deaths. Given that there is no cure for COVID-19, the clinical testing of HCQ is urgently needed to ascertain its potency against the virus as this is the current available treatment option. There is still a need to find other innovative drug candidates as other possible candidate to go into clinical evaluation and testing.


title: Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection

text: Japanese encephalitis virus (JEV) is the leading cause of epidemic encephalitis worldwide. JEV-induced neuroinflammation is characterized by profound neuronal cells damage accompanied by activation of glial cells. Albeit long non-coding RNAs (lncRNAs) have been emerged as important regulatory RNAs with profound effects on various biological processes, it is unknown how lncRNAs regulate JEV-induced inflammation. Here, using microarray approach, we identified 618 lncRNAs and 1,007 mRNAs differentially expressed in JEV-infected mice brain. The functional annotation analysis revealed that differentially regulated transcripts were predominantly involved in various signaling pathways related to host immune and inflammatory responses. The lncRNAs with their potential to regulate JEV-induced inflammatory response were identified by constructing the lncRNA-mRNA coexpression network. Furthermore, silencing of the two selected lncRNAs (E52329 and N54010) resulted in reducing the phosphorylation of JNK and MKK4, which are known to be involved during inflammatory response. Collectively, we first demonstrated the transcriptomic landscape of lncRNAs in mice brain infected with JEV and analyzed the coexpression network of differentially regulated lncRNAs and mRNAs during JEV infection. Our results provide a better understanding of the host response to JEV infection and suggest that the identified lncRNAs may be used as potential therapeutic targets for the management of Japanese encephalitis.


title: SARS-CoV-2: the viral shedding vs infectivity dilemma

text: Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over four million people worldwide. There are multiple reports of prolonged viral shedding in people infected with SARS-CoV-2 but the presence of viral RNA on a test does not necessarily correlate with infectivity. The duration of quarantine required after clinical recovery to definitively prevent transmission is therefore uncertain. In addition, asymptomatic and presymptomatic transmission may occur, and infectivity may be highest early after onset of symptoms, meaning that contact tracing, isolation of exposed individuals and social distancing are essential public health measures to prevent further spread. This review aimed to summarise the evidence around viral shedding vs infectivity of SARS-CoV-2.


title: Contagious bovine pleuropneumonia: A rationale for the development of a mucosal sub-unit vaccine

text: Abstract Contagious bovine pleuropneumonia (CBPP) remains a major cattle disease in Africa with serious socio-economic consequences. Its eradication requires the development of improved vaccines. Knowledge on this disease and its causing agent, Mycoplasma mycoides subsp. mycoides biotype Small Colony (MmmSC), has been progressing significantly in the last years, opening new areas for vaccine design. Advances were achieved in the understanding of the protective immune responses to MmmSC infection and immunopathological mechanisms allowing the pathogen to escape the host immune response. Based on sequencing and genomic studies, some virulence factors and metabolic pathways were unraveled leading to the identification of potential MmmSC vaccine candidates. Based on these findings, this review presents a scientific strategy to design multi-component sub-unit vaccines for mucosal delivery as the most promising approach for efficient long-term protective vaccines to prevent CBPP.


COVID-19 and surgery: Running on good will or guilt?


title: Assessment of Ebola virus disease preparedness in the WHO South-East Asia Region

text: OBJECTIVE: To conduct assessments of Ebola virus disease preparedness in countries of the World Health Organization (WHO) South-East Asia Region. METHODS: Nine of 11 countries in the region agreed to be assessed. During February to November 2015 a joint team from WHO and ministries of health conducted 4–5 day missions to Bangladesh, Bhutan, Indonesia, Maldives, Myanmar, Nepal, Sri Lanka, Thailand and Timor-Leste. We collected information through guided discussions with senior technical leaders and visits to hospitals, laboratories and airports. We assessed each country’s Ebola virus disease preparedness on 41 tasks under nine key components adapted from the WHO Ebola preparedness checklist of January 2015. FINDINGS: Political commitment to Ebola preparedness was high in all countries. Planning was most advanced for components that had been previously planned or tested for influenza pandemics: multilevel and multisectoral coordination; multidisciplinary rapid response teams; public communication and social mobilization; drills in international airports; and training on personal protective equipment. Major vulnerabilities included inadequate risk assessment and risk communication; gaps in data management and analysis for event surveillance; and limited capacity in molecular diagnostic techniques. Many countries had limited planning for a surge of Ebola cases. Other tasks needing improvement included: advice to inbound travellers; adequate isolation rooms; appropriate infection control practices; triage systems in hospitals; laboratory diagnostic capacity; contact tracing; and danger pay to staff to ensure continuity of care. CONCLUSION: Joint assessment and feedback about the functionality of Ebola virus preparedness systems help countries strengthen their core capacities to meet the International Health Regulations.


title: Severe Acute Respiratory Syndrome (SARS) and the GDP. Part II: Implications for GDPs

text: The transmission modes of SARS-coronavirus appear to be through droplet spread, close contact and fomites although air borne transmission has not been ruled out. This clearly places dental personnel at risks as they work in close proximity to their patients employing droplet and aerosol generating procedures. Although the principle of universal precautions is widely advocated and followed throughout the dental community, additional precautionary measures — termed standard precaution may be necessary to help control the spread of this highly contagious disease. Patient assessment should include questions on recent travel to SARS infected areas and, contacts of patients, fever and symptoms of respiratory infections. Special management protocols and modified measures that regulate droplet and aerosol contamination in a dental setting have to be introduced and may include the reduction or avoidance of droplet/aerosol generation, the disinfection of the treatment field, application of rubber dam, pre-procedural antiseptic mouthrinse and the dilution and efficient removal of contaminated ambient air. The gag, cough or vomiting reflexes that lead to the generation of aerosols should also be prevented.


Adp-Ribose-1”-Phosphatase Activities of the Human Coronavirus 229E and Sars Coronavirus X Domains


title: Glycosylation is Required for Coronavirus TGEV to Induce an Efficient Production of IFNα by Blood Mononuclear Cells

text: Porcine peripheral blood mononuclear cells (PBMC) are induced to produce interferon alpha (IFNα) following in vitro exposure to coronavirus TGEV (transmissible gastroenteritis virus)‐infected glutaraldehyde‐fixed cell monolayers or lo TGEV virions. In the present report, we examined the possibility that glycosylation of viral proteins could play a major role in interactions with PBMC leading to the production of IFNα. Con A pretreatment of TGEV‐infected cell monolayers before fixation with glutaraldehyde and exposure to PBMC caused a dose‐dependent inhibition of IFNα induction, implying that masking of carbohydrates at the surface of infected cells lowered IFNα induction. Similarly, inhibition of N‐linked glycosylation by tunicamycin during viral infection of cell monolayers altered their ability to induce IFNα. In addition, complete cleavage of complex type' oligosaccharides by peptide‐N‐glycohydrolase Flowered the capacity of TGEV virions to induce IFNα. Thus, these findings strongly suggest that glycosylation of the viral proteins, and more precisely the presence of complex‐type oligosaccharides, is an important requirement for a completely efficient interaction with PBMC leading to the production of IFN‐α.


title: Birth Defects Data from Surveillance Hospitals in Hubei Province, China, 200l – 2008

text: BACKGROUND: To determine the prevalence and characteristics of birth defects in perinatal infants in Hubei Province during 200l–2008. METHODS: The prevalence of birth defects in perinatal infants delivered after 28 weeks or more was analyzed in Hubei surveillance hospitals during 200l–2008. RESULTS: The incidence of birth defects in perinatal infants from 200l to 2008 was 120.0 per 10,000 births, and was increased by about 41% from 81. 1 in 2001 to 138.5 per 10,000 births in 2008. The incidence in the first 4 years (2005–2008) was much higher than the latter four (2001–2004) (χ(2)=77.64, P <0.05). The difference in prevalence between urban and rural was of no significance in 2008 (χ(2)=0.03, P >0.05), but that between male and female was significant (χ(2)=5.24, P <0.05), as the former prevalence was much higher. The prevalence of birth defects was slightly higher among mothers over 35 years old than those under 35 years old, but with no significance (χ(2)=1.98, P >0.05). The two leading birth defects were cleft lip and/or palate and polydactyly, followed by congenital heart disease, hydrocephaly, external ear malformation and neural tube defects. The prevalence of congenital heart disease was rising. CONCLUSIONS: Eight years’ birth defects data indicate that the birth defect rate was on the rise and the birth defects prevalence in Hubei province should be valued.


title: Effectiveness of non-pharmaceutical measures in preventing pediatric influenza: a case–control study

text: BACKGROUND: Hygiene behavior plays a relevant role in infectious disease transmission. The aim of this study was to evaluate non-pharmaceutical interventions (NPI) in preventing pediatric influenza infections. METHODS: Laboratory confirmed influenza cases occurred during 2009–10 and 2010–11 seasons matched by age and date of consultation. NPI (frequency of hand washing, alcohol-based hand sanitizer use and hand washing after touching contaminated surfaces) during seven days prior to onset of symptoms were obtained from parents of cases and controls. RESULTS: Cases presented higher prevalence of underlying conditions such as pneumonia [OR = 3.23; 95 % CI: 1.38 – 7.58 p = 0.007], asthma [OR = 2.45; 95 % CI: 1.17 – 5.14 p = 0.02] and having more than 1 risk factor [OR = 1.67; 95 % CI: 0.99 – 2.82 p = 0.05]. Hand washing more than 5 times per day [aOR = 0.62; 95 % CI: 0.39 – 0.99 p = 0.04] was the only statistically significant protective factor. When considering two age groups (pre-school age 0–4 yrs and school age 5–17) yrs , only the school age group showed a negative association for influenza infection for both washing more than 5 times per day [aOR = 0.47; 95 % CI: 0.22 – 0.99 p = 0.04] and hand washing after touching contaminated surfaces [aOR = 0.19; 95 % CI: 0.04 – 0.86 p = 0.03]. CONCLUSION: Frequent hand washing should be recommended to prevent influenza infection in the community setting and in special in the school age group.


title: Bovine Caruncular Epithelial Cell Line (BCEC-1) Isolated from the Placenta Forms a Functional Epithelial Barrier in a Polarised Cell Culture Model

text: Abstract In the bovine synepitheliochorial placenta key sites of fetal–maternal interaction are placentomes consisting of maternal caruncles interdigitating with fetal cotyledons. The aim of this study was to establish an epithelial cell line from caruncles of pregnant cows and to develop a model to study restricted trophoblast invasion, pathogenesis of pregnancy associated diseases and pathways of infection and transport. Primary epithelial cells were isolated, successfully subcultured for 32 passages and cryopreserved at various stages. The cultures were termed bovine caruncular epithelial cell line-1 (BCEC-1). Cytokeratin, zonula occludens-1 protein and vimentin but neither α-smooth muscle actin nor desmin were detected by immunofluorescence performed every 5 (±1) passages. These results were confirmed by Western blotting. BCEC-1 were then cultured either without matrix or on fibronectin or collagen coated Transwell® polyester membrane inserts, respectively, enabling separate access to the basal or apical epithelial compartments. Transmission and scanning electron microscopy of BCEC-1 revealed ultrastructural features also observed in vivo, such as apical microvilli and junctional complexes. Transepithelial electrical resistance (TEER) was measured regularly and revealed an increase with advancing confluence in all cultures. Cultures on coated inserts reached confluence and corresponding TEER-levels at an earlier stage. In addition, the cells were tested negative for bovine virus diarrhoea (BVD) virus, but were permissive for the virus. In conclusion, the BCEC-1 cell line retained characteristics of maternal caruncular epithelial cells as observed in vivo and in primary cell cultures and thus will be a highly useful tool for future studies of pathways of invasion, fetal–maternal communication, transport and infection.


title: Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain

text: Host interferon-induced transmembrane proteins (IFITMs) are broad-spectrum antiviral restriction factors. Of these, IFITM3 potently inhibits viruses that enter cells through acidic endosomes, many of which are zoonotic and emerging viruses with bats (order Chiroptera) as their natural hosts. We previously demonstrated that microbat IFITM3 is antiviral. Here, we show that bat IFITMs are characterized by strong adaptive evolution and identify a highly variable and functionally important site—codon 70—within the conserved CD225 domain of IFITMs. Mutation of this residue in microbat IFITM3 impairs restriction of representatives of four different virus families that enter cells via endosomes. This mutant shows altered subcellular localization and reduced S-palmitoylation, a phenotype copied by mutation of conserved cysteine residues in microbat IFITM3. Furthermore, we show that microbat IFITM3 is S-palmitoylated on cysteine residues C71, C72, and C105, mutation of each cysteine individually impairs virus restriction, and a triple C71A-C72A-C105A mutant loses all restriction activity, concomitant with subcellular re-localization of microbat IFITM3 to Golgi-associated sites. Thus, we propose that S-palmitoylation is critical for Chiropteran IFITM3 function and identify a key molecular determinant of IFITM3 S-palmitoylation.


title: Photocatalytic disinfection using titanium dioxide: spectrum and mechanism of antimicrobial activity

text: The photocatalytic properties of titanium dioxide are well known and have many applications including the removal of organic contaminants and production of self-cleaning glass. There is an increasing interest in the application of the photocatalytic properties of TiO(2) for disinfection of surfaces, air and water. Reviews of the applications of photocatalysis in disinfection (Gamage and Zhang 2010; Chong et al., Wat Res 44(10):2997–3027, 2010) and of modelling of TiO(2) action have recently been published (Dalrymple et al. , Appl Catal B 98(1–2):27–38, 2010). In this review, we give an overview of the effects of photoactivated TiO(2) on microorganisms. The activity has been shown to be capable of killing a wide range of Gram-negative and Gram-positive bacteria, filamentous and unicellular fungi, algae, protozoa, mammalian viruses and bacteriophage. Resting stages, particularly bacterial endospores, fungal spores and protozoan cysts, are generally more resistant than the vegetative forms, possibly due to the increased cell wall thickness. The killing mechanism involves degradation of the cell wall and cytoplasmic membrane due to the production of reactive oxygen species such as hydroxyl radicals and hydrogen peroxide. This initially leads to leakage of cellular contents then cell lysis and may be followed by complete mineralisation of the organism. Killing is most efficient when there is close contact between the organisms and the TiO(2) catalyst. The killing activity is enhanced by the presence of other antimicrobial agents such as Cu and Ag.


docid: mexfkial

title: Associations between media use and health information-seeking behavior on vaccinations in South Korea

text: BACKGROUND: Although vaccinations are critical for preventing emerging infectious diseases, scant research has been conducted on risk communication. With socio-economic characteristics, health behavior, and underlying diseases under control, we investigated associations between media use, health information-seeking behavior, health information type, and vaccination in the population. METHODS: This study relied on a national survey of Korean adults (n = 1367). Participants were adult males and females age 20 and older. Web and face-to-face surveys were conducted throughout July 2014. The main outcome was vaccination (categorized as yes or no). Independent variables were time spent on media, frequency of health information-seeking behavior, and types of health information sought. RESULTS: Controlling for co-variates, logistic regression analysis was conducted to identify factors that influence Korean adults being vaccinated. Results revealed that accessible information about emerging infectious diseases, listening to the radio, and reading the newspaper were associated with increased odds of being vaccinated. Active seeking health information as well as being female and of higher socio-economic status were positively correlated with Korean adults being vaccinated. CONCLUSION: It is critical to promote health information-seeking behavior and use diverse media channels to increase acceptance and awareness of emerging infectious diseases and vaccinations. Because there are differences in vaccination awareness depending on social class, it is critical to reduce communication inequality, strengthen accessibility to vaccinations, and devise appropriate risk communication strategies that ensure Korean adults receive vaccinations.


title: Availability, consistency and evidence-base of policies and guidelines on the use of mask and respirator to protect hospital health care workers: a global analysis

text: BACKGROUND: Currently there is an ongoing debate and limited evidence on the use of masks and respirators for the prevention of respiratory infections in health care workers (HCWs). This study aimed to examine available policies and guidelines around the use of masks and respirators in HCWs and to describe areas of consistency between guidelines, as well as gaps in the recommendations, with reference to the WHO and the CDC guidelines. METHODS: Policies and guidelines related to mask and respirator use for the prevention of influenza, SARS and TB were examined. Guidelines from the World Health Organization (WHO), the Center for Disease Control and Prevention (CDC), three high-income countries and six low/middle-income countries were selected. RESULTS: Uniform recommendations are made by the WHO and the CDC in regards to protecting HCWs against seasonal influenza (a mask for low risk situations and a respirator for high risk situations) and TB (use of a respirator). However, for pandemic influenza and SARS, the WHO recommends mask use in low risk and respirators in high risk situations, whereas, the CDC recommends respirators in both low and high risk situations. Amongst the nine countries reviewed, there are variations in the recommendations for all three diseases. While, some countries align with the WHO recommendations, others align with those made by the CDC. The choice of respirator and the level of filtering ability vary amongst the guidelines and the different diseases. Lastly, none of the policies discuss reuse, extended use or the use of cloth masks. CONCLUSION: Currently, there are significant variations in the policies and recommendations around mask and respirator use for protection against influenza, SARS and TB. These differences may reflect the scarcity of level-one evidence available to inform policy development. The lack of any guidelines on the use of cloth masks, despite widespread use in many low and middle-income countries, remains a policy gap. Health organizations and countries should jointly evaluate the available evidence, prioritize research to inform evidence gaps, and develop consistent policy on masks and respirator use in the health care setting.


title: Bifurcation analysis of an SIRS epidemic model with a generalized nonmonotone and saturated incidence rate

text: Abstract In this paper, we study a susceptible-infectious-recovered (SIRS) epidemic model with a generalized nonmonotone and saturated incidence rate k I 2 S 1 + β I + α I 2 , in which the infection function first increases to a maximum when a new infectious disease emerges, then decreases due to psychological effect, and eventually tends to a saturation level due to crowding effect. It is shown that there are a weak focus of multiplicity at most two and a cusp of codimension at most two for various parameter values, and the model undergoes saddle-node bifurcation, Bogdanov-Takens bifurcation of codimension two, Hopf bifurcation, and degenerate Hopf bifurcation of codimension two as the parameters vary. It is shown that there exists a critical value α = α 0 for the psychological effect, and two critical values k = k 0 , k 1 ( k 0 < k 1 ) for the infection rate such that: (i) when α > α 0 , or α ≤ α 0 and k ≤ k 0 , the disease will die out for all positive initial populations; (ii) when α = α 0 and k 0 < k ≤ k 1 , the disease will die out for almost all positive initial populations; (iii) when α = α 0 and k > k 1 , the disease will persist in the form of a positive coexistent steady state for some positive initial populations; and (iv) when α < α 0 and k > k 0 , the disease will persist in the form of multiple positive periodic coexistent oscillations and coexistent steady states for some positive initial populations. Numerical simulations, including the existence of one or two limit cycles and data-fitting of the influenza data in Mainland China, are presented to illustrate the theoretical results.


title: SARS and Population Health Technology

text: The recent global outbreak of SARS (severe acute respiratory syndrome) provides an opportunity to study the use and impact of public health informatics and population health technology to detect and fight a global epidemic. Population health technology is the umbrella term for technology applications that have a population focus and the potential to improve public health. This includes the Internet, but also other technologies such as wireless devices, mobile phones, smart appliances, or smart homes. In the context of an outbreak or bioterrorism attack, such technologies may help to gather intelligence and detect diseases early, and communicate and exchange information electronically worldwide. Some of the technologies brought forward during the SARS epidemic may have been primarily motivated by marketing efforts, or were more directed towards reassuring people that "something is being done," ie, fighting an "epidemic of fear." To understand "fear epidemiology" is important because early warning systems monitoring data from a large number of people may not be able to discriminate between a biological epidemic and an epidemic of fear. The need for critical evaluation of all of these technologies is stressed.


title: Predictors of Mortality in Mechanically Ventilated Critical Pertussis in a low Income Country

text: BACKGROUND: Critical pertussis is characterized by severe respiratory failure, important leukocytosis, pulmonary hypertension, septic shock and encephalopathy. AIM: To describe the clinical course of critical pertussis, and identify predictors of death at the time of presentation for medical care. METHODOLOGY: Retrospective study conducted in children’s hospital Tunisian PICU between 01 January and 31 October 2013. Patients with critical pertussis confirmed by RT-PCR and requiring mechanical ventilation were included. Predictors of death were studied. RESULTS: A total of 17 patients was studied. Median age was 50 days. Mortality was 23%. Predictors risk of mortality were : high PRISM score (Pediatric Risk of Mortality Score) (p=0,007), shock (p=0,002), tachycardia (p=0,005), seizures (p=0,006), altered mental status (p=0,006), elevated WBC count (p=0,003) and hemodynamic support (p=0022). However, the difference did not reach statistical significance in comorbidity, pneumoniae, high pulmonary hypertension or exchange transfusion. Concomitant viral or bacterial co-infection was not related to poor outcome. CONCLUSION: Young infants are at high risk to have critical pertussis. Despite advances in life support and the treatment of organ failure in childhood critical illness, critical pertussis remains difficult to treat.


title: Role of CD25(+) CD4(+) T cells in acute and persistent coronavirus infection of the central nervous system

text: The influence of CD25(+)CD4(+) regulatory T cells (Treg) on acute and chronic viral infection of the central nervous system (CNS) was examined using a glial tropic murine coronavirus. Treg in the CNS were highest during initial T cell mediated virus control, decreased and then remained relatively stable during persistence. Anti-CD25 treatment did not affect CNS recruitment of inflammatory cells. Viral control was initially delayed; however, neither the kinetics of viral control nor viral persistence were affected. By contrast, the absence of Treg during the acute phase resulted in increased demyelination during viral persistence. These data suggest that CNS inflammation, progression of viral control and viral persistence are relatively independent of CD25(+)CD4(+) Treg. However, their absence during acute infection alters the ability of the host to limit tissue damage.


title: Structural insights into RNA recognition and activation of RIG-I-like receptors

text: RIG-I like receptors (RLR) that recognize non-self RNA play critical roles in activating host innate immune pathways in response to viral infections. Not surprisingly, RLRs and their associated signaling networks are also targeted by numerous antagonists that facilitate viral pathogenesis. Although the role of RLRs in orchestrating antiviral signaling has been recognized for some time, our knowledge of the complex regulatory mechanisms that control signaling through these key molecules is incomplete. A series of recent structural studies shed new light into the structural basis for dsRNA recognition and activation of RLRs. Collectively, these studies suggest that the repression of RLRs is facilitated by a cis element that makes multiple contacts with domains within the helicase and that RNA binding initiated by the C-terminal RNA binding domain is important for ATP hydrolysis and release of the CARD domain containing signaling module from the repressed conformation. These studies also highlight potential differences between RIG-I and MDA5, two RLR members. Together with previous studies, these new results bring us a step closer to uncovering the complex regulatory process of a key protein that protects host cells from invading pathogens.


docid: ypsbkvpo

title: Public Health Perspectives of Smokeless Tobacco and Areca Nut Use in the COVID-19 Era


title: THE GERIATRICIAN: THE FRONTLINE SPECIALIST IN THE TREATMENT OF COVID-19 PATIENTS

text: Abstract On February 20, 2020, a man living in the north of Italy was admitted to the emergency room with an atypical pneumonia that later proved to be COVID-19. This was the trigger of one of the most serious clusters of COVID-19 in the world, outside of China. Despite aggressive restraint and inhibition efforts, COVID-19 continues to increase, and the total number of infected patients in Italy is growing daily. After six weeks the total number of patients reached 128,948 cases (April 5, 2020), with the higher case-fatality rate (15,887 deaths) dominated by old and very old patients. This sudden health emergency severely challenged the Italian Health System, in particular acute care hospitals and intensive care units. In one hospital, geriatric observation units were created, the experience of which can be extremely useful for European countries, the United States, and all countries that in the coming days will face a similar situation.


title: Pathogenicity and antigenicity of a new variant of Korean nephropathogenic infectious bronchitis virus

text: Despite the existence of an active vaccination program, recently emerged strains of nephropathogenic infectious bronchitis virus (IBV) in Korea have caused significant economic losses in the poultry industry. In this study, we assessed the pathogenic and antigenic characteristics of a K-IIb type field strain of IBV that emerged in Korea since 2003, such as Kr/Q43/06. Specific pathogen free 1-week-old chickens exhibited severe respiratory symptoms (dyspnea) and nephropathogenic lesions (swollen kidneys with nephritis and urate deposits) following challenge with the recent IBV field strain. The antigenic relatedness (R value), based on a calculated virus neutralization index, of the K-IIb type field strain and K-IIa type strain KM91 (isolated in 1991) was 30%, which indicated that the recent strain, Kr/Q43/06, is a new variant that is antigenically distinct from strain KM91. This report is the first to document the emergence of a new antigenic variant of nephropathogenic IBV in chicken from Korea.


title: Human bocavirus infection in Belgian children with respiratory tract disease

text: Human bocavirus (HBoV) has been detected primarily in children with acute lower respiratory tract disease (LRTD), but its occurrence, clinical profile, and role as a causative agent of RTD are not clear. The aim of this study was to investigate the prevalence and the potential clinical relevance of HBoV. Using molecular tests, we tested 1352 nasopharyngeal samples obtained between October 1, 2017 and April 30, 2018 from children up to the age of 16 with RTD for the presence of HBoV DNA and 20 other respiratory pathogens at three different hospitals in Belgium. HBoV was detected in 77 children with a median age of 10.6 months. Consecutive samples were available for 15 HBoV-positive children and showed persistent HBoV positivity in four of them. Monoinfection was observed in six infants. Four of them were born prematurely and were infected during hospitalization at the neonatal intensive care unit (NICU). Only one of these six monoinfected children was diagnosed with recurrent wheezing due to HBoV. This child was carried to term and had a high viral load. Coinfections, most frequently with rhinovirus (52.1%) and adenovirus (49.3%), were observed in 72 patients. In seventeen of them in which HBoV was present at high viral load or higher viral load than its copathogens, bronchi(oli)tis (n = 8), recurrent wheezing (n = 8) or episodic wheezing (n = 1) were diagnosed. Our results suggest that HBoV infection at high viral load in infants is associated with wheezing (P = 0.013, Cramer’s V = 0.613). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04396-6) contains supplementary material, which is available to authorized users.


title: Analysis of a mathematical model for COVID-19 population dynamics in Lagos, Nigeria

text: This work examines the impact of various non-pharmaceutical control measures (government and personal) on the population dynamics of the novel coronavirus disease 2019 (COVID-19) in Lagos, Nigeria, using an appropriately formulated mathematical model. Using the available data, since its first reported case on 16 March 2020, we seek to develop a predicative tool for the cumulative number of reported cases and the number of active cases in Lagos; we also estimate the basic reproduction number of the disease outbreak in the aforementioned State in Nigeria. Using numerical simulations, we show the effect of control measures, specifically the common social distancing, use of face mask and case detection (via contact tracing and subsequent testings) on the dynamics of COVID-19. We also provide forecasts for the cumulative number of reported cases and active cases for different levels of the control measures being implemented. Numerical simulations of the model show that if at least 55% of the population comply with the social distancing regulation with about 55% of the population effectively making use of face masks while in public, the disease will eventually die out in the population and that, if we can step up the case detection rate for symptomatic individuals to about 0.8 per day, with about 55% of the population complying with the social distancing regulations, it will lead to a great decrease in the incidence (and prevalence) of COVID-19.


How Brazil is dealing with COVID-19 pandemic arrival regarding elective gynecological surgeries


Membrane Fusion


title: Mutagenesis of the transmembrane domain of the SARS coronavirus spike glycoprotein: refinement of the requirements for SARS coronavirus cell entry

text: BACKGROUND: The spike protein (S) of SARS Coronavirus (SARS-CoV) mediates entry of the virus into target cells, including receptor binding and membrane fusion. Close to or in the viral membrane, the S protein contains three distinct motifs: a juxtamembrane aromatic part, a central highly hydrophobic stretch and a cysteine rich motif. Here, we investigate the role of aromatic and hydrophobic parts of S in the entry of SARS CoV and in cell-cell fusion. This was investigated using the previously described SARS pseudotyped particles system (SARSpp) and by fluorescence-based cell-cell fusion assays. RESULTS: Mutagenesis showed that the aromatic domain was crucial for SARSpp entry into cells, with a likely role in pore enlargement. Introduction of lysine residues in the hydrophobic stretch of S also resulted in a block of entry, suggesting the borders of the actual transmembrane domain. Surprisingly, replacement of a glycine residue, situated close to the aromatic domain, with a lysine residue was tolerated, whereas the introduction of a lysine adjacent to the glycine, was not. In a model, we propose that during fusion, the lateral flexibility of the transmembrane domain plays a critical role, as do the tryptophans and the cysteines. CONCLUSIONS: The aromatic domain plays a crucial role in the entry of SARS CoV into target cells. The positioning of the aromatic domain and the hydrophobic domain relative to each other is another essential characteristic of this membrane fusion process.


docid: kaccgoza

title: KEY HIGHLIGHTS of the Canadian Thoracic Society’s Position Statement on the Optimization of Chronic Obstructive Pulmonary Disease Management during the COVID-19 Pandemic


title: The Role of HBZ in HTLV-1-Induced Oncogenesis

text: Human T-cell leukemia virus type 1 (HTLV-1) causes adult T-cell leukemia (ATL) and chronic inflammatory diseases. HTLV-1 bZIP factor (HBZ) is transcribed as an antisense transcript of the HTLV-1 provirus. Among the HTLV-1-encoded viral genes, HBZ is the only gene that is constitutively expressed in all ATL cases. Recent studies have demonstrated that HBZ plays an essential role in oncogenesis by regulating viral transcription and modulating multiple host factors, as well as cellular signaling pathways, that contribute to the development and continued growth of cancer. In this article, I summarize the current knowledge of the oncogenic function of HBZ in cell proliferation, apoptosis, T-cell differentiation, immune escape, and HTLV-1 pathogenesis.


title: Genome and Infection Characteristics of Human Parechovirus Type 1: The Interplay between Viral Infection and Type I Interferon Antiviral System

text: Human parechoviruses (HPeVs), members of the family Picornaviridae, are associated with severe human clinical conditions such as gastrointestinal disease, encephalitis, meningitis, respiratory disease and neonatal sepsis. A new contemporary strain of HPeV1, KVP6 (accession no. KC769584), was isolated from a clinical specimen. Full-genome alignment revealed that HPeV1 KVP6 shares high genome homology with the German strain of HPeV1, 7555312 (accession no. FM178558) and could be classified in the clade 1B group. An intertypic recombination was shown within the P2-P3 genome regions of HPeV1. Cell-type tropism test showed that T84 cells (colon carcinoma cells), A549 cells (lung carcinoma cells) and DBTRG-5MG cells (glioblastoma cells) were susceptible to HPeV1 infection, which might be relevant clinically. A facilitated cytopathic effect and increased viral titers were reached after serial viral passages in Vero cells, with viral genome mutation found in later passages. HPeV1 is sensitive to elevated temperature because 39°C incubation impaired virion production. HPeV1 induced innate immunity with phosphorylation of interferon (IFN) regulatory transcription factor 3 and production of type I IFN in A549 but not T84 cells. Furthermore, type I IFN inhibited HPeV1 production in A549 cells but not T84 cells; T84 cells may be less responsive to type I IFN stimulation. Moreover, HPeV1-infected cells showed downregulated type I IFN activation, which indicated a type I IFN evasion mechanism. The characterization of the complete genome and infection features of HPeV1 provide comprehensive information about this newly isolated HPeV1 for further diagnosis, prevention or treatment strategies.


title: Effective Inhibition of SARS-CoV-2 Entry by Heparin and Enoxaparin Derivatives

text: Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has caused a pandemic of historic proportions and continues to spread globally, with enormous consequences to human health. Currently there is no vaccine, effective therapeutic or prophylactic. Like other betacoronaviruses, attachment and entry of SARS-CoV-2 is mediated by the spike glycoprotein (SGP). In addition to its well-documented interaction with its receptor, human angiotensin converting enzyme 2 (hACE2), SGP has been found to bind to glycosaminoglycans like heparan sulfate, which is found on the surface of virtually all mammalian cells. Here, we pseudotyped SARS-CoV-2 SGP on a third generation lentiviral (pLV) vector and tested the impact of various sulfated polysaccharides on transduction efficiency in mammalian cells. The pLV vector pseudotyped SGP efficiently and produced high titers on HEK293T cells. Various sulfated polysaccharides potently neutralized pLV-S pseudotyped virus with clear structure-based differences in anti-viral activity and affinity to SGP. Concentration-response curves showed that pLV-S particles were efficiently neutralized by a range of concentrations of unfractionated heparin (UFH), enoxaparin, 6-O-desulfated UFH and 6-O-desulfated enoxaparin with an IC(50) of 599 ng/L, 108 μg/L, 177 ng/L, and 586 μg/L respectively. The low serum bioavailability of intranasally administered UFH, along with data suggesting that the nasal epithelium is a portal for initial infection and transmission, suggest that intranasal administration of UFH may be an effective and safe prophylactic treatment.


docid: alhsujpa

title: The increase in total knee replacement surgery in Taiwan: A 15-year retrospective study

text: Total knee replacement (TKR) is considered as one of the most success among clinical interventions for patients with who suffering from knee osteoarthritis (OA). We sought to estimate the incidence of TKR using demographics, incidence rates, lengths of hospital stay, and costs from 1996 to 2010 by analyzing Taiwan's National Health Insurance Research Database. A total of 154,553 patients obtained primary TKR surgery between 1996 and 2010. The diagnosis code for knee OA and the procedure code for TKR were selected from the records. To compare the rate of TKR between covariables, we calculated the TKR risk ratios and 95% confidence interval (CI) of these variables (gender, age, age group, and primary diagnoses). A 2-tailed P-value of .05 was considered statistically significant. The statistical package SPSS version 20.0 (SPSS, Chicago, IL) was used to conduct all the statistical analyzes. We analyzed 154,553 TKRs performed by surgeons in Taiwan from 1996 to 2010. The overall crude incidence increased from 26.4 to 74.55 TKR per 100,000 inhabitants from 1996 to 2010. TKR incidence for the 70 to 79 years age group increased from 227 to 505 per 100,000 people from 1996 to 2010. The age-standardized rate ratios for TKR of women to men ranged from 2.5 to 3.0. The mean average length of stay in hospital was 15 days in 1996 and decreased to 8 days in 2010. During the study period, the adjusted mean cost per patient decreased from US$7485 to US$4827. Health expenditures for TKR were 5% of total National Health Insurance expenditure every year. Over the 15-year period, Taiwan's TKR incidence tripled, which is consistent with population ageing. Arthritis will be a major public health issue in the ageing population in the future.


title: In-Silico Proteomic Exploratory Quest: Crafting T-Cell Epitope Vaccine Against Whipple’s Disease

text: Whipple’s disease is one of the rare maladies in terms of spread but very fatal one as it is linked with many disorders (like Gastroenteritis, Endocarditis etc.). Also, current regimens include less effective drugs which require long duration follows up. This exploratory study was conducted to commence the investigation for crafting multi target epitope vaccine against its bacterial pathogen Tropheryma whipplei. The modern bioinformatics tools like VaxiJen, NETMHCII PAN 3.2, ALLERGEN-FP, PATCH-DOCK, TOXIC-PRED, MHCPRED and IEDB were deployed, which makes the study more intensive in analyzing proteome of T. whipplei as these methods are based on robust result generating statistical algorithms ANN, HMM, and ML. This Immuno-Informatics approach leads us in the prediction of two epitopes: VLMVSAFPL and IRYLAALHL interacting with 4 and 6 HLA DRB1 alleles of MHC Class II respectively. VLMVSAFPL epitope is a part of DNA-directed RNA polymerase subunit beta, and IRYLAALHL epitope is a part of membranous protein insertase YidC of this bacterium. Molecular-Docking and Molecular-Simulation analysis yields the perfect interaction based on Atomic contact energy, binding scores along with RMSD values (0 to 1.5 Ǻ) in selection zone. The IEDB (Immune epitope database) population coverage analysis exhibits satisfactory relevance with respect to world population.


title: Clot in Transit on Transesophageal Echocardiography in a Prone Patient with COVID-19 Acute Respiratory Distress Syndrome

text: • The risk of thromboembolic events in COVID-19 is substantial; • Pulmonary embolism should be considered in cases of clinical deterioration; • Management of clot in transit is controversial.


title: Opportunistic bacterial, viral and fungal infections of the lung

text: Abstract Opportunistic infections are a major cause of morbidity and mortality in severely immunocompromised patients, such as those receiving chemotherapy or biological therapies, patients with haematological malignancy, aplastic anaemia or HIV infection, and recipients of solid-organ or stem cell transplants. The type and degree of the immune defect dictate the profile of potential opportunistic pathogens; T-cell-mediated defects increase the risk of viral (cytomegalovirus, respiratory viruses) and Pneumocystis jirovecii infections, whereas neutrophil defects are associated with bacterial pneumonia and invasive aspergillosis. However, patients often have combinations of immune defects, and a wide range of other opportunistic infections can cause pneumonia. Importantly, conventional non-opportunistic pathogens are frequently encountered in immunocompromised hosts and should not be overlooked. The radiological pattern of disease (best assessed by computed tomography) and speed of onset help to identify the likely pathogen(s); radiological imaging can subsequently be supported by targeted investigation including the early use of bronchoscopy in selected patients. Rapid and expert clinical assessment can identify the most likely pathogens, which can then be treated aggressively, providing the best opportunity for a positive clinical outcome.


title: Potential drug‐drug interactions associated with drugs currently proposed for COVID‐19 treatment in patients receiving other treatments

text: Pharmacologists, pharmacists and other drug experts have been at the forefront during the COVID‐19 outbreak. Pharmacological expertise was required in various areas such as the daily healthcare of patients admitted to our hospitals [1], the implementation of pharmacokinetic and pharmacokinetic‐pharmacodynamic studies in clinical trials of repurposed drugs [2] and even in providing up‐to‐date information to the general population [3].


title: Crisis communication in context: Cultural and political influences underpinning Chinese public relations practice

text: Abstract This study analyzes academic journal articles in order to depict the features of Chinese crisis communication in Mainland China, Hong Kong, and Taiwan. The findings revealed the following features of crisis communication in Chinese societies: collectivistic culture, nationalism, rationalism, face-giving/saving, striving for the “golden mean,” the preference for passive communicative strategies, and the avoidance of extreme strategies. Nevertheless, the differences in political systems—the ubiquitous intervention by authoritarian government on the Mainland, the mistrust of government in post-handover Hong Kong, and the relatively mature democratic polity in Taiwan all lead to unique crisis communication practices.


title: Limiting the spread of highly resistant hospital-acquired microorganisms via critical care transfers: a simulation study

text: PURPOSE: Hospital-acquired infections with highly resistant organisms are an important problem among critically ill patients. Control of these organisms has largely focused within individual hospitals. We examine the extent to which transfers of critically ill patients could be a vector for the wide spread of highly resistant organisms, and compare the efficiency of different approaches to targeting infection control resources. METHODS: We analyzed the network of interhospital transfers of intensive care unit patients in 2005 US Medicare data and 2004–2006 Pennsylvania all-payer data. We simulated the spread of highly resistant hospital-acquired infections by randomly choosing a single hospital to develop a highly resistant organism and following the spread of infection or colonization throughout the network under varying strategies of infection control and varying levels of infectivity. RESULTS: Critical care transfers could spread a highly resistant organism between any two US hospitals in a median of 3 years. Hospitals varied substantially in their importance to limiting potential spread. Targeting resources to a small subset of hospitals on the basis of their position in the transfer network was 16 times more efficient than distributing infection control resources uniformly. Within any set of targeted hospitals, the best strategy for infection control heavily concentrated resources at a few particularly important hospitals, regardless of level of infectivity. CONCLUSIONS: Critical care transfers provide a plausible vector for widespread dissemination of highly resistant hospital-acquired microorganisms. Infection control efforts can be made more efficient by selectively targeting hospitals most important for transmission. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00134-011-2341-y) contains supplementary material, which is available to authorized users.


title: Spatial association between primary Middle East respiratory syndrome coronavirus infection and exposure to dromedary camels in Saudi Arabia

text: Middle East respiratory syndrome coronavirus (MERS‐CoV) is an emerging zoonotic disease. Exposure to dromedary camels (Camelus dromedaries) has been consistently considered the main source of primary human infection. Although Saudi Arabia reports the highest rate of human MERS‐CoV infection and has one of the largest populations of dromedary camels worldwide, their spatial association has not yet been investigated. Thus, this study aimed to examine the correlation between the spatial distribution of primary MERS‐CoV cases with or without a history of camel exposure reported between 2012 and 2019 and dromedary camels at the provincial level in Saudi Arabia. In most provinces, a high proportion of older men develop infections after exposure to camels. Primary human infections during spring and winter were highest in provinces characterized by seasonal breeding and calving, increased camel mobilization and camel–human interactions. A strong and significant association was found between the total number of dromedary camels and the numbers of primary camel‐exposed and non‐exposed MERS‐CoV cases. Furthermore, spatial correlations between MERS‐CoV cases and camel sex, age and dairy status were significant. Via a cluster analysis, we identified Riyadh, Makkah and Eastern provinces as having the most primary MERS‐CoV cases and the highest number of camels. Transmission of MERS‐CoV from camels to humans occurs in most primary cases, but there is still a high proportion of primary infections with an ambiguous link to camels. The results from this study include significant correlations between primary MERS‐CoV cases and camel populations in all provinces, regardless of camel exposure history. This supports the hypothesis of the role of an asymptomatic human carrier or, less likely, an unknown animal host that has direct contact with both infected camels and humans. In this study, we performed a preliminary risk assessment of prioritization measures to control the transmission of infection from camels to humans.


title: The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites

text: BACKGROUND: The gut microbiome is closely associated with the health of the host; although the interaction between the bacterial microbiome and the whole virome has rarely been studied, it is likely of medical importance. Examination of the interactions between the gut bacterial microbiome and virome of rhesus monkey would significantly contribute to revealing the gut microbiome composition. METHODS: Here, we conducted a metagenomic analysis of the gut microbiome of rhesus monkeys in a longitudinal cohort treated with an antibiotic cocktail, and we documented the interactions between the bacterial microbiome and virome. The depletion of viral populations was confirmed at the species level by real-time PCR. We also detected changes in the gut metabolome by GC-MS and LC-MS. RESULTS: A majority of bacteria were depleted after treatment with antibiotics, and the Shannon diversity index decreased from 2.95 to 0.22. Furthermore, the abundance-based coverage estimator (ACE) decreased from 104.47 to 33.84, and the abundance of eukaryotic viruses also changed substantially. In the annotation, 6 families of DNA viruses and 1 bacteriophage family were present in the normal monkeys but absent after gut bacterial microbiome depletion. Intriguingly, we discovered that changes in the gut bacterial microbiome composition may promote changes in the gut virome composition, and tryptophan, arginine, and quinone may play roles in the interaction between the bacterial microbiome and virome. CONCLUSION: Our results indicated that the clearly altered composition of the virome was correlated with depletion in the bacterial community and that metabolites produced by bacteria possibly play important roles in the interaction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-019-1211-z) contains supplementary material, which is available to authorized users.


title: The Emerging Role of RNA as a Therapeutic Target for Small Molecules

text: Recent advances in understanding different RNAs and unique features of their biology have revealed a wealth of information. However, approaches to identify small molecules that target these newly discovered biological regulatory elements have been lacking. The application of new biochemical screening and design-based technologies, coupled with a resurgence of interest in phenotypic screening, has resulted in several compelling successes in targeting RNA. A number of recent advances suggest that achieving the longstanding goal of developing druglike, biologically active small molecules that target RNA is in fact possible. This review highlights advances and successes in approaches to targeting RNA with diverse small molecules, and the potential for these technologies to pave the way to new types of RNA-targeted therapeutics.


title: Global Initiative for Chronic Obstructive Lung Disease strategy for the diagnosis, management and prevention of chronic obstructive pulmonary disease: An Asia–Pacific perspective

text: Abstract: Chronic obstructive pulmonary disease (COPD) is a major public health problem and its prevalence and mortality are increasing throughout the world, including the Asia–Pacific region. To arrest these worldwide trends, the Global Initiative for Chronic Obstructive Lung Disease (GOLD) Expert Panel's global strategy for the diagnosis, management, and prevention of COPD was published in 2001. Based on recently published clinical trials, the GOLD statement was updated in 2003. The Asia–Pacific COPD Roundtable Group, a taskforce of expert respirologists from the Asia–Pacific region, has recently formulated a consensus statement on implementation of the GOLD strategy for COPD in the Asia–Pacific region. The key issues identified by the COPD Roundtable Group for comment are: (i) where there is no access to spirometry, diagnosis of COPD could be suspected on the basis of history, symptoms and physical signs; (ii) inhaled bronchodilators are the preferred regular treatment for COPD in the region, but oral bronchodilators may be considered if the cost of inhaled bronchodilators is a barrier to treatment; (iii) the use of an Metered Dose Inhaler with spacer in place of a nebulizer is recommended in the treatment of acute airflow obstruction in patients with COPD; (iv) influenza vaccination is recommended for all patients with COPD in communities where there is a high likelihood of Severe Acute Respitory Syndrome; and (v) simplified pulmonary rehabilitation programmes should be established in areas where comprehensive programmes are unavailable. Physical exercise training and education on smoking cessation should be core elements of any rehabilitation program. In summary, the COPD Roundtable Group supports implementation of the GOLD strategy for the diagnosis, management and prevention of COPD in the Asia–Pacific region, subject to the additions and modifications to the guidelines suggested above.


title: The neurological insights of the emerging coronaviruses

text: Emerging Viral diseases are incredibly infectious and proficient in inducing pandemics. Unlike the previous emerging coronaviruses (ECoVs) which neurological complexities were uncommon, with neurological features exhibition at 14-25 days post-onset, yet with critical outcomes exhibiting > 50% mortality in central nervous(CNS) presenting pathologies. The COVID 19 neurological consequences occur more frequently even in mild cases, presenting with CNS involvement in up to 25%, musculoskeletal and peripheral manifestation(PNM). Through preceding ECoVs case reports, the PNM not linked to fatal outcomes, however, required, repeated neuro-imaging as notable CT and MRI changes appeared as late as 21 days while the likelihood of Cerebrospinal fluid to test positive for ECoV was 25%, only in the CNS presenting cases. Owing to 44-60% myalgia presentation, risk of the high inflammatory state, and coagulation cascade abnormalities reported in ECoVs, testing for C-reactive protein, serum creatine kinase, and D-dimer level is mandatory. Presently, there is no antiviral medication or vaccination for the ECoVs, early induction of antiviral drugs remains the backbone of management. Neurologically, the therapeutic dosages of anticoagulants are linked to the high incidence of thrombotic complexities, while methylprednisolone is associated with myopathy. Future studies expected to apply more neuro-imaging techniques for CNS exploration and further explore the pathogenesis of the COVID 19 myalgia, anosmia/ageusia reported in the majority of the initial cases.


title: COVID-19 Disease: a critical care perspective

text: Abstract COVID-19 is a new highly infectious disease with an incompletely described clinical course, which has caused a pandemic, with Europe being identified as the third epicentre. COVID-19 has placed unprecedented pressure on critical care services which is likely to stretch resources beyond capacity. The situation is exacerbated by increased staff absence from self-isolation and illness, increased referral of patients with suspected or confirmed COVID-19 who develop respiratory failure, and limited availability of Extra Corporeal Membrane Oxygenation (ECMO) services. In addition, there is the ongoing challenge of patients being transferred between departments and hospitals for ongoing care. In consequence, as current needs continue to rise, innovative approaches are needed to redress shortages and support the continuance of services. This article provides an overview of severe COVID-19 infection, outlining treatment strategies and nursing processes that will need to develop and extend in response to this evolving situation.


title: SARS‐CoV‐2 outbreak and lockdown in a Northern Italy hospital. Comparison with Scandinavian no‐lockdown country

text: The ongoing SARS‐CoV‐2 pandemic has evolved with cases of local transmission soon after the detection of imported cases in affected countries. However, the pandemic did not reach all countries at the same time and our country (Italy) had to act as forerunners.


docid: frvhxuod

title: Chapter 32 Education and training in microbial forensics

text: Abstract Advances in research and development have led to new technologies, tools and analytical capabilities bolstering the field of microbial forensics. However, a parallel commitment to education and training in this field is needed to prepare the next generation of scientists. Education and training are needed to: Improve first responder preparation and awareness, essential to public safety and preservation of the evidence integrity; Provide a larger pool of trained microbial forensics practitioners and; Educate the public and policy makers on the capabilities and limitations of microbial forensics. This chapter provides suggestions for topics, core courses, laboratories, skills, training, education programs, curricular guidelines and resources for microbial forensics that have been codified from a variety of sources including the American Society of Microbiology and American Academy of Forensic Sciences.


title: Prevalence of and risk factors associated with viral and bacterial pathogens in farmed European wild boar

text: Abstract The aim of this study was to estimate in farmed European wild boars the prevalence of and risk factors associated with a range of common porcine viral and bacterial infections, namely, porcine parvovirus (PPV), porcine circovirus type 2 (PCV2), swine influenza virus (SIV), Aujeszky’s disease virus (ADV), classical swine fever virus (CSFV), swine vesicular disease virus (SVDV), coronavirus causing transmissible gastroenteritis (TGEV), porcine reproductive and respiratory syndrome virus (PRRSV), Mycoplasma hyopneumoniae, Lawsonia intracellularis, Brucella spp., and Leptospira spp. A sampling frame was compiled based on a national record of wild boar farmers, and 32 farms were surveyed. Serological screening was carried out on 303 samples from animals slaughtered between 2005 and 2008, and random-effect logistic regression models were developed for pathogens with a ‘non-zero’ prevalence. The apparent animal prevalence for PPV, PCV2, and L. intracellularis was 46.5% (95% confidence interval [CI] 41–52%), 51.1% (95% CI 45–57%) and 59.2% (95% CI 54–65%), respectively. Apparent farm seroprevalence rates for PPV, PCV2 and Lawsonia intracellularis were 56.3% (95% CI, 39–73%), 21.9% (95% CI, 8–36%) and 78.1% (95% CI, 64–92%), respectively. No antibodies were detected against SIV, ADV, CSFV, SVDV, TGEV, PRSSV, Leptospira spp., Brucella spp., or M. hyopneumoniae. Increasing herd size, proximity to dense populations of domestic swine and later sampling times within the survey period were found to be risk factors. Overall, the seroprevalence of these pathogens in farmed wild boar was similar to that in the farmed domestic pig population in Finland. However, it is possible that the rearing of wild boars in fenced estates may predispose them to particular infections, as reflected in higher antibody titres.


title: Pathological Features and Pathogenesis of the Endomyocardial Form of Restrictive Cardiomyopathy in Cats

text: Summary This study reports pathological and molecular features in 41 cases of feline restrictive cardiomyopathy (RCM). Grossly, there were patchy or diffuse areas of endocardial thickening affecting the left ventricle. The more common patchy endocardial lesions occurred as large trabecular or irregular broad bands of fibrous tissue bridging the left ventricular free wall and ventricular septum. Microscopically, regardless of the gross pattern, the thickened endocardium contained various numbers of stellate, spindle-shaped or elongated mesenchymal cells surrounded by fibrous connective tissue. Immunohistochemical findings were indicative of smooth muscle differentiation in mesenchymal cells. These cells proliferated vigorously and produced alcian blue-positive ground substance and collagen fibres; it was considered that the mesenchymal cells contributed to the formation of the endocardial lesions. In addition, multiple left ventricular ‘false tendons’ were invariably included within the trabecular or broad fibrous bands, providing a framework for formation of those bands. Evidence of endocarditis or endomyocarditis was lacking in all 41 cases, and no viral genomes were detected in any of the DNA or RNA samples obtained from 14 of the hearts. These observations suggest that any relationship between feline RCM and a virus-induced inflammatory response seems unlikely.


title: Potential inhibitors of coronavirus 3-chymotrypsin-like protease (3CL(pro)): an in silico screening of alkaloids and terpenoids from African medicinal plants

text: The novel coronavirus disease 2019 (COVID-19) caused by SARS-COV-2 has raised myriad of global concerns. There is currently no FDA approved antiviral strategy to alleviate the disease burden. The conserved 3-chymotrypsin-like protease (3CL(pro)), which controls coronavirus replication is a promising drug target for combating the coronavirus infection. This study screens some African plants derived alkaloids and terpenoids as potential inhibitors of coronavirus 3CL(pro) using in silico approach. Bioactive alkaloids (62) and terpenoids (100) of plants native to Africa were docked to the 3CL(pro) of the novel SARS-CoV-2. The top twenty alkaloids and terpenoids with high binding affinities to the SARS-CoV-2 3CL(pro) were further docked to the 3CL(pro) of SARS-CoV and MERS-CoV. The docking scores were compared with 3CL(pro)-referenced inhibitors (Lopinavir and Ritonavir). The top docked compounds were further subjected to ADEM/Tox and Lipinski filtering analyses for drug-likeness prediction analysis. This ligand-protein interaction study revealed that more than half of the top twenty alkaloids and terpenoids interacted favourably with the coronaviruses 3CL(pro), and had binding affinities that surpassed that of lopinavir and ritonavir. Also, a highly defined hit-list of seven compounds (10-Hydroxyusambarensine, Cryptoquindoline, 6-Oxoisoiguesterin, 22-Hydroxyhopan-3-one, Cryptospirolepine, Isoiguesterin and 20-Epibryonolic acid) were identified. Furthermore, four non-toxic, druggable plant derived alkaloids (10-Hydroxyusambarensine, and Cryptoquindoline) and terpenoids (6-Oxoisoiguesterin and 22-Hydroxyhopan-3-one), that bind to the receptor-binding site and catalytic dyad of SARS-CoV-2 3CL(pro) were identified from the predictive ADME/tox and Lipinski filter analysis. However, further experimental analyses are required for developing these possible leads into natural anti-COVID-19 therapeutic agents for combating the pandemic. Communicated by Ramaswamy H. Sarma


title: Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses

text: The severity and outcome of respiratory viral infections is partially determined by the cellular response mounted by infected lung epithelial cells. Disease prevention and treatment is dependent on our understanding of the shared and unique responses elicited by diverse viruses, yet few studies compare host responses to different viruses while controlling other experimental parameters. We compared changes in gene expression of murine lung epithelial cells infected individually by three respiratory viruses causing mild (rhinovirus, RV1B), moderate (coronavirus, MHV-1), and severe (influenza A virus, PR8) disease in mice. RV1B infection caused numerous gene expression changes, but the differential effect peaked at 12 hours post-infection. PR8 altered an intermediate number of genes whose expression continued to change through 24 hours. MHV-1 had comparatively few effects on host gene expression. The viruses elicited highly overlapping responses in antiviral genes, though MHV-1 induced a lower type I interferon response than the other two viruses. Signature genes were identified for each virus and included host defense genes for PR8, tissue remodeling genes for RV1B, and transcription factors for MHV-1. Our comparative approach identified universal and specific transcriptional signatures of virus infection that can be used to discover mechanisms of pathogenesis in the respiratory tract.


title: Systematic Assembly and Genetic Manipulation of the Mouse Hepatitis Virus A59 Genome

text: We have developed a DNA assembly platform that utilizes the nonspecific, highly variable sequence signatures of type IIs restriction enzymes to assemble a full-length molecular clone of murine hepatitis coronavirus (MHV) strain A59. The approach also allows changes to be engineered into a DNA fragment by designing primers that incorporate the restriction site and the mutations of interest. By adding the type IIs restriction site in the proper orientation, subsequent digestion removes the restriction site and leaves a sticky end comprising the mutation of interest ready to ligate to a second fragment generated in parallel as its complement. In this chapter, we discuss the details of the method to assemble a full-length infectious clone of MHV and then engineer a specific mutation into the clone to demonstrate the power of this unique site-directed “No See’m” mutagenesis approach.


title: Genetic determinants of pathogenesis by feline infectious peritonitis virus

text: Abstract Feline infectious peritonitis (FIP) is a fatal, immune-augmented, and progressive viral disease of cats associated with feline coronavirus (FCoV). Viral genetic determinants specifically associated with FIPV pathogenesis have not yet been discovered. Viral gene signatures in the spike, non-structural protein 3c, and membrane of the coronavirus genome have been shown to often correlate with disease manifestation. An “in vivo mutation transition hypothesis” is widely accepted and postulates that de novo virus mutation occurs in vivo giving rise to virulence. The existence of “distinct circulating avirulent and virulent strains” is an alternative hypothesis of viral pathogenesis. It may be possible that viral dynamics from both hypotheses are at play in the occurrence of FIP. Epidemiologic data suggests that the genetic background of the cat contributes to the manifestation of FIP. Further studies exploring both viral and host genetic determinants of disease in FIP offer specific opportunities for the management of this disease.


title: Data-driven outbreak forecasting with a simple nonlinear growth model

text: Recent events have thrown the spotlight on infectious disease outbreak response. We developed a data-driven method, EpiGro, which can be applied to cumulative case reports to estimate the order of magnitude of the duration, peak and ultimate size of an ongoing outbreak. It is based on a surprisingly simple mathematical property of many epidemiological data sets, does not require knowledge or estimation of disease transmission parameters, is robust to noise and to small data sets, and runs quickly due to its mathematical simplicity. Using data from historic and ongoing epidemics, we present the model. We also provide modeling considerations that justify this approach and discuss its limitations. In the absence of other information or in conjunction with other models, EpiGro may be useful to public health responders.


title: A novel real-time PCR assay panel for detection of common respiratory pathogens in a convenient, strip-tube array format

text: Commercial multiplex assays, built on different chemistries and platforms are widely available for simultaneous detection of pathogens that cause respiratory infections. However, these tests are often difficult to implement in a resource limited setting because of high cost. In this study, we developed and validated a method for simultaneous testing of common respiratory pathogens (Respanel) by real-time PCR in a convenient, strip-tube array format. Primers and probes for sixteen PCR assays were selected from the literature or newly designed. Following optimization of individual PCR assays, strip-tube arrays were prepared by dispensing primer-probe mixes (PPM) into two sets of 8-tube strips. Nucleic acid extracts from specimens were mixed with PCR master mix, and dispensed column-wise into 2X8-wells of a 96-well plate. PPMs from strip-tubes were then added to the wells using a multichannel pipette for real-time PCR. Individual PCR assays were optimized using previously known specimens (n=397) with 91%-100% concordance with culture, DFA or PCR results. Respanel was then tested in a routine manner at two different sites using specimens (n=147) previously tested by Qiagen Resplex I&II or Fast-Track Diagnostics Respiratory Pathogens 21 assays. The sensitivity, specificity and accuracy of Respanel were 94%, 95% and 95%, respectively, against Resplex and 88%, 100% and 99%, respectively, against FTDRP21. Respanel detected 48% more pathogens (p<0.05) than Resplex but the rate of pathogen detection was not significantly different from FTDRP21. Respanel is a convenient and inexpensive assay that is more sensitive than Resplex and comparable to FTDRP21 for the detection of common respiratory pathogens.


title: Characteristics associated with clinical severity and inflammatory phenotype of naturally occurring virus-induced exacerbations of asthma in adults

text: BACKGROUND: In experimental studies viral infections have been shown to induce type 2 inflammation in asthmatics, but whether this is a feature of naturally occurring virus-induced asthma exacerbations is unknown. Thymic stromal lymphopoietin (TSLP) released from the airway epithelium in response to damage, has been suggested as a link between viral infection and type 2 inflammation, but the role of TSLP in asthma exacerbations is unknown. OBJECTIVE: To assess whether type 2 inflammation, as measured by sputum eosinophils and fractional exhaled nitric oxide (FeNO), is a feature of naturally occurring virus-induced exacerbations of asthma and whether TSLP is associated with this type 2 inflammation. METHODS: Patients presenting to hospital with acute asthma were examined during the exacerbation, and after 4 weeks recovery. The assessments included spirometry, FeNO and induced sputum for differential counts and TSLP mRNA levels. Nasal swabs were collected for viral detection. RESULTS: Sputum eosinophils and FeNO were similar between virus-positive (n=44) and negative patients (n=44). In virus-positive patients, TSLP expression was lower at exacerbation than follow-up (p=0.03). High TSLP at exacerbation was associated with lower sputum eosinophils (p=0.01) and higher FEV1 (p=0.03). In virus-positive patients, %-predicted FEV1 negatively correlated with both FeNO and sputum eosinophils (p=0.02 and p=0.05, respectively). CONCLUSION: Our findings support that type 2 inflammation is present in patients during virus-induced asthma exacerbations, to the same degree as non-viral exacerbations, and correlate negatively with FEV1. However, in virus-positive patients, high TSLP expression during exacerbation was associated with low sputum eosinophils, suggesting that the effect of TSLP in vivo, in the setting of an asthma exacerbation, might be different than the type 2 inducing effects observed in experimental studies.


title: Assembling millions of short DNA sequences using SSAKE

text: Summary: Novel DNA sequencing technologies with the potential for up to three orders magnitude more sequence throughput than conventional Sanger sequencing are emerging. The instrument now available from Solexa Ltd, produces millions of short DNA sequences of 25 nt each. Due to ubiquitous repeats in large genomes and the inability of short sequences to uniquely and unambiguously characterize them, the short read length limits applicability for de novo sequencing. However, given the sequencing depth and the throughput of this instrument, stringent assembly of highly identical sequences can be achieved. We describe SSAKE, a tool for aggressively assembling millions of short nucleotide sequences by progressively searching through a prefix tree for the longest possible overlap between any two sequences. SSAKE is designed to help leverage the information from short sequence reads by stringently assembling them into contiguous sequences that can be used to characterize novel sequencing targets. Availability: Contact: rwarren@bcgsc.ca


docid: ulsejzqt

title: Octahydroquinoxalin-2(1H)-One-Based Aminophosphonic Acids and Their Derivatives—Biological Activity towards Cancer Cells

text: In the search for new antitumor agents, aminophosphonic acids and their derivatives based on octahydroquinoxalin-2(1H)-one scaffold were obtained and their cytotoxic properties and a mechanism of action were evaluated. Phosphonic acid and phosphonate moieties increased the antiproliferative activity in comparison to phenolic Mannich bases previously reported. Most of the obtained compounds revealed a strong antiproliferative effect against leukemia cell line (MV-4-11) with simultaneous low cytotoxicity against normal cell line (mouse fibroblasts-BALB/3T3). The most active compound was diphenyl-[(1R,6R)-3-oxo-2,5-diazabicyclo[4.4.0]dec-4-yl]phosphonate. Preliminary evaluation of the mechanism of action showed the proapoptotic effect associated with caspase 3/7 induction.


title: A novel subset of putative stem/progenitor CD34(+)Oct-4(+) cells is the major target for SARS coronavirus in human lung

text: Identification of the nature of severe acute respiratory syndrome (SARS)-infected cells is crucial toward understanding the pathogenesis. Using multicolor colocalization techniques, we previously reported that SARS(+) cells in the lung of fatally infected patients expressed the only known functional receptor, angiotensin-converting enzyme 2, and also a binding receptor, liver/lymph node–specific ICAM-3–grabbing non-integrin (CD209L). In this study, we show that SARS-infected cells also express the stem/progenitor cell markers CD34 and Oct-4, and do not express cytokeratin or surfactant. These putative lung stem/progenitor cells can also be identified in some non-SARS individuals and can be infected by SARS-coronavirus ex vivo. Infection of these cells may contribute to the loss of lung repair capacity that leads to respiratory failure as clinically observed.