title: Time Series Prediction of COVID-19 by Mutation Rate Analysis using Recurrent Neural Network-based LSTM Model

text: SARS-CoV-2, a novel coronavirus mostly known as COVID-19 has created a global pandemic. The world is now immobilized by this infectious RNA virus. As of May 18, already more than 4.8 million people have been infected and 316k people died. This RNA virus has the ability to do the mutation in the human body. Accurate determination of mutation rates is essential to comprehend the evolution of this virus and to determine the risk of emergent infectious disease. This study explores the mutation rate of the whole genomic sequence gathered from the patient's dataset of different countries. The collected dataset is processed to determine the nucleotide mutation and codon mutation separately. Furthermore, based on the size of the dataset, the determined mutation rate is categorized for four different regions: China, Australia, The United States, and the rest of the World. It has been found that a huge amount of Thymine (T) and Adenine (A) are mutated to other nucleotides for all regions, but codons are not frequently mutating like nucleotides. A recurrent neural network-based Long Short Term Memory (LSTM) model has been applied to predict the future mutation rate of this virus. The LSTM model gives Root Mean Square Error (RMSE) of 0.06 in testing and 0.04 in training, which is an optimized value. Using this train and testing process, the nucleotide mutation rate of 400(th) patient in future time has been predicted. About 0.1% increment in mutation rate is found for mutating of nucleotides from T to C and G, C to G and G to T. While a decrement of 0.1% is seen for mutating of T to A, and A to C. It is found that this model can be used to predict day basis mutation rates if more patient data is available in updated time.


M-VII Fetal infections by human parvovirus B19 and cytomegalovirus


title: The role of viruses in the development and exacerbation of atopic disease

text: Objective To examine data in support of the viral hypothesis of atopic disease. Data Sources We retrieved review articles and original research from MEDLINE, OVID, and PubMed (1950-June 2009) that addressed our topic of interest, using the terms respiratory virus, asthma, IgE, atopy, and viral-induced wheeze. Study Selection Articles were selected for their relevance to viruses and their role in asthma. Results Much of the data in support of the viral role in asthma focuses on rhinovirus and respiratory syncytial virus. Epidemiologic studies have used factors such as day-care and family size as surrogates for infection in studies that support and negate the role of viruses in the development of asthma. A large volume of literature supports the theory that virus exacerbates preexisting asthma by setting off the inflammatory cascade. No mechanistic studies fully explain how viral infections can translate or exacerbate atopic disease. We provide information from our mouse model that suggests that dendritic cells, IgE, and FcɛRI are critical to the induction of atopy. Studies of patients taking antiviral agents (eg, ribavirin or palvizumab) support the notion that interfering with respiratory viral infections may decrease the development of atopy. Conclusions Many studies suggest strongly that viral infections may predispose patients to the development of asthma and other atopic diseases. Further, mechanistic studies are necessary to allow for the development of targeted therapeutics to prevent the translation of viral into atopic disease.


Grundrechte in Zeiten von Corona : Zugleich Anmerkung zu BVerfG, Beschl. v. 7.4.2020 – 1 BvR 755/20


Risks and Benefits of Gain-of-Function Experiments with Pathogens of Pandemic Potential, Such as Influenza Virus: a Call for a Science-Based Discussion


Livestock diseases threatening smallholder farmers in Lao people's Democratic Republic


title: Comparative analysis of laboratory indexes of severe and non-severe patients infected with COVID-19

text: BACKGROUND: The pandemic coronavirus disease 2019 (COVID-19) has threaten the global health. The characteristics of laboratory findings of coronavirus are of great significance for clinical diagnosis and treatment. We found indicators that may most effectively predict a non-severe COVID-19 patient develop into a severe patient. METHODS: We conducted a meta-analysis to compare the laboratory findings of severe patients with non-severe patients with COVID-19 from searched articles. RESULTS: Through the analysis of laboratory examination information of patients with COVID-19 from 35 articles (5912 patients), we demonstrated that severe cases possessed higher levels of leukocyte (1.20-fold), neutrophil (1.33-fold), CRP (3.04-fold), PCT (2.00-fold), ESR (1.44-fold), AST (1.40-fold), ALT (1.34-fold), LDH (1.54-fold), CK (1.44-fold), CK-MB (1.39-fold), total bilirubin(1.14-fold), urea (1.28-fold), creatine (1.09-fold), PT (1.03-fold) and D-dimer (2.74-fold), as well as lower levels of lymphocytes (1.44-fold), eosinophil (2.00-fold), monocyte (1.08-fold), Hemoglobin (1.53-fold), PLT (1.15-fold), albumin (1.15-fold), and APTT (1.02-fold). Lymphocyte subsets and series of inflammatory cytokines were also different in severe cases with the non-severe ones, including lower levels of CD4 T cells (2.10-fold) and CD8 T cells (2.00-fold), higher levels of IL-1β (1.02-fold), IL-6 (1.93-fold) and IL-10 (1.55-fold). CONCLUSIONS: Some certain laboratory inspections could predict the progress of the COVID-19 changes, especially lymphocytes, CRP, PCT, ALT, AST, LDH, D-dimer, CD4 T cells and IL6, which provide valuable signals for preventing the deterioration of the disease.


title: Prevención del riesgo infeccioso en el consultorio de pediatría y en el hospital

text: En Francia, el Ministerio de Sanidad establece en su programa nacional de prevención de infecciones asociadas a la asistencia sanitaria o infecciones nosocomiales de 2015 que los centros sanitarios, así como los establecimientos médico-sociales y los médicos locales deben prevenir este tipo de infecciones. Este artículo describe la prevención de la transmisión de microorganismos procedentes de pacientes o ambientales. Dicha prevención incluye siempre la aplicación de una serie de precauciones estándar (lavado y/o desinfección de manos, uso de guantes ante el menor riesgo de contacto con líquidos biológicos, uso de batas, gafas y mascarillas si existe un riesgo de proyección o de aerosolización de sangre o de cualquier otro producto de origen humano), así como la desinfección del material y de las superficies contaminadas. En algunos casos, es preciso adoptar precauciones específicas complementarias, como las basadas en la transmisión por contacto, por ejemplo en caso de gastroenteritis, las basadas en la transmisión por gotas, en caso de infecciones pulmonares u otorrinolaringológicas, y las específicas de la transmisión aérea, en caso de tuberculosis, sarampión o varicela. El artículo describe la prevención de infecciones asociadas a intervenciones invasivas (colocación de dispositivos urinarios, dispositivos intravasculares, actos quirúrgicos) y de infecciones en piel lesionada o en orificios de ostomía. También contempla la prevención de accidentes por exposición a la sangre (AES): uso de materiales de seguridad, definición clara y escrita de la conducta necesaria ante un AES, vacunación del personal. La emergencia de la resistencia a los antibióticos es un desafío para la salud pública. El control de la difusión de bacterias multirresistentes a los antibióticos y de bacterias altamente resistentes está basado a su vez en el control de la prescripción de antibióticos y de la prevención de la difusión de infecciones a partir de pacientes portadores (transmisión cruzada).


title: Increased levels of myelin basic protein transcripts gene in virus-induced demyelination

text: In multiple sclerosis, a demyelinating disease of young adults, there is a paucity of myelin repair in the central nervous system (CNS) which is necessary for the restoration of fast saltatory conduction in axons(1,2). Consequently, this relapsing disease often causes marked disability. In similar diseases of small rodents, however, remyelination can be quite extensive, as in the demyelinating disease caused by the A59 strain of mouse hepatitis virus (MHV-A59)(3,4), a coronavirus of mice. To investigate when and where oligodendrocytes are first triggered to repair CNS myelin in such disease, we have used a complementary DNA probe specific for one major myelin protein gene, myelin basic protein (MBP), which hybridizes with the four forms of MBP messenger RNA in rodents(5). Using Northern blot and in situ hybridization techniques, we previously found that MBP mRNA is first detected at about 5 days after birth, peaks at 18 days and progressively decreases to 25% of the peak levels in the adult(5–7). We now report that in spinal cord sections of adult animals with active demyelination and inflammatory cells, in situ hybridization reveals a dramatic increase in probe binding to MBP-specific mRNA at (2–3) weeks after virus inoculation and before remyelination can be detected by morphological methods. This increase of MBP-specific mRNA is found at the edge of the demyelinating area and extends into surrounding areas of normal-appearing white matter. Thus, in situ hybridization with myelin-specific probes appears to be a useful method for detecting the timing, intensity and location of myelin protein gene reactivation preceding remyelination. This method could be used to elucidate whether such a reactivation occurs in multiple sclerosis brain tissue. Our results suggest that in mice, glial cells react to a demyelinating process with widespread MBP mRNA synthesis which may be triggered by a diffusible factor released in the demyelinated areas.


title: Expression of the peplomer glycoprotein of murine coronavirus JHM using a baculovirus vector

text: Abstract The gene encoding the E2 peplomer glycoprotein of coronavirus mouse hepatitis virus JHM strain (JHMV) has been inserted into the genome of Autographa cafifornica nuclear polyhedrosis baculovirus (AcNPV) in lieu of the coding region of the AcNPV polyhedrin gene. This recombinant virus produced E2 protein in insect cells under the control of the baculovirus polyhedrin promotor. The expressed E2 protein was shown in size and antigenic properties to be similar to the E2 protein produced in mouse cells infected by JHMV. The expressed E2 protein was glycosylated and transported to the cell surface; however, no proteolytic cleavage was detected in insect cells. The sera from rats immunized with partially purified E2 protein derived from insect cells reacted in immunoprecipitation and immunofluorescence experiments with the E2 protein produced in JHMV-infected mouse cells. The antiserum failed to neutralize the infectivity of JHMV. These results suggest that the E2 protein expressed by the recombinant baculovirus in insect cells is similar but not identical to the E2 protein produced in JHMV-infected mouse cells. The inability of the E2 protein expressed in insect cells to produce neutralizing antibody is discussed.


title: Virus–drug interactions—molecular insight into immunosuppression and HCV

text: Liver transplantation is an effective treatment for end-stage liver disease that is attributable to chronic HCV infection. However, long-term outcomes are compromised by universal virological recurrence in the graft. Reinfection that occurs after transplantation has increased resistance to current interferon-based antiviral therapy and often leads to accelerated development of cirrhosis. Important risk factors for severe HCV recurrence are linked to immunosuppression. Owing to the lack of good randomized, controlled trials, the optimal choice of immunosuppressants is still debated. By contrast, much progress has been made in the understanding of HCV biology and the antiviral action of interferons. These new insights have greatly expanded our knowledge of the molecular interplay between HCV and immunosuppressive drugs. In this article, we explore the effect of different immunosuppressants on the complex cellular events involved in HCV infection and interferon signalling. Potential implications for clinical practice and future drug development are discussed.


title: VIDA: a virus database system for the organization of animal virus genome open reading frames

text: VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships. Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html.


title: Improving care of the critically ill: institutional and health-care system approaches

text: Summary Institutional and health-care system approaches complement bedside strategies to improve care of the critically ill. Focusing on the USA and the UK, we discuss seven approaches: education (especially of non-clinical managers, policy-makers, and the public), organisational guidelines, performance reporting, financial and sociobehavioural incentives to health-care professionals and institutions, regulation, legal requirements, and health-care system reorganisation. No single action is likely to have sustained effect and we recommend a combination of approaches. Several recent initiatives that hold promise tie performance reporting to financial incentives. Though performance reporting has been hampered by concerns over cost and accuracy, it remains an essential component and we recommend continued effort in this area. We also recommend more public education and use of organisational guidelines, such as admission criteria and staffing levels in intensive care units. Even if these endeavours are successful, with rising demand for services and continuing pressure to control costs, optimum care of the critically ill will not be realised without a fundamental reorganisation of services. In both the USA and UK, we recommend exploration of regionalised care, akin to US state trauma systems, and greater use of physician-extenders, such as nurse practitioners, to provide enhanced access to specialist care for critical illness.


title: Pretreated household materials carry similar filtration protection against pathogens when compared with surgical masks

text: The past 4 months, the emergence and spread of novel 2019 SARS-Cov-2 (COVID-19) has led to a global pandemic which is rapidly depleting supplies of personal protective equipment worldwide. There are currently over 1.6 million confirmed cases of COVID-19 worldwide which has resulted in more the 100,000 deaths. As these numbers grow daily, hospitals are being forced to reuse surgical masks in hopes of conserving their dwindling supply. Since COVID-19 will most likely have effects that last for many months, our nationwide shortage of masks poses a long term issue that must be addressed immediately. Based on a previous study by Quan et al., a salt-based soaking strategy has been reported to enhance the filtration ability of surgical masks. We propose a similar soaking process which uses materials widely available in anyone's household. We tested this method of pretreating a variety of materials with a salt-based solution by a droplet test using fluorescently stained nanoparticles similar in size to the COVID-19 virus. Our results show that this filter significantly reduces the amount of penetration of these particles. This will allow for healthcare workers to create a disposable added layer of protection to their surgical masks, N95s, or homemade masks by using household available products.


Knowledge for nurses to better care for themselves so they can better care for others during the Covid-19 pandemic and beyond


title: Detection and Phylogenetic Analysis of Group 1 Coronaviruses in South American Bats

text: Bat coronaviruses (Bt-CoVs) are thought to be the precursors of severe acute respiratory syndrome coronavirus. We detected Bt-CoVs in 2 bat species from Trinidad. Phylogenetic analysis of the RNA-dependent RNA polymerase gene and helicase confirmed them as group 1 coronaviruses.


title: Human bocavirus detection in an atopic child affected by pneumonia associated with wheezing

text: Abstract Background Human bocavirus (HBoV) is a newly discovered human parvovirus. HBoV was detected in respiratory samples by PCR, but its aetiologic role in the pathogenesis of acute respiratory infectious diseases is still unclear. Results In this report, we describe an atopic child affected by pneumonia, with a past history of wheezing. A panel of bacteria and respiratory viruses were searched in the nasopharyngeal swab, only human bocavirus was detected by PCR. Conclusions Detection of HboV, as the only microbial agent, in samples from children with wheezing and acute respiratory diseases supports the assumption that this emerging virus could have an aetiologic role in the pathogenesis of respiratory diseases.


Dr. Yang Zhong: An explorer on the road forever


title: Traditional Chinese medicine herbal extracts of Cibotium barometz, Gentiana scabra, Dioscorea batatas, Cassia tora, and Taxillus chinensis inhibit SARS-CoV replication

text: Development of anti-severe acute respiratory syndrome associated coronavirus (SARS-CoV) agents is pivotal to prevent the reemergence of the life-threatening disease, SARS. In this study, more than 200 extracts from Chinese medicinal herbs were evaluated for anti-SARS-CoV activities using a cell-based assay that measured SARS-CoV-induced cytopathogenic effect (CPE) in vitro on Vero E6 cells. Six herbal extracts, one each from Gentianae Radix (龍膽 lóng dǎn; the dried rhizome of Gentiana scabra), Dioscoreae Rhizoma (山藥 shān yào; the tuber of Dioscorea batatas), Cassiae Semen (決明子 jué míng zǐ; the dried seed of Cassia tora) and Loranthi Ramus (桑寄生 sāng jì shēng; the dried stem, with leaf of Taxillus chinensis) (designated as GSH, DBM, CTH and TCH, respectively), and two from Rhizoma Cibotii (狗脊 gǒu jǐ; the dried rhizome of Cibotium barometz) (designated as CBE and CBM), were found to be potent inhibitors of SARS-CoV at concentrations between 25 and 200 μg/ml. The concentrations of the six extracts needed to inhibit 50% of Vero E6 cell proliferation (CC(50)) and 50% of viral replication (EC(50)) were determined. The resulting selective index values (SI = CC(50)/EC(50)) of the most effective extracts CBE, GSH, DBM, CTH and TCH were > 59.4, > 57.5, > 62.1, > 59.4, and > 92.9, respectively. Among these extracts, CBM and DBM also showed significant inhibition of SARS-CoV 3CL protease activity with IC(50) values of 39 μg/ml and 44 μg/ml, respectively. Our findings suggest that these six herbal extracts may have potential as candidates for future development of anti-SARS therapeutics. Abbreviations SARS, severe acute respiratory syndrome CoV, coronavirus CPE, cytopathogenic effect TCM, traditional Chinese medicine


title: Clinical epidemiological analyses of overweight/obesity and abnormal liver function contributing to prolonged hospitalization in patients infected with COVID-19

text: BACKGROUND/OBJECTIVES: During the 2019 coronavirus disease (COVID-19) outbreak, obesity may contribute to COVID-19 transmission and deterioration. In addition, many patients with COVID-19 infection have suffered liver damage which might contribute to a worse prognosis. We conducted a clinical epidemiological analysis to investigate the association of overweight/obesity and abnormal liver function (ALF) with hospitalized duration in patients infected with COVID-19. SUBJECTS/METHODS: Fifty-eight patients with diagnosed COVID-19 (22 women & 36 men; average age: 49.2 ± 13.1 yr) were included, and their clinical data were collected at The Second Affiliated and Yuying Children’s Hospital of Wenzhou Medical University, Zhejiang. Overweight/obesity was determined as body mass index (BMI) ≥24 kg/m(2), ALF was determined as alanine aminotransferase >40 U/L, and prolonged hospitalization was lasting more than the median value of the hospitalized days (19 days) in this population. RESULTS: The proportions of prolonged hospitalization were elevated in patients with overweight/obesity and ALF compared with those without overweight/obesity (62.1% versus 26.1%, P = 0.010) and those without ALF (70.6% versus 41.5%, P = 0.043). Kaplan–Meier analysis showed that the hospitalized duration was increased from the patients with neither overweight/obesity nor ALF to those with either overweight/obesity or ALF, and to those with both of overweight/obesity and ALF (mean with 95% confidence interval: 16.4 [14.5–18.3] versus 25.3 [21.6–29.1] versus 28.3 [24.6–32.0], P for trend = 0.001). Being discharged from hospital in time was inversely and independently associated with BMI (hazard ratio [HR] = 0.75, 95% CI: 0.63–0.90, P for trend = 0.002) and ALT (HR = 0.95, 95% CI: 0.92–0.99, P for trend = 0.007). CONCLUSIONS: Present findings suggested that overweight/obesity and/or ALF contributed to predicting a probability of prolonged hospitalization in patients with COVID-19 infection, to whom extra attentions and precautions should be paid during clinical treatments.


title: Clinical characteristics of refractory COVID-19 pneumonia in Wuhan, China

text: BACKGROUND: Since December 2019, novel coronavirus (SARS-CoV-2)-infected pneumonia (COVID-19) occurred in Wuhan, and rapidly spread throughout China. This study aimed to clarify the characteristics of patients with refractory COVID-19. METHODS: In this retrospective single-center study, we included 155 consecutive patients with confirmed COVID-19 in Zhongnan Hospital of Wuhan University from January 1(st) to February 5(th). The cases were divided into general and refractory COVID-19 groups according to the clinical efficacy after hospitalization, and the difference between groups were compared. RESULTS: Compared with general COVID-19 patients (45.2%), refractory patients had an older age, male sex, more underlying comorbidities, lower incidence of fever, higher levels of maximum temperature among fever cases, higher incidence of breath shortness and anorexia, severer disease assessment on admission, high levels of neutrophil, aspartate aminotransferase (AST), lactate dehydrogenase (LDH) and C-reactive protein, lower levels of platelets and albumin, and higher incidence of bilateral pneumonia and pleural effusion (P<0.05). Refractory COVID-19 patients were more likely to receive oxygen, mechanical ventilation, expectorant, and adjunctive treatment including corticosteroid, antiviral drugs and immune enhancer (P<0.05). After adjustment, those with refractory COVID-19 were also more likely to have a male sex and manifestations of anorexia and fever on admission, and receive oxygen, expectorant and adjunctive agents (P<0.05) when considering the factors of disease severity on admission, mechanical ventilation, and ICU transfer. CONCLUSION: Nearly 50% COVID-19 patients could not reach obvious clinical and radiological remission within 10 days after hospitalization. The patients with male sex, anorexia and no fever on admission predicted poor efficacy.


title: Evolving views on bovine respiratory disease: An appraisal of selected key pathogens – Part 1

text: Abstract Bovine respiratory disease (BRD) is one of the most commonly diagnosed causes of morbidity and mortality in cattle and interactions of factors associated with the animal, the pathogen and the environment are central to its pathogenesis. Emerging knowledge of a role for pathogens traditionally assumed to be minor players in the pathogenesis of BRD reflects an increasingly complex situation that will necessitate regular reappraisal of BRD pathogenesis and control. This review appraises the role of selected key pathogens implicated in BRD pathogenesis to assess how our understanding of their role has evolved in recent years.


title: The Creation of a Psychiatry-Palliative Care Liaison Team: Utilizing Psychiatrists to Extend Palliative Care Delivery and Access during the COVID-19 Crisis

text: CONTEXT: Over the course of March and April 2020, New York City experienced a surge of a hundred and seventy thousand COVID-19 cases, overwhelming hospital systems and leading to an unprecedented need for palliative care services. OBJECTIVES: To present a model for rapid palliative care workforce expansion under crisis conditions, utilizing supervised advanced psychiatry trainees to provide primary palliative services in the acute care and emergency setting. METHODS: In response to the New York City COVID-19 surge, advanced psychiatry trainees at New York-Presbyterian Columbia University Irving Medical Center were rapidly trained and redeployed to a newly formed psychiatry-palliative care liaison team. Under the supervision of consultation-liaison psychiatrists (who also served as team coordinators), these trainees provided circumscribed palliative care services to patients and/or their families, including goals of care discussions and psychosocial support. Palliative care attendings remained available to all team members for more advanced, specialized supervision. RESULTS: The psychiatry-palliative care liaison team effectively provided palliative care services during the early phase and peak of New York City’s COVID-19 crisis, managing up to 16 new cases per day and provided longitudinal follow-up, thereby enabling palliative care specialists to focus on providing services requiring specialist-level palliative care expertise. CONCLUSION: By training and supervising psychiatrists and advanced psychiatry trainees in specific palliative care roles, palliative care teams could more effectively meet markedly increased service needs of varying complexity during the COVID-19 crisis. As new geographic regions experience possible COVID-19 surges in the coming months, this may serve as a model for rapidly increasing palliative care workforce.


title: Turkey industry strategies for control of respiratory and enteric diseases

text: Abstract Current strategies to control respiratory and enteric diseases of turkeys involve sanitation and biosecurity practices to prevent the introduction of infectious agents. In addition, proper husbandry and management practice reduce stress and help maintain a competent immune system. Industry-wide monitoring programs are used in conjunction with isolation, depopulation, and orderly marketing to eliminate pathogens that cause serious economic loss. Vaccines are available and utilized against some pathogens. Effective drug treatment is available and used for some diseases but is most commonly used to control secondary disease losses when treatment is not available for the primary disease.


COVID‐19 Preparedness in Nursing Homes in the Midst of the Pandemic


title: Long-term use of yeast fermentation products in comparison to halofuginone for the control of cryptosporidiosis in neonatal calves

text: Abstract The objective of this study was to compare the effect of non-GMO Saccharomyces cerevisiae fermentation products (SCFP) with that of a halofuginone treatment against Cryptosporidium parvum infection in pre-weaned calves on a commercial dairy farm. A total of 123 neonatal female calves, housed in individual hutches, were enrolled sequentially based on date of birth in 41 blocks of 3 animals each. Calves within each block were allocated to one of 3 treatments: remaining untreated, fed with SCFP (Diamond V SmartCare® at 1 g/d in milk and NutriTek® at 5 g/d in starter grain) for the first 63 days of life, or treated with halofuginone (0.1 mg/kg/d) for the first 7 days of life. Fecal samples collected on days 4–21 post-partum were examined for both Cryptosporidium oocysts and coproantigen. The presence and intensity of diarrhea were monitored by scoring daily for the first 4 weeks of life. Calves were weighed at 0, 21, 42 and 63 days of age. Almost all calves were Cryptosporidium-positive at least once during the study. Halofuginone significantly reduced the number of Cryptosporidium-positive fecal samples as compared to the two other groups. Based on the coproantigen scores, both halofuginone and SCFP feeding significantly reduced the intensity of Cryptosporidium infection as compared to the untreated group. Diarrhea was recorded in almost all calves at least once. Neither the proportion of diarrheic calves nor the intensity and duration of diarrhea differed among the 3 treatment groups significantly. The mean daily weight gain during the first 3 weeks of life was significantly lower in halofuginone treated calves than in both other groups; however, at the end of the study period the total weight gain did not significantly differ among the 3 treatment groups. In conclusion, the clinical results and weight gains of pre-weaning supplementation with the SCFP were neither better nor worse than the 7-day halofuginone treatment suggesting that the SCFP feeding may be from the clinical point of view a natural alternative measure, instead of halofuginone treatment, in bovine cryptosporidiosis.


title: The Restructuring of Structural Heart Disease Practice During The Covid-19 Pandemic

text: Abstract Patients with structural heart disease (SHD) are at increased risk of adverse outcomes from the coronavirus disease 19 (COVID-19) due to advanced age and comorbidity. In the midst of a global pandemic of a novel infectious disease, reality-based considerations comprise an important starting point for formulating clinical management pathways. The aim of these “crisis-driven” recommendations is (1) to ensure appropriate and timely treatment of SHD patients, (2) to minimize the risk of COVID-19 exposure to patients and healthcare workers, and (3) to limit resource utilization under conditions of constraint. While the degree of disruption to usual practice will vary across the United States and elsewhere, we hope that early experiences from a Heart Team operating in the current global epicenter of COVID-19 may prove useful for others adapting their practice in advance of local surges of COVID-19.


docid: bitofnje

title: Assessing the application of a pseudovirus system for emerging SARS-CoV-2 and re-emerging avian influenza virus H5 subtypes in vaccine development

text: Highly pathogenic emerging and re-emerging viruses continuously threaten lives worldwide. In order to provide prophylactic prevention from the emerging and re-emerging viruses, vaccine is suggested as the most efficient way to prevent individuals from the threat of viral infection. Nonetheless, the highly pathogenic viruses need to be handled in a high level of biosafety containment, which hinders vaccine development. To shorten the timeframe of vaccine development, the pseudovirus system has been widely applied to examine vaccine efficacy or immunogenicity in the emerging and re-emerging viruses. Here we developed pseudovirus systems for emerging SARS coronavirus 2 (SARS-CoV-2) and re-emerging avian influenza virus H5 subtypes which can be handled in the biosafety level 2 facility. Through the generated pseudovirus of SARS-CoV-2 and avian influenza virus H5 subtypes, we successfully established a neutralization assay to quantify the neutralizing activity of antisera against the viruses. In addition, the result of re-emerging avian influenza virus H5Nx pseudoviruses provided valuable information for antigenic evolution and immunogenicity analysis in vaccine candidate selection. Together, our study assessed the potency of pseudovirus systems in vaccine efficacy, antigenic analysis, and immunogenicity in the vaccine development of emerging and re-emerging viruses. Instead of handling live highly pathogenic viruses in a high biosafety level facility, using pseudovirus systems would speed up the process of vaccine development to provide community protection against emerging and re-emerging viral diseases with high pathogenicity.


title: Ebola Virus Disease in Humans: Pathophysiology and Immunity

text: Viruses of the Ebolavirus genus cause sporadic epidemics of severe and systemic febrile disease that are fueled by human-to-human transmission. Despite the notoriety of ebolaviruses, particularly Ebola virus (EBOV), as prominent viral hemorrhagic fever agents, and the international concern regarding Ebola virus disease (EVD) outbreaks, very little is known about the pathophysiology of EVD in humans and, in particular, about the human immune correlates of survival and immune memory. This lack of basic knowledge about physiological characteristics of EVD is probably attributable to the dearth of clinical and laboratory data gathered from past outbreaks. The unprecedented magnitude of the EVD epidemic that occurred in West Africa from 2013 to 2016 has allowed, for the first time, evaluation of clinical, epidemiological, and immunological parameters in a significant number of patients using state-of-the-art laboratory equipment. This review will summarize the data from the literature regarding human pathophysiologic and immunologic responses to filoviral infection.


docid: tkyngspy

title: Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

text: Abstract The new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted “CellPhoneDB” analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.


title: Epidemiological Aspects and Psychological Reactions to COVID-19 of Dental Practitioners in the Northern Italy Districts of Modena and Reggio Emilia

text: The outbreak and diffusion of the Severe Acute Respiratory Syndrome-Coronavirus-2 (Sars-CoV-2) and COronaVIrus Disease 19 (COVID-19) have caused an emergency status in the health system, including in the dentistry environment. Italy registered the third highest number of COVID-19 cases in the world and the second highest in Europe. An anonymous online survey composed of 40 questions has been sent to dentists practicing in the area of Modena and Reggio Emilia, one of the areas in Italy most affected by COVID-19. The survey was aimed at highlighting the practical and emotional consequences of COVID-19 emergence on daily clinical practice. Specifically, it assessed dentists’ behavioral responses, emotions and concerns following the Sars-CoV-2 pandemic restrictive measures introduced by the Italian national administrative order of 10 March 2020 (DM-10M20), as well as the dentists’ perception of infection likelihood for themselves and patients. Furthermore, the psychological impact of COVID-19 was assessed by means of the Generalized Anxiety Disorder-7 test (GAD-7), that measures the presence and severity of anxiety symptoms. Using local dental associations (ANDI-Associazione Nazionale Dentisti Italiani, CAO-Commissione Albo Odontoiatri) lists, the survey was sent by email to all dentists in the district of Modena and Reggio Emilia (874 practitioners) and was completed by 356 of them (40%). All dental practitioners closed or reduced their activity to urgent procedures, 38.2% prior to and 61.8% after the DM-10M20. All reported a routinely use of the most common protective personal equipment (PPE), but also admitted that the use of PPE had to be modified during COVID-19 pandemic. A high percentage of patients canceled their previous appointments after the DM-10M20. Almost 85% of the dentists reported being worried of contracting the infection during clinical activity. The results of the GAD-7 (General Anxiety Disorder-7) evaluation showed that 9% of respondents reported a severe anxiety. To conclude, the COVID-19 emergency is having a highly negative impact on the activity of dentists practicing in the area of Modena and Reggio Emilia. All respondents reported practice closure or strong activity reduction. The perception of this negative impact was accompanied by feelings of concern (70.2%), anxiety (46.4%) and fear (42.4%). The majority of them (89.6%) reported concerns about their professional future and the hope for economic measures to help dental practitioners.


title: Mechanisms of viral impact on asthma exacerbations

text: Abstract Rationale Respiratory viruses are a frequent cause of wheezing in infants and children. 60 - 85% of asthma exacerbations in children and up to 50% of asthma exacerbations in adults are attributed to respiratory viruses. Previous studies investigated the role of rhinoviruses, RS-viruses and adenoviruses in development of asthma exacerbations in children hospitalized in the clinic of the Institute of Immunology (Moscow, Russia). Rhinovirus was the most frequently detected – 33 samples (24.8% of all tested samples), adenovirus – 5 samples (3.8%), RSV– 4 samples (3.0%), and mixed infections (rhinovirus and RSV) – 1 sample (0.7%). Among positive samples rhinovirus accounted for 76.7%, adenovirus - 11.6%, RSV - 9.3%, and mixed infection - 2.3%. Methods Primers for PCR diagnostics of Parainfluenza viruses of 1, 2 and 3 type and coronaviruses OC43 and 229E were developed. Investigation of HLA-alleles and genotypes was conducted in patients with virus-induced bronchial asthma to reveal HLA-associated markers of susceptibility to viral-induced asthma. Results An increased frequency of HLA-DRB1∗13 specificity and reduced frequencies of HLA-DRB1∗04 and HLA-DRB1∗11 specificities were noted in the viral-induced asthmatics compared to the healthy control group. A minimal increase of HLA-DRB1 homozygotes - 21% was also noted in comparison with the control group - 14%. Conclusions Investigation of HLA-haplotype in patients with viral-induced outbreaks of asthma via HLA-genotyping may reveal more evident associations between HLA-haplotypes and individual respiratory viral infections.


Plasma therapies and parabiosis in the COVID-19 era


title: Evaluation of swine enteroids as in vitro models for Lawsonia intracellularis infection(,)

text: The enteric pathogen Lawsonia intracellularis is one of the main causes of diarrhea and compromised weight gain in pigs worldwide. Traditional cell-line cultures have been used to study L. intracellularis pathogenesis. However, these systems fail to reproduce the epithelial changes observed in the intestines of L. intracellularis-infected pigs, specifically, the changes in intestinal cell constitution and gene expression. A more physiologically accurate and state-of-the-art model is provided by swine enteroids derived from stem cell-containing crypts from healthy pigs. The objective of this study was to verify the feasibility of two-dimensional swine enteroids as in vitro models for L. intracellularis infection. We established both three- and two-dimensional swine enteroid cultures derived from intestinal crypts. The two-dimensional swine enteroids were infected by L. intracellularis in four independent experiments. Enteroid-infected samples were collected 3 and 7 d postinfection for analysis using real-time quantitative PCR and L. intracellularis immunohistochemistry. In this study, we show that L. intracellularis is capable of infecting and replicating intracellularly in two-dimensional swine enteroids derived from ileum.


title: Delivering urgent urological surgery during the COVID‐19 pandemic in the United Kingdom: Outcomes from our initial 52 patients.

text: Since first reported in December 2019, the novel RNA betacoronavirus disease (COVID‐19) has spread rapidly across the world with, as of the 3rd May 2020, 3.3 million confirmed cases with more than 230,000 deaths worldwide and more than 200 countries affected. The most common symptoms reported include dry cough, fever and fatigue with ground‐glass opacification bilaterally in the lungs on imaging and lymphopenia on haematological analysis. In severe cases the patients can develop acute respiratory distress syndrome (ARDS) or multi organ failure which can lead to death. Transmission of the virus (SARS‐CoV‐2) is via direct contact or via droplets spread by a cough or sneeze from an infected individual. The difficulty in disease detection and containment has been the long course of COVID‐19. Current evidence shows an incubation period of up to 14 days post exposure to the virus, and on average most patients first display symptoms on day five after initial exposure. More importantly, carriers are contagious even during this preceding asymptomatic incubation phase of the disease.


title: Bivalirudin for Maintenance Anticoagulation During Veno-Venous Extracorporeal Membrane Oxygenation for COVID-19

text: In its severe manifestation, COVID-19 compromises oxygenation in a manner that is refractory to maximal conventional support and requires escalation to extracorporeal membrane oxygenation (ECMO). Maintaining ECMO support for extended durations requires a delicately balanced anticoagulation strategy to maintain circuit viability by preventing thrombus deposition, while avoiding excessive anticoagulation yielding hemorrhage; a task that is complicated in COVID-19 secondary to an inherent hypercoagulable state. Bivalirudin, a member of the direct thrombin inhibitor drug class, offers potential advantages during ECMO including to its ability to exert its effect by directly attaching to and inhibiting freely circulating and fibrin-bound thrombin. Herein, we report the successful use of an anticoagulation strategy employing the off-label use of a continuous infusion of bivalirudin in a case of severe hypoxemic and hypercarbic respiratory failure caused by COVID-19 requiring VV-ECMO. Importantly, therapeutic anticoagulation intensity was rapidly achieved with stable pharmacokinetics and there was no need for any circuit interventions throughout the patient's 27 day ECMO course. In COVID-19, bivalirudin offers a potential option for maintaining systemic anticoagulation during ECMO in a manner that may mitigate the pro-thrombotic nature of the underlying pathophysiologic state.


title: Azaphenantherene derivatives as inhibitor of SARS CoV-2 Mpro: Synthesis, Physicochemical, Quantum chemical and Molecular docking analysis

text: Abstract The crystal structure of 2-(1H-indol-3-yl)-4-phenyl-5,6-dihydrobenzo[h]quinoline-3-carbonitrile (Ia) and 2-(5-bromo-1H-indol-3-yl)-4-(4-methoxyphenyl)-5,6-dihydrobenzo[h]quinoline-3-carbonitrile (Ib) were elucidated using single crystal X-ray diffraction. The cyclohexadiene ring adopts screw boat conformation in compound (Ia) and distorted screw boat in compound (Ib). The pyridine ring is effectively planar. The qualitative and quantitative analyses of hydrogen bonding interactions in the compounds were done using Hirshfeld surface analysis, QTAIM and NCI. DFT/B3LYP level of theory was used to optimize both the compounds. These compounds drug-like behaviors were studied using HOMO-LUMO analysis. The molecular docking analysis against Mpro was carried out for the synthesized compounds and some suggested drugs for COVID-19. The docking results were then analyzed.


title: A novel algorithm to define infection tendencies in H1N1 cases in Mainland China

text: Abstract Incidences of H1N1 viral infections in Mainland China are collected by the Ministry of Health, the People's Republic of China. The number of confirmed cases and the timing of these outbreaks from May 13 to July 22, 2009 were obtained and subjected to a novel mathematical model to simulate the infection profile (time vs number). The model was predicated upon the grey prediction theory which allows assignment of future trends using limited numbers of data points. During the period of our analysis, the number of confirmed H1N1 cases in Mainland China increased from 1 to 1772. The efficiency of our model to simulate these data points was evaluated using Sum of squares of error (SSE), Relative standard error (RSE), Mean absolute deviation (MAD) and Average relative error (ARE). Results from these analyses were compared to similar calculations based upon the grey prediction algorithm. Using our equation, defined herein as equation D–R, results showed that SSE=6742.00, RSE=10.69, MAD=7.07, ARE=2.47% were all consistent with the D–R algorithm performing well in the estimation of future trends of H1N1 cases in Mainland China. Calculations using the grey theory had no predictive value [ARE for GM(1,1)=−104.63%]. To validate this algorithm, we performed a second analysis using new data obtained from cases reported to the WHO and CDC in the US between April 26 and June 8, 2009. In like manner, the model was equally predictive. The success of the D–R mathematical model suggests that it may have broader application to other viral infections among the human population in China and may be modified for application to other regions of the world.


title: Identification of a novel B-cell epitope in the spike protein of porcine epidemic diarrhea virus

text: BACKGROUND: Porcine epidemic diarrhea virus (PEDV) infection causes an acute enteric tract infectious disease characterized by vomiting, anorexia, dehydration, weight loss and high mortality in neonatal piglets. During PEDV infection, the spike protein (S) is a major virion structural protein interacting with receptors and inducing neutralizing antibodies. However, the neutralizing B-cell epitopes within PEDV S protein have not been well studied. METHODS: To accurately identify the important immunodominant region of S1, the purified truncated S1 proteins (SA, SB, SC, SD and SE) were used to immunize BALB/c mice to prepare polyclonal antibodies. The antisera titers were determined by indirect ELISA, western blot and IFA after four immunizations to find the important immunodominant region of S1, and then purified the immunodominant region of S1 protein and immunized mice to generate the special antibodies, and then used recombinant peptides to determine the B-cell epitopes of monoclonal antibodies. RESULTS: Five antisera of recombinant proteins of the spike protein region of PEDV were generated and we found that only the polyclonal antibody against part of the S1 region (signed as SE protein, residues 666–789) could recognize the native PEDV. Purified SE protein was used to immunize BALB/c mice and generate mAb 2E10. Pepscan of the SE protein demonstrated that SE16 ((722)SSTFNSTREL(731)) is the minimal linear epitope required for reactivity with the mAb 2E10. Further investigation indicated that the epitope SE16 was localized on the surface of PEDV S protein in the 3D structure. CONCLUSIONS: A mAb 2E10 that is specifically bound to PEDV was generated and identified a specific linear B-cell epitope (SE16, (722)SSTFNSTREL(731)) of the mAb. The epitope region of PEDV S1 localized in the different regions in comparison with the earlier identified epitopes. These findings enhance the understanding of the PEDV spike protein structure for vaccine design and provide a potential use for developing diagnostic methods to detect PEDV.


title: Development of an SPE–HPLC–MS method for simultaneous determination and pharmacokinetic study of bioactive constituents of Yu Ping Feng San in rat plasma after oral administration

text: Abstract Ethnopharmacological relevance Yu Ping Feng San (YPFS, in Chinese: Jade Windscreen Powder), a well-known traditional Chinese medicine, is commonly used to cure the diseases of respiratory systems and immune systems. Aim of the study A selective and sensitive high-performance liquid chromatography coupled with mass spectrometry method (HPLC–MS) was developed and validated for simultaneous quantification of cycloastragenol, formononetin, calycosin, 4′-O-β-glucopyranosyl-5-O-methylvisamminol (GMV) and cimifugin in rat plasma after oral administration of Yu Ping Feng San decoction. Materials and methods Plasma samples were extracted via solid-phase extraction (SPE), separated on a Zorbax SB-C18 column, detected by single quadruple mass spectrometry with an electrospray ionization interface, and quantified using selected ion monitoring mode. The current SPE–HPLC–MS assay was validated for linearity, intra-day and inter-day precisions, accuracy, extraction recovery and stability. The method was applied to a comparative pharmacokinetic study after administration of Yu Ping Feng San to rats at different doses (10, 20 and 40g/kg). Results The calibration curves were linear over the ranges 0.50–50ng/mL and 17.36–1736ng/mL. Intra- and inter-day precisions (relative standard deviations) were from 0.45% to 10.95%, and accuracy (relative recovery) from 95% to 115%. The extraction recoveries were greater than 88.42% for all analytes. Dose-dependence was shown for some constituents in the drug concentration–time profiles. Among all the active ingredients detected, cimifugin had the highest blood concentration (881–1510ng/mL), and cycloastragenol had the longest retention time in the rat body (15.06–20.44h). Conclusion This analytical method is a selective, sensitive, precise, accurate, and reliable assay for simultaneous determination of cycloastragenol, calycosin, formononetin, GMV, and cimifugin in rat plasma.


title: Telmisartan as tentative angiotensin receptor blocker therapeutic for COVID‐19

text: In late 2019, a new coronavirus emerged in Wuhan Province, China, causing lung complications similar to those produced by the SARS coronavirus in the 2002–2003 epidemic. This new disease was named COVID‐19 and the causative virus SARS‐CoV‐2. The SARS‐CoV‐2 virus enters the airway and binds, by means of the S protein on its surface to the membrane protein ACE2 in type 2 alveolar cells. The S protein‐ACE2 complex is internalized by endocytosis leading to a partial decrease or total loss of the enzymatic function ACE2 in the alveolar cells and in turn increasing the tissue concentration of pro‐inflammatory angiotensin II by decreasing its degradation and reducing the concentration of its physiological antagonist angiotensin 1–7. High levels of angiotensin II on the lung interstitium can promote apoptosis initiating an inflammatory process with release of proinflammatory cytokines, establishing a self‐powered cascade, leading eventually to ARDS. Recently, Gurwitz proposed the tentative use of agents such as losartan and telmisartan as alternative options for treating COVID‐19 patients prior to development of ARDS. In this commentary article, the authors make the case for the election of telmisartan as such alternative on the basis of its pharmacokinetic and pharmacodynamic properties and present an open‐label randomized phase II clinical trial for the evaluation of telmisartan in COVID‐19 patients (https://www.clinicaltrials.gov/ct2/show/NCT04355936).


title: Competing Crises: COVID‐19 Countermeasures and Social Isolation among Older Adults in Long Term Care

text: While debate over the appropriate scope and goals of COVID‐19 lockdowns has raged, all public health agencies have been clear on one matter: older adults have the highest rates of mortality (Comas‐Herrera et al., 2020) and should be isolated (Public Health Agency of Canada, 2020). Older adults and individuals with complex health conditions are most vulnerable to the virus. Yet, social isolation contributes to the onset and intensifies depression, feelings of despair and, in older adults with dementia, further cognitive decline.


title: Expression of antisense RNA fails to inhibit influenza virus replication

text: Abstract Cell lines were constructed which permanently express influenza virus-specific RNA. Two approaches were followed. C127 cells were transformed with bovine papilloma virus (BPV) vectors and the resulting cell lines were found to inhibit the replication of influenza virus at low multiplicity of infection (MOI 0.05). However, examination of cellular RNA using single-stranded probes revealed the presence of both ( + )sense and antisense RNA transcripts (45–70 copies per cell). In this BPV-based system the inhibitory activity appeared to be associated with a nonspecific, interferon (IFN)-mediated effect. In the second approach, an expression system was used which involved 293 cells, a chimeric human cytomegalovirus (CMV)/human immunodeficiency virus (HIV) promoter, and methotrexate- (Mtx)-mediated gene amplification. Cells were found to express up to 7500 copies of influenza virus-specific RNA per cell at a steady state level. In this system no RNA transcripts of the opposite orientation were found. However, all cell lines permanently expressing either (−)sense or ( + )sense viral RNA failed to reduce influenza virus titers in a multi-cycle replication experiment (MOI 0.01).


title: Utilization management in microbiology

text: Abstract The available literature concerning utilization management in the clinical microbiology laboratory is relatively limited compared with that for high-volume, automated testing in the central Core Laboratory. However, the same strategies employed elsewhere in the clinical laboratory operation can be applied to utilization management challenges in microbiology, including decision support systems, application of evidence-based medicine, screening algorithms and gatekeeper functions. The results of testing in the microbiology laboratory have significant effects on the cost of clinical care, especially costs related to antimicrobial agents and infection control practices. Consequently many of the successful utilization management interventions described in clinical microbiology have targeted not just the volume of tests performed in the laboratory, but also the downstream costs of care. This article will review utilization management strategies in clinical microbiology, including specific examples from our institution and other healthcare organizations.


title: Additive Effects of Mechanical Marrow Ablation and PTH Treatment on de Novo Bone Formation in Mature Adult Rats

text: Mechanical ablation of bone marrow in young rats induces rapid but transient bone growth, which can be enhanced and maintained for three weeks by the administration of parathyroid hormone (PTH). Additionally, marrow ablation, followed by PTH treatment for three months leads to increased cortical thickness. In this study, we sought to determine whether PTH enhances bone formation after marrow ablation in aged rats. Aged rats underwent unilateral femoral marrow ablation and treatment with PTH or vehicle for four weeks. Both femurs from each rat were analyzed by X-ray and pQCT, then analyzed either by microCT, histology or biomechanical testing. Marrow ablation alone induced transient bone formation of low abundance that persisted over four weeks, while marrow ablation followed by PTH induced bone formation of high abundance that also persisted over four weeks. Our data confirms that the osteo-inducive effect of marrow ablation and the additive effect of marrow ablation, followed by PTH, occurs in aged rats. Our observations open new avenues of investigations in the field of tissue regeneration. Local marrow ablation, in conjunction with an anabolic agent, might provide a new platform for rapid site-directed bone growth in areas of high bone loss, such as in the hip and wrist, which are subject to fracture.


title: Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines

text: To trace the possible route of introduction of porcine epidemic diarrhea virus (PEDV), the phylogenetic relationships of PEDV strains in the regions of epidemicity in the Philippines to PEDV strains that are endemic in other countries were investigated. Partial nucleotide sequences of the S1 spike gene was determined from the PEDV-positive samples and compared with S1 sequences from other countries. Phylogenetic analysis indicated that PEDV strains in the Philippines segregate into two groups. Members of group 1 are related to strains from the USA, Taiwan, Japan and Canada, while those in group 2 are related to strains from China and Vietnam.


title: Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

text: The human respiratory tract is constantly exposed to a wide variety of viruses, microbes and inorganic particulates from environmental air, water and food. Physical characteristics of inhaled particles and airway mucosal immunity determine which viruses and microbes will persist in the airways. Here we present the first metagenomic study of DNA viral communities in the airways of diseased and non-diseased individuals. We obtained sequences from sputum DNA viral communities in 5 individuals with cystic fibrosis (CF) and 5 individuals without the disease. Overall, diversity of viruses in the airways was low, with an average richness of 175 distinct viral genotypes. The majority of viral diversity was uncharacterized. CF phage communities were highly similar to each other, whereas Non-CF individuals had more distinct phage communities, which may reflect organisms in inhaled air. CF eukaryotic viral communities were dominated by a few viruses, including human herpesviruses and retroviruses. Functional metagenomics showed that all Non-CF viromes were similar, and that CF viromes were enriched in aromatic amino acid metabolism. The CF metagenomes occupied two different metabolic states, probably reflecting different disease states. There was one outlying CF virome which was characterized by an over-representation of Guanosine-5′-triphosphate,3′-diphosphate pyrophosphatase, an enzyme involved in the bacterial stringent response. Unique environments like the CF airway can drive functional adaptations, leading to shifts in metabolic profiles. These results have important clinical implications for CF, indicating that therapeutic measures may be more effective if used to change the respiratory environment, as opposed to shifting the taxonomic composition of resident microbiota.


Management of gynecologic cancer: choosing radiotherapy wisely by 3 Southern Ontario academic centers during the COVID-19 pandemic


title: Virus assembly, allostery, and antivirals

text: Assembly of virus capsids and surface proteins must be regulated to ensure that the resulting complex is an infectious virion. Here we examine assembly of virus capsids, focusing on hepatitis B virus and bacteriophage MS2, and formation of glycoproteins in the alphaviruses. These systems are structurally and biochemically well-characterized and are simplest-case paradigms of self-assembly. Published data suggest that capsid and glycoprotein assembly is subject to allosteric regulation, that is, regulation at the level of conformational change. The hypothesis that allostery is a common theme in viruses suggests that deregulation of capsid and glycoprotein assembly by small molecule effectors will be an attractive antiviral strategy, as has been demonstrated with hepatitis B virus.


Perceptions on COVID19: A ground-level analysis to guide public policy


Heart failure related hospitalisation and management during COVID‐19 pandemic: are we ready to reflect?


title: Genomic Motifs as a Novel Indicator of the Relationship between Strains Isolated from the Epidemic of Porcine Epidemic Diarrhea in 2013-2014

text: Porcine epidemic diarrhea virus (PEDV) is a positive-sense RNA virus that causes infectious gastroenteritis in pigs. Following a PED outbreak that occurred in China in 2010, the disease was identified for the first time in the United States in April 2013, and was reported in many other countries worldwide from 2013 to 2014. As a novel approach to elucidate the epidemiological relationship between PEDV strains, we explored their genome sequences to identify the motifs that were shared within related strains. Of PED outbreaks reported in many countries during 2013–2014, 119 PEDV strains in Japan, USA, Canada, Mexico, Germany, and Korea were selected and used in this study. We developed a motif mining program, which aimed to identify a specific region of the genome that was exclusively shared by a group of PEDV strains. Eight motifs were identified (M1–M8) and they were observed in 41, 9, 18, 6, 10, 14, 2, and 2 strains, respectively. Motifs M1–M6 were shared by strains from more than two countries, and seemed to originate from one PEDV strain, Indiana12.83/USA/2013, among the 119 strains studied. BLAST search for motifs M1–M6 revealed that M3–M5 were almost identical to the strain ZMDZY identified in 2011 in China, while M1 and M2 were similar to other Chinese strains isolated in 2011–2012. Consequently, the PED outbreaks in these six countries may be closely related, and multiple transmissions of PEDV strains between these countries may have occurred during 2013–2014. Although tools such as phylogenetic tree analysis with whole genome sequences are increasingly applied to reveal the connection between isolates, its interpretation is sometimes inconclusive. Application of motifs as a tool to examine the whole genome sequences of causative agents will be more objective and will be an explicit indicator of their relationship.


docid: vmsdhccp

title: Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults


title: A Longitudinal Study on the Mental Health of General Population during the COVID-19 Epidemic in China

text: Abstract In addition to being a public physical health emergency, Coronavirus disease 2019 (COVID-19) affected global mental health, as evidenced by panic-buying worldwide as cases soared. Little is known about changes in levels of psychological impact, stress, anxiety and depression during this pandemic. This longitudinal study surveyed the general population twice - during the initial outbreak, and the epidemic's peak four weeks later, surveying demographics, symptoms, knowledge, concerns, and precautionary measures against COVID-19. There were 1738 respondents from 190 Chinese cities (1210 first-survey respondents, 861 second-survey respondents; 333 respondents participated in both). Psychological impact and mental health status were assessed by the Impact of Event Scale-Revised (IES-R) and the Depression, Anxiety and Stress Scale (DASS-21), respectively. IES-R measures PTSD symptoms in survivorship after an event. DASS -21 is based on tripartite model of psychopathology that comprise a general distress construct with distinct characteristics. This study found that there was a statistically significant longitudinal reduction in mean IES-R scores (from 32.98 to 30.76, p<0.01) after 4 weeks. Nevertheless, the mean IES-R score of the first- and second-survey respondents were above the cut-off scores (>24) for PTSD symptoms, suggesting that the reduction in scores was not clinically significant. During the initial evaluation, moderate-to-severe stress, anxiety and depression were noted in 8.1%, 28.8% and 16.5%, respectively and there were no significant longitudinal changes in stress, anxiety and depression levels (p>0.05). Protective factors included high level of confidence in doctors, perceived survival likelihood and low risk of contracting COVID-19, satisfaction with health information, personal precautionary measures. As countries around the world brace for an escalation in cases, Governments should focus on effective methods of disseminating unbiased COVID-19 knowledge, teaching correct containment methods, ensuring availability of essential services/commodities, and providing sufficient financial support.


title: Does COVID‐19 really call for an overhaul of nursing curricula or promoting the power, status and representation of nursing?

text: The COVID‐19 pandemic has presented us with many well documented challenges as well as causing death, disability and economic devastation. All around the globe people were caught unprepared for the pandemic despite the warnings of public health experts. Many of these warnings were not considered serious and moves towards nationalism and populism have challenged global collaboration.


title: Impacts of SARS on health-seeking behaviors in general population in Hong Kong

text: Abstract Background. The severe acute respiratory syndrome (SARS) epidemic that occurred in Hong Kong in 2003 caused serious public health consequences. Its impacts on health-seeking behaviors of the general public have not been assessed. Methods. Two cross-sectional, random telephone surveys interviewed 1603 Hong Kong adult residents in the post-SARS epidemic period, June and September 2003 to investigate changes in the post-SARS period. Results. Noteworthy percentages of the respondents self-reported increased frequencies of practicing favorable health-seeking behaviors in June 2003, as compared with the pre-SARS period. Few respondents reported the opposite. This was observed in different dimensions: health services seeking, adoption of healthier lifestyle, spending more resources on health, adoption of good personal hygiene, mask use when ill with influenza, and avoidance of risk behaviors. The frequencies of practicing most of these health-seeking behaviors, as measured in June and September 2003, were comparable. Further increases in healthy diet and weight control, etc., were observed during that period. Those who worried about contracting SARS were more likely to have improved health-seeking behaviors. Conclusions. The community in Hong Kong responded to the SARS epidemic by practicing more favorable health-seeking behaviors. Public health workers should utilize these opportunities to foster favorable changes.


title: Single-cell Analysis of ACE2 Expression in Human Kidneys and Bladders Reveals a Potential Route of 2019-nCoV Infection

text: Since December 2019, a novel coronavirus named 2019 coronavirus (2019-nCoV) has emerged in Wuhan of China and spread to several countries worldwide within just one month. Apart from fever and respiratory complications, acute kidney injury has been observed in some patients with 2019-nCoV. In a short period of time, angiotensin converting enzyme II (ACE2), have been proposed to serve as the receptor for the entry of 2019-nCoV, which is the same for severe acute respiratory syndrome coronavirus (SARS). To investigate the possible cause of kidney damage in 2019-nCoV patients, we used both published kidney and bladder cell atlas data and an independent unpublished kidney single cell RNA-Seq data generated in-house to evaluate ACE2 gene expressions in all cell types in healthy kidneys and bladders. Our results showed the enriched expression of all subtypes of proximal tubule cells of kidney and low but detectable levels of expression in bladder epithelial cells. These results indicated the urinary system is a potential route for 2019-nCoV infection, along with the respiratory system and digestion system. Our findings suggested the kidney abnormalities of SARS and 2019-nCoV patients may be due to proximal tubule cells damage and subsequent systematic inflammatory response induced kidney injury. Beyond that, laboratory tests of viruses and related indicators in urine may be needed in some special patients of 2019-nCoV.


title: Genomics and outbreak investigation: from sequence to consequence

text: Outbreaks of infection can be devastating for individuals and societies. In this review, we examine the applications of new high-throughput sequencing approaches to the identification and characterization of outbreaks, focusing on the application of whole-genome sequencing (WGS) to outbreaks of bacterial infection. We describe traditional epidemiological analysis and show how WGS can be informative at multiple steps in outbreak investigation, as evidenced by many recent studies. We conclude that high-throughput sequencing approaches can make a significant contribution to the investigation of outbreaks of bacterial infection and that the integration of WGS with epidemiological investigation, diagnostic assays and antimicrobial susceptibility testing will precipitate radical changes in clinical microbiology and infectious disease epidemiology in the near future. However, several challenges remain before WGS can be routinely used in outbreak investigation and clinical practice.


title: Anticorps monoclonaux : tours et détours technologiques pour de nouveaux espoirs thérapeutiques

text: Abstract Engineering monoclonal antibodies, now widely used in the clinic, has made it possible to develop a new generation of antibodies with optimized functional properties. These antibodies should allow a significant improvement of the treatment of diseases where only few drugs are available, if any. However, the cost of treatments with monoclonal antibodies requires further improvements in production and purification technologies, and raises the question of generic antibodies. The present review summarizes some of the technological past and present challenges in the field. To cite this article: D. Bourel, J.-L. Teillaud, C. R. Biologies 329 (2006).


title: Implementing a negative-pressure isolation ward for a surge in airborne infectious patients

text: BACKGROUND: During a large-scale airborne infectious disease outbreak, the number of patients needing hospital-based health care services may exceed available negative-pressure isolation room capacity. METHODS: To test one method of increasing hospital surge capacity, a temporary negative-pressure isolation ward was established at a fully functioning hospital. Negative pressure was achieved in a 30-bed hospital ward by adjusting the ventilation system. Differential pressure was continuously measured at 22 locations, and ventilation airflow was characterized throughout the ward. RESULTS: The pressure on the test ward relative to the main hospital hallway was −29 Pa on average, approximately 10 times higher than the Centers for Disease Control and Prevention guidance for airborne infection control. No occurrences of pressure reversal occurred at the entrances to the ward, even when staff entered the ward. Pressures within the ward changed, with some rooms becoming neutrally or slightly positively pressurized. CONCLUSIONS: This study showed that establishing a temporary negative-pressure isolation ward is an effective method to increase surge capacity in a hospital.


title: Direct Sequencing of SARS-Coronavirus S and N Genes from Clinical Specimens Shows Limited Variation

text: Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged, in November 2002, as a novel agent causing severe respiratory illness. To study sequence variation in the SARS-CoV genome, we determined the nucleic acid sequence of the S and N genes directly from clinical specimens from 10 patients—1 specimen with no matched SARS-CoV isolate, from 2 patients; multiple specimens from 3 patients; and matched clinical-specimen/ cell-culture-isolate pairs from 6 patients. We identified 3 nucleotide substitutions that were most likely due to natural variation and 2 substitutions that arose after cell-culture passage of the virus. These data demonstrate the overall stability of the S and N genes of SARS-CoV over 3 months during which a minimum of 4 generations for transmission events occurred. These findings are a part of the expanding investigation of the evolution of how this virus adapts to a new host.


title: Genistein inhibits African swine fever virus replication in vitro by disrupting viral DNA synthesis

text: Abstract African swine fever virus (ASFV) is the causal agent of a highly-contagious and fatal disease of domestic pigs, leading to serious socio-economic consequences in affected countries. Once, neither an anti-viral drug nor an effective vaccines are available, studies on new anti-ASFV molecules are urgently need. Recently, it has been shown that ASFV type II topoisomerase (ASFV-topo II) is inhibited by several fluoroquinolones (bacterial DNA topoisomerase inhibitors), raising the idea that this viral enzyme can be a potential target for drug development against ASFV. Here, we report that genistein hampers ASFV infection at non-cytotoxic concentrations in Vero cells and porcine macrophages. Interestingly, the antiviral activity of this isoflavone, previously described as a topo II poison in eukaryotes, is maximal when it is added to cells at middle-phase of infection (8 hpi), disrupting viral DNA replication, blocking the transcription of late viral genes as well as the synthesis of late viral proteins, reducing viral progeny. Further, the single cell electrophoresis analysis revealed the presence of fragmented ASFV genomes in cells exposed to genistein, suggesting that this molecule also acts as an ASFV-topo II poison and not as a reversible inhibitor. No antiviral effects were detected when genistein was added before or at entry phase of ASFV infection. Molecular docking studies demonstrated that genistein may interact with four residues of the ATP-binding site of ASFV-topo II (Asn-144, Val-146, Gly-147 and Leu-148), showing more binding affinity (−4.62 kcal/mol) than ATP4− (−3.02 kcal/mol), emphasizing the idea that this viral enzyme has an essential role during viral genome replication and can be a good target for drug development against ASFV.


Molecular Interactions of Group 1 Coronaviruses with Feline APN


title: Angiotensin-Converting Enzyme 2 (ACE2) Is a Key Modulator of the Renin Angiotensin System in Health and Disease

text: Angiotensin-converting enzyme 2 (ACE2) shares some homology with angiotensin-converting enzyme (ACE) but is not inhibited by ACE inhibitors. The main role of ACE2 is the degradation of Ang II resulting in the formation of angiotensin 1–7 (Ang 1–7) which opposes the actions of Ang II. Increased Ang II levels are thought to upregulate ACE2 activity, and in ACE2 deficient mice Ang II levels are approximately double that of wild-type mice, whilst Ang 1–7 levels are almost undetectable. Thus, ACE2 plays a crucial role in the RAS because it opposes the actions of Ang II. Consequently, it has a beneficial role in many diseases such as hypertension, diabetes, and cardiovascular disease where its expression is decreased. Not surprisingly, current therapeutic strategies for ACE2 involve augmenting its expression using ACE2 adenoviruses, recombinant ACE2 or compounds in these diseases thereby affording some organ protection.


Grand Challenge in Human/Animal Virology: Unseen, Smallest Replicative Entities Shape the Whole Globe


docid: ffykwraw

title: Reproduction, growth, and development of rats during chronic exposure to multiple field strengths of 60-Hz electric fields

text: Abstract A study with multiple exposure groups and large group sizes was performed to establish whether exposure to 60-Hz electric fields would result in reproductive and developmental toxicity. A response model was developed from previous results and tested in groups of rats exposed to electric fields at various field strengths. Female rats were mated, and sperm-positive animals randomly distributed among four groups: sham-exposed or exposed to 10, 65, or 130 kV/m, 60-Hz vertical electric fields. Animals were exposed for 19 hr/day throughout the experiment. During gestation, exposure to the higher field strengths resulted in slightly depressed weight gains of dams. Offspring were born in the field and remained with their dams through the suckling period. Numbers of pups per litter and pup mortality did not differ among the exposure groups. Dams exposed at 65 kV/m lost slightly more weight through the lactation period than the control group. Male pups exposed to higher field strengths gained slightly less weight from 4 to 21 days of age than did sham-exposed animals. At weaning, two F1 females per litter (randomly selected) continued on the same exposure regimen were mated at 11 weeks of age to unexposed males, and euthanized at 20 days of gestation. Uterine contents were evaluated, and all liver fetuses were weighed and examined for external, visceral, and skeletal malformations. Fertility and gestational weight gain of F1 females were not affected by exposure, nor was prenatal viability or fetal body weight. No significant increase in the incidence of litters with malformations was observed. Although no developmental toxicity was detected, exposures produced physical changes in the dams, evidenced as a rust-colored deposit on the muzzle and ears (chromodacryorrhea) that increased in incidence and severity at 65 and 130 kV/m. Incidence of chromodacryorrhea was not significantly different between sham-exposed rats and those exposed at 10 kV/m.


Wear N95 Mask With Plastic Handle Reduce Pressure Injury


title: Microbiological findings in bronchoalveolar lavage fluid from lung transplant patients in Sweden

text: BACKGROUND: Lung transplant patients experience a high risk of airway infections and microbial colonization of the lung due to constant exposure to the environment through inhaled microorganisms, denervation, reduced ciliary transport, and decreased cough. METHODS: In this nationwide prospective study on Swedish lung transplant patients, we evaluated the microbiological panorama of bacteria, fungi, and virus found in bronchoalveolar lavage fluid (BALF) obtained the first year after lung transplantation (LTx). Differences in microbiological findings depending of concomitant signs of infection and background factors were assessed. RESULTS: A total of 470 bronchoscopies from 126 patients were evaluated. Sixty‐two percent (n = 293) of BALF samples had positive microbiological finding(s). Forty‐six percent (n = 217) had bacterial growth, 29% (n = 137) fungal growth, and 9% (n = 43) were positive in viral PCR. In 38% of BALF samples (n = 181), a single microbe was found, whereas a combination of bacteria, fungi or virus was found in 24% (n = 112) of bronchoscopies. The most common microbiological findings were Candida albicans, Pseudomonas aeruginosa and coagulase negative Staphylococcus (in 42 (33%), 36 (29%), and 25 (20%) patients, respectively). Microbiological findings were similar in BALF from patients with and without signs of lung infection and the frequency of multidrug resistant (MDR) bacteria was low. No significant association was found between background factors and time to first lung infection. CONCLUSION: This study gives important epidemiologic insights and reinforces that microbiological findings have to be evaluated in the light of clinical symptoms and endobronchial appearance in the assessment of lung infections in lung transplant patients.


title: Gene expression pattern differences in primary human pulmonary epithelial cells infected with MERS-CoV or SARS-CoV-2

text: Coronaviruses such as MERS-CoV and SARS-CoV-2 infect the human respiratory tract and can cause severe pneumonia. Disease severity and outcomes are different for these two infections: the human mortality rate for MERS-CoV and SARS-CoV-2 is over 30% and less than 10%, respectively. Here, using microarray assay, we analyzed the global alterations in gene expression induced by MERS-CoV or SARS-CoV-2 infections in primary human pulmonary epithelial cells. Overall, the number of differentially expressed genes was higher in human lung cells infected with MERS-CoV than in cells with SARS-CoV-2. Out of 44,556 genes analyzed, 127 and 50 were differentially expressed in cells infected with MERS-CoV and SARS-CoV-2, respectively (> 2-fold increase, compared to uninfected cells). Of these, only eight genes, including the one coding for CXCL8, were similarly modulated (upregulated or downregulated) by the two coronaviruses. Importantly, these results were virus-specific and not conditioned by differences in viral load, and viral growth curves were similar in human lung cells infected with both viruses. Our results suggest that these distinct gene expression profiles, detected early after infection by these two coronaviruses, may help us understand the differences in clinical outcomes of MERS-CoV and SARS-CoV-2 infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04730-3) contains supplementary material, which is available to authorized users.


title: New insights into the evolution of the Trypanosoma cruzi clade provided by a new trypanosome species tightly linked to Neotropical Pteronotus bats and related to an Australian lineage of trypanosomes

text: BACKGROUND: Bat trypanosomes are implicated in the evolution of the T. cruzi clade, which harbours most African, European and American trypanosomes from bats and other trypanosomes from African, Australian and American terrestrial mammals, including T. cruzi and T. rangeli, the agents of the American human trypanosomiasis. The diversity of bat trypanosomes globally is still poorly understood, and the common ancestor, geographical origin, and evolution of species within the T. cruzi clade remain largely unresolved. METHODS: Trypanosome sequences were obtained from cultured parasites and from museum archived liver/blood samples of bats captured from Guatemala (Central America) to the Brazilian Atlantic Coast. Phylogenies were inferred using Small Subunit (SSU) rRNA, glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH), and Spliced Leader (SL) RNA genes. RESULTS: Here, we described Trypanosoma wauwau n. sp. from Pteronotus bats (Mormoopidae) placed in the T. cruzi clade, then supporting the bat-seeding hypothesis whereby the common ancestor of this clade likely was a bat trypanosome. T. wauwau was sister to the clade T. spp-Neobats from phyllostomid bats forming an assemblage of trypanosome species exclusively of Noctilionoidea Neotropical bats, which was sister to an Australian clade of trypanosomes from indigenous marsupials and rodents, which possibly evolved from a bat trypanosome. T. wauwau was found in 26.5 % of the Pteronotus bats examined, and phylogeographical analysis evidenced the wide geographical range of this species. To date, this species was not detected in other bats, including those that were sympatric or shared shelters with Pteronotus. T. wauwau did not develop within mammalian cells, and was not infective to Balb/c mice or to triatomine vectors of T. cruzi and T. rangeli. CONCLUSIONS: Trypanosoma wauwau n. sp. was linked to Pteronotus bats. The positioning of the clade T. wauwau/T.spp-Neobats as the most basal Neotropical bat trypanosomes and closely related to an Australian lineage of trypanosomes provides additional evidence that the T. cruzi clade trypanosomes likely evolved from bats, and were dispersed in bats within and between continents from ancient to unexpectedly recent times. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-015-1255-x) contains supplementary material, which is available to authorized users.


title: Consequences pathologiques d'un episode grippal severe (virus swine A/H1N1 dans les conditions naturelles chez la truie non immune en debut de gestation

text: Résumé L'apparition subite et généralisée de manifestations de fièvre, d'anorexie et de toux sur un groupe de truies nullipares dans un élevage dont les animaux sont par ailleurs l'objet d'un protocole d'étude, a justifié la mise en place d'un dispositif particulier d'observation. Les signes cliniques sont enregistrés quotidiennement et notamment la température rectale. Une cinétique sérologique est réalisée et les anticorpos anti Aujeszky, coronavirus GET-like, grippe, A/H1N1, grippe A/H3N2 et Mycoplasma hypopneumoniae sont recherchés. Des recherches virales sont conduites sur mucosités nasales d'animaux en hyperthermie ainsi que sur avortons. L'étude clinique montre une hyperthermie plus ou moins prononcée sur les animaux, les troubles persistant généralement 2 à 5 jours. Le diagnostic de grippe mettant en cause le virus H1N1 swine apparenté A/FIN/1/82 a été établi à la fois par la sérologie (séroconversion) et la mise en évidence du virus sur écouvillon nasal ainsi que sur avorton. L'examen des poumons de truies réformées après l'épisode grippal montre des lésions étendues de Bronchopneumonie et Pasteurella multocida est mise en évidence. Les conséquences zootechniques ont été considérables en particulier chez les truies venant d'être mises à la reproduction. Ainsi sur 13 truies inséminées depuis moins d'une semaine, 3 mise bas seulement on été obtenues. Elles comportent 5,5 et 12 porcelets. 7 truies sont revenues en chaleurs et enfin 3 diagnostiquées vides à 21 jours par échotomographie ont été réformées et examinées à l'abattoir. Sur 8 truies inséminées depuis environ un mois et confirmées gestantes, 2 résorptions embryonnaires sont intervenues, les 6 autres truies donnant naissance à des portées normales. Enfin sur 18 truies gestantes de plus de 45 jours, un avortement a été observé. Abstract Pathological consequences of a severe outbreak of swine influenza (H1N1 virus) in the non immune sow at the beginning of pregnancy, under natural conditions. A sudden acute outbreak of fever, depression, anorexia and coughing in a group of nulliparous sows from a herd that was currently under epidemiological investigation lead to build a particular disposal of observation. The clinical signs were daily recorded including rectal temperature. Blood was taken from the sows at the beginning of the troubles and 3 weeks later for the detection of Aujesky's disease, coronavirus TGE-like, Influenza viruses A/H1N1 and A/H3N2 and Mycoplasma hyopneumoniae. Viral detection was attempted from nasal swabs and aborted fetuses during the acute phase. The clinical study showed fever reaching near 41°C on most of the pigs and lasting usually from 2 to 5 days. The diagnosis of Influenza (virus swine H1N1) was established both on serology (massive seroconversion) and on the detection of the virus from the nasal swabs and from an aborted fetus. The control of the lungs of sows “not in pig” and culled showed extended lesions of bronchopneumonia and Pasteurella multocida was found. The technical consequences of this severe outbreak of Influenza on reproduction were mainly important at the beginning of pregnancy. Over 13 sows inseminated less than 1 week before the outbreak, only 3 farrowed (respectively 5,5 and 12 piglets); 7 returned to oestrus and 3 “not a pig” at 21 days (echotomography) did not show signs of heat and were culled. Over 8 pregnant sows (1 month of pregnancy), 6 farrowed normal litters and total embryonic resorption occurred in 2 sows. Over 18 pregnant sows (more than 45 days gestation) one aborted.


title: Insights into Cleavage Specificity from the Crystal Structure of Foot-and-Mouth Disease Virus 3C Protease Complexed with a Peptide Substrate

text: Abstract Picornavirus replication is critically dependent on the correct processing of a polyprotein precursor by 3C protease(s) (3Cpro) at multiple specific sites with related but non-identical sequences. To investigate the structural basis of its cleavage specificity, we performed the first crystallographic structural analysis of non-covalent complexes of a picornavirus 3Cpro with peptide substrates. The X-ray crystal structure of the foot-and-mouth disease virus 3Cpro, mutated to replace the catalytic Cys by Ala and bound to a peptide (APAKQ|LLNFD) corresponding to the P5–P5′ region of the VP1-2A cleavage junction in the viral polyprotein, was determined up to 2.5 Å resolution. Comparison with free enzyme reveals significant conformational changes in 3Cpro on substrate binding that lead to the formation of an extended interface of contact primarily involving the P4–P2′ positions of the peptide. Strikingly, the deep S1′ specificity pocket needed to accommodate P1′-Leu only forms when the peptide binds. Substrate specificity was investigated using peptide cleavage assays to show the impact of amino acid substitutions within the P5–P4′ region of synthetic substrates. The structure of the enzyme–peptide complex explains the marked substrate preferences for particular P4, P2 and P1 residue types, as well as the relative promiscuity at P3 and on the P′ side of the scissile bond. Furthermore, crystallographic analysis of the complex with a modified VP1-2A peptide (APAKE|LLNFD) containing a Gln-to-Glu substitution reveals an identical mode of peptide binding and explains the ability of foot-and-mouth disease virus 3Cpro to cleave sequences containing either P1-Gln or P1-Glu. Structure-based mutagenesis was used to probe interactions within the S1′ specificity pocket and to provide direct evidence of the important contribution made by Asp84 of the Cys-His-Asp catalytic triad to proteolytic activity. Our results provide a new level of detail in our understanding of the structural basis of polyprotein cleavage by 3Cpro.


title: lncRNA expression signatures in response to enterovirus 71 infection

text: Abstract Outbreaks of hand, foot, and mouth disease caused by enterovirus 71 (EV71) have become considerable threats to the health of infants and young children. To identify the cellular long noncoding RNAs (lncRNAs) involved in the host response to EV71 infection, we performed comprehensive lncRNA and mRNA profiling in EV71-infected rhabdomyosarcoma cells through microarray. We observed the differential expression of more than 4800 lncRNAs during infection. Further analysis showed 160 regulated enhancer-like lncRNA and nearby mRNA pairs, as well as 313 regulated Rinn’s lncRNA [M. Guttman I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, B.W. Carey, J.P. Cassady, M.N. Cabili, R. Jaenisch, T.S. Mikkelsen, T. Jacks, N. Hacohen, B.E. Bernstein, M. Kellis, A. Regev, J.L. Rinn, E.S. Lander. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458 (2009) 223–227, A.M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, B.E. Bernstein, A. van Oudenaarden, A. Regev, E.S. Lander, J.L. Rinn. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106 (2009) 11667–11672] and nearby mRNA pairs. The results provided information for further research on the prevention and treatment of EV71 infection, as well as on distinguishing severe and mild EV71 cases.


title: Use of Tocilizumab for COVID-19-Induced Cytokine Release Syndrome A Cautionary Case Report

text: Novel coronavirus disease 2019 (COVID-19) emerged in late December 2019 in Wuhan, China. Since then, COVID-19 has become a pandemic affecting more than 1.5 million people worldwide. Patients with COVID-19 have a wide spectrum of manifestations, one being cytokine release syndrome (CRS) and its fatal correlate, secondary hemophagocytic lymphohistiocytosis (sHLH). Anti-cytokine therapy such as tocilizumab, an IL-6 receptor antagonist, is a potential treatment for COVID-19; however, data regarding the efficacy of this anti-IL-6 therapy are currently lacking. We report two cases of patients who received a diagnosis of COVID-19 complicated by CRS and were treated with tocilizumab. Both patients progressed to sHLH despite treatment with tocilizumab, and one developed viral myocarditis, challenging the safety and clinical usefulness of tocilizumab in the treatment of COVID-19-induced CRS. These cases highlight the need for clinical trials to determine optimal patient selection and timing for the use of tocilizumab during this disease process.


title: Response of calves persistently infected with noncytopathic bovine viral diarrhea virus (BVDV) subtype 1b after vaccination with heterologous BVDV strains in modified live virus vaccines and Mannheimia haemolytica bacterin-toxoid

text: Seronegative persistently infected (PI) calves with bovine viral diarrhea virus (BVDV) subtype 1b were vaccinated with each of four modified live virus (MLV) BVDV vaccines and a Mannheimia haemolytica bacterin-toxoid. Nasal swabs and peripheral blood leukocytes (PBL) were collected for virus isolation and serums were collected after vaccination and tested for BVDV1a, BVDV1b, BVDV2, bovine herpesvirus-1 (BHV-1), bovine parainfluenza-3 virus (PI-3V), and bovine respiratory syncytial virus (BRSV) antibodies. M. haemolytica and Pasteurella multocida antibodies were detected using ELISA procedures. None of the PI calves developed mucosal disease (MD) after MLV vaccination. None of the BVDV PI calves seroconverted to BVDV1b after MLV vaccination. Calves receiving MLV vaccines seroconverted to the respective type/subtype in the vaccine. Calves receiving a MLV vaccine with noncytopathic (NCP) BVDV1 (subtype not designated) did not seroconvert to BVDV1a, BVDV1b, or BVDV2. The PI calves were positive for BVDV subtype 1b, in the PBL and nasal swabs throughout the study. Calves receiving each of three vaccines with known BVDV1a strains had BVDV1a positive samples after vaccination, in some but not all calves, up to Day 28. The PI BVDV1b calves did not respond with increased M. haemolytica antibodies after vaccination compared to BVDV negative calves receiving the same M. haemolytica vaccine.


title: Reactivation of SARS‐CoV‐2 after Recovery

text: Coronavirus disease 2019 (COVID‐19) has now spread worldwide as a global pandemic.(1) We report on an 8‐year‐old boy who might be a patient with reactivation of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in a family cluster.


title: Risk Factors for Human Infection with Avian Influenza A H5N1, Vietnam, 2004

text: To evaluate risk factors for human infection with influenza A subtype H5N1, we performed a matched case-control study in Vietnam. We enrolled 28 case-patients who had laboratory-confirmed H5N1 infection during 2004 and 106 age-, sex-, and location-matched control-respondents. Data were analyzed by matched-pair analysis and multivariate conditional logistic regression. Factors that were independently associated with H5N1 infection were preparing sick or dead poultry for consumption <7 days before illness onset (matched odds ratio [OR] 8.99, 95% confidence interval [CI] 0.98–81.99, p = 0.05), having sick or dead poultry in the household <7 days before illness onset (matched OR 4.94, 95% CI 1.21–20.20, p = 0.03), and lack of an indoor water source (matched OR 6.46, 95% CI 1.20–34.81, p = 0.03). Factors not significantly associated with infection were raising healthy poultry, preparing healthy poultry for consumption, and exposure to persons with an acute respiratory illness.


title: Bacterial and viral respiratory tract microbiota and host characteristics in children with lower respiratory tract infections: a matched case-control study

text: BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of childhood morbidity and mortality. Potentially pathogenic organisms are present in the respiratory tract in both symptomatic and asymptomatic children, but their presence does not necessarily indicate disease. We aimed to assess the concordance between upper and lower respiratory tract microbiota during LRTIs and the use of nasopharyngeal microbiota to discriminate LRTIs from health. METHODS: First, we did a prospective study of children aged between 4 weeks and 5 years who were admitted to the paediatric intensive care unit (PICU) at Wilhelmina Children's Hospital (Utrecht, Netherlands) for a WHO-defined LRTI requiring mechanical ventilation. We obtained paired nasopharyngeal swabs and deep endotracheal aspirates from these participants (the so-called PICU cohort) between Sept 10, 2013, and Sept 4, 2016. We also did a matched case-control study (1:2) with the same inclusion criteria in children with LRTIs at three Dutch teaching hospitals and in age-matched, sex-matched, and time-matched healthy children recruited from the community. Nasopharyngeal samples were obtained at admission for cases and during home visits for controls. Data for child characteristics were obtained by questionnaires and from pharmacy printouts and medical charts. We used quantitative PCR and 16S rRNA-based sequencing to establish viral and bacterial microbiota profiles, respectively. We did sparse random forest classifier analyses on the bacterial data, viral data, metadata, and the combination of all three datasets to distinguish cases from controls. FINDINGS: 29 patients were enrolled in the PICU cohort. Intra-individual concordance in terms of viral microbiota profiles (96% agreement [95% CI 93–99]) and bacterial microbiota profiles (58 taxa with a median Pearson's r 0·93 [IQR 0·62–0·99]; p<0·05 for all 58 taxa) was high between nasopharyngeal and endotracheal aspirate samples, supporting the use of nasopharyngeal samples as proxy for lung microbiota during LRTIs. 154 cases and 307 matched controls were prospectively recruited to our case-control cohort. Individually, bacterial microbiota (area under the curve 0·77), viral microbiota (0·70), and child characteristics (0·80) poorly distinguished health from disease. However, a classification model based on combined bacterial and viral microbiota plus child characteristics distinguished children with LRTIs from their matched controls with a high degree of accuracy (area under the curve 0·92). INTERPRETATION: Our data suggest that the nasopharyngeal microbiota can serve as a valid proxy for lower respiratory tract microbiota in childhood LRTIs, that clinical LRTIs in children result from the interplay between microbiota and host characteristics, rather than a single microorganism, and that microbiota-based diagnostics could improve future diagnostic and treatment protocols. FUNDING: Spaarne Gasthuis, University Medical Center Utrecht, and the Netherlands Organization for Scientific Research.


Collapsing glomerulopathy in a COVID-19 patient.