title: Modulation of Extracellular ISG15 Signaling by Pathogens and Viral Effector Proteins

text: ISG15 is a ubiquitin-like modifier that also functions extracellularly, signaling through the LFA-1 integrin to promote interferon (IFN)-γ release from natural killer (NK) and T cells. The signals that lead to the production of extracellular ISG15 and the relationship between its two core functions remain unclear. We show that both epithelial cells and lymphocytes can secrete ISG15, which then signals in either an autocrine or paracrine manner to LFA-1-expressing cells. Microbial pathogens and Toll-like receptor (TLR) agonists result in both IFN-β-dependent and -independent secretion of ISG15, and residues required for ISG15 secretion are mapped. Intracellular ISGylation inhibits secretion, and viral effector proteins, influenza B NS1, and viral de-ISGylases, including SARS-CoV-2 PL(pro), have opposing effects on secretion of ISG15. These results establish extracellular ISG15 as a cytokine-like protein that bridges early innate and IFN-γ-dependent immune responses, and indicate that pathogens have evolved to differentially inhibit the intracellular and extracellular functions of ISG15.


docid: rxornpqu

title: Infectivity and cross-immunity studies of Theileria lestoquardi and Theileria annulata in sheep and cattle: I. In vivo responses

text: In a series of experiments, sporozoite stabilates of a Theileria lestoquardi (Lahr) and a T. annulata (Ankara) stock prepared from Hyalomma anatolicum anatolicum ticks, were used to examine the infectivity of both parasite species for sheep and cattle and to study the development of cross-immunity between these parasite species. In the first experiment sheep and cattle were inoculated with T. lestoquardi sporozoites. Surviving animals and naive sheep and cattle were, in the second experiment, inoculated with T. annulata. In the third experiment, naive sheep and sheep previously infected with T. annulata, were inoculated with T. lestoquardi. The following responses to inoculations were monitored: clinical and haematological signs of infection, appearance of parasitic stages of the parasites in lymph node biopsies and in peripheral blood and serological response to T. lestoquardi and T. annulata schizont antigens. While T. lestoquardi readily infected sheep and caused severe disease, it did not infect cattle. On the other hand, T. annulata infected both cattle and sheep. However, whereas cattle became severely affected, infected sheep showed mild clinical symptoms only and piroplasms did not develop. Despite their different behaviour in the host species examined, cross-immunity studies suggested that the parasite species are very closely related. Experiments in sheep indicated that T. lestoquardi infection protected against subsequent T. annulata infection. On the other hand, recovery from T. annulata infection did not prevent infection by sporozoites of T. lestoquardi, resulting in the establishment of schizonts and their subsequent development into piroplasms, although it protected against the major clinical effects of T. lestoquardi infection.


Environmental Engineers and Scientists Have Important Roles to Play in Stemming Outbreaks and Pandemics Caused by Enveloped Viruses


title: Next-Generation Sequencing in Veterinary Medicine: How Can the Massive Amount of Information Arising from High-Throughput Technologies Improve Diagnosis, Control, and Management of Infectious Diseases?

text: The development of high-throughput molecular technologies and associated bioinformatics has dramatically changed the capacities of scientists to produce, handle, and analyze large amounts of genomic, transcriptomic, and proteomic data. A clear example of this step-change is represented by the amount of DNA sequence data that can be now produced using next-generation sequencing (NGS) platforms. Similarly, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometry have promoted the identification and quantification of proteins in a given sample. These advancements in biotechnology have increasingly been applied to the study of animal infectious diseases and are beginning to revolutionize the way that biological and evolutionary processes can be studied at the molecular level. Studies have demonstrated the value of NGS technologies for molecular characterization, ranging from metagenomic characterization of unknown pathogens or microbial communities to molecular epidemiology and evolution of viral quasispecies. Moreover, high-throughput technologies now allow detailed studies of host-pathogen interactions at the level of their genomes (genomics), transcriptomes (transcriptomics), or proteomes (proteomics). Ultimately, the interaction between pathogen and host biological networks can be questioned by analytically integrating these levels (integrative OMICS and systems biology). The application of high-throughput biotechnology platforms in these fields and their typical low-cost per information content has revolutionized the resolution with which these processes can now be studied. The aim of this chapter is to provide a current and prospective view on the opportunities and challenges associated with the application of massive parallel sequencing technologies to veterinary medicine, with particular focus on applications that have a potential impact on disease control and management.


title: Epidemiology and characterization of avian infectious bronchitis virus strains circulating in southern China during the period from 2013–2015

text: Two hundred and six strains of avian infectious bronchitis virus (IBV) were isolated from chickens showing signs of disease in southern China during the period from 2013–2015. The nucleotide and amino acid sequences from the isolated field strains were compared to 42 published references. Nucleotide homologies ranged from 63.1–99.9% and amino acid homologies ranging from 60.2–100%. At least seven IBV genotypes were co-circulating in commercial chicken farms in southern China. The IBV isolates were genetically diverse and underwent continuing evolution. The QX-type, TW I-type, and 4/91-type were the most common genotypes during the three-year observation period and accounted for 88.8% of the isolated strains. Notably, the prevalence of the TW I-type strains has been increasing in recent years and has become the most common genotype in China. The emergence of variant IBV strains can be attributed to recombination. Serologic analysis and antigenic 3D cartography of 4 reference and 14 field isolated strains indicated the surveyed IBVs had diverse serology types and that the serotype of the isolated QX-type and TW I-type strains was distinct from the vaccines strains. Therefore, long-term continuing surveillance is necessary for IBV prevention and control.


docid: iwlxwfda

title: El impacto de la pandemia del COVID-19 en la utilización de los servicios urológicos de urgencias

text: ABSTRACT Objectives: To compare the number of patients attending the Urology ED of Centro Hospitalar Universitário do Porto (CHUP), as well as their demographic characteristics, the reasons for admission, the clinical severity under the Manchester triage system (MTS), and the need for emergency surgery or hospitalization, during the pandemic and the equivalent period in 2019. Material and Methods: Data were collected from patients attending the Urology emergency ward of CHUP during three weeks - from March 11th 2020 to April 1st 2020 - and from the same period the previous year (from March 11th to April 1st 2019). Results: During the pandemic, 46.4% fewer patients visited our urological ED (122 vs 263). There was no significant difference of the mean age or the number of old patients (with 65 or more years old) between the two periods. However, significantly fewer female patients sought emergency urological services during the COVID-19 pandemic period (32.7% vs. 14.8%, p<0.05). No significant differences were noted between different clinical severity groups under the MTS. In 2019, significantly less patients required hospitalization. The most common reasons for admission, during both periods, were hematuria, renal colic and urinary tract infections (UTI). The authors recognize that the study has several limitations, namely, those inherent to its retrospective nature. Conclusion: COVID-19 significantly influenced people’s urological care-seeking behaviour. Based on the results of this study, we have reasons to speculate that people’s requirements for urological services might grow explosively in the post-COVID-19 period. There should be further studies about the real state of long-term urological services and the consequences that this pandemic may have in terms of morbimortality not directly related to the virus.


title: Future liasing of the lockdown during COVID-19 pandemic: The dawn is expected at hand from the darkest hour

text: The lockdown during COVID-19 pandemic has converted the world into new experimental laboratories, which may reveal temporal or spatial comparative analysis data. However, some startling information is gathered in terms of reduced premature mortality cases associated with air and water quality improvement, enhanced e-learning on a broader platform, work from home, and successful e-health. The decline in vehicular density on roads and congestion leads to reduced energy consumption and associated greenhouse gases (GHG) and other pollutants emission. The lockdown has also been identified as a possible emergency measure to combat severe air pollution episodes. Similarly, industrial pollution has been recognized as one of the primary causes of water resource pollution and would, therefore, bring change in policy vis-à-vis groundwater pollution control. Our findings suggest that the results of successful e-learning and work from home would be a permanent shift from conventional modes in the near future due to a drastic reduction in socio-economic cost. Our critical analysis also highlights that with such temporary lockdown measures acute/chronic ill-effects of anthropogenic perturbations on planet earth can be effectively estimated through sociocultural, socioeconomical and socio-political/sociotechnological nexus.


The perspective of surgical residents on current and future training in light of the COVID‐19 pandemic


CONSECUENCIAS DE LA COVID-19 SOBRE LAS PERSONAS CON DIABETES


title: A systematic review of asymptomatic infections with COVID-19

text: Since the outbreak of coronavirus disease 2019 (COVID-19) in late December 2019, it has brought significant harm and challenges to over 200 countries and regions around the world. However, there is increasing evidence that many patients with COVID-19 are asymptomatic or have only mild symptoms, but they are able to transmit the virus to others. There are difficulties in screening for asymptomatic infections, which makes it more difficult for national prevention and control of this epidemic. This article reviews the characteristics, treatment, and outcomes of asymptomatic infections with COVID-19, hoping it would be helpful for early prevention and control of this severe public health threat worldwide.


Chapter 61 Disorders of the Ear


title: Immune protection conferred by three commonly used commercial live attenuated vaccines against the prevalent local strains of avian infectious bronchitis virus in southern China

text: Live attenuated vaccines are critical in the control of avian infectious bronchitis. It is necessary to know the protection conferred by commonly used commercial live vaccines. In this study, specific pathogen-free chicks were vaccinated with the commercial live vaccines H120, 4/91 and LDT3-A. Blood samples were collected at weekly intervals for the detection of IBV-specific antibodies and quantification of CD4(+) and CD8(+) T lymphocytes. At 21 days post-inoculation the vaccinated birds were challenged with the IBV prevalent local strains GX-YL5, GX-GL11079 and GX-NN09032, respectively. Trachea and kidney samples were collected at 5 days post-challenge for the detection of the virus. The results showed that the H120 group exhibited medium antibody levels, the lowest percentages of CD4(+), CD8(+) T lymphocytes and the highest viral loads. The 4/91 group showed the lowest antibody levels, but the highest percentages of CD4(+), CD8(+) T lymphocytes and the lowest viral loads. The LDT3-A group showed the highest antibody levels, the medium percentages of CD4(+), CD8(+) T lymphocytes and the medium viral loads. The protection rates of H120, 4/91 and LDT3-A groups were 41.7–58.3%, 75.0–83.7% and 66.7–75.0%, respectively. The present study demonstrated that the vaccines H120, 4/91 and LDT3-A could stimulate the immunized chicks to produce different levels of humoral and cellular immunity to resist the infection of IBV, but couldn’t provide complete protection against the prevalent local strains of IBV in southern China. Also, the vaccine 4/91 offered the best immune protection among the three vaccines.


Lung perfusion [(99m)Tc]-MAA SPECT/CT to rule out pulmonary embolism in COVID-19 patients with contraindications for iodine contrast


COVID-19 jeopardizes the response to coming natural disasters


title: Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates

text: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that re-emerged in 2004 and has caused massive outbreaks in recent years. The lack of a licensed vaccine or treatment options emphasize the need to obtain more insight into the viral life cycle and CHIKV-host interactions. Infectious cDNA clones are important tools for such studies, and for mechanism of action studies on antiviral compounds. Existing CHIKV cDNA clones are based on a single genome from an individual clinical isolate, which is expected to have evolved specific characteristics in response to the host environment, and possibly also during subsequent cell culture passaging. To obtain a virus expected to have the general characteristics of the recent E1-226V CHIKV isolates, we have constructed a new CHIKV full-length cDNA clone, CHIKV LS3, based on the consensus sequence of their aligned genomes. Here we report the characterization of this synthetic virus and a green fluorescent protein-expressing variant (CHIKV LS3-GFP). Their characteristics were compared to those of natural strain ITA07-RA1, which was isolated during the 2007 outbreak in Italy. In cell culture the synthetic viruses displayed phenotypes comparable to the natural isolate, and in a mouse model they caused lethal infections that were indistinguishable from infections with a natural strain. Compared to ITA07-RA1 and clinical isolate NL10/152, the synthetic viruses displayed similar sensitivities to several antiviral compounds. 3-deaza-adenosine was identified as a new inhibitor of CHIKV replication. Cyclosporin A had no effect on CHIKV replication, suggesting that cyclophilins -opposite to what was found for other +RNA viruses- do not play an essential role in CHIKV replication. The characterization of the consensus sequence-based synthetic viruses and their comparison to natural isolates demonstrated that CHIKV LS3 and LS3-GFP are suitable and representative tools to study CHIKV-host interactions, screen for antiviral compounds and unravel their mode of action.


title: Clinical and Genetic Characteristics of Covid-19 Patients from UK Biobank

text: OBJECTIVE: To explore both clinical and genetic risk factors for Covid-19 in a cohort from the United Kingdom. DESIGN: Prospective cohort study. PARTICIPANTS: 669 positive Covid-19 patients within a cohort of 502,536 UK Biobank participants, recruited between 2006 and 2010. MAIN OUTCOME MEASURES: The main outcome measure was Covid-19 positive status, determined by the presence of any positive test for a single individual. We also assessed risk factors for inpatient and outpatient status for Covid-19 positive individuals. RESULTS: We found that black participants were at over three times increased risk of testing positive for Covid-19, relative to white participants, even after adjusting for confounders (adjusted relative risk [ARR] 3.14, 95% confidence interval [CI] 2.28 to 4.31). Asian participants were also at higher risk of Covid-19 (ARR 2.03, 95% CI 1.40 to 2.95). Next, we analyzed the association of comorbidities with Covid-19. We found that participants were at increased risk of Covid-19 if they had chronic obstructive pulmonary disease (ARR 1.54, 95% CI 1.02 to 2.31) or ischemic heart disease (ARR 1.56, 95% CI 1.18 to 2.07). However, there was no evidence that either angiotensin converting enzyme inhibitors (ARR 1.32, 95% CI 0.95 to 1.84) or angiotensin II receptor blockers (ARR 1.37, 95% CI 0.94 to 1.98) increased the risk of Covid-19. We confirmed that blood type A was associated with Covid-19 relative to blood type O individuals, and we also found that the HLA variant DQA1_509 was enriched in Covid-19 positive cases, even after Bonferroni correction (P = 1.0 × 10(−5)). CONCLUSIONS: In this study, we found that black and Asian participants were at increased risk of Covid-19, even after adjusting for confounders. We also identified a novel genetic association with the HLA variant DQA1_509. Further investigations of genetic associations with Covid-19 may lead to important discoveries of genetic drivers of severe disease.


title: Reliable quantification of rhinovirus species C using real-time PCR

text: Abstract Background Rhinovirus C (RV-C) is an important respiratory pathogen of children, but little is known about its contribution to disease severity, though viral load appears to be important. Difficulty in RV-C cultivation and target sequence variation has precluded the development of a PCR based quantification method. Objective The aim of this study was to develop and validate reverse transcription quantitative PCR (RT-qPCR) assays for a broad range of circulating RV-C genotypes in nasopharyngeal aspirates (NPAs). Study design Four assays were designed to quantify a 296bp region located within the 5′ untranslated region (UTR) of RV-C types. These assays were based on in silico analysis of available RV-C sequences. Probes were designed to provide 100% homology to the corresponding RV-C genotypes. Results The linear dynamic range of each of the four assays spanned eight orders of magnitude (104–1011 copies/mL). The limit of detection for assays 1–4 was estimated to be 1147 copies/mL, 765 copies/mL, 1138 copies/mL and 1470 copies/mL respectively. Each assay demonstrated a strong linear relationship (r2 =>0.995) and amplification efficiency greater than 95%. Repeatability and reproducibility of the method were shown to be high, with coefficients of variations lower than 8% and 15% respectively.


docid: sqhebpyg

title: Impact of supplemental protein source offered to primiparous heifers during gestation on II. Progeny performance and carcass characteristics

text: A 3-yr study using primiparous crossbred beef heifers (n = 114) was conducted to determine the effects of protein supplement during late gestation on progeny performance and carcass characteristics. Pregnant heifers were stratified by heifer development system, initial BW, and AI service sire and placed in an individual feeding system. Heifers were offered meadow hay (8 to 11% CP) from early November to mid-February and provided no supplement (CON; n = 37), 0.83 kg/d (DM basis) of a dried distillers grains with solubles–based supplement (HI; n = 39), or 0.83 kg/d (DM basis) of a dried corn gluten feed–based supplement (LO; n = 38). Supplements were designed to be isonitrogenous (28% CP) and isocaloric but to differ in RUP with HI (59% RUP) having greater levels of RUP than LO (34% RUP). After the individual feeding period, heifers were placed in a drylot for calving. All heifers were bred using a fixed-timed AI protocol and pairs were moved to a commercial ranch in the Nebraska Sandhills for summer grazing. Calf weaning BW did not differ (P = 0.14) based on maternal diet. However, feedlot entry BW was greater (P = 0.03) for HI compared with CON calves. Average daily gain during the initial feedlot phase tended (P = 0.10) to be greatest for calves born to CON dams and lowest for calves born to LO dams. However, overall ADG was similar (P = 0.50) for the entire feedlot period. Residual feed intake during the reimplant and total feeding period was improved in calves born to supplemented dams in yr 2 and 3 compared with calves born to CON dams. There was no difference in final BW among treatments (P = 0.71). Hot carcass weight was similar (P = 0.72) among treatments; however, steers had greater (P < 0.01) HCW than heifers. Furthermore, percent empty body fat and 12th rib fat thickness were lowest (P = 0.05 and P = 0.04) for calves born to LO dams. Tenderness measured by Warner-Bratzler shear force was increased (P = 0.03) in longissimus samples from calves from CON dams compared to calves from LO dams. Similarly, crude fat levels tended to be greater (P = 0.07) for calves from CON dams compared with calves from LO dams. Based on these data, providing RUP supplements, similar to those used in this study, to primiparous heifers in late gestation consuming ad libitum grass hay resulted in increased initial feedlot BW for HI compared to CON calves, improved feed efficiency, and altered carcass characteristics in calves born to supplemented compared with CON dams.


title: Prevalence and analysis of associated risk factors for Cryptosporidium infection in lambs in Jammu district

text: An epidemiologic study was carried out to investigate the prevalence and analysis of risk of Cryptosporidium infection in lambs in Jammu district. Faecal samples of 120 lambs of different age groups viz., <1 month, 1–3 months and 3–6 months were assessed. Cryptosporidium oocysts were identified by using modified Zeihl Neelsen technique. Statistical analysis showed that infection rates were significantly higher in lambs of <1 month age group (65 %) than other two age groups (p < 0.05). Similarly, cryptosporidial infection rates were significantly higher in diarrhoeic (54.41 %) than in non diarrhoeic lambs (34.61 %). Winter records highest prevalence (73.33 %) which varied significantly. Sex wise higher prevalence was observed in females (51.56 %) as compared to males (39.28 %). The relationship between intensity of infection and various epidemiological factors showed that highest intensity was observed in lambs of 0–1 month age group, having diarrhoea, in winter season.


title: Superiority of Transcriptional Profiling Over Procalcitonin for Distinguishing Bacterial From Viral Lower Respiratory Tract Infections in Hospitalized Adults

text: Background. Distinguishing between bacterial and viral lower respiratory tract infection (LRTI) remains challenging. Transcriptional profiling is a promising tool for improving diagnosis in LRTI. Methods. We performed whole blood transcriptional analysis in 118 patients (median age [interquartile range], 61 [50–76] years) hospitalized with LRTI and 40 age-matched healthy controls (median age, 60 [46–70] years). We applied class comparisons, modular analysis, and class prediction algorithms to identify and validate diagnostic biosignatures for bacterial and viral LRTI. Results. Patients were classified as having bacterial (n = 22), viral (n = 71), or bacterial-viral LRTI (n = 25) based on comprehensive microbiologic testing. Compared with healthy controls, statistical group comparisons (P < .01; multiple-test corrections) identified 3376 differentially expressed genes in patients with bacterial LRTI, 2391 in viral LRTI, and 2628 in bacterial-viral LRTI. Patients with bacterial LRTI showed significant overexpression of inflammation and neutrophil genes (bacterial > bacterial-viral > viral), and those with viral LRTI displayed significantly greater overexpression of interferon genes (viral > bacterial-viral > bacterial). The K–nearest neighbors algorithm identified 10 classifier genes that discriminated between bacterial and viral LRTI with a 95% sensitivity (95% confidence interval, 77%–100%) and 92% specificity (77%–98%), compared with a sensitivity of 38% (18%–62%) and a specificity of 91% (76%–98%) for procalcitonin. Conclusions. Transcriptional profiling is a helpful tool for diagnosis of LRTI.


title: Cardiac Involvement in COVID-19—Assessment with Echocardiography and Cardiac Magnetic Resonance Imaging

text: The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), started at the beginning of December 2019, in Wuhan, Hubei, China. Since then, the disease has been spreading quickly all over the world with dramatic consequences for global health. That is the reason why it was declared pandemic since March 11th, 2020. The clinical presentation of SARS-CoV-2 is quite variable. Respiratory symptoms dominate its clinical manifestations, but based on current observations, it can significantly affect the heart as well, thus leading to myocardial injury. Imaging plays a key role in the cardiovascular management of these patients, with the aim of improving their outcomes. This review article provides an overview as to strengths and weaknesses of cardiac magnetic resonance compared with echocardiography in the difficult management of these patients.


title: The expression level of angiotensin-converting enzyme 2 determines the severity of COVID-19: lung and heart tissue as targets

text: Researchers have reported some useful information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leading to CoV disease 2019 (COVID-19). Several studies have been performed in order to develop antiviral drugs, from which a few have been prescribed to patients. Also, several diagnostic tests have been designed to accelerate the process of identifying and treating COVID-19. It has been well-documented that the surface of host cells is covered by some receptors, known as angiotensin-converting enzyme 2 (ACE2), which mediates the binding and entry of CoV. After entering, the viral RNA interrupts the cell proliferation system to activate self-proliferation. However, having all the information about the outbreakof the SARS-COV-2, it is not still clear which factors determine the severity of lung and heart function impairment induced by COVID-19. A major step in exploring SARS-COV-2 pathogenesis is to determine the distribution of ACE2 in different tissues . In this review, the structure and origin of CoV, the role of ACE2 as a receptor of SARS-COV-2 on the surface of host cells, and the ACE2 distribution in different tissues with a focus on lung and cardiovascular system have been discussed. It was also revealed that acute and chronic cardiovascular diseases (CVDs) may result in the clinical severity of COVID-19. In conclusion, this review may provide useful information in developing some promising strategies to end up with a worldwide COVID-19 pandemic. Communicated by Ramaswamy H. Sarma


title: Wildlife health investigations: needs, challenges and recommendations

text: In a fast changing world with growing concerns about biodiversity loss and an increasing number of animal and human diseases emerging from wildlife, the need for effective wildlife health investigations including both surveillance and research is now widely recognized. However, procedures applicable to and knowledge acquired from studies related to domestic animal and human health can be on partly extrapolated to wildlife. This article identifies requirements and challenges inherent in wildlife health investigations, reviews important definitions and novel health investigation methods, and proposes tools and strategies for effective wildlife health surveillance programs. Impediments to wildlife health investigations are largely related to zoological, behavioral and ecological characteristics of wildlife populations and to limited access to investigation materials. These concerns should not be viewed as insurmountable but it is imperative that they are considered in study design, data analysis and result interpretation. It is particularly crucial to remember that health surveillance does not begin in the laboratory but in the fields. In this context, participatory approaches and mutual respect are essential. Furthermore, interdisciplinarity and open minds are necessary because a wide range of tools and knowledge from different fields need to be integrated in wildlife health surveillance and research. The identification of factors contributing to disease emergence requires the comparison of health and ecological data over time and among geographical regions. Finally, there is a need for the development and validation of diagnostic tests for wildlife species and for data on free-ranging population densities. Training of health professionals in wildlife diseases should also be improved. Overall, the article particularly emphasizes five needs of wildlife health investigations: communication and collaboration; use of synergies and triangulation approaches; investments for the long term; systematic collection of metadata; and harmonization of definitions and methods.


Some recent work at the common cold unit, Salisbury


title: Americans’ COVID-19 Stress, Coping, and Adherence to CDC Guidelines

text: IMPORTANCE: Documenting Americans’ stress responses to an unprecedented pandemic and their degree of adherence to CDC guidelines is essential for mental health interventions and policy-making. OBJECTIVE: To provide the first snapshot of immediate impact of COVID-19 on Americans’ stress, coping, and guideline adherence. DESIGN: Data were collected from an online workers’ platform for survey research (Amazon’s Mechanical Turk) from April 7 to 9, 2020. The current data represents the baseline of a longitudinal study. Best practices for ensuring high-quality data were employed. PARTICIPANTS: Individuals who are 18 years of age or older, living in the USA, and English-speaking were eligible for the study. Of 1086 unique responses, 1015 completed responses are included. SETTING: Population-based. MAIN OUTCOMES: Exposure to and stressfulness of COVID-19 stressors, coping strategies, and adherence to CDC guidelines. RESULTS: The sample was 53.9% women (n = 547), with an average age of 38.9 years (SD = 13.50, range = 18–88), most of whom were White (n = 836, 82.4%), non-Hispanic (n = 929, 91.5%), and straight/heterosexual (n = 895, 88.2%); 40% were currently married (n = 407), and 21.6% (n = 219) were caregivers. About half (50.5%) endorsed having at least “mostly” enough money to meet their needs. Respondents’ locations across the USA ranged from 18.5% in the Northeast to 37.8% in the South. The most commonly experienced stressors were reading/hearing about the severity and contagiousness of COVID-19, uncertainty about length of quarantine and social distancing requirements, and changes to social and daily personal care routines. Financial concerns were rated most stressful. Younger age, female gender, and caregiver status increased risk for stressor exposure and greater degree of stressfulness. The most frequently reported strategies to manage stress were distraction, active coping, and seeking emotional social support. CDC guideline adherence was generally high, but several key social distancing and hygiene behaviors showed suboptimal adherence, particularly for men and younger adults. CONCLUSIONS AND RELEVANCE: Americans have high COVID-19 stress exposure and some demographic subgroups appear particularly vulnerable to stress effects. Subgroups less likely to adhere to CDC guidelines may benefit from targeted information campaigns. these findings may guide mental health interventions and inform policy-making regarding implications of specific public health measures.


Rapid deployment of pathology services to a remote Australian quarantine setting during the COVID-19 pandemic


title: Screening of melatonin, α-tocopherol, folic acid, acetyl-l-carnitine and resveratrol for anti-dengue 2 virus activity

text: OBJECTIVE: Infections with the mosquito transmitted dengue virus (DENV) are a significant public health burden in many parts of the world. Despite the introduction of a commercial vaccine in some parts of the world, the majority of the populations at risk of infection remain unprotected against this disease, and there is currently no treatment for DENV infection. Natural compounds offer the prospect of cheap and sustainable therapeutics to reduce the disease burden during infection, and thus potentially alleviate the risk of more severe disease. This study evaluated the potential anti-DENV 2 activity of five natural compounds namely melatonin, α-tocopherol, folic acid, acetyl-l-carnitine and resveratrol in two different cell lines. RESULTS: Screening of the compounds showed that one compound (acetyl-l-carnitine) showed no effect on DENV infection, three compounds (melatonin, α-tocopherol and folic acid) slightly increased levels of infection, while the 5th compound, resveratrol, showed some limited anti-DENV activity, with resveratrol reducing virus output with an EC(50) of less than 25 μM. These results suggest that some commonly taken natural compounds may have beneficial effects on DENV infection, but that others may potentially add to the disease burden. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13104-018-3417-3) contains supplementary material, which is available to authorized users.


docid: stgfzlvs

title: After the pandemic


title: Adaptive evolution of bat dipeptidyl peptidase 4 (dpp4): implications for the origin and emergence of Middle East respiratory syndrome coronavirus

text: BACKGROUND: The newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV) that first appeared in Saudi Arabia during the summer of 2012 has to date (20th September 2013) caused 58 human deaths. MERS-CoV utilizes the dipeptidyl peptidase 4 (DPP4) host cell receptor, and analysis of the long-term interaction between virus and receptor provides key information on the evolutionary events that lead to the viral emergence. FINDINGS: We show that bat DPP4 genes have been subject to significant adaptive evolution, suggestive of a long-term arms-race between bats and MERS related CoVs. In particular, we identify three positively selected residues in DPP4 that directly interact with the viral surface glycoprotein. CONCLUSIONS: Our study suggests that the evolutionary lineage leading to MERS-CoV may have circulated in bats for a substantial time period.


title: Metagenomic Next-Generation Sequencing Reveal Presence of a Novel Ungulate Bocaparvovirus in Alpacas

text: Viruses belonging to the genus Bocaparvovirus (BoV) are a genetically diverse group of DNA viruses known to cause respiratory, enteric, and neurological diseases in animals, including humans. An intestinal sample from an alpaca (Vicugna pacos) herd with reoccurring diarrhea and respiratory disease was submitted for next-generation sequencing, revealing the presence of a BoV strain. The alpaca BoV strain (AlBoV) had a 58.58% whole genome nucleotide percent identity to a camel BoV from Dubai, belonging to a tentative ungulate BoV 8 species (UBoV8). Recombination events were lacking with other UBoV strains. The AlBoV genome was comprised of the NS1, NP1, and VP1 proteins. The NS1 protein had the highest amino acid percent identity range (57.89–67.85%) to the members of UBoV8, which was below the 85% cut-off set by the International Committee on Taxonomy of Viruses. The low NS1 amino acid identity suggests that AlBoV is a tentative new species. The whole genome, NS1, NP1, and VP1 phylogenetic trees illustrated distinct branching of AlBoV, sharing a common ancestor with UBoV8. Walker loop and Phospholipase A2 (PLA2) motifs that are vital for virus infectivity were identified in NS1 and VP1 proteins, respectively. Our study reports a novel BoV strain in an alpaca intestinal sample and highlights the need for additional BoV research.


title: A Comparison of Mortality-related Risk Factors of COVID-19, SARS, and MERS: A Systematic Review and Meta-analysis

text: Objective: Coronavirus Disease 2019 (COVID-19) is a pandemic. This systematic review compares mortality risk factors including clinical, demographic and laboratory features of COVID-19, Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). The aim is to provide new strategies for COVID-19 prevention and treatment. Methods: We performed a systematic review with meta-analysis, using five databases to compare the predictors of death for COVID-19, SARS and MERS. A random-effects model meta-analysis calculated odds ratios (OR) and 95% confidence intervals (95% CI). Results: 845 articles up through 11/4/2020 were retrieved, but only 28 studies were included in this meta-analysis. The results showed that males had a higher likelihood of death than females (OR = 1.82, 95% CI 1.56-2.13). Age (OR = 7.86, 95% CI 5.46-11.29), diabetes comorbidity (OR = 3.73, 95% CI 2.35-5.90), chronic lung disease (OR = 3.43, 95% CI 1.80-6.52) and hypertension (OR = 3.38, 95% CI 2.45-4.67) were the mortality risk factors. The laboratory indicators lactic dehydrogenase (OR = 37.52, 95% CI 24.68-57.03), C-reactive protein (OR = 12.11, 95% CI 5.24-27.98), and neutrophils (OR = 17.56, 95% CI 10.67-28.90) had stronger correlations with COVID-19 mortality than with SARS or MERS mortality. Consolidation and ground-glass opacity imaging features were similar among COVID-19, SARS, and MERS patients. Conclusions: COVID-19’s mortality factors are similar to those of SARS and MERS. Age and laboratory indicators could be effective predictors of COVID-19 mortality outcomes.


title: Cardiac involvement in COVID‐19 patients: Risk factors, predictors, and complications: A review

text: BACKGROUND: Respiratory complications have been well remarked in the novel coronavirus disease (SARS‐CoV‐2/COVID‐19), yet an emerging body of research indicates that cardiac involvement may be implicated in poor outcomes for these patients. AIMS: This review seeks to gather and distill the existing body of literature that describes the cardiac implications of COVID‐19. MATERIALS AND METHODS: The English literature was reviewed for papers dealing with the cardiac effects of COVID‐19. RESULTS: Notably, COVID‐19 patients with pre‐existing cardiovascular disease are counted in greater frequency in intensive care unit settings, and ultimately suffer greater rates of mortality. Other studies have noted cardiac presentations for COVID‐19, rather than respiratory, such as acute pericarditis and left ventricular dysfunction. In some patients there has been evidence of acute myocardial injury, with correspondingly increased serum troponin I levels. With regard to surgical interventions, there is a dearth of data describing myocardial protection during cardiac surgery for COVID‐19 patients. Although some insights have been garnered in the study of cardiovascular diseases for these patients, these insights remain fragmented and have yet to cement clear guidelines for actionable clinical practice. CONCLUSION: While some information is available, further studies are imperative for a more cohesive understanding of the cardiac pathophysiology in COVID‐19 patients to promote more informed treatment and, ultimately, better clinical outcomes.


title: Viruses in wastewater sludges and in effluents used for irrigation

text: Abstract Disposal of sewage wastes is a problem of increasing magnitude in the United States. New control measures enacted by Congress require consideration of land disposal of sludges and effluents. The volume of wastes involved and the possibility of contaminating ground water supplies and vegetation has great public health significance. The effectiveness of the sewage treatment process to remove chemical and biological contaminants and the operational efficiency of many sewage treatment plants are factors that must be given careful consideration before final selection of disposal methodology. The quality of our future water and food supplies will be affected either beneficially or adversely by current management decisions.


title: Candidate new rotavirus species in Schreiber's bats, Serbia

text: Abstract The genus Rotavirus comprises eight species designated A to H and one tentative species, Rotavirus I. In a virus metagenomic analysis of Schreiber's bats sampled in Serbia in 2014 we obtained sequences likely representing novel rotavirus species. Whole genome sequencing and phylogenetic analysis classified the representative strain into a tentative tenth rotavirus species, we provisionally called Rotavirus J. The novel virus shared a maximum of 50% amino acid sequence identity within the VP6 gene to currently known members of the genus. This study extends our understanding of the genetic diversity of rotaviruses in bats.


title: Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor

text: Coronaviruses infect animals and humans causing a wide range of diseases. The diversity of coronaviruses in many mammalian species is contributed by relatively high mutation and recombination rates during replication. This dynamic nature of coronaviruses may facilitate cross-species transmission and shifts in tissue or cell tropism in a host, resulting in substantial change in virulence. Feline enteric coronavirus (FECV) causes inapparent or mild enteritis in cats, but a highly fatal disease, called feline infectious peritonitis (FIP), can arise through mutation of FECV to FIP virus (FIPV). The pathogenesis of FIP is intimately associated with immune responses and involves depletion of T cells, features shared by some other coronaviruses like Severe Acute Respiratory Syndrome Coronavirus. The increasing risks of highly virulent coronavirus infections in humans or animals call for effective antiviral drugs, but no such measures are yet available. Previously, we have reported the inhibitors that target 3C-like protease (3CLpro) with broad-spectrum activity against important human and animal coronaviruses. Here, we evaluated the therapeutic efficacy of our 3CLpro inhibitor in laboratory cats with FIP. Experimental FIP is 100% fatal once certain clinical and laboratory signs become apparent. We found that antiviral treatment led to full recovery of cats when treatment was started at a stage of disease that would be otherwise fatal if left untreated. Antiviral treatment was associated with a rapid improvement in fever, ascites, lymphopenia and gross signs of illness and cats returned to normal health within 20 days or less of treatment. Significant reduction in viral titers was also observed in cats. These results indicate that continuous virus replication is required for progression of immune-mediated inflammatory disease of FIP. These findings may provide important insights into devising therapeutic strategies and selection of antiviral compounds for further development for important coronaviruses in animals and humans.


Epitope specificity of demyelinating MOG-specific autoantibody responses


title: Angiotensin-converting enzyme 2 inhibits lung injury induced by respiratory syncytial virus

text: Respiratory syncytial virus (RSV) infection is a major cause of severe lower respiratory illness in infants and young children, but the underlying mechanisms responsible for viral pathogenesis have not been fully elucidated. To date, no drugs or vaccines have been employed to improve clinical outcomes for RSV-infected patients. In this paper, we report that angiotensin-converting enzyme-2 (ACE2) protected against severe lung injury induced by RSV infection in an experimental mouse model and in pediatric patients. Moreover, ACE2 deficiency aggravated RSV-associated disease pathogenesis, mainly by its action on the angiotensin II type 1 receptor (AT1R). Furthermore, administration of a recombinant ACE2 protein alleviated the severity of RSV-induced lung injury. These findings demonstrate that ACE2 plays a critical role in preventing RSV-induced lung injury, and suggest that ACE2 is a promising potential therapeutic target in the management of RSV-induced lung disease.


title: Xenotransplantation: Infectious Risk Revisited

text: Xenotransplantation is a possible solution for the shortage of tissues for human transplantation. Multiple hurdles exist to clinical xenotransplantation, including immunologic barriers, metabolic differences between pigs – the source species most commonly considered – and humans, and ethical concerns. Since clinical trials were first proposed almost 10 years ago, the degree of risk for infection transmitted from the xenograft donor to the recipient has been extensively investigated. A number of potential viral pathogens have been identified including porcine endogenous retrovirus (PERV), porcine cytomegalovirus (PCMV), and porcine lymphotropic herpesvirus (PLHV). Sensitive diagnostic assays have been developed for each virus. Human‐tropic PERV are exogenous recombinants between PERV‐A and PERV‐C sequences and are present in only a subset of swine. Porcine cytomegalovirus can be excluded from herds of source animals by early weaning of piglets. In contrast, the risks associated with PLHV remain undefined. Microbiologic studies and assays for potential xenogeneic pathogens have furthered understanding of risks associated with xenotransplantation. Thus far, clinical xenotransplantation of pig tissues has not resulted in transmission of viral infection to humans; significant risks for disease transmission from swine to humans have not been confirmed. If immunologic hurdles can be overcome, it is reasonable to initiate carefully monitored clinical trials.


title: Primary care influenza‐like illness surveillance in Ho Chi Minh City, Vietnam 2013‐2015

text: BACKGROUND: Year‐round transmission of influenza has been detected in Vietnam through both national surveillance and other epidemiological studies. Understanding the demographic and clinical features of influenza‐like illness (ILI) presenting to primary care in urban Vietnam is vital to understand these transmission dynamics. METHODS: An observational study of patients with ILI in Ho Chi Minh City, Vietnam, was conducted between August 2013 and November 2015 in a mix of public and private primary care settings. Molecular testing for influenza A and influenza B and 12 other respiratory viruses was performed. RESULTS: A total of 1152 ILI patients were recruited. 322 and 136 subjects tested positive for influenza A and influenza B, respectively. 193 subjects tested positive for another respiratory virus; most commonly rhinovirus and parainfluenza virus 3. Influenza was detected in 81% of the 116 study weeks. Three peaks of influenza activity were detected; an H3N2 peak April‐June 2014, an influenza B peak July‐December 2014, and a mixed H3N2 and H1N1 peak March‐September 2015. Subjects recruited from private clinics were more likely to have higher income and to have reported previous influenza vaccination. Antibiotic use was common (50.3%) despite limited evidence of bacterial infection. CONCLUSION: Influenza in southern Vietnam has complex transmission dynamics including periods of intense influenza activity of alternating types and subtypes. Broadening surveillance from hospital to the community in tropical settings is feasible and a valuable for improving our understanding of the global spread and evolution of the virus.


title: Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing

text: BACKGROUND: Unbiased deep sequencing offers the potential for improved adventitious virus screening in vaccines and biotherapeutics. Successful implementation of such assays will require appropriate control materials to confirm assay performance and sensitivity. METHODS: A common reference material containing 25 target viruses was produced and 16 laboratories were invited to process it using their preferred adventitious virus detection assay. RESULTS: Fifteen laboratories returned results, obtained using a wide range of wet-lab and informatics methods. Six of 25 target viruses were detected by all laboratories, with the remaining viruses detected by 4–14 laboratories. Six non-target viruses were detected by three or more laboratories. CONCLUSION: The study demonstrated that a wide range of methods are currently used for adventitious virus detection screening in biological products by deep sequencing and that they can yield significantly different results. This underscores the need for common reference materials to ensure satisfactory assay performance and enable comparisons between laboratories.


title: Excretion and persistence of bovine coronavirus in neonatal calves

text: Following oral inoculation, the excretion of a virulent or an attenuated strain of bovine coronavirus in calf feces and their persistence in spiral colon, ileum, and jejunum were studied using hemagglutination and direct fluorescent antibody tests, respectively. The virus was excreted in feces for only 3 days at high titers and then intermittently at low titers. However, viral antigen was detected in crypt or Peyer's patches for at least 3 weeks after infection in 1 of 3 calves given virulent virus and 1 of 2 calves given attenuated virus.


title: Telemedicine and Outpatient Subspecialty Visits among Pediatric Medicaid Beneficiaries

text: Abstract Objective Live-interactive telemedicine is increasingly covered by state Medicaid programs, but whether telemedicine is improving equity in utilization of subspecialty care is not known. We examined patterns of telemedicine use for outpatient pediatric subspecialty care within state Medicaid programs. Methods We identified children ≤17 years old in 2014 Medicaid Analysis eXtract data for 12 states. We identified telemedicine-using and telemedicine non-using medical and surgical subspecialists. Among children cared for by telemedicine-using subspecialists, we assessed child and subspecialist characteristics associated with any telemedicine visit using logistic regression with subspecialist-level random effects. Among children cared for by telemedicine-using and non-using subspecialists, we compared visit rates across child characteristics by assessing negative binomial regression interaction terms. Results Of 12,237,770 pediatric Medicaid beneficiaries, 2,051,690 (16.8%) had ≥1 subspecialist visit. Of 42,695 subspecialists identified, 146 (0.3%) had ≥1 telemedicine claim. Among children receiving care from telemedicine-using subspecialists, likelihood of any telemedicine use was increased for rural children (OR 10.4, 95%CI 6.3-17.1 compared to large metropolitan referent group) and those >90 miles from the subspecialist (OR 13.4, 95% CI 10.2-17.7 compared to 0-30 mile referent group). Compared to children receiving care from telemedicine non-using subspecialists, matched children receiving care from telemedicine-using subspecialists had larger differences in visit rates by distance to care, county rurality, ZIP code median income, and child race/ethnicity (p<0.001 for interaction terms). Conclusion Children in rural communities and at distance to subspecialists had increased likelihood of telemedicine use. Use overall was low, and results indicated that early telemedicine policies and implementation did not close disparities in subspecialty visit rates by child geographic and sociodemographic characteristics.


title: Epidemiology of Infectious Diarrhea

text: Abstract Diarrhea is a very frequent symptom. A great variety of chemical agents, microorganisms, and biotoxins can cause diarrhea, acute or persistent, slight or serious. From the epidemiological point of view, the cases can be sporadic or epidemic, and identification of the infection source and transmission mechanism is important for prevention and control. Knowledge of the etiology is a great help. The entrance route to the human body is usually through the digestive system. From some source in an individual's surroundings, the causal agent somehow reaches the mouth of the susceptible person. The hands play a fundamental role in many situations. This article revises the most important epidemiological characteristics of the agents that produce diarrhea as a main symptom, placing an emphasis on epidemiological point of view and environmental transmission mechanisms. Some aspects regarding individual susceptibility (genetic or other types) are also mentioned. Because the long-term consequences of infectious gastroenteritis are less well known, a small section dedicated to the long-term consequences of infectious gastroenteritis has been included. With suitable prevention, not only the acute consequences but also the aftereffects of these diseases can be avoided.


title: Broad-spectrum antiviral activity of chebulagic acid and punicalagin against viruses that use glycosaminoglycans for entry

text: BACKGROUND: We previously identified two hydrolyzable tannins, chebulagic acid (CHLA) and punicalagin (PUG) that blocked herpes simplex virus type 1 (HSV-1) entry and spread. These compounds inhibited viral glycoprotein interactions with cell surface glycosaminoglycans (GAGs). Based on this property, we evaluated their antiviral efficacy against several different viruses known to employ GAGs for host cell entry. RESULTS: Extensive analysis of the tannins’ mechanism of action was performed on a panel of viruses during the attachment and entry steps of infection. Virus-specific binding assays and the analysis of viral spread during treatment with these compounds were also conducted. CHLA and PUG were effective in abrogating infection by human cytomegalovirus (HCMV), hepatitis C virus (HCV), dengue virus (DENV), measles virus (MV), and respiratory syncytial virus (RSV), at μM concentrations and in dose-dependent manners without significant cytotoxicity. Moreover, the natural compounds inhibited viral attachment, penetration, and spread, to different degrees for each virus. Specifically, the tannins blocked all these steps of infection for HCMV, HCV, and MV, but had little effect on the post-fusion spread of DENV and RSV, which could suggest intriguing differences in the roles of GAG-interactions for these viruses. CONCLUSIONS: CHLA and PUG may be of value as broad-spectrum antivirals for limiting emerging/recurring viruses known to engage host cell GAGs for entry. Further studies testing the efficacy of these tannins in vivo against certain viruses are justified.


title: Late‐onset noninfectious interstitial lung disease following autologous haematopoietic stem cell transplantation in paediatric patients

text: BACKGROUND AND OBJECTIVE: High‐dose chemotherapy (HDCT) followed by autologous haematopoietic stem cell transplantation (HSCT) is widely used in paediatric cancer patients, but few data about noninfectious interstitial lung disease (ILD) following this treatment are available. Therefore, we aimed to evaluate the incidence, clinical features and risk factors of noninfectious ILD after HDCT in paediatric patients. METHODS: This was a retrospective cohort study of paediatric solid tumour patients who underwent HDCT and autologous HSCT between 1997 and 2012. ILD was diagnosed using clinical symptoms and radiography after excluding cardiac, renal and infectious causes. Risk factors were analysed using a Cox proportional hazard regression model. RESULTS: Three hundred and forty patients were enrolled, and the median age was 3 years (interquartile range 1–7). Eight patients (2.4%) were diagnosed with noninfectious ILD. The median duration of symptom onset was 30 months (range 7–74). Six (75%) of eight ILD patients died during the study period, even though steroids were administered for treatment. High‐dose cyclophosphamide use (hazard ratio = 11.37, 95% confidence interval = 1.38–93.32, P = 0.023) and sex (hazard ratio = 0.10, 95% confidence interval = 0.01–0.84, P = 0.034) were associated with late‐onset, noninfectious ILD upon multivariate analysis. CONCLUSION: The incidence of noninfectious ILD after HDCT and autologous HSCT was not negligible, and the clinical features of ILD showed late onset and a poor prognosis. Female gender and high‐dose cyclophosphamide treatment may be risk factors for noninfectious ILD, but further studies with a larger number of ILD patients are suggested.


title: Reduction in Clostridium difficile Infection Rates after Mandatory Hospital Public Reporting: Findings from a Longitudinal Cohort Study in Canada

text: BACKGROUND: The role of public reporting in improving hospital quality of care is controversial. Reporting of hospital-acquired infection rates has been introduced in multiple health care systems, but its relationship to infection rates has been understudied. Our objective was to determine whether mandatory public reporting by hospitals is associated with a reduction in hospital rates of Clostridium difficile infection. METHODS AND FINDINGS: We conducted a longitudinal, population-based cohort study in Ontario (Canada's largest province) between April 1, 2002, and March 31, 2010. We included all patients (>1 y old) admitted to 180 acute care hospitals. Using Poisson regression, we developed a model to predict hospital- and age-specific monthly rates of C. difficile disease per 10,000 patient-days prior to introduction of public reporting on September 1, 2008. We then compared observed monthly rates of C. difficile infection in the post-intervention period with rates predicted by the pre-intervention predictive model. In the pre-intervention period there were 33,634 cases of C. difficile infection during 39,221,113 hospital days, with rates increasing from 7.01 per 10,000 patient-days in 2002 to 10.79 in 2007. In the first calendar year after the introduction of public reporting, there was a decline in observed rates of C. difficile colitis in Ontario to 8.92 cases per 10,000 patient-days, which was significantly lower than the predicted rate of 12.16 (95% CI 11.35–13.04) cases per 10,000 patient-days (p<0.001). Over this period, public reporting was associated with a 26.7% (95% CI 21.4%–31.6%) reduction in C. difficile cases, or a projected 1,970 cases averted per year (95% CI 1,476–2,500). The effect was specific to C. difficile, with rates of community-acquired gastrointestinal infections and urinary tract infections unchanged. A limitation of our study is that this observational study design cannot rule out the influence of unmeasured temporal confounders. CONCLUSIONS: Public reporting of hospital C. difficile rates was associated with a substantial reduction in the population burden of this infection. Future research will be required to discern the direct mechanism by which C. difficile infection rates may have been reduced in response to public reporting. Please see later in the article for the Editors' Summary


title: Viral Pathogens and Acute Lung Injury: Investigations Inspired by the SARS Epidemic and the 2009 H1N1 Influenza Pandemic

text: Acute viral pneumonia is an important cause of acute lung injury (ALI), although not enough is known about the exact incidence of viral infection in ALI. Polymerase chain reaction-based assays, direct fluorescent antigen (DFA) assays, and viral cultures can detect viruses in samples from the human respiratory tract, but the presence of the virus does not prove it to be a pathogen, nor does it give information regarding the interaction of viruses with the host immune response and bacterial flora of the respiratory tract. The severe acute respiratory syndrome (SARS) epidemic and the 2009 H1N1 influenza pandemic provided a better understanding of how viral pathogens mediate lung injury. Although the viruses initially infect the respiratory epithelium, the relative role of epithelial damage and endothelial dysfunction has not been well defined. The inflammatory host immune response to H1N1 infection is a major contributor to lung injury. The SARS coronavirus causes lung injury and inflammation in part through actions on the nonclassical renin angiotensin pathway. The lessons learned from the pandemic outbreaks of SARS coronavirus and H1N1 capture key principles of virally mediated ALI. There are pathogen-specific pathways underlying virally mediated ALI that converge onto a common end pathway resulting in diffuse alveolar damage. In terms of therapy, lung protective ventilation is the cornerstone of supportive care. There is little evidence that corticosteroids are beneficial, and they might be harmful. Future therapeutic strategies may be targeted to specific pathogens, the pathogenetic pathways in the host immune response, or enhancing repair and regeneration of tissue damage.


title: Risk of SARS-CoV-2 infection among contacts of individuals with COVID-19 in Hangzhou, China

text: Abstract Objectives This study determined the rate of secondary infection among contacts of individuals with confirmed COVID-19 in Hangzhou according to the type of contact, the intensity of the contact, and their relationship with the index patient. Study design Retrospective cohort study. Methods The analysis used the data of 2,994 contacts of 144 individuals with confirmed SARS-CoV-2 infection. The contacts were categorized according to the information source, type of contact, location, intensity of contact, and relationship with the index patient. Results The incidence of infection differed significantly according to contact type. Of the contacts, 186 (6.2%) developed symptoms and 71 (2.4%) had confirmed infection with SARS-CoV-2. The main symptoms were cough and fever. Compared to those who had brief contact with the index case, those who had dined with the index case had a 2.6 times greater risk of infection; those who had shared transport, visited, or had contact with the index case in a medical institution had a 3.6 times greater risk of infection; and household contacts had 41.7 times greater risk of infection. Family members had a 31.6 times greater risk of infection than healthcare providers or other patients exposed to an index case. Conclusions The form and frequency of contact are the main factors affecting the risk of infection among contacts of individuals with COVID-19. Centralized isolation and observation of close contacts of individuals with confirmed SARS-CoV-2 infection, in addition to population-based control measures, can reduce the risk of secondary infections and curb the spread of the infection.


title: Departmental Experience and Lessons Learned With Accelerated Introduction of Telemedicine During the COVID-19 Crisis

text: Despite the use of digital technology in healthcare, telemedicine has not been readily adopted. During the COVID-19 pandemic, healthcare systems have begun crisis management planning. To appropriately allocate resources and prevent virus exposure while maintaining effective patient care, our orthopaedic surgery department rapidly introduced a robust telemedicine program during a 5-day period. Implementation requires attention to patient triage, technological resources, credentialing, education of providers and patients, scheduling, and regulatory considerations. This article provides practical instruction based on our experience for physicians who wish to implement telemedicine during the COVID-19 pandemic. Between telemedicine encounters and necessary in-person visits, providers may be able to achieve 50% of their typical clinic volume within 2 weeks. When handling the massive disruption to the routine patient care workflow, it is critical to understand the key factors associated with an accelerated introduction of telemedicine for the safe and effective continuation of orthopaedic care during this pandemic. LEVEL OF EVIDENCE: V


title: Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a

text: Abstract Spike and nucleocapsid are structural proteins of severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) and major targets for cytotoxic T lymphocytes (CTLs). In contrast, non-structural proteins encoded by two-thirds of viral genome are poorly characterized for cell-mediated immunity. We previously demonstrated that nucleocapsid-derived peptides chemically coupled to the surface of liposomes effectively elicited SARS-CoV-specific CTLs in mice. Here, we attempted to identify HLA-A*0201-restricted CTL epitopes derived from a non-structural polyprotein 1a (pp1a) of SARS-CoV, and investigated whether liposomal peptides derived from pp1a were effective for CTL induction. Out of 30 peptides predicted on computational algorithms, nine peptides could significantly induce interferon gamma (IFN-γ)-producing CD8+ T cells in mice. These peptides were coupled to the surface of liposomes, and inoculated into mice. Six liposomal peptides effectively induced IFN-γ-producing CD8+ T cells and seven liposomal peptides including the six peptides primed CTLs showing in vivo killing activities. Further, CTLs induced by the seven liposomal peptides lysed an HLA-A*0201 positive cell line expressing naturally processed, pp1a-derived peptides. Of note, one of the liposomal peptides induced high numbers of long-lasting memory CTLs. These data suggest that surface-linked liposomal peptides derived from pp1a might offer an efficient CTL-based vaccine against SARS.


title: Neisseria gonorrhoeae uses cellular proteins CXCL10 and IL8 to enhance HIV‐1 transmission across cervical mucosa

text: PROBLEM: Neisseria gonorrhoeae (NG) infection has been shown to increase sexual transmission of HIV‐1. However, the mechanism of NG‐induced enhanced HIV‐1 transmission is unknown. METHODS: (a) The cervical tissues were exposed to NG, and cytokine induction was monitored by measuring cytokine proteins in culture supernatants and cytokine mRNAs in tissues. (b) Transcription and replication of HIV‐1 in TZM‐bl, U1, and ACH2 cells were measured by Beta‐Gal activity and p24 proteins in the supernatant, respectively. (c) HIV‐1 transmission was assayed in an organ culture system by measuring transmitted HIV‐1 in supernatant and HIV‐1 gag mRNA in the tissues. (d) Transcriptome analysis was done using second generation sequencing. RESULTS: (a) NG induced membrane ruffling of epithelial layer, caused migration of CD3+ cells to the intraepithelial region, and induced high levels of inflammatory cytokines IL‐1β and TNF‐α. (b) NG‐induced supernatants (NGIS) increased HIV‐1 transcription, induced HIV‐1 from latently infected cells, and increased transmission of HIV‐1 across cervical mucosa. (c) Transcriptome analysis of the epithelial layer of the tissues exposed to NG, and HIV‐1 showed significant upregulation of CXCL10 and IL8. IL‐1β increased the induction of CXCL10 and IL‐8 expression in cervical mucosa with a concomitant increase in HIV‐1 transmission. CONCLUSION: We present a model in which IL‐1β produced from cervical epithelium during NG exposure increases CXCL10 and IL8 in epithelia. This in turn causes upon HIV‐1 infection, the migration of HIV‐1 target cells toward the subepithelium, resulting in increased HIV‐1 transcription in the sub‐mucosa and subsequent enhancement of transmission across cervical mucosa.


title: Near-Complete Genome Sequence of Infectious Bronchitis Virus Strain VFAR-047 (GI-16 Lineage), Isolated in Peru

text: Here, we report the near-complete genome sequence of the infectious bronchitis virus (IBV) strain VFAR-047, isolated in Peru in 2014. This strain was classified into GI lineage 16 (GI-16) based on both the genome and Spike 1 (S1) sequence analysis. Furthermore, four potential recombination events with other GI-16 and GI-11 strains were identified.


Data-Directed Drug Design


title: ANDES: Statistical tools for the ANalyses of DEep Sequencing

text: BACKGROUND: The advancements in DNA sequencing technologies have allowed researchers to progress from the analyses of a single organism towards the deep sequencing of a sample of organisms. With sufficient sequencing depth, it is now possible to detect subtle variations between members of the same species, or between mixed species with shared biomarkers, such as the 16S rRNA gene. However, traditional sequencing analyses of samples from largely homogeneous populations are often still based on multiple sequence alignments (MSA), where each sequence is placed along a separate row and similarities between aligned bases can be followed down each column. While this visual format is intuitive for a small set of aligned sequences, the representation quickly becomes cumbersome as sequencing depths cover loci hundreds or thousands of reads deep. FINDINGS: We have developed ANDES, a software library and a suite of applications, written in Perl and R, for the statistical ANalyses of DEep Sequencing. The fundamental data structure underlying ANDES is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment (MSA). Tools include the root mean square deviation (RMSD) plot, which allows for the visual comparison of multiple samples on a position-by-position basis, and the computation of base conversion frequencies (transition/transversion rates), variation (Shannon entropy), inter-sample clustering and visualization (dendrogram and multidimensional scaling (MDS) plot), threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values. CONCLUSIONS: As new sequencing technologies evolve, deep sequencing will become increasingly cost-efficient and the inter and intra-sample comparisons of largely homogeneous sequences will become more common. We have provided a software package and demonstrated its application on various empirically-derived datasets. Investigators may download the software from Sourceforge at https://sourceforge.net/projects/andestools.


title: Factors associated with death in hospitalized pneumonia patients with 2009 H1N1 influenza in Shenyang, China

text: BACKGROUND: During the spring of 2009, a pandemic influenza A (H1N1) virus emerged and spread globally. We describe the clinical characteristics and factors associated with the death of patients who were hospitalized with 2009 H1N1 influenza pneumonia in Shenyang, China, from November to December 2009. METHODS: We carried out a retrospective chart review of 68 patients who were hospitalized with pneumonia and confirmed to have 2009 H1N1 virus infection by a real time RT-PCR assay of respiratory specimens. RESULTS: Of the 68 patients we studied, 30 (44%) were admitted to an intensive care unit and 10 (14.7%) died. The median age of patients was 41 years (range, 18-66), and only one patient was over 65 years of age. The male to female ratio was 2.78:1 (50:18). Of the 68 patients, 23 (34%) had at least one underlying medical condition, 9 (13%) had a cigarette index ≥400 and 22 (32%) were obese. All patients underwent chest radiography on admission and the findings were consistent with pneumonia in all cases. All patients were treated with oseltamivir and treatment was initiated at a median time of seven days after the onset of illness. The laboratory test results indicated lymphopenia, hypoproteinemia and elevated lactic dehydrogenase and C reactive protein levels. Of the 68 patients, 33 (52%) showed a reduction in CD4 T cell counts. Of the 58 patients who survived, 31 (53%) had lymphopenia and 27 recovered from this condition after five days. Of the 10 patients who died, nine (90%) had lymphopenia and only two patients recovered from this condition after five days. Obesity and recovery from lymphopenia after five days were factors associated with death, as determined by multivariate logistic-regression analysis (obesity, odds ratio = 23.06; lymphocytopenia reversion, odds ration = 28.69). CONCLUSIONS: During the evaluation period in Shenyang, China, 2009 H1N1 influenza caused severe illness requiring hospitalization in 68 patients, 10 (14.7%) of which died. Many of these patients were considered healthy adults and few were elderly (65 years or older). Obesity and lymphopenia, which was not restored after five days of treatment, were factors associated with poor outcomes of 2009 H1N1 influenza infection.


title: Neuroinvasive potential of a primary respiratory pathogen SARS- CoV2: Summarizing the evidences

text: BACKROUND AND AIMS: After the emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in the last two decades, the world is facing its new challenge in SARS-CoV-2 pandemic with unfathomable global responses. The characteristic clinical symptoms for Coronavirus (COVID-19) affected patients are high fever, dry-cough, dyspnoea, lethal pneumonia whereas some patients also show additional neurological signs such as headache, nausea, vomiting etc. The accumulative evidences suggest that SARS-CoV-2 is not only confined within the respiratory tract but may also invade the central nervous system (CNS) and peripheral nervous system (PNS) inducing some fatal neurological diseases. Here, we analyze the phylogenetic perspective of SARS-CoV-2 with other strains of β-Coronaviridae from a standpoint of neurological spectrum disorders. METHODOLOGY: A Pubmed/Medline, NIH Lit Covid, Cochrane library and some open data bases (BioRxiv, MedRxiv,preprint.org and others) search were carried out by using keywords relevant to our topic of discussion. The extracted literatures are scrutinized by the authors. RESULTS: 58 literatures including original articles, case reports and case series were selected by the authors to analyze the differential distribution of neurological impairments in COVID-19 positive patients along with angiotensin-converting enzyme-2 (ACE2) expression dynamics in neuronal and non-neuronal tissue in CNS and PNS with neuroinvasive potential of SARS-CoV2. CONCLUSION: We discuss the need for modulations in clinical approach from a neurological point of view, as a measure towards reducing disease transmission, morbidity and mortality in SARS-CoV2 positive patients.


docid: nokowfdi

title: “Don’t forget the migrants”: exploring preparedness and response strategies to combat the potential spread of MERS-CoV virus through migrant workers in Sri Lanka

text: From September 2012 to July 2013, 81 laboratory-confirmed cases of infection with Middle East respiratory syndrome coronavirus (MERS-CoV), including 45 deaths (a case fatality ratio of 55%) have been reported from eight countries. Human-to-human transmission is now confirmed showing potential for another pandemic of zoonotic disease, with an extremely high mortality rate. Effective surveillance strategies are required in countries with a high influx of migrants from the Middle East to mitigate the probable importation of MERS-CoV. We discuss here the risk of MERS-CoV in major labor sending countries and list the probable strategies for control and prevention of MERS-CoV using Sri Lanka as an example. It is conservatively estimated that 10% of Sri Lanka’s population work as international labor migrants (1.8 to 2 million workers), with 93% residing in the Middle East. An average of 720 workers depart each day, with the majority of these workers (71%) departing to the Kingdom of Saudi Arabia (the country with 81.5% of total MERS-CoV cases). We also describe other inbound migration categories such as tourists and resident visa holders relevant to the context of preparedness and planning. The importance of partnerships between public health authorities at national and regional levels with labor migration networks to establish institutional and/or policy mechanisms are highlighted for ensuring effective preparedness and response planning. Strategies that can be taken by public health authorities working in both labor sending and labor receiving counties are also described. The strategies described here may be useful for other labor sending country contexts in Asia with a high frequency and volume of migrant workers to and from the Gulf region.


docid: kxivgxbg

title: Experimental infection of dromedaries with Middle East respiratory syndrome-Coronavirus is accompanied by massive ciliary loss and depletion of the cell surface receptor dipeptidyl peptidase 4

text: Middle East respiratory syndrome (MERS) represents an important respiratory disease accompanied by lethal outcome in one-third of human patients. Recent data indicate that dromedaries represent an important source of infection, although information regarding viral cell tropism and pathogenesis is sparse. In the current study, tissues of eight dromedaries receiving inoculation of MERS-Coronavirus (MERS-CoV) after recombinant Modified-Vaccinia-Virus-Ankara (MVA-S)-vaccination (n = 4), MVA-vaccination (mock vaccination, n = 2) and PBS application (mock vaccination, n = 2), respectively, were investigated. Tissues were analyzed by histology, immunohistochemistry, immunofluorescence, and scanning electron microscopy. MERS-CoV infection in mock-vaccinated dromedaries revealed high numbers of MERS-CoV-nucleocapsid positive cells, T cells, and macrophages within nasal turbinates and trachea at day four post infection. Double immunolabeling demonstrated cytokeratin (CK) 18 expressing epithelial cells to be the prevailing target cell of MERS-CoV, while CK5/6 and CK14 expressing cells did not co-localize with virus. In addition, virus was occasionally detected in macrophages. The acute disease was further accompanied by ciliary loss along with a lack of dipeptidyl peptidase 4 (DPP4), known to mediate virus entry. DPP4 was mainly expressed by human lymphocytes and dromedary monocytes, but overall the expression level was lower in dromedaries. The present study underlines significant species-specific manifestations of MERS and highlights ciliary loss as an important finding in dromedaries. The obtained results promote a better understanding of coronavirus infections, which pose major health challenges.


title: Dynamic evolution of lung abnormalities evaluated by quantitative CT techniques in patients with COVID-19 infection

text: Chest CT evaluation is often vital to determine patients suspected of COVID-19 pneumonia. The aim of this study was to determine the evolution of lung abnormalities evaluated by quantitative CT techniques in patients with COVID-19 infection from initial diagnosis to recovery. This retrospective study included 16 patients with COVID-19 infection from 30 January 2020 through 11 March 2020. Repeat chest CT examinations were obtained for three or more scans per patient. We measured total volume and mean CT value of lung lesions in each patient per scan, and then calculated the mass, which equals to volume × (CT value + 1000). Dynamic evolution of chest CT imaging as a function of time was fitted by non-linear regression model in terms of mass, volume and CT value, respectively. According to the fitting curves, we redefined the evolution of lung abnormalities: progressive stage (0–5 days), infection emerged and rapidly aggravated; peak stage (5–15 days), the greatest severity at approximate 7–8 days after onset; and absorption stage (15–30 days), the lesions slowly and gradually resolved.


title: Pigment Epithelium-Derived Factor (PEDF) Protects Osteoblastic Cell Line from Glucocorticoid-Induced Apoptosis via PEDF-R

text: Pigment epithelial-derived factor (PEDF) is known as a widely expressed multifunctional secreted glycoprotein whose biological actions are cell-type dependent. Recent studies demonstrated that PEDF displays cytoprotective activity in several cell types. However, it remains unknown whether PEDF is involved in glucocorticoid-induced osteoblast death. The aim of this study was to examine the role of PEDF in osteoblast survival in response to dexamethasone, an active glucocorticoid analogue, and explore the underlying mechanism. In the present study, dexamethasone (DEX) was used to induce MC3T3-E1 pre-osteoblast apoptosis. PEDF mRNA and protein levels and cell apoptosis were determined respectively. Then PEDF receptor (PEDF-R)- and lysophosphatidic acid (LPA)-related signal transductions were assessed. Here we show that DEX down-regulates PEDF expression, which contributes to osteoblast apoptosis. As a result, exogenous recombinant PEDF (rPEDF) inhibited DEX-induced cell apoptosis. We confirmed that PEDF-R was expressed on MC3T3-E1 pre-osteoblast membrane and could bind to PEDF which increased the level of LPA and activated the phosphorylation of Akt. Our results suggest that PEDF attenuated DEX-induced apoptosis in MC3T3-E1 pre-osteoblasts through LPA-dependent Akt activation via PEDF-R.


title: Association between genetic polymorphisms and osteonecrosis in steroid treatment populations: a detailed stratified and dose-response meta-analysis

text: Steroid treatment has become recognized as an important risk factor for avascular osteonecrosis of the femoral head. However, not all patients who receive long-term, high-dose steroids develop osteonecrosis, indicating that there are individual differences in occurrence. We explored the relationship between polymorphisms and steroid-induced osteonecrosis of the femoral head (SONFH) incidence with variables. We used a multilevel mixed-effects logistic regression model, which is an expansion of logistic regression, for each type of steroid, primary disease, drug dose, applied duration, and single-nucleotide polymorphism (SNP). We also conducted a dose-response meta-analysis to analyze the cumulative dosage and SONFH risk in mutation carriers. There were significant correlations between the ABCB1 rs1045642 mutant and SONFH in the prednisone-use and methylprednisolone/prednisone-use populations. The ABCB1 rs2032582 mutant homozygote had a protective effect in the methylprednisolone/prednisolone renal transplant population. For ApoB rs693, mutation increased the incidence of SONFH in prednisone-use and methylprednisolone/prednisolone-use populations and renal transplant patients. For ApoB rs1042031, mutation increased the risk of SONFH in the prednisone-use population. The PAI-1 rs1799768 mutation had a protective effect on the SONFH risk prednisone-use and renal transplant populations. ABCB1 rs1045642 mutations have a protective effect against SONFH, and ApoB rs693 and rs1042031 increase the SONFH risk. Cumulative dosage and treatment duration had little effect on the results. In addition, there was a dose-effect correlation in ABCB1 rs1045642 and rs2032582 mutation carriers.


title: Improving pedestrian level low wind velocity environment in high-density cities: A general framework and case study

text: Abstract An acceptable pedestrian level wind environment is essential to maintain an enjoyable outdoor space for city residents. Low wind velocity environment can lead to uncomfortable outdoor thermal experience in hot and humid summer, and it is unable to remove the pollutants out of city canyons. However, the average wind velocity at pedestrian level is significantly lowered by closely spaced tall buildings in modern megacities. To improve the low wind velocity environment at pedestrian level in high-density cities, a general framework and detailed guidelines are needed. This study is the first time to develop such a framework, and provide detailed guidelines for improving pedestrian level low wind velocity environment in high-density cities. Additionally, a detailed review and summarisation of evaluation criteria and improvement measures are presented in this paper, which provide additional options for urban planners. To investigate the performance of the framework, the Hong Kong Polytechnic University campus was utilised as a case study. Results showed that pedestrian level wind comfort was greatly improved with the developed framework. The outcomes of this study can assist city planners to improve the low wind velocity environment, and can help policy makers to establish sustainable urban planning policies.


title: Emerging Technologies for Use in the Study, Diagnosis, and Treatment of Patients with COVID-19

text: INTRODUCTION: The COVID-19 pandemic has caused an unprecedented health and economic worldwide crisis. Innovative solutions are imperative given limited resources and immediate need for medical supplies, healthcare support and treatments. AIM: The purpose of this review is to summarize emerging technologies being implemented in the study, diagnosis, and treatment of COVID-19. RESULTS: Key focus areas include the applications of artificial intelligence, the use of Big Data and Internet of Things, the importance of mathematical modeling for predictions, utilization of technology for community screening, the use of nanotechnology for treatment and vaccine development, the utility of telemedicine, the implementation of 3D-printing to manage new demands and the potential of robotics. CONCLUSION: The review concludes by highlighting the need for collaboration in the scientific community with open sharing of knowledge, tools, and expertise.


title: Mathematical analysis of the role of hospitalization/isolation in controlling the spread of Zika fever

text: Abstract The Zika virus is transmitted to humans primarily through Aedes mosquitoes and through sexual contact. It is documented that the virus can be transmitted to newborn babies from their mothers. We consider a deterministic model for the transmission dynamics of the Zika virus infectious disease that spreads in, both humans and vectors, through horizontal and vertical transmission. The total populations of both humans and mosquitoes are assumed to be constant. Our models consist of a system of eight differential equations describing the human and vector populations during the different stages of the disease. We have included the hospitalization/isolation class in our model to see the effect of the controlling strategy. We determine the expression for the basic reproductive number R 0 in terms of horizontal as well as vertical disease transmission rates. An in-depth stability analysis of the model is performed, and it is consequently shown, that the model has a globally asymptotically stable disease-free equilibrium when the basic reproduction number R 0 < 1. It is also shown that when R 0 > 1, there exists a unique endemic equilibrium. We showed that the endemic equilibrium point is globally asymptotically stable when it exists. We were able to prove this result in a reduced model. Furthermore, we conducted an uncertainty and sensitivity analysis to recognize the impact of crucial model parameters on R 0. The uncertainty analysis yields an estimated value of the basic reproductive number R 0 = 1.54. Assuming infection prevalence in the population under constant control, optimal control theory is used to devise an optimal hospitalization/isolation control strategy for the model. The impact of isolation on the number of infected individuals and the accumulated cost is assessed and compared with the constant control case.


title: Improved expression of porcine epidemic diarrhea antigen by fusion with cholera toxin B subunit and chloroplast transformation in Nicotiana tabacum

text: The porcine epidemic diarrhea virus (PEDV) belongs to the coronavirus family, which causes acute diarrhea in pigs with higher mortality in piglets less than 2 weeks old. The PEDV is one of the major concerns of the pig industry around the world, including Asian countries and Noth America since first identified in Europe. Currently, there is no PEDV licensed vaccine to effectively prevent this disease. This study was performed for the development of a mucosal PEDV vaccine and B subunit of cholera toxin (CTB) as a carrier was employed to surpass the tolerogenic nature of GALT and induce potent immune responses against the target antigen fused to CTB. An epitope (S1D) alone or conjugated with CTB was constructed into the tobacco chloroplasts expression vector which is controlled under the chloroplast rRNA operon promoter with T7g10 5′ UTR and the psbA 3′UTR as a terminator. The homoplastomic lines were obtained by third round screening via organogenesis from the leaf tissues which were verified by PCR with antigen and chloroplast specific primers and then confirmed by Southern blot analysis. While the expression level of the S1D alone as detected by Western blotting was approximately 0.07% of total soluble protein, the CTB-S1D fusion protein was expressed up to 1.4%. The fusion protein showed binding to the intestinal membrane GM1-ganglioside receptor, demonstrating its functionality. The result shows that the highest expression of S1D could be achieved by fusion with a stable CTB protein and chloroplast transformation. Furthermore, the CTB-S1D expressed in chloroplasts of Nicotiana tabacum cv. Maryland could be assembled to pentameric form which increases the possibility to develop a mucosal vaccine against PEDV.


title: Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations

text: The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease M(pro), because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2′-Fluoro-2′-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (−7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity −6.06 and −4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.


Open source clinical science for emerging infections


title: Human astroviruses: in silico analysis of the untranslated region and putative binding sites of cellular proteins

text: Human astrovirus (HAstV) constitutes a major cause of acute gastroenteritis in children. The viral 5′ and 3′ untranslated regions (UTR) have been involved in the regulation of several molecular mechanisms. However, in astrovirues have been less characterized. Here, we analyzed the secondary structures of the 5′ and 3′ UTR of HAstV, as well as their putative target sites that might be recognized by cellular factors. To our knowledge, this is the first bioinformatic analysis that predicts the HAstV 5′ UTR secondary structure. The analysis showed that both the UTR sequence and secondary structure are highly conserved in all HAstVs analyzed, suggesting their regulatory role of viral activities. Notably, the UTRs of HAstVs contain putative binding sites for the serine/arginine-rich factors SRSF2, SRSF5, SRSF6, SRSF3, and the multifunctional hnRNPE2 protein. More importantly, putative binding sites for PTB were localized in single-stranded RNA sequences, while hnRNPE2 sites were localized in double-stranded sequence of the HAstV 5′ and 3′ UTR structures. These analyses suggest that the combination of SRSF proteins, hnRNPE2 and PTB described here could be involved in the maintenance of the secondary structure of the HAstVs, possibly allowing the recruitment of the replication complex that selects and recruits viral RNA replication templates. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11033-018-4498-8) contains supplementary material, which is available to authorized users.


title: Déshydratation aiguë du nourrisson

text: Résumé Le nourrisson de moins d’un an et surtout de moins de six mois est à haut risque de déshydratation dont la première cause est la diarrhée. Celle-ci est majoritairement d’origine virale. La prise en charge d’une déshydratation comporte la correction de celle-ci et le maintien des besoins hydriques et nutritionnels. L’évaluation de la sévérité de la déshydratation est l’élément clé qui va guider la thérapeutique. La perte de poids, exprimée en pourcentage du poids corporel avant l’épisode de déshydratation, constitue la méthode de référence mais elle est souvent difficile ou impossible à obtenir. Aussi, les signes cliniques tels que l’altération de l’aspect général, l’allongement du temps de recoloration cutanée, la constatation d’un pli cutané persistant, des yeux creux, une sécheresse des muqueuses, une absence de larmes sont les principaux éléments qui, avec la tachycardie, la pression artérielle et la diurèse, permettent d’apprécier la sévérité de la déshydratation. Le traitement repose sur la correction rapide du déficit du secteur extracellulaire. Une expansion volémique par 20ml/kg d’un soluté cristalloïde isotonique administré par voie intraveineuse ou intra-osseuse peut être nécessaire à la phase initiale dans les cas les plus sévères (déshydratation supérieure à 10 %). Dans tous les autres cas, la réhydratation par voie orale visant à corriger le déficit hydrique en quatre heures est la technique de choix, qui est démontrée efficace, sûre et rapide. Elle utilise des solutés de réhydratation adaptés qui répondent à des critères spécifiques. Leur utilisation précoce constitue la prévention la plus efficace des formes graves et doit être plus largement répandue. Summary Dehydration in infant under the age of one year, even more under six months old, due to viral diarrhoea in most cases, is particularly risky. Management of dehydration consists in rehydrating and maintaining nutritional needs. The key to choosing the right treatment is to assess dehydration gravity according to weight loss, expressed in percentages of body weight before dehydration, which can be tough or impossible to obtain. So, clinical signs like impairment of general aspect, lengthening of cutaneous recoloration time, persistent cutaneous crease, hollow eyes, mucous membranes dryness or tear lack, with tachycardia, arterial pressure and diuresis, can help in diagnosing dehydration gravity. Treatment is based on correcting extracellular area deficit. In severe cases, it is possible to treat with 20ml/kg of isotonic cristalloide solute intravenously (dehydration greater than 10%). In all other cases, the technique mostly used is oral rehydration, aimed for correcting hydrical deficit in four hours, which has proved to be efficient, secure and fast. It consists in using rehydration solutes fitting specific criteria. Using them precociously allows most efficient prevention of acute forms.


title: Using IL‐2R/lymphocytes for predicting the clinical progression of patients with COVID‐19

text: Effective laboratory markers for the estimation of disease severity and predicting the clinical progression of coronavirus disease‐2019 (COVID‐19) is urgently needed. Laboratory tests, including blood routine, cytokine profiles and infection markers, were collected from 389 confirmed COVID‐19 patients. The included patients were classified into mild (n = 168), severe (n = 169) and critical groups (n = 52). The leukocytes, neutrophils, infection biomarkers [such as C‐reactive protein (CRP), procalcitonin (PCT) and ferritin] and the concentrations of cytokines [interleukin (IL)‐2R, IL‐6, IL‐8, IL‐10 and tumor necrosis factor (TNF)‐α] were significantly increased, while lymphocytes were significantly decreased with increased severity of illness. The amount of IL‐2R was positively correlated with the other cytokines and negatively correlated with lymphocyte number. The ratio of IL‐2R to lymphocytes was found to be remarkably increased in severe and critical patients. IL‐2R/lymphocytes were superior compared with other markers for the identification of COVID‐19 with critical illness, not only from mild but also from severe illness. Moreover, the cytokine profiles and IL‐2R/lymphocytes were significantly decreased in recovered patients, but further increased in disease‐deteriorated patients, which might be correlated with the outcome of COVID‐19. Lymphopenia and increased levels of cytokines were closely associated with disease severity. The IL‐2R/lymphocyte was a prominent biomarker for early identification of severe COVID‐19 and predicting the clinical progression of the disease.


title: SARS-CoV and SARS-CoV-2 main protease residue interaction networks change when bound to inhibitor N3

text: COVID-19 is a respiratory disease caused by the coronavirus SARS-CoV-2. SARS-CoV-2 has many similarities with SARS-CoV. Both viruses rely on a protease called the main protease, or M(pro), for replication. Therefore, inhibiting M(pro) may be a successful strategy for treating COVID-19. Structures are available in the Protein Data Bank of the main proteases of SARS-CoV and SARS-CoV-2 with and without inhibitor N3. Comparing these structures revealed residue interaction network changes associated with N3 inhibition. Comparing network clustering with and without inhibitor N3 identified the formation of a cluster of residues 17, 18, 30-33, 70, 95, 98, 103, 117, 122, and 177 as a network change in both viral proteases when bound to inhibitor N3. Betweenness and stress centrality differences as well as differences in bond energies and relative B-factors when comparing free M(pro) to inhibitor-bound M(pro) identified residues 131, 175, 182, and 185 as possibly conformationally relevant when bound to the inhibitor N3. Taken together, these results provide insight into conformational changes of betacoronavirus M(pro)s when bound to an inhibitor.